U.S. patent application number 14/463253 was filed with the patent office on 2014-12-04 for functional genomics using crispr-cas systems, compositions, methods, knock out libraries and applications thereof.
The applicant listed for this patent is THE BROAD INSTITUTE INC., MASSACHUSETTS INSTITUTE OF TECHNOLOGY. Invention is credited to Neville Espi Sanjana, Ophir Shalem, Feng Zhang.
Application Number | 20140357530 14/463253 |
Document ID | / |
Family ID | 49887332 |
Filed Date | 2014-12-04 |
United States Patent
Application |
20140357530 |
Kind Code |
A1 |
Zhang; Feng ; et
al. |
December 4, 2014 |
FUNCTIONAL GENOMICS USING CRISPR-CAS SYSTEMS, COMPOSITIONS,
METHODS, KNOCK OUT LIBRARIES AND APPLICATIONS THEREOF
Abstract
The present invention generally relates to compositions, methods
applications and screens used in functional genomics that focus on
gene function in a cell and that may use vector systems and other
aspects related to Clustered Regularly Interspaced Short
Palindromic Repeats (CRISPR)-Cas systems and components thereof.
Provided are vectors and vector systems, some of which encode one
or more components of a CRISPR complex, as well as methods for the
design and use of such vectors. Also provided are methods of
directing CRISPR complex formation in eukaryotic cells and methods
for utilizing the CRISPR-Cas system.
Inventors: |
Zhang; Feng; (Cambridge,
MA) ; Sanjana; Neville Espi; (Cambridge, MA) ;
Shalem; Ophir; (Boston, MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
THE BROAD INSTITUTE INC.
MASSACHUSETTS INSTITUTE OF TECHNOLOGY |
CAMBRIDGE
CAMBRIDGE |
MA
MA |
US
US |
|
|
Family ID: |
49887332 |
Appl. No.: |
14/463253 |
Filed: |
August 19, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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PCT/US2013/074800 |
Dec 12, 2013 |
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14463253 |
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61736527 |
Dec 12, 2012 |
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61802174 |
Mar 15, 2013 |
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Current U.S.
Class: |
506/16 |
Current CPC
Class: |
C12N 15/1034 20130101;
C12N 15/1093 20130101; C12N 15/635 20130101; C12N 15/1082 20130101;
C12N 15/907 20130101; C12N 2750/14143 20130101; C12N 15/63
20130101; C12N 15/102 20130101 |
Class at
Publication: |
506/16 |
International
Class: |
C12N 15/10 20060101
C12N015/10 |
Goverment Interests
STATEMENT AS TO FEDERALLY SPONSORED RESEARCH
[0004] This invention was made with government support under the
NIH Pioneer Award (1DP1MH100706) awarded by the National Institutes
of Health. The government has certain rights in the invention.
Claims
1. A genome wide library comprising a plurality of CRISPR-Cas
system guide RNAs comprising guide sequences that are capable of
targeting a plurality of target sequences in a plurality of genomic
loci in a population of eukaryotic cells.
2. The library of claim 1, wherein the population of cells is a
population of embryonic stem (ES) cells.
3. The library of claim 1, wherein the target sequence in the
genomic locus is a non-coding sequence.
4. The library of claim 1, wherein gene function of one or more
gene products is altered by said targeting.
5. The library of claim 1, wherein said targeting results in a
knockout of gene function.
6. The library of claim 1, wherein the targeting is of about 100 or
more sequences.
7. The library of claim 1, wherein the targeting is of about 1000
or more sequences.
8. The library of claim 1, wherein the targeting is of about 20,000
or more sequences.
9. The library of claim 1, wherein the targeting is of the entire
genome.
10. The library of claim 1, wherein the targeting is of a panel of
target sequences focused on a relevant or desirable pathway.
11. The library of claim 10, wherein the pathway is an immune
pathway.
12. The library of claim 5, wherein targeting is of about 100 or
more sequences.
13. The library of claim 5, wherein targeting is of about 1000 or
more sequences.
14. The library of claim 5, wherein targeting is of about 20,000 or
more sequences.
15. The library of claim 5, wherein targeting is of the entire
genome.
16. The library of claim 5, wherein the targeting is of a panel of
target sequences focused on a relevant or desirable pathway.
17. The library of claim 16, wherein the pathway is an immune
pathway.
18. The library of claim 16, wherein the pathway is a cell division
pathway.
19. The library of claim 5, wherein the knockout of gene function
comprises: introducing into each cell in the population of cells a
vector system of one or more vectors comprising an engineered,
non-naturally occurring CRISPR-Cas system comprising I. a Cas
protein, and II. one or more guide RNAs, wherein components I and
II may be same or on different vectors of the system, integrating
components I and II into each cell, wherein the guide sequence
targets a unique gene in each cell, wherein the Cas protein is
operably linked to a regulatory element, wherein when transcribed,
the guide RNA comprising the guide sequence directs
sequence-specific binding of a CRISPR-Cas system to a target
sequence in the genomic loci of the unique gene, inducing cleavage
of the genomic loci by the Cas protein, and confirming different
knockout mutations in a plurality of unique genes in each cell of
the population of cells thereby generating a gene knockout cell
library.
20. The library of claim 19, wherein the one or more vectors are
plasmid vectors.
21. The library of claim 19, wherein the regulatory element is an
inducible promoter.
22. The library of claim 19, wherein the inducible promoter is a
doxycycline inducible promoter.
23. The library of claim 19, wherein the confirming of different
knockout mutations is by whole exome sequencing.
24. The library of claim 19, wherein the knockout mutation is
achieved in 100 or more unique genes.
25. The library of claim 19, wherein the knockout mutation is
achieved in 1000 or more unique genes.
26. The library of claim 19, wherein the knockout mutation is
achieved in 20,000 or more unique genes.
27. The library of claim 19, wherein the knockout mutation is
achieved in the entire genome,
28. The library of claim 19, wherein the knockout of gene function
is achieved in a plurality of unique genes which function in a
particular physiological pathway or condition.
29. The library of claim 28, wherein the pathway or condition is an
immune pathway or condition.
30. The library of claim 28, wherein the pathway or condition is a
cell division pathway or condition.
Description
RELATED APPLICATIONS AND INCORPORATION BY REFERENCE
[0001] This application is a continuation of US international
application PCT/US2013/074800 filed Dec. 12, 2013, which claims
benefit of and priority to U.S. provisional patent application Nos.
61/736,527 filed Dec. 12, 2012 and 61/802,174 filed Mar. 15,
2013.
[0002] Reference is also made to U.S. provisional patent
application Nos. 61/960,777 filed on Sep. 25, 2013 and 61/961,980
filed on Oct. 28, 2013. Reference is made to U.S. provisional
patent applications 61/758,468; 61/769,046; 61/802,174; 61/806,375;
61/814,263; 61/819,803 and 61/828,130 filed on Jan. 30, 2013; Feb.
25, 2013; Mar. 15, 2013; Mar. 28, 2013; Apr. 20, 2013; May 6, 2013
and May 28, 2013 respectively. Reference is also made to U.S.
provisional patent applications 61/836,123, 61/847,537, 61/862,355
and 61/871,301 filed on Jun. 17, 2013; Jul. 17, 2013, Aug. 5, 2013
and Aug. 28, 2013 respectively. Reference is also made to U.S.
provisional patent applications 61/736,527 and 61/748,427 on Dec.
12, 2012 and Jan. 2, 2013, respectively. Reference is also made to
U.S. provisional patent application 61/791,409 filed on Mar. 15,
2013. Reference is also made to U.S. provisional patent application
61/799,800 filed Mar. 15, 2013. Reference is also made to U.S.
provisional patent applications 61/835,931, 61/835,936, 61/836,127,
61/836,101, 61/836,080, and 61/835,973 each filed Jun. 17,
2013.
[0003] The foregoing applications, and all documents cited therein
or during their prosecution ("appln cited documents") and all
documents cited or referenced in the appln cited documents, and all
documents cited or referenced herein ("herein cited documents"),
and all documents cited or referenced in herein cited documents,
together with any manufacturer's instructions, descriptions,
product specifications, and product sheets for any products
mentioned herein or in any document incorporated by reference
herein, are hereby incorporated herein by reference, and may be
employed in the practice of the invention. More specifically, all
referenced documents are incorporated by reference to the same
extent as if each individual document was specifically and
individually indicated to be incorporated by reference.
FIELD OF THE INVENTION
[0005] The present invention generally relates to compositions,
methods, applications and screens used in functional genomics that
focus on gene function in a cell and that may use vector systems
and other aspects related to Clustered Regularly Interspaced Short
Palindromic Repeats (CRISPR)-Cas systems and components
thereof.
BACKGROUND OF THE INVENTION
[0006] Recent advances in genome sequencing techniques and analysis
methods have significantly accelerated the ability to catalog and
map genetic factors associated with a diverse range of biological
functions and diseases. Functional genomics is a field of molecular
biology that may be considered to utilize the vast wealth of data
produced by genomic projects (such as genome sequencing projects)
to describe gene (and protein) functions and interactions. Contrary
to classical genomics, functional genomics focuses on the dynamic
aspects such as gene transcription, translation, and
protein-protein interactions, as opposed to the static aspects of
the genomic information such as DNA sequence or structures, though
these static aspects are very important and supplement one's
understanding of cellular and molecular mechanisms. Functional
genomics attempts to answer questions about the function of DNA at
the levels of genes, RNA transcripts, and protein products. A key
characteristic of functional genomics studies is a genome-wide
approach to these questions, generally involving high-throughput
methods rather than a more traditional "gene-by-gene" approach.
Given the vast inventory of genes and genetic information it is
advantageous to use genetic screens to provide information of what
these genes do, what cellular pathways they are involved in and how
any alteration in gene expression can result in a particular
biological process.
[0007] Functional genomic screens and libraries attempt to
characterize gene function in the context of living cells and hence
are likely to generate biologically significant data. There are
three key elements for a functional genomics screen: a good reagent
to perturb the gene, a good tissue culture model and a good readout
of cell state. Good reagents that allow for precise genome
targeting technologies are needed to enable systematic reverse
engineering of causal genetic variations by allowing selective
perturbation of individual genetic elements, as well as to advance
synthetic biology, biotechnological, and medical applications.
Although genome-editing techniques such as designer zinc fingers,
transcription activator-like effectors (TALEs), or homing
meganucleases are available for producing targeted genome
perturbations, there remains a need for new genome engineering
technologies that are affordable, easy to set up, scalable, and
amenable to targeting multiple positions within the eukaryotic
genome.
SUMMARY OF THE INVENTION
[0008] The CRISPR-Cas system does not require the generation of
customized proteins to target specific sequences but rather a
single Cas enzyme can be programmed by a short RNA molecule to
recognize a specific DNA target. Adding the CRISPR-Cas system to
the repertoire of genome sequencing techniques and analysis methods
may significantly simplify the methodology and accelerate the
ability to catalog and map genetic factors associated with a
diverse range of biological functions and diseases. To utilize the
CRISPR-Cas system effectively for genome editing without
deleterious effects, it is critical to understand aspects of
engineering, optimization and tissue/organ specific delivery of
these genome engineering tools, which are aspects of the claimed
invention.
[0009] There exists a pressing need for alternative and robust
systems and techniques for sequence targeting with a wide array of
applications. Aspects of this invention address this need and
provide related advantages. An exemplary CRISPR complex comprises a
CRISPR enzyme complexed with a guide sequence hybridized to a
target sequence within the target polynucleotide. The guide
sequence is linked to a tracr mate sequence, which in turn
hybridizes to a tracr sequence.
[0010] One aspect of the invention comprehends a genome wide
library that may comprise a plurality of CRISPR-Cas system guide
RNAs that may comprise guide sequences that are capable of
targeting a plurality of target sequences in a plurality of genomic
loci, wherein said targeting results in a knockout of gene
function. This library may potentially comprise guide RNAs that
target each and every gene in the genome of an organism. In some
embodiments of the invention the organism or subject is a eukaryote
(including mammal including human) or a non-human eukaryote or a
non-human animal or a non-human mammal. In some embodiments, the
organism or subject is a non-human animal, and may be an arthropod,
for example, an insect, or may be a nematode. In some methods of
the invention the organism or subject is a plant. In some methods
of the invention the organism or subject is a mammal or a non-human
mammal. A non-human mammal may be for example a rodent (preferably
a mouse or a rat), an ungulate, or a primate. In some methods of
the invention the organism or subject is algae, including
microalgae, or is a fungus.
[0011] In another aspect, the invention provides a method of
generating a gene knockout cell library comprising introducing into
each cell in a population of cells a vector system of one or more
vectors that may comprise an engineered, non-naturally occurring
CRISPR-Cas system comprising I. a Cas protein, and II. one or more
guide RNAs of the library of the invention, wherein components I
and II may be on the same or on different vectors of the system,
integrating components I and II into each cell, wherein the guide
sequence targets a unique gene in each cell,
wherein the Cas protein is operably linked to a regulatory element,
wherein when transcribed, the guide RNA comprising the guide
sequence directs sequence-specific binding of a CRISPR-Cas system
to a target sequence in the genomic loci of the unique gene,
inducing cleavage of the genomic loci by the Cas protein, and
confirming different knockout mutations in a plurality of unique
genes in each cell of the population of cells thereby generating a
gene knockout cell library. In an embodiment of the invention, the
Cas protein is a Cas9 protein. In another embodiment, the one or
more vectors are plasmid vectors. In a further embodiment, the
regulatory element operably linked to the Cas protein is an
inducible promoter, e.g. a doxycycline inducible promoter. The
invention comprehends that the population of cells is a population
of eukaryotic cells, and in a preferred embodiment, the population
of cells is a population of embryonic stem (ES) cells. In another
embodiment the confirming of different knockout mutations is by
whole exome sequencing. The invention also provides kits that
comprise the genome wide libraries mentioned herein. The kit may
comprise a single container comprising vectors or plasmids
comprising the library of the invention. The kit may also comprise
a panel comprising a selection of unique CRISPR-Cas system guide
RNAs comprising guide sequences from the library of the invention,
wherein the selection is indicative of a particular physiological
condition. The invention comprehends that the targeting is of about
100 or more sequences, about 1000 or more sequences or about 20,000
or more sequences or the entire genome. Furthermore, a panel of
target sequences may be focused on a relevant or desirable pathway,
such as an immune pathway or cell division.
[0012] In another aspect the invention provides for use of genome
wide libraries for functional genomic studies. Such studies focus
on the dynamic aspects such as gene transcription, translation, and
protein-protein interactions, as opposed to the static aspects of
the genomic information such as DNA sequence or structures, though
these static aspects are very important and supplement one's
understanding of cellular and molecular mechanisms. Functional
genomics attempts to answer questions about the function of DNA at
the levels of genes, RNA transcripts, and protein products. A key
characteristic of functional genomics studies is a genome-wide
approach to these questions, generally involving high-throughput
methods rather than a more traditional "gene-by-gene" approach.
Given the vast inventory of genes and genetic information it is
advantageous to use genetic screens to provide information of what
these genes do, what cellular pathways they are involved in and how
any alteration in gene expression can result in particular
biological process.
[0013] In one aspect, the invention provides methods for using one
or more elements of a CRISPR-Cas system. The CRISPR complex of the
invention provides an effective means for modifying a target
polynucleotide. The CRISPR complex of the invention has a wide
variety of utilities including modifying (e.g., deleting,
inserting, translocating, inactivating, activating) a target
polynucleotide in a multiplicity of cell types in various tissues
and organs. As such the CRISPR complex of the invention has a broad
spectrum of applications in, e.g., gene or genome editing, gene
therapy, drug discovery, drug screening, disease diagnosis, and
prognosis.
[0014] Aspects of the invention relate to Cas9 enzymes having
improved target specificity in a CRISPR-Cas9 system having guide
RNAs having optimal activity, smaller in length than wild-type Cas9
enzymes and nucleic acid molecules coding therefor, and chimeric
Cas9 enzymes, as well as methods of improving the target
specificity of a Cas9 enzyme or of designing a CRISPR-Cas9 system
comprising designing or preparing guide RNAs having optimal
activity and/or selecting or preparing a Cas9 enzyme having a
smaller size or length than wild-type Cas9 whereby packaging a
nucleic acid coding therefor into a delivery vector is advanced as
there is less coding therefor in the delivery vector than for
wild-type Cas9, and/or generating chimeric Cas9 enzymes.
[0015] Also provided are uses of the present sequences, vectors,
enzymes or systems, in medicine or in therapy. Also provided are
uses of the same in gene or genome editing. Also provided are the
present sequences, vectors, enzymes, or systems for use in medicine
or in therapy; or for use in gene or genome editing. Still further
provided are uses of the present sequences, vectors, enzymes, or
systems in the manufacture of a medicament.
[0016] In an additional aspect of the invention, a Cas9 enzyme may
comprise one or more mutations and may be used as a generic DNA
binding protein with or without fusion to a functional domain. The
mutations may be artificially introduced mutations or gain- or
loss-of-function mutations. The mutations may include but are not
limited to mutations in one of the catalytic domains (D10 and H840)
in the RuvC and HNH catalytic domains, respectively. Further
mutations have been characterized. In one aspect of the invention,
the functional domain may be a transcriptional activation domain,
which may be VP64. In other aspects of the invention, the
functional domain may be a transcriptional repressor domain, which
may be KRAB or SID4X. Other aspects of the invention relate to the
mutated Cas 9 enzyme being fused to domains which include but are
not limited to a transcriptional activator, repressor, a
recombinase, a transposase, a histone remodeler, a demethylase, a
DNA methyltransferase, a cryptochrome, a light
inducible/controllable domain or a chemically
inducible/controllable domain.
[0017] In a further embodiment, the invention provides for methods
to generate mutant tracrRNA and direct repeat sequences or mutant
chimeric guide sequences that allow for enhancing performance of
these RNAs in cells. Aspects of the invention also provide for
selection of said sequences.
[0018] Aspects of the invention also provide for methods of
simplifying the cloning and delivery of components of the CRISPR
complex. In a preferred embodiment of the invention, a suitable
promoter, such as the U6 promoter, is amplified with a DNA oligo
and added onto the guide RNA. The resulting PCR product can then be
transfected into cells to drive expression of the guide RNA.
Aspects of the invention also relate to the guide RNA being
transcribed in vitro or ordered from a synthesis company and
directly transfected.
[0019] In one aspect, the invention provides for methods to improve
activity by using a more active polymerase. In a preferred
embodiment, the expression of guide RNAs under the control of the
T7 promoter is driven by the expression of the T7 polymerase in the
cell. In an advantageous embodiment, the cell is a eukaryotic cell.
In a preferred embodiment the eukaryotic cell is a human cell. In a
more preferred embodiment the human cell is a patient specific
cell.
[0020] In one aspect, the invention provides for methods of
reducing the toxicity of Cas enzymes. In certain aspects, the Cas
enzyme is any Cas9 as described herein, for instance any
naturally-occurring bacterial Cas9 as well as any chimaeras,
mutants, homologs or orthologs. In a preferred embodiment, the Cas9
is delivered into the cell in the form of mRNA. This allows for the
transient expression of the enzyme thereby reducing toxicity. In
another preferred embodiment, the invention also provides for
methods of expressing Cas9 under the control of an inducible
promoter, and the constructs used therein.
[0021] In another aspect, the invention provides for methods of
improving the in vivo applications of the CRISPR-Cas system. In the
preferred embodiment, the Cas enzyme is wildtype Cas9 or any of the
modified versions described herein, including any
naturally-occurring bacterial Cas9 as well as any chimaeras,
mutants, homologs or orthologs. An advantageous aspect of the
invention provides for the selection of Cas9 homologs that are
easily packaged into viral vectors for delivery. Cas9 orthologs
typically share the general organization of 3-4 RuvC domains and a
HNH domain. The 5' most RuvC domain cleaves the non-complementary
strand, and the HNH domain cleaves the complementary strand. All
notations are in reference to the guide sequence.
[0022] The catalytic residue in the 5' RuvC domain is identified
through homology comparison of the Cas9 of interest with other Cas9
orthologs (from S. pyogenes type II CRISPR locus, S. thermophilus
CRISPR locus 1, S. thermophilus CRISPR locus 3, and Franciscilla
novicida type II CRISPR locus), and the conserved Asp residue (D10)
is mutated to alanine to convert Cas9 into a complementary-strand
nicking enzyme. Similarly, the conserved His and Asn residues in
the HNH domains are mutated to Alanine to convert Cas9 into a
non-complementary-strand nicking enzyme. In some embodiments, both
sets of mutations may be made, to convert Cas9 into a non-cutting
enzyme.
[0023] In some embodiments, the CRISPR enzyme is a type I or III
CRISPR enzyme, preferably a type II CRISPR enzyme. This type II
CRISPR enzyme may be any Cas enzyme. A preferred Cas enzyme may be
identified as Cas9 as this can refer to the general class of
enzymes that share homology to the biggest nuclease with multiple
nuclease domains from the type II CRISPR system. Most preferably,
the Cas9 enzyme is from, or is derived from, spCas9 or saCas9. By
derived, Applicants mean that the derived enzyme is largely based,
in the sense of having a high degree of sequence homology with, a
wildtype enzyme, but that it has been mutated (modified) in some
way as described herein
[0024] It will be appreciated that the terms Cas and CRISPR enzyme
are generally used herein interchangeably, unless otherwise
apparent. As mentioned above, many of the residue numberings used
herein refer to the Cas9 enzyme from the type II CRISPR locus in
Streptococcus pyogenes. However, it will be appreciated that this
invention includes many more Cas9s from other species of microbes,
such as SpCas9, SaCas9, St1Cas9 and so forth. Further examples are
provided herein. The skilled person will be able to determine
appropriate corresponding residues in Cas9 enzymes other than
SpCas9 by comparison of the relevant amino acid sequences. Thus,
where a specific amino acid replacement is referred to using the
SpCas9 numbering, then, unless the context makes it apparent this
is not intended to refer to other Cas9 enzymes, the disclosure is
intended to encompass corresponding modifications in other Cas9
enzymes.
[0025] An example of a codon optimized sequence, in this instance
optimized for humans (i.e. being optimized for expression in
humans) is provided herein, see the SaCas9 human codon optimized
sequence. Whilst this is preferred, it will be appreciated that
other examples are possible and codon optimization for a host
species is known.
[0026] In further embodiments, the invention provides for methods
of enhancing the function of Cas9 by generating chimeric Cas9
proteins. Chimeric Cas9 proteins may be new Cas9 containing
fragments from more than one naturally occurring Cas9. These
methods may comprise fusing N-terminal fragments of one Cas9
homolog with C-terminal fragments of another Cas9 homolog. These
methods also allow for the selection of new properties displayed by
the chimeric Cas9 proteins.
[0027] It will be appreciated that in the present methods, where
the organism is an animal or a plant, the modification may occur ex
vivo or in vitro, for instance in a cell culture and in some
instances not in vivo. In other embodiments, it may occur in vivo.
Where the modification occurs ex vivo or in vitro, a modified cell
may be used to generate a complete organism, or a modified cell may
be introduced or reintroduced into a host organism.
[0028] In one aspect, the invention provides a method of modifying
an organism or a non-human organism by manipulation of a target
sequence in a genomic locus of interest comprising: delivering a
non-naturally occurring or engineered composition comprising:
A)--I. a CRISPR-Cas system chimeric RNA (chiRNA) polynucleotide
sequence, wherein the polynucleotide sequence comprises: (a) a
guide sequence capable of hybridizing to a target sequence in a
eukaryotic cell, (b) a tracr mate sequence, and (c) a tracr
sequence, and II. a polynucleotide sequence encoding a CRISPR
enzyme comprising at least one or more nuclear localization
sequences, wherein (a), (b) and (c) are arranged in a 5' to 3'
orientation, wherein when transcribed, the tracr mate sequence
hybridizes to the tracr sequence and the guide sequence directs
sequence-specific binding of a CRISPR complex to the target
sequence, and wherein the CRISPR complex comprises the CRISPR
enzyme complexed with (1) the guide sequence that is hybridized to
the target sequence, and (2) the tracr mate sequence that is
hybridized to the tracr sequence and the polynucleotide sequence
encoding a CRISPR enzyme is DNA or RNA, or (B) I. polynucleotides
comprising: (a) a guide sequence capable of hybridizing to a target
sequence in a eukaryotic cell, and (b) at least one or more tracr
mate sequences, II. a polynucleotide sequence encoding a CRISPR
enzyme, and III. a polynucleotide sequence comprising a tracr
sequence, wherein when transcribed, the tracr mate sequence
hybridizes to the tracr sequence and the guide sequence directs
sequence-specific binding of a CRISPR complex to the target
sequence, and wherein the CRISPR complex comprises the CRISPR
enzyme complexed with (1) the guide sequence that is hybridized to
the target sequence, and (2) the tracr mate sequence that is
hybridized to the tracr sequence, and the polynucleotide sequence
encoding a CRISPR enzyme is DNA or RNA.
[0029] Any or all of the polynucleotide sequence encoding a CRISPR
enzyme, guide sequence, tracr mate sequence or tracr sequence, may
be RNA. The polynucleotides encoding the sequence encoding a CRISPR
enzyme, the guide sequence, tracr mate sequence or tracr sequence
may be RNA and may be delivered via liposomes, nanoparticles,
exosomes, microvesicles, or a gene-gun.
[0030] It will be appreciated that where reference is made to a
polynucleotide, which is RNA and is said to `comprise` a feature
such as a tracr mate sequence, the RNA sequence includes the
feature. Where the polynucleotide is DNA and is said to comprise a
feature such as a tracr mate sequence, the DNA sequence is or can
be transcribed into the RNA including the feature at issue. Where
the feature is a protein, such as the CRISPR enzyme, the DNA or RNA
sequence referred to is, or can be, translated (and in the case of
DNA transcribed first).
[0031] Accordingly, in certain embodiments the invention provides a
method of modifying an organism, e.g., mammal including human or a
non-human mammal or organism by manipulation of a target sequence
in a genomic locus of interest comprising delivering a
non-naturally occurring or engineered composition comprising a
viral or plasmid vector system comprising one or more viral or
plasmid vectors operably encoding a composition for expression
thereof, wherein the composition comprises: (A) a non-naturally
occurring or engineered composition comprising a vector system
comprising one or more vectors comprising I. a first regulatory
element operably linked to a CRISPR-Cas system chimeric RNA
(chiRNA) polynucleotide sequence, wherein the polynucleotide
sequence comprises (a) a guide sequence capable of hybridizing to a
target sequence in a eukaryotic cell, (b) a tracr mate sequence,
and (c) a tracr sequence, and II. a second regulatory element
operably linked to an enzyme-coding sequence encoding a CRISPR
enzyme comprising at least one or more nuclear localization
sequences (or optionally at least one or more nuclear localization
sequences as some embodiments can involve no NLS), wherein (a), (b)
and (c) are arranged in a 5' to 3' orientation, wherein components
I and II are located on the same or different vectors of the
system, wherein when transcribed, the tracr mate sequence
hybridizes to the tracr sequence and the guide sequence directs
sequence-specific binding of a CRISPR complex to the target
sequence, and wherein the CRISPR complex comprises the CRISPR
enzyme complexed with (1) the guide sequence that is hybridized to
the target sequence, and (2) the tracr mate sequence that is
hybridized to the tracr sequence, or (B) a non-naturally occurring
or engineered composition comprising a vector system comprising one
or more vectors comprising I. a first regulatory element operably
linked to (a) a guide sequence capable of hybridizing to a target
sequence in a eukaryotic cell, and (b) at least one or more tracr
mate sequences, II. a second regulatory element operably linked to
an enzyme-coding sequence encoding a CRISPR enzyme, and III. a
third regulatory element operably linked to a tracr sequence,
wherein components I, II and III are located on the same or
different vectors of the system, wherein when transcribed, the
tracr mate sequence hybridizes to the tracr sequence and the guide
sequence directs sequence-specific binding of a CRISPR complex to
the target sequence, and wherein the CRISPR complex comprises the
CRISPR enzyme complexed with (1) the guide sequence that is
hybridized to the target sequence, and (2) the tracr mate sequence
that is hybridized to the tracr sequence. In some embodiments,
components I, II and III are located on the same vector. In other
embodiments, components I and II are located on the same vector,
while component III is located on another vector. In other
embodiments, components I and III are located on the same vector,
while component II is located on another vector. In other
embodiments, components II and III are located on the same vector,
while component I is located on another vector. In other
embodiments, each of components I, II and III is located on
different vectors. The invention also provides a viral or plasmid
vector system as described herein.
[0032] Preferably, the vector is a viral vector, such as a lenti-
or baculo- or preferably adeno-viral/adeno-associated viral
vectors, but other means of delivery are known (such as yeast
systems, microvesicles, gene guns/means of attaching vectors to
gold nanoparticles) and are provided. In some embodiments, one or
more of the viral or plasmid vectors may be delivered via
liposomes, nanoparticles, exosomes, microvesicles, or a
gene-gun.
[0033] By manipulation of a target sequence, Applicants also mean
the epigenetic manipulation of a target sequence. This may be of
the chromatin state of a target sequence, such as by modification
of the methylation state of the target sequence (i.e. addition or
removal of methylation or methylation patterns or CpG islands),
histone modification, increasing or reducing accessibility to the
target sequence, or by promoting 3D folding.
[0034] It will be appreciated that where reference is made to a
method of modifying an organism or mammal including human or a
non-human mammal or organism by manipulation of a target sequence
in a genomic locus of interest, this may apply to the organism (or
mammal) as a whole or just a single cell or population of cells
from that organism (if the organism is multicellular). In the case
of humans, for instance, Applicants envisage, inter alia, a single
cell or a population of cells and these may preferably be modified
ex vivo and then re-introduced. In this case, a biopsy or other
tissue or biological fluid sample may be necessary. Stem cells are
also particularly preferred in this regard. But, of course, in vivo
embodiments are also envisaged.
[0035] In certain embodiments the invention provides a method of
treating or inhibiting a condition caused by a defect in a target
sequence in a genomic locus of interest in a subject (e.g., mammal
or human) or a non-human subject (e.g., mammal) in need thereof
comprising modifying the subject or a non-human subject by
manipulation of the target sequence and wherein the condition is
susceptible to treatment or inhibition by manipulation of the
target sequence comprising providing treatment comprising:
delivering a non-naturally occurring or engineered composition
comprising an AAV or lentivirus vector system comprising one or
more AAV or lentivirus vectors operably encoding a composition for
expression thereof, wherein the target sequence is manipulated by
the composition when expressed, wherein the composition comprises:
(A) a non-naturally occurring or engineered composition comprising
a vector system comprising one or more vectors comprising I. a
first regulatory element operably linked to a CRISPR-Cas system
chimeric RNA (chiRNA) polynucleotide sequence, wherein the
polynucleotide sequence comprises (a) a guide sequence capable of
hybridizing to a target sequence in a eukaryotic cell, (b) a tracr
mate sequence, and (c) a tracr sequence, and II. a second
regulatory element operably linked to an enzyme-coding sequence
encoding a CRISPR enzyme comprising at least one or more nuclear
localization sequences (or optionally at least one or more nuclear
localization sequences as some embodiments can involve no NLS)
wherein (a), (b) and (c) are arranged in a 5' to 3' orientation,
wherein components I and II are located on the same or different
vectors of the system, wherein when transcribed, the tracr mate
sequence hybridizes to the tracr sequence and the guide sequence
directs sequence-specific binding of a CRISPR complex to the target
sequence, and wherein the CRISPR complex comprises the CRISPR
enzyme complexed with (1) the guide sequence that is hybridized to
the target sequence, and (2) the tracr mate sequence that is
hybridized to the tracr sequence, or (B) a non-naturally occurring
or engineered composition comprising a vector system comprising one
or more vectors comprising I. a first regulatory element operably
linked to (a) a guide sequence capable of hybridizing to a target
sequence in a eukaryotic cell, and (b) at least one or more tracr
mate sequences, II. a second regulatory element operably linked to
an enzyme-coding sequence encoding a CRISPR enzyme, and III. a
third regulatory element operably linked to a tracr sequence,
wherein components I, II and III are located on the same or
different vectors of the system, wherein when transcribed, the
tracr mate sequence hybridizes to the tracr sequence and the guide
sequence directs sequence-specific binding of a CRISPR complex to
the target sequence, and wherein the CRISPR complex comprises the
CRISPR enzyme complexed with (1) the guide sequence that is
hybridized to the target sequence, and (2) the tracr mate sequence
that is hybridized to the tracr sequence. In some embodiments,
components I, II and III are located on the same vector. In other
embodiments, components I and II are located on the same vector,
while component III is located on another vector. In other
embodiments, components I and III are located on the same vector,
while component II is located on another vector. In other
embodiments, components II and III are located on the same vector,
while component I is located on another vector. In other
embodiments, each of components I, II and III is located on
different vectors. The invention also provides a viral (e.g. AAV or
lentivirus) vector system as described herein.
[0036] Some methods of the invention can include inducing
expression. In some methods of the invention the organism or
subject is a eukaryote (including mammal including human) or a
non-human eukaryote or a non-human animal or a non-human mammal. In
some embodiments, the organism or subject is a non-human animal,
and may be an arthropod, for example, an insect, or may be a
nematode. In some methods of the invention the organism or subject
is a plant. In some methods of the invention the organism or
subject is a mammal or a non-human mammal. A non-human mammal may
be for example a rodent (preferably a mouse or a rat), an ungulate,
or a primate. In some methods of the invention the organism or
subject is algae, including microalgae, or is a fungus. In some
methods of the invention the viral vector is an AAV or a
lentivirus, and can be part of a vector system as described herein.
In some methods of the invention the CRISPR enzyme is a Cas9. In
some methods of the invention the expression of the guide sequence
is under the control of the T7 promoter and is driven by the
expression of T7 polymerase.
[0037] The invention in some embodiments comprehends a method of
delivering a CRISPR enzyme comprising delivering to a cell mRNA
encoding the CRISPR enzyme. In some of these methods the CRISPR
enzyme is a Cas9.
[0038] The invention also provides methods of preparing the vector
systems of the invention, in particular the viral vector systems as
described herein. The invention in some embodiments comprehends a
method of preparing the AAV of the invention comprising
transfecting plasmid(s) containing or consisting essentially of
nucleic acid molecule(s) coding for the AAV into AAV-infected
cells, and supplying AAV rep and/or cap obligatory for replication
and packaging of the AAV. In some embodiments the AAV rep and/or
cap obligatory for replication and packaging of the AAV are
supplied by transfecting the cells with helper plasmid(s) or helper
virus(es). In some embodiments the helper virus is a poxvirus,
adenovirus, herpesvirus or baculovirus. In some embodiments the
poxvirus is a vaccinia virus. In some embodiments the cells are
mammalian cells. And in some embodiments the cells are insect cells
and the helper virus is baculovirus. In other embodiments, the
virus is a lentivirus.
[0039] In plants, pathogens are often host-specific. For example,
Fusarium oxyvsporum f. sp. lycopersici causes tomato wilt but
attacks only tomato, and F. oxysporum f. dianthii Puccinia graminis
f. sp. tritici attacks only wheat. Plants have existing and induced
defenses to resist most pathogens. Mutations and recombination
events across plant generations lead to genetic variability that
gives rise to susceptibility, especially as pathogens reproduce
with more frequency than plants. In plants there can be non-host
resistance, e.g., the host and pathogen are incompatible. There can
also be Horizontal Resistance, e.g., partial resistance against all
races of a pathogen, typically controlled by many genes and
Vertical Resistance, e.g., complete resistance to some races of a
pathogen but not to other races, typically controlled by a few
genes. In a Gene-for-Gene level, plants and pathogens evolve
together, and the genetic changes in one balance changes in other.
Accordingly, using Natural Variability, breeders combine most
useful genes for Yield, Quality, Uniformity, Hardiness, Resistance.
The sources of resistance genes include native or foreign
Varieties, Heirloom Varieties, Wild Plant Relatives, and Induced
Mutations, e.g., treating plant material with mutagenic agents.
Using the present invention, plant breeders are provided with a new
tool to induce mutations. Accordingly, one skilled in the art can
analyze the genome of sources of resistance genes, and in Varieties
having desired characteristics or traits employ the present
invention to induce the rise of resistance genes, with more
precision than previous mutagenic agents and hence accelerate and
improve plant breeding programs.
[0040] The invention further comprehends a composition of the
invention or a CRISPR enzyme thereof (including or alternatively
mRNA encoding the CRISPR enzyme) for use in medicine or in therapy.
In some embodiments the invention comprehends a composition
according to the invention or a CRISPR enzyme thereof (including or
alternatively mRNA encoding the CRISPR enzyme) for use in a method
according to the invention. In some embodiments the invention
provides for the use of a composition of the invention or a CRISPR
enzyme thereof (including or alternatively mRNA encoding the CRISPR
enzyme) in ex vivo gene or genome editing. In certain embodiments
the invention comprehends use of a composition of the invention or
a CRISPR enzyme thereof (including or alternatively mRNA encoding
the CRISPR enzyme) in the manufacture of a medicament for ex vivo
gene or genome editing or for use in a method according of the
invention. The invention comprehends in some embodiments a
composition of the invention or a CRISPR enzyme thereof (including
or alternatively mRNA encoding the CRISPR enzyme), wherein the
target sequence is flanked at its 3' end by a PAM (protospacer
adjacent motif) sequence comprising 5'-motif, especially where the
Cas9 is (or is derived from) S. pyogenes or S. aureus Cas9. For
example, a suitable PAM is 5'-NRG or 5'-NNGRR (where N is any
Nucleotide) for SpCas9 or SaCas9 enzymes (or derived enzymes),
respectively, as mentioned below.
[0041] It will be appreciated that SpCas9 or SaCas9 are those from
or derived from S. pyogenes or S. aureus Cas9.
[0042] Aspects of the invention comprehend improving the
specificity of a CRISPR enzyme, e.g. Cas9, mediated gene targeting
and reducing the likelihood of off-target modification by the
CRISPR enzyme, e.g. Cas9. The invention in some embodiments
comprehends a method of modifying an organism or a non-human
organism with a reduction in likelihood of off-target modifications
by manipulation of a first and a second target sequence on opposite
strands of a DNA duplex in a genomic locus of interest in a cell
comprising delivering a non-naturally occurring or engineered
composition comprising:
[0043] I. a first CRISPR-Cas system chimeric RNA (chiRNA)
polynucleotide sequence,
wherein the first polynucleotide sequence comprises: (a) a first
guide sequence capable of hybridizing to the first target sequence,
(b) a first tracr mate sequence, and (c) a first tracr
sequence,
[0044] II. a second CRISPR-Cas system chiRNA polynucleotide
sequence, wherein the second polynucleotide sequence comprises:
(a) a second guide sequence capable of hybridizing to the second
target sequence, (b) a second tracr mate sequence, and (c) a second
tracr sequence, and
[0045] III. a polynucleotide sequence encoding a CRISPR enzyme
comprising at least one or more nuclear localization sequences and
comprising one or more mutations, wherein (a), (b) and (c) are
arranged in a 5' to 3' orientation, wherein when transcribed, the
first and the second tracr mate sequence hybridize to the first and
second tracr sequence respectively and the first and the second
guide sequence directs sequence-specific binding of a first and a
second CRISPR complex to the first and second target sequences
respectively, wherein the first CRISPR complex comprises the CRISPR
enzyme complexed with (1) the first guide sequence that is
hybridized to the first target sequence, and (2) the first tracr
mate sequence that is hybridized to the first tracr sequence,
wherein the second CRISPR complex comprises the CRISPR enzyme
complexed with (1) the second guide sequence that is hybridized to
the second target sequence, and (2) the second tract mate sequence
that is hybridized to the second tracr sequence, wherein the
polynucleotide sequence encoding a CRISPR enzyme is DNA or RNA, and
wherein the first guide sequence directs cleavage of one strand of
the DNA duplex near the first target sequence and the second guide
sequence directs cleavage of the other strand near the second
target sequence inducing a double strand break, thereby modifying
the organism or the non-human organism with a reduction in
likelihood of off-target modifications.
[0046] In some methods of the invention any or all of the
polynucleotide sequence encoding the CRISPR enzyme, the first and
the second guide sequence, the first and the second tracr mate
sequence or the first and the second tracr sequence, is/are RNA. In
further embodiments of the invention the polynucleotides encoding
the sequence encoding the CRISPR enzyme, the first and the second
guide sequence, the first and the second tracr mate sequence or the
first and the second tracr sequence, is/are RNA and are delivered
via liposomes, nanoparticles, exosomes, microvesicles, or a
gene-gun. In certain embodiments of the invention, the first and
second tracr mate sequence share 100% identity and/or the first and
second tracr sequence share 100% identity. In some embodiments, the
polynucleotides may be comprised within a vector system comprising
one or more vectors. In preferred embodiments of the invention the
CRISPR enzyme is a Cas9 enzyme, e.g. SpCas9. In an aspect of the
invention the CRISPR enzyme comprises one or more mutations in a
catalytic domain, wherein the one or more mutations are selected
from the group consisting of D10A, E762A, H840A, N854A, N863A and
D986A. In a highly preferred embodiment the CRISPR enzyme has the
D10A mutation. In preferred embodiments, the first CRISPR enzyme
has one or more mutations such that the enzyme is a complementary
strand nicking enzyme, and the second CRISPR enzyme has one or more
mutations such that the enzyme is a non-complementary strand
nicking enzyme. Alternatively the first enzyme may be a
non-complementary strand nicking enzyme, and the second enzyme may
be a complementary strand nicking enzyme.
[0047] In preferred methods of the invention the first guide
sequence directing cleavage of one strand of the DNA duplex near
the first target sequence and the second guide sequence directing
cleavage of the other strand near the second target sequence
results in a 5' overhang. In embodiments of the invention the 5'
overhang is at most 200 base pairs, preferably at most 100 base
pairs, or more preferably at most 50 base pairs. In embodiments of
the invention the 5' overhang is at least 26 base pairs, preferably
at least 30 base pairs or more preferably 34-50 base pairs.
[0048] The invention in some embodiments comprehends a method of
modifying an organism or a non-human organism with a reduction in
likelihood of off-target modifications by manipulation of a first
and a second target sequence on opposite strands of a DNA duplex in
a genomic locus of interest in a cell comprising delivering a
non-naturally occurring or engineered composition comprising a
vector system comprising one or more vectors comprising
[0049] I. a first regulatory element operably linked to
(a) a first guide sequence capable of hybridizing to the first
target sequence, and (b) at least one or more tracr mate
sequences,
[0050] II. a second regulatory element operably linked to
(a) a second guide sequence capable of hybridizing to the second
target sequence, and (b) at least one or more tracr mate
sequences,
[0051] III. a third regulatory element operably linked to an
enzyme-coding sequence encoding a CRISPR enzyme, and
[0052] IV. a fourth regulatory element operably linked to a tracr
sequence,
[0053] wherein components I, II, III and IV are located on the same
or different vectors of the system, when transcribed, the tracr
mate sequence hybridizes to the tracr sequence and the first and
the second guide sequence direct sequence-specific binding of a
first and a second CRISPR complex to the first and second target
sequences respectively, wherein the first CRISPR complex comprises
the CRISPR enzyme complexed with (1) the first guide sequence that
is hybridized to the first target sequence, and (2) the tracr mate
sequence that is hybridized to the tracr sequence, wherein the
second CRISPR complex comprises the CRISPR enzyme complexed with
(1) the second guide sequence that is hybridized to the second
target sequence, and (2) the tracr mate sequence that is hybridized
to the tracr sequence, wherein the polynucleotide sequence encoding
a CRISPR enzyme is DNA or RNA, and wherein the first guide sequence
directs cleavage of one strand of the DNA duplex near the first
target sequence and the second guide sequence directs cleavage of
the other strand near the second target sequence inducing a double
strand break, thereby modifying the organism or the non-human
organism with a reduction in likelihood of off-target
modifications.
[0054] The invention also provides a vector system as described
herein. The system may comprise one, two, three or four different
vectors. Components I, II, III and IV may thus be located on one,
two, three or four different vectors, and all combinations for
possible locations of the components are herein envisaged, for
example: components I, II, III and IV can be located on the same
vector; components I, II, III and IV can each be located on
different vectors; components I, II, III and IV may be located on a
total of two or three different vectors, with all combinations of
locations envisaged, etc.
[0055] In some methods of the invention any or all of the
polynucleotide sequence encoding the CRISPR enzyme, the first and
the second guide sequence, the first and the second tracr mate
sequence or the first and the second tracr sequence, is/are RNA. In
further embodiments of the invention the first and second tracr
mate sequence share 100% identity and/or the first and second tracr
sequence share 100% identity. In preferred embodiments of the
invention the CRISPR enzyme is a Cas9 enzyme, e.g. SpCas9. In an
aspect of the invention the CRISPR enzyme comprises one or more
mutations in a catalytic domain, wherein the one or more mutations
are selected from the group consisting of D10A, E762A, H840A.
N854A, N863A and D986A. In a highly preferred embodiment the CRISPR
enzyme has the D10A mutation. In preferred embodiments, the first
CRISPR enzyme has one or more mutations such that the enzyme is a
complementary strand nicking enzyme, and the second CRISPR enzyme
has one or more mutations such that the enzyme is a
non-complementary strand nicking enzyme. Alternatively the first
enzyme may be a non-complementary strand nicking enzyme, and the
second enzyme may be a complementary strand nicking enzyme. In a
further embodiment of the invention, one or more of the viral
vectors are delivered via liposomes, nanoparticles, exosomes,
microvesicles, or a gene-gun.
[0056] In preferred methods of the invention the first guide
sequence directing cleavage of one strand of the DNA duplex near
the first target sequence and the second guide sequence directing
cleavage of other strand near the second target sequence results in
a 5' overhang. In embodiments of the invention the 5' overhang is
at most 200 base pairs, preferably at most 100 base pairs, or more
preferably at most 50 base pairs. In embodiments of the invention
the 5' overhang is at least 26 base pairs, preferably at least 30
base pairs or more preferably 34-50 base pairs.
[0057] The invention in some embodiments comprehends a method of
modifying a genomic locus of interest with a reduction in
likelihood of off-target modifications by introducing into a cell
containing and expressing a double stranded DNA molecule encoding a
gene product of interest an engineered, non-naturally occurring
CRISPR-Cas system comprising a Cas protein having one or more
mutations and two guide RNAs that target a first strand and a
second strand of the DNA molecule respectively, whereby the guide
RNAs target the DNA molecule encoding the gene product and the Cas
protein nicks each of the first strand and the second strand of the
DNA molecule encoding the gene product, whereby expression of the
gene product is altered; and, wherein the Cas protein and the two
guide RNAs do not naturally occur together.
[0058] In preferred methods of the invention the Cas protein
nicking each of the first strand and the second strand of the DNA
molecule encoding the gene product results in a 5' overhang. In
embodiments of the invention the 5' overhang is at most 200 base
pairs, preferably at most 100 base pairs, or more preferably at
most 50 base pairs. In embodiments of the invention the 5' overhang
is at least 26 base pairs, preferably at least 30 base pairs or
more preferably 34-50 base pairs.
[0059] Embodiments of the invention also comprehend the guide RNAs
comprising a guide sequence fused to a tracr mate sequence and a
tracr sequence. In an aspect of the invention the Cas protein is
codon optimized for expression in a eukaryotic cell, preferably a
mammalian cell or a human cell. In further embodiments of the
invention the Cas protein is a type II CRISPR-Cas protein, e.g. a
Cas 9 protein. In a highly preferred embodiment the Cas protein is
a Cas9 protein, e.g. SpCas9. In aspects of the invention the Cas
protein has one or more mutations selected from the group
consisting of D10A, E762A, H840A, N854A, N863A and D986A. In a
highly preferred embodiment the Cas protein has the D10A
mutation.
[0060] Aspects of the invention relate to the expression of the
gene product being decreased or a template polynucleotide being
further introduced into the DNA molecule encoding the gene product
or an intervening sequence being excised precisely by allowing the
two 5' overhangs to reanneal and ligate or the activity or function
of the gene product being altered or the expression of the gene
product being increased. In an embodiment of the invention, the
gene product is a protein.
[0061] The invention also comprehends an engineered, non-naturally
occurring CRISPR-Cas system comprising a Cas protein having one or
more mutations and two guide RNAs that target a first strand and a
second strand respectively of a double stranded DNA molecule
encoding a gene product in a cell, whereby the guide RNAs target
the DNA molecule encoding the gene product and the Cas protein
nicks each of the first strand and the second strand of the DNA
molecule encoding the gene product, whereby expression of the gene
product is altered; and, wherein the Cas protein and the two guide
RNAs do not naturally occur together.
[0062] In aspects of the invention the guide RNAs may comprise a
guide sequence fused to a tracr mate sequence and a tracr sequence.
In an embodiment of the invention the Cas protein is a type II
CRISPR-Cas protein. In an aspect of the invention the Cas protein
is codon optimized for expression in a eukaryotic cell, preferably
a mammalian cell or a human cell. In further embodiments of the
invention the Cas protein is a type II CRISPR-Cas protein, e.g. a
Cas 9 protein. In a highly preferred embodiment the Cas protein is
a Cas9 protein, e.g. SpCas9. In aspects of the invention the Cas
protein has one or more mutations selected from the group
consisting of D10A, E762A, H840A, N854A, N863A and D986A. In a
highly preferred embodiment the Cas protein has the D10A
mutation.
[0063] Aspects of the invention relate to the expression of the
gene product being decreased or a template polynucleotide being
further introduced into the DNA molecule encoding the gene product
or an intervening sequence being excised precisely by allowing the
two 5' overhangs to reanneal and ligate or the activity or function
of the gene product being altered or the expression of the gene
product being increased. In an embodiment of the invention, the
gene product is a protein.
[0064] The invention also comprehends an engineered, non-naturally
occurring vector system comprising one or more vectors
comprising:
a) a first regulatory element operably linked to each of two
CRISPR-Cas system guide RNAs that target a first strand and a
second strand respectively of a double stranded DNA molecule
encoding a gene product, b) a second regulatory element operably
linked to a Cas protein, wherein components (a) and (b) are located
on same or different vectors of the system, whereby the guide RNAs
target the DNA molecule encoding the gene product and the Cas
protein nicks each of the first strand and the second strand of the
DNA molecule encoding the gene product, whereby expression of the
gene product is altered; and, wherein the Cas protein and the two
guide RNAs do not naturally occur together.
[0065] In aspects of the invention the guide RNAs may comprise a
guide sequence fused to a tracr mate sequence and a tracr sequence.
In an embodiment of the invention the Cas protein is a type II
CRISPR-Cas protein. In an aspect of the invention the Cas protein
is codon optimized for expression in a eukaryotic cell, preferably
a mammalian cell or a human cell. In further embodiments of the
invention the Cas protein is a type II CRISPR-Cas protein, e.g. a
Cas 9 protein. In a highly preferred embodiment the Cas protein is
a Cas9 protein, e.g. SpCas9. In aspects of the invention the Cas
protein has one or more mutations selected from the group
consisting of D10A, E762A, H840A, N854A, N863A and D986A. In a
highly preferred embodiment the Cas protein has the D10A
mutation.
[0066] Aspects of the invention relate to the expression of the
gene product being decreased or a template polynucleotide being
further introduced into the DNA molecule encoding the gene product
or an intervening sequence being excised precisely by allowing the
two 5' overhangs to reanneal and ligate or the activity or function
of the gene product being altered or the expression of the gene
product being increased. In an embodiment of the invention, the
gene product is a protein. In preferred embodiments of the
invention the vectors of the system are viral vectors. In a further
embodiment, the vectors of the system are delivered via liposomes,
nanoparticles, exosomes, microvesicles, or a gene-gun.
[0067] In one aspect, the invention provides a method of modifying
a target polynucleotide in a eukaryotic cell. In some embodiments,
the method comprises allowing a CRISPR complex to bind to the
target polynucleotide to effect cleavage of said target
polynucleotide thereby modifying the target polynucleotide, wherein
the CRISPR complex comprises a CRISPR enzyme complexed with a guide
sequence hybridized to a target sequence within said target
polynucleotide, wherein said guide sequence is linked to a tracr
mate sequence which in turn hybridizes to a tracr sequence. In some
embodiments, said cleavage comprises cleaving one or two strands at
the location of the target sequence by said CRISPR enzyme. In some
embodiments, said cleavage results in decreased transcription of a
target gene. In some embodiments, the method further comprises
repairing said cleaved target polynucleotide by homologous
recombination with an exogenous template polynucleotide, wherein
said repair results in a mutation comprising an insertion,
deletion, or substitution of one or more nucleotides of said target
polynucleotide. In some embodiments, said mutation results in one
or more amino acid changes in a protein expressed from a gene
comprising the target sequence. In some embodiments, the method
further comprises delivering one or more vectors to said eukaryotic
cell, wherein the one or more vectors drive expression of one or
more of: the CRISPR enzyme, the guide sequence linked to the tracr
mate sequence, and the tracr sequence. In some embodiments, said
vectors are delivered to the eukaryotic cell in a subject. In some
embodiments, said modifying takes place in said eukaryotic cell in
a cell culture. In some embodiments, the method further comprises
isolating said eukaryotic cell from a subject prior to said
modifying. In some embodiments, the method further comprises
returning said eukaryotic cell and/or cells derived therefrom to
said subject.
[0068] In one aspect, the invention provides a method of modifying
expression of a polynucleotide in a eukaryotic cell. In some
embodiments, the method comprises allowing a CRISPR complex to bind
to the polynucleotide such that said binding results in increased
or decreased expression of said polynucleotide; wherein the CRISPR
complex comprises a CRISPR enzyme complexed with a guide sequence
hybridized to a target sequence within said polynucleotide, wherein
said guide sequence is linked to a tracr mate sequence which in
turn hybridizes to a tracr sequence. In some embodiments, the
method further comprises delivering one or more vectors to said
eukaryotic cells, wherein the one or more vectors drive expression
of one or more of: the CRISPR enzyme, the guide sequence linked to
the tracr mate sequence, and the tracr sequence.
[0069] In one aspect, the invention provides a method of generating
a model eukaryotic cell comprising a mutated disease gene. In some
embodiments, a disease gene is any gene associated with an increase
in the risk of having or developing a disease. In some embodiments,
the method comprises (a) introducing one or more vectors into a
eukaryotic cell, wherein the one or more vectors drive expression
of one or more of: a CRISPR enzyme, a guide sequence linked to a
tracr mate sequence, and a tracr sequence; and (b) allowing a
CRISPR complex to bind to a target polynucleotide to effect
cleavage of the target polynucleotide within said disease gene,
wherein the CRISPR complex comprises the CRISPR enzyme complexed
with (1) the guide sequence that is hybridized to the target
sequence within the target polynucleotide, and (2) the tracr mate
sequence that is hybridized to the tracr sequence, thereby
generating a model eukaryotic cell comprising a mutated disease
gene. In some embodiments, said cleavage comprises cleaving one or
two strands at the location of the target sequence by said CRISPR
enzyme. In some embodiments, said cleavage results in decreased
transcription of a target gene. In some embodiments, the method
further comprises repairing said cleaved target polynucleotide by
homologous recombination with an exogenous template polynucleotide,
wherein said repair results in a mutation comprising an insertion,
deletion, or substitution of one or more nucleotides of said target
polynucleotide. In some embodiments, said mutation results in one
or more amino acid changes in a protein expression from a gene
comprising the target sequence.
[0070] In one aspect the invention provides for a method of
selecting one or more prokaryotic cell(s) by introducing one or
more mutations in a gene in the one or more prokaryotic cell (s),
the method comprising: introducing one or more vectors into the
prokaryotic cell (s), wherein the one or more vectors drive
expression of one or more of: a CRISPR enzyme, a guide sequence
linked to a tracr mate sequence, a tracr sequence, and an editing
template; wherein the editing template comprises the one or more
mutations that abolish CRISPR enzyme cleavage; allowing homologous
recombination of the editing template with the target
polynucleotide in the cell(s) to be selected; allowing a CRISPR
complex to bind to a target polynucleotide to effect cleavage of
the target polynucleotide within said gene, wherein the CRISPR
complex comprises the CRISPR enzyme complexed with (1) the guide
sequence that is hybridized to the target sequence within the
target polynucleotide, and (2) the tracr mate sequence that is
hybridized to the tracr sequence, wherein binding of the CRISPR
complex to the target polynucleotide induces cell death, thereby
allowing one or more prokaryotic cell(s) in which one or more
mutations have been introduced to be selected. In a preferred
embodiment, the CRISPR enzyme is Cas9. In another aspect of the
invention the cell to be selected may be a eukaryotic cell. Aspects
of the invention allow for selection of specific cells without
requiring a selection marker or a two-step process that may include
a counter-selection system.
[0071] In one aspect, the invention provides for methods of
modifying a target polynucleotide in a eukaryotic cell. In some
embodiments, the method comprises allowing a CRISPR complex to bind
to the target polynucleotide to effect cleavage of said target
polynucleotide thereby modifying the target polynucleotide, wherein
the CRISPR complex comprises a CRISPR enzyme complexed with a guide
sequence hybridized to a target sequence within said target
polynucleotide, wherein said guide sequence is linked to a tracr
mate sequence which in turn hybridizes to a tracr sequence.
[0072] In other embodiments, this invention provides a method of
modifying expression of a polynucleotide in a eukaryotic cell. The
method comprises increasing or decreasing expression of a target
polynucleotide by using a CRISPR complex that binds to the
polynucleotide.
[0073] Where desired, to effect the modification of the expression
in a cell, one or more vectors comprising a tracr sequence, a guide
sequence linked to the tracr mate sequence, a sequence encoding a
CRISPR enzyme is delivered to a cell. In some methods, the one or
more vectors comprises a regulatory element operably linked to an
enzyme-coding sequence encoding said CRISPR enzyme comprising a
nuclear localization sequence; and a regulatory element operably
linked to a tracr mate sequence and one or more insertion sites for
inserting a guide sequence upstream of the tracr mate sequence.
When expressed, the guide sequence directs sequence-specific
binding of a CRISPR complex to a target sequence in a cell.
Typically, the CRISPR complex comprises a CRISPR enzyme complexed
with (1) the guide sequence that is hybridized to the target
sequence, and (2) the tracr mate sequence that is hybridized to the
tracr sequence.
[0074] In some methods, a target polynucleotide can be inactivated
to effect the modification of the expression in a cell. For
example, upon the binding of a CRISPR complex to a target sequence
in a cell, the target polynucleotide is inactivated such that the
sequence is not transcribed, the coded protein is not produced, or
the sequence does not function as the wild-type sequence does. For
example, a protein or microRNA coding sequence may be inactivated
such that the protein is not produced.
[0075] In certain embodiments, the CRISPR enzyme comprises one or
more mutations selected from the group consisting of D10A, E762A.
H840A, N854A, N863A or D986A and/or the one or more mutations is in
a RuvC1 or HNH domain of the CRISPR enzyme or is a mutation as
otherwise as discussed herein. In some embodiments, the CRISPR
enzyme has one or more mutations in a catalytic domain, wherein
when transcribed, the tracr mate sequence hybridizes to the tracr
sequence and the guide sequence directs sequence-specific binding
of a CRISPR complex to the target sequence, and wherein the enzyme
further comprises a functional domain. In some embodiments, the
functional domain is a transcriptional activation domain,
preferably VP64. In some embodiments, the functional domain is a
transcription repression domain, preferably KRAB. In some
embodiments, the transcription repression domain is SID, or
concatemers of SID (eg SID4X). In some embodiments, the functional
domain is an epigenetic modifying domain, such that an epigenetic
modifying enzyme is provided. In some embodiments, the functional
domain is an activation domain, which may be the P65 activation
domain.
[0076] In some embodiments, the CRISPR enzyme is a type I or III
CRISPR enzyme, but is preferably a type II CRISPR enzyme. This type
II CRISPR enzyme may be any Cas enzyme. A Cas enzyme may be
identified as Cas9 as this can refer to the general class of
enzymes that share homology to the biggest nuclease with multiple
nuclease domains from the type II CRISPR system. Most preferably,
the Cas9 enzyme is from, or is derived from, spCas9 or saCas9. By
derived, Applicants mean that the derived enzyme is largely based,
in the sense of having a high degree of sequence homology with, a
wildtype enzyme, but that it has been mutated (modified) in some
way as described herein.
[0077] It will be appreciated that the terms Cas and CRISPR enzyme
are generally used herein interchangeably, unless otherwise
apparent. As mentioned above, many of the residue numberings used
herein refer to the Cas9 enzyme from the type II CRISPR locus in
Streptococcus pyogenes. However, it will be appreciated that this
invention includes many more Cas9s from other species of microbes,
such as SpCas9, SaCa9, St1Cas9 and so forth.
[0078] An example of a codon optimized sequence, in this instance
optimized for humans (i.e. being optimized for expression in
humans) is provided herein, see the SaCas9 human codon optimized
sequence. Whilst this is preferred, it will be appreciated that
other examples are possible and codon optimization for a host
species is known.
[0079] Preferably, delivery is in the form of a vector which may be
a viral vector, such as a lenti- or baculo- or preferably
adeno-viral/adeno-associated viral vectors, but other means of
delivery are known (such as yeast systems, microvesicles, gene
guns/means of attaching vectors to gold nanoparticles) and are
provided. A vector may mean not only a viral or yeast system (for
instance, where the nucleic acids of interest may be operably
linked to and under the control of (in terms of expression, such as
to ultimately provide a processed RNA) a promoter), but also direct
delivery of nucleic acids into a host cell. While in herein methods
the vector may be a viral vector and this is advantageously an AAV,
other viral vectors as herein discussed can be employed, such as
lentivirus. For example, baculoviruses may be used for expression
in insect cells. These insect cells may, in turn be useful for
producing large quantities of further vectors, such as AAV or
lentivirus vectors adapted for delivery of the present invention.
Also envisaged is a method of delivering the present CRISPR enzyme
comprising delivering to a cell mRNA encoding the CRISPR enzyme. It
will be appreciated that in certain embodiments the CRISPR enzyme
is truncated, and/or comprised of less than one thousand amino
acids or less than four thousand amino acids, and/or is a nuclease
or nickase, and/or is codon-optimized, and/or comprises one or more
mutations, and/or comprises a chimeric CRISPR enzyme, and/or the
other options as herein discussed. AAV and lentiviral vectors are
preferred.
[0080] In certain embodiments, the target sequence is flanked or
followed, at its 3' end, by a PAM suitable for the CRISPR enzyme,
typically a Cas and in particular a Cas9.
[0081] For example, a suitable PAM is 5'-NRG or 5'-NNGRR for SpCas9
or SaCas9 enzymes (or derived enzymes), respectively.
[0082] It will be appreciated that SpCas9 or SaCas9 are those from
or derived from S. pyogenes or S. aureus Cas9.
[0083] Accordingly, it is an object of the invention to not
encompass within the invention any previously known product,
process of making the product, or method of using the product such
that Applicants reserve the right and hereby disclose a disclaimer
of any previously known product, process, or method. It is further
noted that the invention does not intend to encompass within the
scope of the invention any product, process, or making of the
product or method of using the product, which does not meet the
written description and enablement requirements of the USPTO (35
U.S.C. .sctn.112, first paragraph) or the EPO (Article 83 of the
EPC), such that Applicants reserve the right and hereby disclose a
disclaimer of any previously described product, process of making
the product, or method of using the product.
[0084] It is noted that in this disclosure and particularly in the
claims and/or paragraphs, terms such as "comprises", "comprised",
"comprising" and the like can have the meaning attributed to it in
U.S. Patent law; e.g., they can mean "includes", "included",
"including", and the like; and that terms such as "consisting
essentially of" and "consists essentially of" have the meaning
ascribed to them in U.S. Patent law, e.g., they allow for elements
not explicitly recited, but exclude elements that are found in the
prior art or that affect a basic or novel characteristic of the
invention.
[0085] These and other embodiments are disclosed or are obvious
from and encompassed by, the following Detailed Description.
BRIEF DESCRIPTION OF THE DRAWINGS
[0086] The novel features of the invention are set forth with
particularity in the appended claims. A better understanding of the
features and advantages of the present invention will be obtained
by reference to the following detailed description that sets forth
illustrative embodiments, in which the principles of the invention
are utilized, and the accompanying drawings of which:
[0087] FIG. 1 shows a schematic model of the CRISPR system. The
Cas9 nuclease from Streptococcus pyogenes (yellow) is targeted to
genomic DNA by a synthetic guide RNA (sgRNA) consisting of a 20-nt
guide sequence (blue) and a scaffold (red). The guide sequence
base-pairs with the DNA target (blue), directly upstream of a
requisite 5'-NGG protospacer adjacent motif (PAM; magenta), and
Cas9 mediates a double-stranded break (DSB)-3 bp upstream of the
PAM (red triangle).
[0088] FIG. 2A-F shows an exemplary CRISPR system, a possible
mechanism of action, an example adaptation for expression in
eukaryotic cells, and results of tests assessing nuclear
localization and CRISPR activity.
[0089] FIG. 3A-D shows results of an evaluation of SpCas9
specificity for an example target.
[0090] FIG. 4A-G show an exemplary vector system and results for
its use in directing homologous recombination in eukaryotic
cells.
[0091] FIG. 5 provides a table of protospacer sequences and
summarizes modification efficiency results for protospacer targets
designed based on exemplary S. pyogenes and S. thermophilus CRISPR
systems with corresponding PAMs against loci in human and mouse
genomes. Cells were transfected with Cas9 and either
pre-crRNA/tracrRNA or chimeric RNA, and analyzed 72 hours after
transfection. Percent indels are calculated based on Surveyor assay
results from indicated cell lines (N=3 for all protospacer targets,
errors are S.E.M., N.D. indicates not detectable using the Surveyor
assay, and N.T. indicates not tested in this study).
[0092] FIG. 6A-C shows a comparison of different tracrRNA
transcripts for Cas9-mediated gene targeting.
[0093] FIG. 7 shows a schematic of a surveyor nuclease assay for
detection of double strand break-induced micro-insertions and
-deletions.
[0094] FIG. 8A-B shows exemplary bicistronic expression vectors for
expression of CRISPR system elements in eukaryotic cells.
[0095] FIG. 9A-C shows histograms of distances between adjacent S.
pyogenes SF370 locus 1 PAM (NGG) (FIG. 9A) and S. thermophilus LMD9
locus 2 PAM (NNAGAAW) (FIG. 9B) in the human genome; and distances
for each PAM by chromosome (Chr) (FIG. 9C).
[0096] FIG. 10A-D shows an exemplary CRISPR system, an example
adaptation for expression in eukaryotic cells, and results of tests
assessing CRISPR activity.
[0097] FIG. 11A-C shows exemplary manipulations of a CRISPR system
for targeting of genomic loci in mammalian cells.
[0098] FIG. 12A-B shows the results of a Northern blot analysis of
crRNA processing in mammalian cells.
[0099] FIG. 13A-B shows an exemplary selection of protospacers in
the human PVALB and mouse Th loci.
[0100] FIG. 14 shows example protospacer and corresponding PAM
sequence targets of the S. thermophilus CRISPR system in the human
EMX1 locus.
[0101] FIG. 15 provides a table of sequences for primers and probes
used for Surveyor, RFLP, genomic sequencing, and Northern blot
assays.
[0102] FIG. 16A-C shows exemplary manipulation of a CRISPR system
with chimeric RNAs and results of SURVEYOR assays for system
activity in eukaryotic cells.
[0103] FIG. 17A-B shows a graphical representation of the results
of SURVEYOR assays for CRISPR system activity in eukaryotic
cells.
[0104] FIG. 18 shows an exemplary visualization of some S. pyogenes
Cas9 target sites in the human genome using the UCSC genome
browser.
[0105] FIG. 19A-D shows a circular depiction of the phylogenetic
analysis revealing five families of Cas9s, including three groups
of large Cas9s (.about.1400 amino acids) and two of small Cas9s
(.about.1100 amino acids).
[0106] FIG. 20A-F shows the linear depiction of the phylogenetic
analysis revealing five families of Cas9s, including three groups
of large Cas9s (.about.1400 amino acids) and two of small Cas9s
(.about.1100 amino acids).
[0107] FIG. 21A-D shows genome editing via homologous
recombination. (a) Schematic of SpCas9 nickase, with D10A mutation
in the RuvC I catalytic domain. (b) Schematic representing
homologous recombination (HR) at the human EMX1 locus using either
sense or antisense single stranded oligonucleotides as repair
templates. Red arrow above indicates sgRNA cleavage site; PCR
primers for genotyping (Tables J and K) are indicated as arrows in
right panel. (c) Sequence of region modified by HR. d, SURVEYOR
assay for wildtype (wt) and nickase (D10A) SpCas9-mediated indels
at the EMX1 target 1 locus (n=3). Arrows indicate positions of
expected fragment sizes.
[0108] FIG. 22A-B shows single vector designs for SpCas9.
[0109] FIG. 23 shows a graph representing the length distribution
of Cas9 orthologs.
[0110] FIG. 24A-M shows sequences where the mutation points are
located within the SpCas9 gene.
[0111] FIG. 25A shows the Conditional Cas9, Rosa26 targeting vector
map.
[0112] FIG. 25B shows the Constitutive Cas9, Rosa26 targeting
vector map.
[0113] FIG. 26 shows a schematic of the important elements in the
Constitutive and Conditional Cas9 constructs.
[0114] FIG. 27 shows delivery and in vivo mouse brain Cas9
expression data.
[0115] FIG. 28 shows RNA delivery of Cas9 and chimeric RNA into
cells (A) Delivery of a GFP reporter as either DNA or mRNA into
Neuro-2A cells. (B) Delivery of Cas9 and chimeric RNA against the
Icam2 gene as RNA results in cutting for one of two spacers tested.
(C) Delivery of Cas9 and chimeric RNA against the F7 gene as RNA
results in cutting for one of two spacers tested.
[0116] FIG. 29 shows how DNA double-strand break (DSB) repair
promotes gene editing. In the error-prone non-homologous end
joining (NHEJ) pathway, the ends of a DSB are processed by
endogenous DNA repair machineries and rejoined together, which can
result in random insertion/deletion (indel) mutations at the site
of junction. Indel mutations occurring within the coding region of
a gene can result in frame-shift and a premature stop codon,
leading to gene knockout. Alternatively, a repair template in the
form of a plasmid or single-stranded oligodeoxynucleotides (ssODN)
can be supplied to leverage the homology-directed repair (HDR)
pathway, which allows high fidelity and precise editing.
[0117] FIG. 30A-C shows anticipated results for HDR in HEK and
HUES9 cells. (a) Either a targeting plasmid or an ssODN (sense or
antisense) with homology arms can be used to edit the sequence at a
target genomic locus cleaved by Cas9 (red triangle). To assay the
efficiency of HDR, we introduced a HindIII site (red bar) into the
target locus, which was PCR-amplified with primers that anneal
outside of the region of homology. Digestion of the PCR product
with HindIII reveals the occurrence of HDR events. (b) ssODNs,
oriented in either the sense or the antisense (s or a) direction
relative to the locus of interest, can be used in combination with
Cas9 to achieve efficient HDR-mediated editing at the target locus.
A minimal homology region of 40 bp, and preferably 90 bp, is
recommended on either side of the modification (red bar). (c)
Example of the effect of ssODNs on HDR in the EMX1 locus is shown
using both wild-type Cas9 and Cas9 nickase (D10A). Each ssODN
contains homology arms of 90 bp flanking a 12-bp insertion of two
restriction sites.
[0118] FIG. 31A-C shows the repair strategy for Cystic Fibrosis
delta F508 mutation.
[0119] FIG. 32A-B (a) shows a schematic of the GAA repeat expansion
in FXN intron 1 and (b) shows a schematic of the strategy adopted
to excise the GAA expansion region using the CRISPR/Cas system.
[0120] FIG. 33 shows a screen for efficient SpCas9 mediated
targeting of Tet1-3 and Dnmt1, 3a and 3b gene loci. Surveyor assay
on DNA from transfected N2A cells demonstrates efficient DNA
cleavage by using different gRNAs.
[0121] FIG. 34 shows a strategy of multiplex genome targeting using
a 2-vector system in an AAV1/2 delivery system. Tet1-3 and Dnmt1,
3a and 3b gRNA under the control of the U6 promoter. GFP-KASH under
the control of the human synapsin promoter. Restriction sides shows
simple gRNA replacement strategy by subcloning. HA-tagged SpCas9
flanked by two nuclear localization signals (NLS) is shown. Both
vectors are delivered into the brain by AAV1/2 virus in a 1:1
ratio.
[0122] FIG. 35 shows verification of multiplex DNMT targeting
vector #1 functionality using Surveyor assay. N2A cells were
co-transfected with the DNMT targeting vector #1 (+) and the SpCas9
encoding vector for testing SpCas9 mediated cleavage of DNMTs genes
family loci. gRNA only (-) is negative control. Cells were
harvested for DNA purification and downstream processing 48 h after
transfection.
[0123] FIG. 36 shows verification of multiplex DNMT targeting
vector #2 functionality using Surveyor assay. N2A cells were
co-transfected with the DNMT targeting vector #1 (+) and the SpCas9
encoding vector for testing SpCas9 mediated cleavage of DNMTs genes
family loci. gRNA only (-) is negative control. Cells were
harvested for DNA purification and downstream processing 48 h after
transfection.
[0124] FIG. 37 shows schematic overview of short promoters and
short polyA versions used for HA-SpCas9 expression in vivo. Sizes
of the encoding region from L-ITR to R-ITR are shown on the
right.
[0125] FIG. 38 shows schematic overview of short promoters and
short polyA versions used for HA-SaCas9 expression in vivo. Sizes
of the encoding region from L-ITR to R-ITR are shown on the
right.
[0126] FIG. 39 shows expression of SpCas9 and SaCas9 in N2A cells.
Representative Western blot of HA-tagged SpCas9 and SaCas9 versions
under the control of different short promoters and with or short
polyA (spA) sequences. Tubulin is loading control. mCherry (mCh) is
a transfection control. Cells were harvested and further processed
for Western blotting 48 h after transfection.
[0127] FIG. 40 shows screen for efficient SaCas9 mediated targeting
of Tet3 gene locus. Surveyor assay on DNA from transfected N2A
cells demonstrates efficient DNA cleavage by using different gRNAs
with NNGGGT PUM sequence. GFP transfected cells and cells
expressing only SaCas9 are controls.
[0128] FIG. 41 shows expression of HA-SaCas9 in the mouse brain.
Animals were injected into dentate gyri with virus driving
expression of HA-SaCas9 under the control of human Synapsin
promoter. Animals were sacrificed 2 weeks after surgery. HA tag was
detected using rabbit monoclonal antibody C29F4 (Cell Signaling).
Cell nuclei stained in blue with DAPI stain.
[0129] FIG. 42 shows expression of SpCas9 and SaCas9 in cortical
primary neurons in culture 7 days after transduction.
Representative Western blot of HA-tagged SpCas9 and SaCas9 versions
under the control of different promoters and with bgh or short
polyA (spA) sequences. Tubulin is loading control.
[0130] FIG. 43 shows LIVE/DEAD stain of primary cortical neurons 7
days after transduction with AAV1 particles carrying SpCas9 with
different promoters and multiplex gRNAs constructs (example shown
on the last panel for DNMTs). Neurons after AAV transduction were
compared with control untransduced neurons. Red nuclei indicate
permeabilized, dead cells (second line of panels). Live cells are
marked in green color (third line of panels).
[0131] FIG. 44 shows LIVE/DEAD stain of primary cortical neurons 7
days after transduction with AAV1 particles carrying SaCas9 with
different promoters. Red nuclei indicate permeabilized, dead cells
(second line of panels). Live cells are marked in green color
(third line of panels).
[0132] FIG. 45 shows comparison of morphology of neurons after
transduction with AAV1 virus carrying SpCas9 and gRNA multiplexes
for TETs and DNMTs genes loci. Neurons without transduction are
shown as a control.
[0133] FIG. 46 shows verification of multiplex DNMT targeting
vector #1 functionality using Surveyor assay in primary cortical
neurons. Cells were co-transduced with the DNMT targeting vector #1
and the SpCas9 viruses with different promoters for testing SpCas9
mediated cleavage of DNMTs genes family loci.
[0134] FIG. 47 shows in vivo efficiency of SpCas9 cleavage in the
brain. Mice were injected with AAV1/2 virus carrying gRNA multiplex
targeting DNMT family genes loci together with SpCas9 viruses under
control of 2 different promoters: mouse Mecp2 and rat Map1b. Two
weeks after injection brain tissue was extracted and nuclei were
prepped and sorted using FACS, based on the GFP expression driven
by Synapsin promoter from gRNA multiplex construct. After gDNA
extraction Surveyor assay was run. + indicates GFP positive nuclei
and - control, GFP-negative nuclei from the same animal. Numbers on
the gel indicate assessed SpCas9 efficiency.
[0135] FIG. 48 shows purification of GFP-KASH labeled cell nuclei
from hippocampal neurons. The outer nuclear membrane (ONM) of the
cell nuclear membrane is tagged with a fusion of GFP and the KASH
protein transmembrane domain. Strong GFP expression in the brain
after one week of stereotactic surgery and AAV1/2 injection.
Density gradient centrifugation step to purify cell nuclei from
intact brain. Purified nuclei are shown. Chromatin stain by
Vybrant.RTM. DyeCycle.TM. Ruby Stain is shown in red, GFP labeled
nuclei are green. Representative FACS profile of GFP+ and GFP- cell
nuclei (Magenta: Vybrant.RTM. DyeCycle.TM. Ruby Stain, Green:
GFP).
[0136] FIG. 49 shows efficiency of SpCas9 cleavage in the mouse
brain. Mice were injected with AAV1/2 virus carrying gRNA multiplex
targeting TET family genes loci together with SpCas9 viruses under
control of 2 different promoters: mouse Mecp2 and rat Map1b. Three
weeks after injection brain tissue was extracted, nuclei were
prepped and sorted using FACS, based on the GFP expression driven
by Synapsin promoter from gRNA multiplex construct. After gDNA
extraction Surveyor assay was run. + indicates GFP positive nuclei
and - control, GFP-negative nuclei from the same animal. Numbers on
the gel indicate assessed SpCas9 efficiency.
[0137] FIG. 50 shows GFP-KASH expression in cortical neurons in
culture. Neurons were transduced with AAV1 virus carrying gRNA
multiplex constructs targeting TET genes loci. The strongest signal
localize around cells nuclei due to KASH domain localization.
[0138] FIG. 51 shows (top) a list of spacing (as indicated by the
pattern of arrangement for two PAM sequences) between pairs of
guide RNAs. Only guide RNA pairs satisfying patterns 1, 2, 3, 4
exhibited indels when used with SpCas9(D10A) nickase. (bottom) Gel
images showing that combination of SpCas9(D10A) with pairs of guide
RNA satisfying patterns 1, 2, 3, 4 led to the formation of indels
in the target site.
[0139] FIG. 52 shows a list of U6 reverse primer sequences used to
generate U6-guide RNA expression cassettes. Each primer needs to be
paired with the U6 forward primer "gcactgagggcctatttcccatgattc" to
generate amplicons containing U6 and the desired guide RNA.
[0140] FIG. 53 shows a Genomic sequence map from the human Emx1
locus showing the locations of the 24 patterns listed in FIG.
33.
[0141] FIG. 54 shows on (right) a gel image indicating the
formation of indels at the target site when variable 5' overhangs
are present after cleavage by the Cas9 nickase targeted by
different pairs of guide RNAs. on (left) a table indicating the
lane numbers of the gel on the right and various parameters
including identifying the guide RNA pairs used and the length of
the 5' overhang present following cleavage by the Cas9 nickase.
[0142] FIG. 55 shows a Genomic sequence map from the human Emx1
locus showing the locations of the different pairs of guide RNAs
that result in the gel patterns of FIG. 54 (right) and which are
further described in Example 35.
[0143] The figures herein are for illustrative purposes only and
are not necessarily drawn to scale.
DETAILED DESCRIPTION OF THE INVENTION
[0144] The invention relates to the engineering and optimization of
systems, methods and compositions used for the control of gene
expression involving sequence targeting, such as genome
perturbation or gene-editing, that relate to the CRISPR-Cas system
and components thereof. In advantageous embodiments, the Cas enzyme
is Cas9.
[0145] An advantage of the present methods is that the CRISPR
system avoids off-target binding and its resulting side effects.
This is achieved using systems arranged to have a high degree of
sequence specificity for the target DNA.
[0146] Cas9 optimization may be used to enhance function or to
develop new functions, one can generate chimeric Cas9 proteins.
Examples that the Applicants have generated are provided in Example
12. Chimeric Cas9 proteins can be made by combining fragments from
different Cas9 homologs. For example, two example chimeric Cas9
proteins from the Cas9s described herein. For example, Applicants
fused the N-term of St1Cas9 (fragment from this protein is in bold)
with C-term of SpCas9. The benefit of making chimeric Cas9s include
any or all of: reduced toxicity, improved expression in eukaryotic
cells; enhanced specificity; reduced molecular weight of protein,
for example, making the protein smaller by combining the smallest
domains from different Cas9 homologs; and/or altering the PAM
sequence requirement.
[0147] The Cas9 may be used as a generic DNA binding protein. For
example, and as shown in Example 13, Applicants used Cas9 as a
generic DNA binding protein by mutating the two catalytic domains
(D10 and H840) responsible for cleaving both strands of the DNA
target. In order to upregulate gene transcription at a target locus
Applicants fused a transcriptional activation domain (VP64) to
Cas9. Other transcriptional activation domains are known. As shown
in Example 17, transcriptional activation is possible. As also
shown in Example 17, gene repression (in this case of the
beta-catenin gene) is possible using a Cas9 repressor (DNA-binding
domain) that binds to the target gene sequence, thus repressing its
activity.
[0148] Cas9 and one or more guide RNA can be delivered using adeno
associated virus (AAV), lentivirus, adenovirus or other plasmid or
viral vector types, in particular, using formulations and doses
from, for example, U.S. Pat. No. 8,454,972 (formulations, doses for
adenovirus), U.S. Pat. No. 8,404,658 (formulations, doses for AAV)
and U.S. Pat. No. 5,846,946 (formulations, doses for DNA plasmids)
and from clinical trials and publications regarding the clinical
trials involving lentivirus, AAV and adenovirus. For examples, for
AAV, the route of administration, formulation and dose can be as in
U.S. Pat. No. 8,454,972 and as in clinical trials involving AAV.
For Adenovirus, the route of administration, formulation and dose
can be as in U.S. Pat. No. 8,404,658 and as in clinical trials
involving adenovirus. For plasmid delivery, the route of
administration, formulation and dose can be as in U.S. Pat. No.
5,846,946 and as in clinical studies involving plasmids. Doses may
be based on or extrapolated to an average 70 kg individual, and can
be adjusted for patients, subjects, mammals of different weight and
species. Frequency of administration is within the ambit of the
medical or veterinary practitioner (e.g., physician, veterinarian),
depending on usual factors including the age, sex, general health,
other conditions of the patient or subject and the particular
condition or symptoms being addressed.
[0149] The viral vectors can be injected into the tissue of
interest. For cell-type specific genome modification, the
expression of Cas9 can be driven by a cell-type specific promoter.
For example, liver-specific expression might use the Albumin
promoter and neuron-specific expression might use the Synapsin I
promoter.
[0150] Transgenic animals are also provided. Preferred examples
include animals comprising Cas9, in terms of polynucleotides
encoding Cas9 or the protein itself. Mice, rats and rabbits are
preferred. To generate transgenic mice with the constructs, as
exemplified herein one may inject pure, linear DNA into the
pronucleus of a zygote from a pseudo pregnant female, e.g. a CB56
female. Founders may then be identified, genotyped, and backcrossed
to CB57 mice. The constructs may then be cloned and optionally
verified, for instance by Sanger sequencing. Knock outs are
envisaged where for instance one or more genes are knocked out in a
model. However, are knockins are also envisaged (alone or in
combination). An example knockin Cas9 mouse was generated and this
is exemplified, but Cas9 knockins are preferred. To generate a Cas9
knock in mice one may target the same constitutive and conditional
constructs to the Rosa26 locus, as described herein (FIGS. 25A-B
and 26). Methods of US Patent Publication Nos. 20120017290 and
20110265198 assigned to Sangamo BioSciences, Inc. directed to
targeting the Rosa locus may be modified to utilize the CRISPR Cas
system of the present invention. In another embodiment, the methods
of US Patent Publication No. 20130236946 assigned to Cellectis
directed to targeting the Rosa locus may also be modified to
utilize the CRISPR Cas system of the present invention.
[0151] Utility of the conditional Cas9 mouse: Applicants have shown
in 293 cells that the Cas9 conditional expression construct can be
activated by co-expression with Cre. Applicants also show that the
correctly targeted R1 mESCs can have active Cas9 when Cre is
expressed. Because Cas9 is followed by the P2A peptide cleavage
sequence and then EGFP Applicants identify successful expression by
observing EGFP. Applicants have shown Cas9 activation in mESCs.
This same concept is what makes the conditional Cas9 mouse so
useful. Applicants may cross their conditional Cas9 mouse with a
mouse that ubiquitously expresses Cre (ACTB-Cre line) and may
arrive at a mouse that expresses Cas9 in every cell. It should only
take the delivery of chimeric RNA to induce genome editing in
embryonic or adult mice. Interestingly, if the conditional Cas9
mouse is crossed with a mouse expressing Cre under a tissue
specific promoter, there should only be Cas9 in the tissues that
also express Cre. This approach may be used to edit the genome in
only precise tissues by delivering chimeric RNA to the same
tissue.
[0152] As mentioned above, transgenic animals are also provided, as
are transgenic plants, especially crops and algae. The transgenic
plants may be useful in applications outside of providing a disease
model. These may include food or feed production through expression
of, for instance, higher protein, carbohydrate, nutrient or vitamin
levels than would normally be seen in the wildtype. In this regard,
transgenic plants, especially pulses and tubers, and animals,
especially mammals such as livestock (cows, sheep, goats and pigs),
but also poultry and edible insects, are preferred.
[0153] Transgenic algae or other plants such as rape may be
particularly useful in the production of vegetable oils or biofuels
such as alcohols (especially methanol and ethanol), for instance.
These may be engineered to express or overexpress high levels of
oil or alcohols for use in the oil or biofuel industries.
[0154] In terms of in vivo delivery, AAV is advantageous over other
viral vectors for a couple of reasons:
[0155] Low toxicity (this may be due to the purification method not
requiring ultra centrifugation of cell particles that can activate
the immune response)
[0156] Low probability of causing insertional mutagenesis because
it doesn't integrate into the host genome.
[0157] AAV has a packaging limit of 4.5 or 4.75 Kb. This means that
Cas9 as well as a promoter and transcription terminator have to be
all fit into the same viral vector. Constructs larger than 4.5 or
4.75 Kb will lead to significantly reduced virus production. SpCas9
is quite large, the gene itself is over 4.1 Kb, which makes it
difficult for packing into AAV. Therefore embodiments of the
invention include utilizing homologs of Cas9 that are shorter. For
example:
TABLE-US-00001 Species Cas9 Size Corynebacter diphtheriae 3252
Eubacterium ventriosum 3321 Streptococcus pasteurianus 3390
Lactobacillus farciminis 3378 Sphaerochaeta globus 3537
Azospirillum B510 3504 Gluconacetobacter diazotrophicus 3150
Neisseria cinerea 3246 Roseburia intestinalis 3420 Parvibaculum
lavamentivorans 3111 Staphylococcus aureus 3159 Nitratifractor
salsuginis DSM 16511 3396 Campylobacter lari CF89-12 3009
Streptococcus thermophilus LMD-9 3396
[0158] These species are therefore, in general, preferred Cas9
species. Applicants have shown delivery and in vivo mouse brain
Cas9 expression data.
[0159] Two ways to package Cas9 coding nucleic acid molecules,
e.g., DNA, into viral vectors to mediate genome modification in
vivo are preferred:
[0160] To achieve NHEJ-mediated gene knockout:
[0161] Single virus vector:
[0162] Vector containing two or more expression cassettes:
[0163] Promoter-Cas9 coding nucleic acid molecule-terminator
[0164] Promoter-gRNA1-terminator
[0165] Promoter-gRNA2-terminator
[0166] Promoter-gRNA(N)-terminator (up to size limit of vector)
[0167] Double virus vector:
[0168] Vector 1 containing one expression cassette for driving the
expression of Cas9
[0169] Promoter-Cas9 coding nucleic acid molecule-terminator
[0170] Vector 2 containing one more expression cassettes for
driving the expression of one or more guideRNAs
[0171] Promoter-gRNA 1-terminator
[0172] Promoter-gRNA(N)-terminator (up to size limit of vector)
[0173] To mediate homology-directed repair. In addition to the
single and double virus vector approaches described above, an
additional vector is used to deliver a homology-direct repair
template.
[0174] Promoter used to drive Cas9 coding nucleic acid molecule
expression can include:
[0175] AAV ITR can serve as a promoter: this is advantageous for
eliminating the need for an additional promoter element (which can
take up space in the vector). The additional space freed up can be
used to drive the expression of additional elements (gRNA, etc.).
Also, ITR activity is relatively weaker, so can be used to reduce
toxicity due to over expression of Cas9.
[0176] For ubiquitous expression, can use promoters: CMV, CAG, CBh,
PGK, SV40, Ferritin heavy or light chains, etc.
[0177] For brain expression, can use promoters: SynapsinI for all
neurons, CaMKIIalpha for excitatory neurons, GAD67 or GAD65 or VGAT
for GABAergic neurons, etc.
[0178] For liver expression, can use Albumin promoter.
[0179] For lung expression, can use SP-B.
[0180] For endothelial cells, can use ICAM.
[0181] For hematopoietic cells can use IFNbeta or CD45.
[0182] For Osteoblasts can use OG-2.
[0183] Promoter used to drive guide RNA can include:
[0184] Pol III promoters such as U6 or H1
[0185] Use of Pol II promoter and intronic cassettes to express
gRNA
[0186] As to AAV, the AAV can be AAV1, AAV2, AAV5 or any
combination thereof. One can select the AAV of the AAV with regard
to the cells to be targeted; e.g., one can select AAV serotypes 1,
2, 5 or a hybrid or capsid AAV1, AAV2, AAV5 or any combination
thereof for targeting brain or neuronal cells; and one can select
AAV4 for targeting cardiac tissue. AAV8 is useful for delivery to
the liver. The above promoters and vectors are preferred
individually.
[0187] RNA delivery is also a useful method of in vivo delivery.
FIG. 27 shows delivery and in vivo mouse brain Cas9 expression
data. It is possible to deliver Cas9 and gRNA (and, for instance,
HR repair template) into cells using liposomes or nanoparticles.
Thus delivery of the CRISPR enzyme, such as a Cas9 and/or delivery
of the RNAs of the invention may be in RNA form and via
microvesicles, liposomes or nanoparticles. For example, Cas9 mRNA
and gRNA can be packaged into liposomal particles for delivery in
vivo. Liposomal transfection reagents such as lipofectamine from
Life Technologies and other reagents on the market can effectively
deliver RNA molecules into the liver.
[0188] Enhancing NHEJ or HR efficiency is also helpful for
delivery. It is preferred that NHEJ efficiency is enhanced by
co-expressing end-processing enzymes such as Trex2 (Dumitrache et
al. Genetics. 2011 August; 188(4): 787-797). It is preferred that
HR efficiency is increased by transiently inhibiting NHEJ
machineries such as Ku70 and Ku86. HR efficiency can also be
increased by co-expressing prokaryotic or eukaryotic homologous
recombination enzymes such as RecBCD, RecA.
[0189] Various means of delivery are described herein, and further
discussed in this section.
[0190] Viral delivery: The CRISPR enzyme, for instance a Cas9,
and/or any of the present RNAs, for instance a guide RNA, can be
delivered using adeno associated virus (AAV), lentivirus,
adenovirus or other viral vector types, or combinations thereof.
Cas9 and one or more guide RNAs can be packaged into one or more
viral vectors. In some embodiments, the viral vector is delivered
to the tissue of interest by, for example, an intramuscular
injection, while other times the viral delivery is via intravenous,
transdermal, intranasal, oral, mucosal, or other delivery methods.
Such delivery may be either via a single dose, or multiple doses.
One skilled in the art understands that the actual dosage to be
delivered herein may vary greatly depending upon a variety of
factors, such as the vector chose, the target cell, organism, or
tissue, the general condition of the subject to be treated, the
degree of transformation/modification sought, the administration
route, the administration mode, the type of
transformation/modification sought, etc.
[0191] Such a dosage may further contain, for example, a carrier
(water, saline, ethanol, glycerol, lactose, sucrose, calcium
phosphate, gelatin, dextran, agar, pectin, peanut oil, sesame oil,
etc.), a diluent, a pharmaceutically-acceptable carrier (e.g.,
phosphate-buffered saline), a pharmaceutically-acceptable
excipient, an adjuvant to enhance antigenicity, an
immunostimulatory compound or molecule, and/or other compounds
known in the art. The adjuvant herein may contain a suspension of
minerals (alum, aluminum hydroxide, aluminum phosphate) on which
antigen is adsorbed; or water-in-oil emulsion in which antigen
solution is emulsified in oil (MF-59, Freund's incomplete
adjuvant), sometimes with the inclusion of killed mycobacteria
(Freund's complete adjuvant) to further enhance antigenicity
(inhibits degradation of antigen and/or causes influx of
macrophages). Adjuvants also include immunostimulatory molecules,
such as cytokines, costimulatory molecules, and for example,
immunostimulatory DNA or RNA molecules, such as CpG
oligonucleotides. Such a dosage formulation is readily
ascertainable by one skilled in the art. The dosage may further
contain one or more pharmaceutically acceptable salts such as, for
example, a mineral acid salt such as a hydrochloride, a
hydrobromide, a phosphate, a sulfate, etc.; and the salts of
organic acids such as acetates, propionates, malonates, benzoates,
etc. Additionally, auxiliary substances, such as wetting or
emulsifying agents, pH buffering substances, gels or gelling
materials, flavorings, colorants, microspheres, polymers,
suspension agents, etc. may also be present herein. In addition,
one or more other conventional pharmaceutical ingredients, such as
preservatives, humectants, suspending agents, surfactants,
antioxidants, anticaking agents, fillers, chelating agents, coating
agents, chemical stabilizers, etc. may also be present, especially
if the dosage form is a reconstitutable form. Suitable exemplary
ingredients include microcrystalline cellulose,
carboxymethylcellulose sodium, polysorbate 80, phenylethyl alcohol,
chlorobutanol, potassium sorbate, sorbic acid, sulfur dioxide,
propyl gallate, the parabens, ethyl vanillin, glycerin, phenol,
parachlorophenol, gelatin, albumin and a combination thereof. A
thorough discussion of pharmaceutically acceptable excipients is
available in REMINGTON'S PHARMACEUTICAL SCIENCES (Mack Pub. Co.,
N.J. 1991) which is incorporated by reference herein.
[0192] In an embodiment herein the delivery is via an adenovirus,
which may be at a single booster dose containing at least
1.times.10.sup.5 particles (also referred to as particle units, pu)
of adenoviral vector. In an embodiment herein, the dose preferably
is at least about 1.times.10.sup.6 particles (for example, about
1.times.10.sup.6-1.times.10.sup.12 particles), more preferably at
least about 1.times.10.sup.7 particles, more preferably at least
about 1.times.10.sup.8 particles (e.g., about
1.times.10.sup.8-1.times.10.sup.11 particles or about
1.times.10.sup.8-1.times.10.sup.12 particles), and most preferably
at least about 1.times.10.sup.0 particles (e.g., about
1.times.10.sup.9-1.times.10.sup.10 particles or about
1.times.10.sup.9-.times.10.sup.12 particles), or even at least
about 1.times.10.sup.10 particles (e.g., about
1.times.10.sup.10-1.times.10.sup.12 particles) of the adenoviral
vector. Alternatively, the dose comprises no more than about
1.times.10.sup.14 particles, preferably no more than about
1.times.10.sup.13 particles, even more preferably no more than
about 1.times.10.sup.12 particles, even more preferably no more
than about 1.times.10.sup.11 particles, and most preferably no more
than about 1.times.10.sup.10 particles (e.g., no more than about
1.times.10.sup.9 articles). Thus, the dose may contain a single
dose of adenoviral vector with, for example, about 1.times.10.sup.6
particle units (pu), about 2.times.10.sup.6 pu, about
4.times.10.sup.6 pu, about 1.times.10.sup.7 pu, about
2.times.10.sup.7 pu, about 4.times.10.sup.7 pu, about
1.times.10.sup.8 pu, about 2.times.10.sup.8 pu, about
4.times.10.sup.8 pu, about 1.times.10.sup.9 pu, about
2.times.10.sup.9 pu, about 4.times.10.sup.9 pu, about
1.times.10.sup.10 pu, about 2.times.10.sup.10 pu, about
4.times.10.sup.10 pu, about 1.times.10.sup.11 pu, about
2.times.10.sup.11 pu, about 4.times.10.sup.11 pu, about
1.times.10.sup.12 pu, about 2.times.10.sup.12 pu, or about
4.times.10.sup.12 pu of adenoviral vector. See, for example, the
adenoviral vectors in U.S. Pat. No. 8,454,972 B2 to Nabel, et. al.,
granted on Jun. 4, 2013; incorporated by reference herein, and the
dosages at col 29, lines 36-58 thereof. In an embodiment herein,
the adenovirus is delivered via multiple doses.
[0193] In an embodiment herein, the delivery is via an AAV. A
therapeutically effective dosage for in vivo delivery of the AAV to
a human is believed to be in the range of from about 20 to about 50
ml of saline solution containing from about 1.times.10.sup.10 to
about 1.times.10.sup.10 functional AAV/ml solution. The dosage may
be adjusted to balance the therapeutic benefit against any side
effects. In an embodiment herein, the AAV dose is generally in the
range of concentrations of from about 1.times.10.sup.5 to
1.times.10.sup.50 genomes AAV, from about 1.times.10.sup.8 to
1.times.10.sup.20 genomes AAV, from about 1.times.10.sup.10 to
about 1.times.10.sup.16 genomes, or about 1.times.10.sup.11 to
about 1.times.10.sup.16 genomes AAV. A human dosage may be about
1.times.10.sup.13 genomes AAV. Such concentrations may be delivered
in from about 0.001 ml to about 100 ml, about 0.05 to about 50 ml,
or about 10 to about 25 ml of a carrier solution. Other effective
dosages can be readily established by one of ordinary skill in the
art through routine trials establishing dose response curves. See,
for example, U.S. Pat. No. 8,404,658 B2 to Hajjar, et al., granted
on Mar. 26, 2013, at col. 27, lines 45-60.
[0194] In an embodiment herein the delivery is via a plasmid. In
such plasmid compositions, the dosage should be a sufficient amount
of plasmid to elicit a response. For instance, suitable quantities
of plasmid DNA in plasmid compositions can be from about 0.1 to
about 2 mg, or from about 1 .mu.g to about 10 .mu.g.
[0195] The doses herein are based on an average 70 kg individual.
The frequency of administration is within the ambit of the medical
or veterinary practitioner (e.g., physician, veterinarian), or
scientist skilled in the art.
[0196] Lentiviruses are complex retroviruses that have the ability
to infect and express their genes in both mitotic and post-mitotic
cells. The most commonly known lentivirus is the human
immunodeficiency virus (HIV), which uses the envelope glycoproteins
of other viruses to target a broad range of cell types.
[0197] Lentiviruses may be prepared as follows. After cloning
pCasES10 (which contains a lentiviral transfer plasmid backbone),
HEK293FT at low passage (p=5) were seeded in a T-75 flask to 50%
confluence the day before transfection in DMEM with 10% fetal
bovine serum and without antibiotics. After 20 hours, media was
changed to OptiMEM (serum-free) media and transfection was done 4
hours later. Cells were transfected with 10 .mu.g of lentiviral
transfer plasmid (pCasES10) and the following packaging plasmids: 5
.mu.g of pMD2.G (VSV-g pseudotype), and 7.5 .mu.g of psPAX2
(gag/pol/rev/tat). Transfection was done in 4 mL OptiMEM with a
cationic lipid delivery agent (50 uL Lipofectamine 2000 and 100 ul
Plus reagent). After 6 hours, the media was changed to
antibiotic-free DMEM with 10% fetal bovine serum.
[0198] Lentivirus may be purified as follows. Viral supernatants
were harvested after 48 hours. Supernatants were first cleared of
debris and filtered through a 0.45 um low protein binding (PVDF)
filter. They were then spun in a ultracentrifuge for 2 hours at
24,000 rpm. Viral pellets were resuspended in 50 ul of DMEM
overnight at 4 C. They were then aliquotted and immediately frozen
at -80 C.
[0199] In another embodiment, minimal non-primate lentiviral
vectors based on the equine infectious anemia virus (EIAV) are also
contemplated, especially for ocular gene therapy (see, e.g.,
Balagaan, J Gene Med 2006; 8: 275-285, Published online 21 Nov.
2005 in Wiley InterScience (www.interscience.wiley.com). DOI:
10.1002/jgm.845). In another embodiment, RetinoStat.RTM., an equine
infectious anemia virus-based lentiviral gene therapy vector that
expresses angiostatic proteins endostain and angiostatin that is
delivered via a subretinal injection for the treatment of the web
form of age-related macular degeneration is also contemplated (see,
e.g., Binley et al., HUMAN GENE THERAPY 23:980-991 (September
2012)) may be modified for the CRISPR-Cas system of the present
invention.
[0200] In another embodiment, self-inactivating lentiviral vectors
with an siRNA targeting a common exon shared by HIV tat/rev, a
nucleolar-localizing TAR decoy, and an anti-CCR5-specific
hammerhead ribozyme (see, e.g., DiGiusto et al. (2010) Sci Transl
Med 2:36ra43) may be used/and or adapted to the CRISPR-Cas system
of the present invention. A minimum of 2.5.times.10.sup.6 CD34+
cells per kilogram patient weight may be collected and
prestimulated for 16 to 20 hours in X-VIVO 15 medium (Lonza)
containing 2 mML-glutamine, stem cell factor (100 ng/ml), Flt-3
ligand (Flt-3L) (100 ng/ml), and thrombopoietin (10 ng/ml)
(CellGenix) at a density of 2.times.10.sup.6 cells/ml.
Prestimulated cells may be transduced with lentiviral at a
multiplicity of infection of 5 for 16 to 24 hours in 75-cm.sup.2
tissue culture flasks coated with fibronectin (25 mg/cm.sup.2)
(RetroNectin, Takara Bio Inc.).
[0201] Lentiviral vectors have been disclosed as in the treatment
for Parkinson's Disease, see, e.g., US Patent Publication No.
20120295960 and U.S. Pat. Nos. 7,303,910 and 7,351,585. Lentiviral
vectors have also been disclosed for the treatment of ocular
diseases, see e.g., US Patent Publication Nos. 20060281180,
20090007284, US20110117189; US20090017543; US20070054961,
US20100317109. Lentiviral vectors have also been disclosed for
delivery to the train, see, e.g., US Patent Publication Nos.
US20110293571; US20110293571, US20040013648, US20070025970,
US20090111106 and U.S. Pat. No. 7,259,015.
[0202] RNA delivery: The CRISPR enzyme, for instance a Cas9, and/or
any of the present RNAs, for instance a guide RNA, can also be
delivered in the form of RNA. Cas9 mRNA can be generated using in
vitro transcription. For example, Cas9 mRNA can be synthesized
using a PCR cassette containing the following elements:
T7_promoter-kozak sequence (GCCACC)-Cas9-3' UTR from beta
globin-polyA tail (a string of 120 or more adenines). The cassette
can be used for transcription by T7 polymerase. Guide RNAs can also
be transcribed using in vitro transcription from a cassette
containing T7_promoter-GG-guide RNA sequence.
[0203] To enhance expression and reduce toxicity, the CRISPR enzyme
and/or guide RNA can be modified using pseudo-U or 5-Methyl-C.
[0204] mRNA delivery methods are especially promising for liver
delivery currently. In particular, for AAV8 is particularly
preferred for delivery to the liver.
[0205] CRISPR enzyme mRNA and guide RNA might also be delivered
separately. CRISPR enzyme mRNA can be delivered prior to the guide
RNA to give time for CRISPR enzyme to be expressed. CRISPR enzyme
mRNA might be administered 1-12 hours (preferably around 2-6 hours)
prior to the administration of guide RNA.
[0206] Alternatively, CRISPR enzyme mRNA and guide RNA can be
administered together. Advantageously, a second booster dose of
guide RNA can be administered 1-12 hours (preferably around 2-6
hours) after the initial administration of CRISPR enzyme mRNA+guide
RNA.
[0207] Additional administrations of CRISPR enzyme mRNA and/or
guide RNA might be useful to achieve the most efficient levels of
genome modification.
[0208] For minimization of toxicity and off-target effect, it will
be important to control the concentration of CRISPR enzyme mRNA and
guide RNA delivered. Optimal concentrations of CRISPR enzyme mRNA
and guide RNA can be determined by testing different concentrations
in a cellular or animal model and using deep sequencing the analyze
the extent of modification at potential off-target genomic loci.
For example, for the guide sequence targeting
5'-GAGTCCGAGCAGAAGAAGAA-3' in the EMX1 gene of the human genome,
deep sequencing can be used to assess the level of modification at
the following two off-target loci, 1: 5'-GAGTCCTAGCAGGAGAAGAA-3'
and 2: 5'-GAGTCTAAGCAGAAGAAGAA-3'. The concentration that gives the
highest level of on-target modification while minimizing the level
of off-target modification should be chosen for in vivo
delivery.
[0209] Alternatively, to minimize the level of toxicity and
off-target effect, CRISPR enzyme nickase mRNA (for example S.
pyogenes Cas9 with the D10A mutation) can be delivered with a pair
of guide RNAs targeting a site of interest. The two guide RNAs need
to be spaced as follows. Guide sequences in red (single underline)
and blue (double underline) respectively (these examples are based
on the PAM requirement for Streptococcus pyogenes Cas9).
TABLE-US-00002 Overhang length (bp) Guide RNA design (guide
sequence and PAM color coded) 14
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNN-5'
13
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNN-5'
12
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNN-5'
11
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNN-5'
10
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNN-5' 9
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNN-5' 8
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNN-5' 7
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNN-5' 6
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNN-5' 5
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNN-5' 4
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNN-5' 3
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
2 5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNN-5' 1
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
blunt
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
1
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
2
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
3
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
4
5'-NNNNNNNNNNNNNNNNNNNNCCNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
5
5'-NNNNNNNNNNNNNNNNNNNNCCNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
6
5'-NNNNNNNNNNNNNNNNNNNNCCNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
7
5'-NNNNNNNNNNNNNNNNNNNNCCNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNGGNCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
8
5'-NNNNNNNNNNNNNNNNNNNNNCCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNNGGCCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
12
5'-NNNNNNNNNNNNNNNNNNNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNNNNCCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
13
5'-NNNNNNNNNNNNNNNNNNNNNNCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNNNNCCNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
14
5'-NNNNNNNNNNNNNNNNNNNNNNCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNNNNCCNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
15
5'-NNNNNNNNNNNNNNNNNNNNNNCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNNNNCCNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
16
5'-NNNNNNNNNNNNNNNNNNNNNNCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNNNCCNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
17
5'-NNNNNNNNNNNNNNNNNNNNNNCGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN-3'
3'-NNNNNNNNNNNNNNNNNNNNNNNCCNNNNNGGNNNNNNNNNNNNNNNNNNNNNNNNNNNN-5'
[0210] Further interrogation of the system have given Applicants
evidence of the 5'overhang (see, e.g., Ran et al., Cell. 2013 Sep.
12; 154(6):1380-9 and U.S. Provisional Patent Application Ser. No.
61/871,301 filed Aug. 28, 2013). Applicants have further identified
parameters that relate to efficient cleavage by the Cas9 nickase
mutant when combined with two guide RNAs and these parameters
include but are not limited to the length of the 5' overhang. In
embodiments of the invention the 5' overhang is at most 200 base
pairs, preferably at most 100 base pairs, or more preferably at
most 50 base pairs. In embodiments of the invention the 5' overhang
is at least 26 base pairs, preferably at least 30 base pairs or
more preferably 34-50 base pairs or 1-34 base pairs. In other
preferred methods of the invention the first guide sequence
directing cleavage of one strand of the DNA duplex near the first
target sequence and the second guide sequence directing cleavage of
other strand near the second target sequence results in a blunt cut
or a 3' overhang. In embodiments of the invention the 3' overhang
is at most 150, 100 or 25 base pairs or at least 15, 10 or 1 base
pairs. In preferred embodiments the 3' overhang is 1-100
basepairs.
[0211] Aspects of the invention relate to the expression of the
gene product being decreased or a template polynucleotide being
further introduced into the DNA molecule encoding the gene product
or an intervening sequence being excised precisely by allowing the
two 5' overhangs to reanneal and ligate or the activity or function
of the gene product being altered or the expression of the gene
product being increased. In an embodiment of the invention, the
gene product is a protein.
[0212] Only sgRNA pairs creating 5' overhangs with less than 8 bp
overlap between the guide sequences (offset greater than -8 bp)
were able to mediate detectable indel formation. Importantly, each
guide used in these assays is able to efficiently induce indels
when paired with wildtype Cas9, indicating that the relative
positions of the guide pairs are the most important parameters in
predicting double nicking activity.
[0213] Since Cas9n and Cas9H840A nick opposite strands of DNA,
substitution of Cas9n with Cas9H840A with a given sgRNA pair should
result in the inversion of the overhang type. For example, a pair
of sgRNAs that will generate a 5' overhang with Cas9n should in
principle generate the corresponding 3' overhang instead.
Therefore, sgRNA pairs that lead to the generation of a 3' overhang
with Cas9n might be used with Cas9H840A to generate a 5' overhang.
Unexpectedly, Applicants tested Cas9H840A with a set of sgRNA pairs
designed to generate both 5' and 3' overhangs (offset range from
-278 to +58 bp), but were unable to observe indel formation.
Further work may be needed to identify the necessary design rules
for sgRNA pairing to allow double nicking by Cas9H840A.
[0214] Targeted deletion of genes is preferred. Examples are
exemplified in Example 18. Preferred are, therefore, genes involved
in cholesterol biosynthesis, fatty acid biosynthesis, and other
metabolic disorders, genes encoding mis-folded proteins involved in
amyloid and other diseases, oncogenes leading to cellular
transformation, latent viral genes, and genes leading to
dominant-negative disorders, amongst other disorders. As
exemplified here, Applicants prefer gene delivery of a CRISPR-Cas
system to the liver, brain, ocular, epithelial, hematopoetic, or
another tissue of a subject or a patient in need thereof, suffering
from metabolic disorders, amyloidosis and protein-aggregation
related diseases, cellular transformation arising from genetic
mutations and translocations, dominant negative effects of gene
mutations, latent viral infections, and other related symptoms,
using either viral or nanoparticle delivery system.
[0215] Therapeutic applications of the CRISPR-Cas system include
Glaucoma, Amyloidosis, and Huntington's disease. These are
exemplified in Example 20 and the features described therein are
preferred alone or in combination.
[0216] Another example of a polyglutamine expansion disease that
may be treated by the present invention includes spinocerebellar
ataxia type 1 (SCA1). Upon intracerebellar injection, recombinant
adenoassociated virus (AAV) vectors expressing short hairpin RNAs
profoundly improve motor coordination, restored cerebellar
morphology and resolved characteristic ataxin-inclusions in
Purkinje cells of SCA1 mice (see, e.g., Xia et al., Nature
Medicine. Vol. 10, No. 8, August 2004). In particular, AAV1 and
AAV5 vectors are preferred and AAV titers of about
1.times.10.sup.12 vector genomes/ml are desirable.
[0217] As an example, chronic infection by HIV-1 may be treated or
prevented. In order to accomplish this, one may generate CRISPR-Cas
guide RNAs that target the vast majority of the HIV-1 genome while
taking into account HIV-1 strain variants for maximal coverage and
effectiveness. One may accomplish delivery of the CRISPR-Cas system
by conventional adenoviral or lentiviral-mediated infection of the
host immune system. Depending on approach, host immune cells could
be a) isolated, transduced with CRISPR-Cas, selected, and
re-introduced in to the host or b) transduced in vivo by systemic
delivery of the CRISPR-Cas system. The first approach allows for
generation of a resistant immune population whereas the second is
more likely to target latent viral reservoirs within the host. This
is discussed in more detail in the Examples section.
[0218] In another example, US Patent Publication No. 20130171732
assigned to Sangamo BioSciences, Inc. relates to insertion of an
anti-HIV transgene into the genome, methods of which may be applied
to the CRISPR Cas system of the present invention. In another
embodiment, the CXCR4 gene may be targeted and the TALE system of
US Patent Publication No. 20100291048 assigned to Sangamo
BioSciences, Inc. may be modified to the CRISPR Cas system of the
present invention. The method of US Patent Publication Nos.
20130137104 and 20130122591 assigned to Sangamo BioSciences, Inc.
and US Patent Publication No. 20100146651 assigned to Cellectis may
be more generally applicable for transgene expression as it
involves modifying a hypoxanthine-guanine phosphoribosyltransferase
(HPRT) locus for increasing the frequency of gene modification.
[0219] It is also envisaged that the present invention generates a
gene knockout cell library. Each cell may have a single gene
knocked out. This is exemplified in Example 23.
[0220] One may make a library of ES cells where each cell has a
single gene knocked out, and the entire library of ES cells will
have every single gene knocked out. This library is useful for the
screening of gene function in cellular processes as well as
diseases. To make this cell library, one may integrate Cas9 driven
by an inducible promoter (e.g. doxycycline inducible promoter) into
the ES cell. In addition, one may integrate a single guide RNA
targeting a specific gene in the ES cell. To make the ES cell
library, one may simply mix ES cells with a library of genes
encoding guide RNAs targeting each gene in the human genome. One
may first introduce a single BxB1 attB site into the AAVS1 locus of
the human ES cell. Then one may use the BxB1 integrase to
facilitate the integration of individual guide RNA genes into the
BxB1 attB site in AAVS1 locus. To facilitate integration, each
guide RNA gene may be contained on a plasmid that carries of a
single attP site. This way BxB1 will recombine the attB site in the
genome with the attP site on the guide RNA containing plasmid. To
generate the cell library, one may take the library of cells that
have single guide RNAs integrated and induce Cas9 expression. After
induction, Cas9 mediates double strand break at sites specified by
the guide RNA.
[0221] Chronic administration of protein therapeutics may elicit
unacceptable immune responses to the specific protein. The
immunogenicity of protein drugs can be ascribed to a few
immunodominant helper T lymphocyte (HTL) epitopes. Reducing the MHC
binding affinity of these HTL epitopes contained within these
proteins can generate drugs with lower immunogenicity (Tangri S, et
al. ("Rationally engineered therapeutic proteins with reduced
immunogenicity" J Immunol. 2005 Mar. 15; 174(6):3187-96.) In the
present invention, the immunogenicity of the CRISPR enzyme in
particular may be reduced following the approach first set out in
Tangri et al with respect to erythropoietin and subsequently
developed. Accordingly, directed evolution or rational design may
be used to reduce the immunogenicity of the CRISPR enzyme (for
instance a Cas9) in the host species (human or other species).
[0222] In Example 28, Applicants used 3 guideRNAs of interest and
able to visualize efficient DNA cleavage in vivo occurring only in
a small subset of cells. Essentially, what Applicants have shown
here is targeted in vivo cleavage. In particular, this provides
proof of concept that specific targeting in higher organisms such
as mammals can also be achieved. It also highlights multiplex
aspect in that multiple guide sequences (i.e. separate targets) can
be used simultaneously (in the sense of co-delivery). In other
words, Applicants used a multiple approach, with several different
sequences targeted at the same time, but independently.
[0223] A suitable example of a protocol for producing AAV, a
preferred vector of the invention is provided in Example 34.
[0224] Trinucleotide repeat disorders are preferred conditions to
be treated. These are also exemplified herein.
[0225] For example, US Patent Publication No. 20110016540,
describes use of zinc finger nucleases to genetically modify cells,
animals and proteins associated with trinucleotide repeat expansion
disorders. Trinucleotide repeat expansion disorders are complex,
progressive disorders that involve developmental neurobiology and
often affect cognition as well as sensori-motor functions.
[0226] Trinucleotide repeat expansion proteins are a diverse set of
proteins associated with susceptibility for developing a
trinucleotide repeat expansion disorder, the presence of a
trinucleotide repeat expansion disorder, the severity of a
trinucleotide repeat expansion disorder or any combination thereof.
Trinucleotide repeat expansion disorders are divided into two
categories determined by the type of repeat. The most common repeat
is the triplet CAG, which, when present in the coding region of a
gene, codes for the amino acid glutamine (Q). Therefore, these
disorders are referred to as the polyglutamine (polyQ) disorders
and comprise the following diseases: Huntington Disease (HD);
Spinobulbar Muscular Atrophy (SBMA); Spinocerebellar Ataxias (SCA
types 1, 2, 3, 6, 7, and 17); and Dentatorubro-Pallidoluysian
Atrophy (DRPLA). The remaining trinucleotide repeat expansion
disorders either do not involve the CAG triplet or the CAG triplet
is not in the coding region of the gene and are, therefore,
referred to as the non-polyglutamine disorders. The
non-polyglutamine disorders comprise Fragile X Syndrome (FRAXA);
Fragile XE Mental Retardation (FRAXE); Friedreich Ataxia (FRDA);
Myotonic Dystrophy (DM); and Spinocerebellar Ataxias (SCA types 8,
and 12).
[0227] The proteins associated with trinucleotide repeat expansion
disorders are typically selected based on an experimental
association of the protein associated with a trinucleotide repeat
expansion disorder to a trinucleotide repeat expansion disorder.
For example, the production rate or circulating concentration of a
protein associated with a trinucleotide repeat expansion disorder
may be elevated or depressed in a population having a trinucleotide
repeat expansion disorder relative to a population lacking the
trinucleotide repeat expansion disorder. Differences in protein
levels may be assessed using proteomic techniques including but not
limited to Western blot, immunohistochemical staining, enzyme
linked immunosorbent assay (ELISA), and mass spectrometry.
Alternatively, the proteins associated with trinucleotide repeat
expansion disorders may be identified by obtaining gene expression
profiles of the genes encoding the proteins using genomic
techniques including but not limited to DNA microarray analysis,
serial analysis of gene expression (SAGE), and quantitative
real-time polymerase chain reaction (Q-PCR).
[0228] Non-limiting examples of proteins associated with
trinucleotide repeat expansion disorders include AR (androgen
receptor), FMR1 (fragile X mental retardation 1), HTT (huntingtin),
DMPK (dystrophia myotonica-protein kinase), FXN (frataxin), ATXN2
(ataxin 2), ATN1 (atrophin 1), FEN1 (flap structure-specific
endonuclease 1), TNRC6A (trinucleotide repeat containing 6A),
PABPN1 (poly(A) binding protein, nuclear 1), JPH3 (junctophilin 3),
MED15 (mediator complex subunit 15), ATXN1 (ataxin 1), ATXN3
(ataxin 3), TBP (TATA box binding protein), CACNA1A (calcium
channel, voltage-dependent, P/Q type, alpha 1A subunit), ATXN80S
(ATXN8 opposite strand (non-protein coding)), PPP2R2B (protein
phosphatase 2, regulatory subunit B, beta), ATXN7 (ataxin 7),
TNRC6B (trinucleotide repeat containing 6B), TNRC6C (trinucleotide
repeat containing 6C), CELF3 (CUGBP, Elav-like family member 3),
MAB21L1 (mab-21-like 1 (C. elegans)), MSH2 (mutS homolog 2, colon
cancer, nonpolyposis type I (E. coli)). TMEM185A (transmembrane
protein 185A), SIX5 (SIX homeobox 5). CNPY3 (canopy 3 homolog
(zebrafish)), FRAXE (fragile site, folic acid type, rare,
fra(X)q28) E), GNB2 (guanine nucleotide binding protein (G
protein), beta polypeptide 2), RPL14 (ribosomal protein L14), ATXN8
(ataxin 8), INSR (insulin receptor), TTR (transthyretin), EP400
(E1A binding protein p400), GIGYF2 (GRB10 interacting GYF protein
2), OGG1 (8-oxoguanine DNA glycosylase). STC1 (stanniocalcin 1),
CNDP1 (carnosine dipeptidase 1 (metallopeptidase M20 family)),
C10orf2 (chromosome 10 open reading frame 2), MAML3 mastermind-like
3 (Drosophila), DKC1 (dyskeratosis congenita 1, dyskerin), PAXIP1
(PAX interacting (with transcription-activation domain) protein 1),
CASK (calcium/calmodulin-dependent serine protein kinase (MAGUK
family)), MAPT (microtubule-associated protein tau), SP1 (Sp1
transcription factor), POLG (polymerase (DNA directed), gamma),
AFF2 (AF4/FMR2 family, member 2), THBS1 (thrombospondin 1), TP53
(tumor protein p53), ESR1 (estrogen receptor 1), CGGBP1 (CGG
triplet repeat binding protein 1), ABT1 (activator of basal
transcription 1), KLK3 (kallikrein-related peptidase 3), PRNP
(prion protein), JUN (jun oncogene), KCNN3 (potassium
intermediate/small conductance calcium-activated channel, subfamily
N, member 3), BAX (BCL2-associated X protein), FRAXA (fragile site,
folic acid type, rare, fra(X)(q27.3) A (macroorchidism, mental
retardation)). KBTBD10 (kelch repeat and BTB (POZ) domain
containing 10), MBNL1 (muscleblind-like (Drosophila)), RAD51 (RAD51
homolog (RecA homolog, E. coli) (S. cerevisiae)), NCOA3 (nuclear
receptor coactivator 3), ERDA1 (expanded repeat domain, CAG/CTG 1),
TSC1 (tuberous sclerosis 1), COMP (cartilage oligomeric matrix
protein), GCLC (glutamate-cysteine ligase, catalytic subunit), RRAD
(Ras-related associated with diabetes). MSH3 (mutS homolog 3 (E.
coli)), DRD2 (dopamine receptor D2), CD44 (CD44 molecule (Indian
blood group)), CTCF (CCCTC-binding factor (zinc finger protein)),
CCND1 (cyclin D1), CLSPN (claspin homolog (Xenopus laevis)), MEF2A
(myocyte enhancer factor 2A), PTPRU (protein tyrosine phosphatase,
receptor type, U), GAPDH (glyceraldehyde-3-phosphate
dehydrogenase), TRIM22 (tripartite motif-containing 22), WT1 (Wilms
tumor 1), AHR (aryl hydrocarbon receptor), GPX1 (glutathione
peroxidase 1), TPMT (thiopurine S-methyltransferase), NDP (Norrie
disease (pseudoglioma)), ARX (aristaless related homeobox), MUS81
(MUS81 endonuclease homolog (S. cerevisiae)), TYR (tyrosinase
(oculocutaneous albinism IA)), EGR1 (early growth response 1), UNG
(uracil-DNA glycosylase). NUMBL (numb homolog (Drosophila)-like),
FABP2 (fatty acid binding protein 2, intestinal), EN2 (engrailed
homeobox 2), CRYGC (crystallin, gamma C). SRP14 (signal recognition
particle 14 kDa (homologous Alu RNA binding protein)), CRYGB
(crystallin, gamma B), PDCD1 (programmed cell death 1), HOXA1
(homeobox A1), ATXN2L (ataxin 2-like), PMS2 (PMS2 postmeiotic
segregation increased 2 (S. cerevisiae)), GLA (galactosidase,
alpha), CBL (Cas-Br-M (murine) ecotropic retroviral transforming
sequence), FTH1 (ferritin, heavy polypeptide 1), IL12RB2
(interleukin 12 receptor, beta 2), OTX2 (orthodenticle homeobox 2),
HOXA5 (homeobox A5), POLG2 (polymerase (DNA directed), gamma 2,
accessory subunit), DLX2 (distal-less homeobox 2), SIRPA
(signal-regulatory protein alpha). OTX1 (orthodenticle homeobox 1),
AHRR (aryl-hydrocarbon receptor repressor), MANF (mesencephalic
astrocyte-derived neurotrophic factor), TMEM158 (transmembrane
protein 158 (gene/pseudogene)), and ENSG00000078687.
[0229] Preferred proteins associated with trinucleotide repeat
expansion disorders include HTT (Huntingtin), AR (androgen
receptor), FXN (frataxin), Atxn3 (ataxin), Atxn1 (ataxin), Atxn2
(ataxin), Atxn7 (ataxin), Atxn10 (ataxin), DMPK (dystrophia
myotonica-protein kinase), Atn1 (atrophin 1), CBP (creb binding
protein), VLDLR (very low density lipoprotein receptor), and any
combination thereof.
[0230] According to another aspect, a method of gene therapy for
the treatment of a subject having a mutation in the CFTR gene is
provided and comprises administering a therapeutically effective
amount of a CRISPR-Cas gene therapy particle, optionally via a
biocompatible pharmaceutical carrier, to the cells of a subject.
Preferably, the target DNA comprises the mutation deltaF508. In
general, it is of preferred that the mutation is repaired to the
wildtype. In this case, the mutation is a deletion of the three
nucleotides that comprise the codon for phenylalanine (F) at
position 508. Accordingly, repair in this instance requires
reintroduction of the missing codon into the mutant.
[0231] To implement this Gene Repair Strategy, it is preferred that
an adenovirus/AAV vector system is introduced into the host cell,
cells or patient. Preferably, the system comprises a Cas9 (or Cas9
nickase) and the guide RNA along with a adenovirus/AAV vector
system comprising the homology repair template containing the F508
residue. This may be introduced into the subject via one of the
methods of delivery discussed earlier. The CRISPR-Cas system may be
guided by the CFTRdelta 508 chimeric guide RNA. It targets a
specific site of the CFTR genomic locus to be nicked or cleaved.
After cleavage, the repair template is inserted into the cleavage
site via homologous recombination correcting the deletion that
results in cystic fibrosis or causes cystic fibrosis related
symptoms. This strategy to direct delivery and provide systemic
introduction of CRISPR systems with appropriate guide RNAs can be
employed to target genetic mutations to edit or otherwise
manipulate genes that cause metabolic, liver, kidney and protein
diseases and disorders such as those in Table B.
[0232] The CRISPR/Cas9 systems of the present invention can be used
to correct genetic mutations that were previously attempted with
limited success using TALEN and ZFN. For example, WO2013163628 A2,
Genetic Correction of Mutated Genes, published application of Duke
University describes efforts to correct, for example, a frameshift
mutation which causes a premature stop codon and a truncated gene
product that can be corrected via nuclease mediated non-homologous
end joining such as those responsible for Duchenne Muscular
Dystrophy, ("DMD") a recessive, fatal, X-linked disorder that
results in muscle degeneration due to mutations in the dystrophin
gene. The majority of dystrophin mutations that cause DMD are
deletions of exons that disrupt the reading frame and cause
premature translation termination in the dystrophin gene.
Dystrophin is a cytoplasmic protein that provides structural
stability to the dystroglycan complex of the cell membrane that is
responsible for regulating muscle cell integrity and function. The
dystrophin gene or "DMD gene" as used interchangeably herein is 2.2
megabases at locus Xp21. The primary transcription measures about
2,400 kb with the mature mRNA being about 14 kb. 79 exons code for
the protein which is over 3500 amino acids. Exon 51 is frequently
adjacent to frame-disrupting deletions in DMD patients and has been
targeted in clinical trials for oligonucleotide-based exon
skipping. A clinical trial for the exon 51 skipping compound
eteplirsen recently reported a significant functional benefit
across 48 weeks, with an average of 47% dystrophin positive fibers
compared to baseline. Mutations in exon 51 are ideally suited for
permanent correction by NHEJ-based genome editing.
[0233] The methods of US Patent Publication No. 20130145487
assigned to Cellectis, which relates to meganuclease variants to
cleave a target sequence from the human dystrophin gene (DMD), may
also be modified to for the CRISPR Cas system of the present
invention.
[0234] The invention uses nucleic acids to bind target DNA
sequences. This is advantageous as nucleic acids are much easier
and cheaper to produce than proteins, and the specificity can be
varied according to the length of the stretch where homology is
sought. Complex 3-D positioning of multiple fingers, for example is
not required.
[0235] The terms "polynucleotide", "nucleotide", "nucleotide
sequence", "nucleic acid" and "oligonucleotide" are used
interchangeably. They refer to a polymeric form of nucleotides of
any length, either deoxyribonucleotides or ribonucleotides, or
analogs thereof. Polynucleotides may have any three dimensional
structure, and may perform any function, known or unknown. The
following are non-limiting examples of polynucleotides: coding or
non-coding regions of a gene or gene fragment, loci (locus) defined
from linkage analysis, exons, introns, messenger RNA (mRNA),
transfer RNA, ribosomal RNA, short interfering RNA (siRNA),
short-hairpin RNA (shRNA), micro-RNA (miRNA), ribozymes, cDNA,
recombinant polynucleotides, branched polynucleotides, plasmids,
vectors, isolated DNA of any sequence, isolated RNA of any
sequence, nucleic acid probes, and primers. The term also
encompasses nucleic-acid-like structures with synthetic backbones,
see, e.g., Eckstein, 1991; Baserga et al., 1992; Milligan, 1993; WO
97/03211; WO 96/39154; Mata, 1997; Strauss-Soukup, 1997; and
Samstag, 1996. A polynucleotide may comprise one or more modified
nucleotides, such as methylated nucleotides and nucleotide analogs.
If present, modifications to the nucleotide structure may be
imparted before or after assembly of the polymer. The sequence of
nucleotides may be interrupted by non-nucleotide components. A
polynucleotide may be further modified after polymerization, such
as by conjugation with a labeling component.
[0236] As used herein the term "wild type" is a term of the art
understood by skilled persons and means the typical form of an
organism, strain, gene or characteristic as it occurs in nature as
distinguished from mutant or variant forms.
[0237] As used herein the term "variant" should be taken to mean
the exhibition of qualities that have a pattern that deviates from
what occurs in nature.
[0238] The terms "non-naturally occurring" or "engineered" are used
interchangeably and indicate the involvement of the hand of man.
The terms, when referring to nucleic acid molecules or polypeptides
mean that the nucleic acid molecule or the polypeptide is at least
substantially free from at least one other component with which
they are naturally associated in nature and as found in nature.
[0239] "Complementarity" refers to the ability of a nucleic acid to
form hydrogen bond(s) with another nucleic acid sequence by either
traditional Watson-Crick base pairing or other non-traditional
types. A percent complementarity indicates the percentage of
residues in a nucleic acid molecule which can form hydrogen bonds
(e.g., Watson-Crick base pairing) with a second nucleic acid
sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%,
80%, 90%, and 100% complementary). "Perfectly complementary" means
that all the contiguous residues of a nucleic acid sequence will
hydrogen bond with the same number of contiguous residues in a
second nucleic acid sequence. "Substantially complementary" as used
herein refers to a degree of complementarity that is at least 60%,
65%, 70%, 75%, 80%, 85%, 90%, 95%, 97%, 98%, 99%, or 100% over a
region of 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22,
23, 24, 25, 30, 35, 40, 45, 50, or more nucleotides, or refers to
two nucleic acids that hybridize under stringent conditions.
[0240] As used herein, "stringent conditions" for hybridization
refer to conditions under which a nucleic acid having
complementarity to a target sequence predominantly hybridizes with
the target sequence, and substantially does not hybridize to
non-target sequences. Stringent conditions are generally
sequence-dependent, and vary depending on a number of factors. In
general, the longer the sequence, the higher the temperature at
which the sequence specifically hybridizes to its target sequence.
Non-limiting examples of stringent conditions are described in
detail in Tijssen (1993), Laboratory Techniques In Biochemistry And
Molecular Biology-Hybridization With Nucleic Acid Probes Part I,
Second Chapter "Overview of principles of hybridization and the
strategy of nucleic acid probe assay", Elsevier, N.Y. Where
reference is made to a polynucleotide sequence, then complementary
or partially complementary sequences are also envisaged. These are
preferably capable of hybridising to the reference sequence under
highly stringent conditions. Generally, in order to maximize the
hybridization rate, relatively low-stringency hybridization
conditions are selected: about 20 to 25.degree. C. lower than the
thermal melting point (T.sub.m). The T.sub.m is the temperature at
which 50% of specific target sequence hybridizes to a perfectly
complementary probe in solution at a defined ionic strength and pH.
Generally, in order to require at least about 85% nucleotide
complementarity of hybridized sequences, highly stringent washing
conditions are selected to be about 5 to 15.degree. C. lower than
the T.sub.m. In order to require at least about 70% nucleotide
complementarity of hybridized sequences, moderately-stringent
washing conditions are selected to be about 15 to 30.degree. C.
lower than the T.sub.m. Highly permissive (very low stringency)
washing conditions may be as low as 50.degree. C. below the
T.sub.m, allowing a high level of mis-matching between hybridized
sequences. Those skilled in the art will recognize that other
physical and chemical parameters in the hybridization and wash
stages can also be altered to affect the outcome of a detectable
hybridization signal from a specific level of homology between
target and probe sequences. Preferred highly stringent conditions
comprise incubation in 50% formamide, 5.times.SSC, and 1% SDS at
42.degree. C., or incubation in 5.times.SSC and 1% SDS at
65.degree. C., with wash in 0.2.times.SSC and 0.1% SDS at
65.degree. C.
[0241] "Hybridization" refers to a reaction in which one or more
polynucleotides react to form a complex that is stabilized via
hydrogen bonding between the bases of the nucleotide residues. The
hydrogen bonding may occur by Watson Crick base pairing, Hoogstein
binding, or in any other sequence specific manner. The complex may
comprise two strands forming a duplex structure, three or more
strands forming a multi stranded complex, a single self-hybridizing
strand, or any combination of these. A hybridization reaction may
constitute a step in a more extensive process, such as the
initiation of PCR, or the cleavage of a polynucleotide by an
enzyme. A sequence capable of hybridizing with a given sequence is
referred to as the "complement" of the given sequence.
[0242] As used herein, the term "genomic locus" or "locus" (plural
loci) is the specific location of a gene or DNA sequence on a
chromosome. A "gene" refers to stretches of DNA or RNA that encode
a polypeptide or an RNA chain that has functional role to play in
an organism and hence is the molecular unit of heredity in living
organisms. For the purpose of this invention it may be considered
that genes include regions which regulate the production of the
gene product, whether or not such regulatory sequences are adjacent
to coding and/or transcribed sequences. Accordingly, a gene
includes, but is not necessarily limited to, promoter sequences,
terminators, translational regulatory sequences such as ribosome
binding sites and internal ribosome entry sites, enhancers,
silencers, insulators, boundary elements, replication origins,
matrix attachment sites and locus control regions.
[0243] As used herein, "expression of a genomic locus" or "gene
expression" is the process by which information from a gene is used
in the synthesis of a functional gene product. The products of gene
expression are often proteins, but in non-protein coding genes such
as rRNA genes or tRNA genes, the product is functional RNA. The
process of gene expression is used by all known life--eukaryotes
(including multicellular organisms), prokaryotes (bacteria and
archaea) and viruses to generate functional products to survive. As
used herein "expression" of a gene or nucleic acid encompasses not
only cellular gene expression, but also the transcription and
translation of nucleic acid(s) in cloning systems and in any other
context. As used herein, "expression" also refers to the process by
which a polynucleotide is transcribed from a DNA template (such as
into and mRNA or other RNA transcript) and/or the process by which
a transcribed mRNA is subsequently translated into peptides,
polypeptides, or proteins. Transcripts and encoded polypeptides may
be collectively referred to as "gene product." If the
polynucleotide is derived from genomic DNA, expression may include
splicing of the mRNA in a eukaryotic cell.
[0244] The terms "polypeptide", "peptide" and "protein" are used
interchangeably herein to refer to polymers of amino acids of any
length. The polymer may be linear or branched, it may comprise
modified amino acids, and it may be interrupted by non amino acids.
The terms also encompass an amino acid polymer that has been
modified; for example, disulfide bond formation, glycosylation,
lipidation, acetylation, phosphorylation, or any other
manipulation, such as conjugation with a labeling component. As
used herein the term "amino acid" includes natural and/or unnatural
or synthetic amino acids, including glycine and both the D or L
optical isomers, and amino acid analogs and peptidomimetics.
[0245] As used herein, the term "domain" or "protein domain" refers
to a part of a protein sequence that may exist and function
independently of the rest of the protein chain.
[0246] As described in aspects of the invention, sequence identity
is related to sequence homology. Homology comparisons may be
conducted by eye, or more usually, with the aid of readily
available sequence comparison programs. These commercially
available computer programs may calculate percent (%) homology
between two or more sequences and may also calculate the sequence
identity shared by two or more amino acid or nucleic acid
sequences. In some preferred embodiments, the capping region of the
dTALEs described herein have sequences that are at least 95%
identical or share identity to the capping region amino acid
sequences provided herein.
[0247] Sequence homologies may be generated by any of a number of
computer programs known in the art, for example BLAST or FASTA,
etc. A suitable computer program for carrying out such an alignment
is the GCG Wisconsin Bestfit package (University of Wisconsin,
U.S.A; Devereux et al., 1984, Nucleic Acids Research 12:387).
Examples of other software than may perform sequence comparisons
include, but are not limited to, the BLAST package (see Ausubel et
al., 1999 ibid--Chapter 18), FASTA (Atschul et al., 1990, J. Mol.
Biol., 403-410) and the GENEWORKS suite of comparison tools. Both
BLAST and FASTA are available for offline and online searching (see
Ausubel et al., 1999 ibid, pages 7-58 to 7-60). However it is
preferred to use the GCG Bestfit program.
[0248] Percentage (%) sequence homology may be calculated over
contiguous sequences, i.e., one sequence is aligned with the other
sequence and each amino acid or nucleotide in one sequence is
directly compared with the corresponding amino acid or nucleotide
in the other sequence, one residue at a time. This is called an
"ungapped" alignment. Typically, such ungapped alignments are
performed only over a relatively short number of residues.
[0249] Although this is a very simple and consistent method, it
fails to take into consideration that, for example, in an otherwise
identical pair of sequences, one insertion or deletion may cause
the following amino acid residues to be put out of alignment, thus
potentially resulting in a large reduction in % homology when a
global alignment is performed. Consequently, most sequence
comparison methods are designed to produce optimal alignments that
take into consideration possible insertions and deletions without
unduly penalizing the overall homology or identity score. This is
achieved by inserting "gaps" in the sequence alignment to try to
maximize local homology or identity.
[0250] However, these more complex methods assign "gap penalties"
to each gap that occurs in the alignment so that, for the same
number of identical amino acids, a sequence alignment with as few
gaps as possible--reflecting higher relatedness between the two
compared sequences--may achieve a higher score than one with many
gaps. "Affinity gap costs" are typically used that charge a
relatively high cost for the existence of a gap and a smaller
penalty for each subsequent residue in the gap. This is the most
commonly used gap scoring system. High gap penalties may, of
course, produce optimized alignments with fewer gaps. Most
alignment programs allow the gap penalties to be modified. However,
it is preferred to use the default values when using such software
for sequence comparisons. For example, when using the GCG Wisconsin
Bestfit package the default gap penalty for amino acid sequences is
-12 for a gap and -4 for each extension.
[0251] Calculation of maximum % homology therefore first requires
the production of an optimal alignment, taking into consideration
gap penalties. A suitable computer program for carrying out such an
alignment is the GCG Wisconsin Bestfit package (Devereux et al.,
1984 Nuc. Acids Research 12 p 387). Examples of other software that
may perform sequence comparisons include, but are not limited to,
the BLAST package (see Ausubel et al., 1999 Short Protocols in
Molecular Biology, 4 h Ed.--Chapter 18), FASTA (Altschul et al.,
1990 J. Mol. Biol. 403-410) and the GENEWORKS suite of comparison
tools. Both BLAST and FASTA are available for offline and online
searching (see Ausubel et al., 1999, Short Protocols in Molecular
Biology, pages 7-58 to 7-60). However, for some applications, it is
preferred to use the GCG Bestfit program. A new tool, called BLAST
2 Sequences is also available for comparing protein and nucleotide
sequences (see FEMS Microbiol Lett. 1999 174(2): 247-50; FEAMS
Microbiol Lett. 1999 177(1): 187-8 and the website of the National
Center for Biotechnology information at the website of the National
Institutes for Health).
[0252] Although the final % homology may be measured in terms of
identity, the alignment process itself is typically not based on an
all-or-nothing pair comparison. Instead, a scaled similarity score
matrix is generally used that assigns scores to each pair-wise
comparison based on chemical similarity or evolutionary distance.
An example of such a matrix commonly used is the BLOSUM62
matrix--the default matrix for the BLAST suite of programs. GCG
Wisconsin programs generally use either the public default values
or a custom symbol comparison table, if supplied (see user manual
for further details). For some applications, it is preferred to use
the public default values for the GCG package, or in the case of
other software, the default matrix, such as BLOSUM62.
[0253] Alternatively, percentage homologies may be calculated using
the multiple alignment feature in DNASIS.TM. (Hitachi Software),
based on an algorithm, analogous to CLUSTAL (Higgins D G &
Sharp P M (1988), Gene 73(1), 237-244). Once the software has
produced an optimal alignment, it is possible to calculate %
homology, preferably % sequence identity. The software typically
does this as part of the sequence comparison and generates a
numerical result.
[0254] The sequences may also have deletions, insertions or
substitutions of amino acid residues which produce a silent change
and result in a functionally equivalent substance. Deliberate amino
acid substitutions may be made on the basis of similarity in amino
acid properties (such as polarity, charge, solubility,
hydrophobicity, hydrophilicity, and/or the amphipathic nature of
the residues) and it is therefore useful to group amino acids
together in functional groups. Amino acids may be grouped together
based on the properties of their side chains alone. However, it is
more useful to include mutation data as well. The sets of amino
acids thus derived are likely to be conserved for structural
reasons. These sets may be described in the form of a Venn diagram
(Livingstone C. D. and Barton G. J. (1993) "Protein sequence
alignments: a strategy for the hierarchical analysis of residue
conservation" Comput. Appl. Biosci. 9: 745-756) (Taylor W. R.
(1986) "The classification of amino acid conservation" J. Theor.
Biol. 119; 205-218). Conservative substitutions may be made, for
example according to the table below which describes a generally
accepted Venn diagram grouping of amino acids.
TABLE-US-00003 Set SuB-set Hydrophobic F M I L V A G C Aromatic F W
Y H Aliphatic I L V Polar W Y H K R E D C S T N Q Charged H K R E D
Positively H K R charged Negatively E D charged Small V C A G S P T
N D Tiny A G S
[0255] Embodiments of the invention include sequences (both
polynucleotide or polypeptide) which may comprise homologous
substitution (substitution and replacement are both used herein to
mean the interchange of an existing amino acid residue or
nucleotide, with an alternative residue or nucleotide) that may
occur i.e., like-for-like substitution in the case of amino acids
such as basic for basic, acidic for acidic, polar for polar, etc.
Non-homologous substitution may also occur i.e., from one class of
residue to another or alternatively involving the inclusion of
unnatural amino acids such as ornithine (hereinafter referred to as
Z), diaminobutyric acid ornithine (hereinafter referred to as B),
norleucine ornithine (hereinafter referred to as O), pyriylalanine,
thienylalanine, naphthylalanine and phenylglycine.
[0256] Variant amino acid sequences may include suitable spacer
groups that may be inserted between any two amino acid residues of
the sequence including alkyl groups such as methyl, ethyl or propyl
groups in addition to amino acid spacers such as glycine or
.beta.-alanine residues. A further form of variation, which
involves the presence of one or more amino acid residues in peptoid
form, may be well understood by those skilled in the art. For the
avoidance of doubt, "the peptoid form" is used to refer to variant
amino acid residues wherein the .alpha.-carbon substituent group is
on the residue's nitrogen atom rather than the .alpha.-carbon.
Processes for preparing peptides in the peptoid form are known in
the art, for example Simon R J et al., PNAS (1992) 89(20),
9367-9371 and Horwell D C, Trends Biotechnol. (1995) 13(4),
132-134.
[0257] The practice of the present invention employs, unless
otherwise indicated, conventional techniques of immunology,
biochemistry, chemistry, molecular biology, microbiology, cell
biology, genomics and recombinant DNA, which are within the skill
of the art. See Sambrook, Fritsch and Maniatis, MOLECULAR CLONING:
A LABORATORY MANUAL, 2nd edition (1989); CURRENT PROTOCOLS IN
MOLECULAR BIOLOGY (F. M. Ausubel, et al. eds., (1987)); the series
METHODS IN ENZYMOLOGY (Academic Press, Inc.): PCR 2: A PRACTICAL
APPROACH (M. J. MacPherson, B. D. Hames and G. R. Taylor eds.
(1995)), Harlow and Lane, eds. (1988) ANTIBODIES, A LABORATORY
MANUAL, and ANIMAL CELL CULTURE (R.I. Freshney, ed. (1987)).
[0258] In one aspect, the invention provides for vectors that are
used in the engineering and optimization of CRISPR-Cas systems.
[0259] A used herein, a "vector" is a tool that allows or
facilitates the transfer of an entity from one environment to
another. It is a replicon, such as a plasmid, phage, or cosmid,
into which another DNA segment may be inserted so as to bring about
the replication of the inserted segment. Generally, a vector is
capable of replication when associated with the proper control
elements. In general, the term "vector" refers to a nucleic acid
molecule capable of transporting another nucleic acid to which it
has been linked. Vectors include, but are not limited to, nucleic
acid molecules that are single-stranded, double-stranded, or
partially double-stranded; nucleic acid molecules that comprise one
or more free ends, no free ends (e.g. circular); nucleic acid
molecules that comprise DNA, RNA, or both; and other varieties of
polynucleotides known in the art. One type of vector is a
"plasmid," which refers to a circular double stranded DNA loop into
which additional DNA segments can be inserted, such as by standard
molecular cloning techniques. Another type of vector is a viral
vector, wherein virally-derived DNA or RNA sequences are present in
the vector for packaging into a virus (e.g. retroviruses,
replication defective retroviruses, adenoviruses, replication
defective adenoviruses, and adeno-associated viruses (AAVs)). Viral
vectors also include polynucleotides carried by a virus for
transfection into a host cell. Certain vectors are capable of
autonomous replication in a host cell into which they are
introduced (e.g. bacterial vectors having a bacterial origin of
replication and episomal mammalian vectors). Other vectors (e.g.,
non-episomal mammalian vectors) are integrated into the genome of a
host cell upon introduction into the host cell, and thereby are
replicated along with the host genome. Moreover, certain vectors
are capable of directing the expression of genes to which they are
operatively-linked. Such vectors are referred to herein as
"expression vectors." Common expression vectors of utility in
recombinant DNA techniques are often in the form of plasmids.
[0260] Recombinant expression vectors can comprise a nucleic acid
of the invention in a form suitable for expression of the nucleic
acid in a host cell, which means that the recombinant expression
vectors include one or more regulatory elements, which may be
selected on the basis of the host cells to be used for expression,
that is operatively-linked to the nucleic acid sequence to be
expressed. Within a recombinant expression vector, "operably
linked" is intended to mean that the nucleotide sequence of
interest is linked to the regulatory element(s) in a manner that
allows for expression of the nucleotide sequence (e.g. in an in
vitro transcription/translation system or in a host cell when the
vector is introduced into the host cell). With regards to
recombination and cloning methods, mention is made of U.S. patent
application Ser. No. 10/815,730, published Sep. 2, 2004 as US
2004-0171156 A1, the contents of which are herein incorporated by
reference in their entirety.
[0261] Aspects of the invention relate to bicistronic vectors for
chimeric RNA and Cas9. Bicistronic expression vectors for chimeric
RNA and Cas9 are preferred. In general and particularly in this
embodiment Cas9 is preferably driven by the CBh promoter. The
chimeric RNA may preferably be driven by a U6 promoter. Ideally the
two are combined. The chimeric guide RNA typically consists of a 20
bp guide sequence (Ns) and this may be joined to the tracr sequence
(running from the first "U" of the lower strand to the end of the
transcript). The tracr sequence may be truncated at various
positions as indicated. The guide and tracr sequences are separated
by the tracr-mate sequence, which may be GUUUUAGAGCUA. This may be
followed by the loop sequence GAAA as shown. Both of these are
preferred examples. Applicants have demonstrated Cas9-mediated
indels at the human EMX1 and PVALB loci by SURVEYOR assays. ChiRNAs
are indicated by their "+n" designation, and crRNA refers to a
hybrid RNA where guide and tracr sequences are expressed as
separate transcripts. Throughout this application, chimeric RNA may
also be called single guide, or synthetic guide RNA (sgRNA). The
loop is preferably GAAA, but it is not limited to this sequence or
indeed to being only 4 bp in length. Indeed, preferred loop forming
sequences for use in hairpin structures are four nucleotides in
length, and most preferably have the sequence GAAA. However, longer
or shorter loop sequences may be used, as may alternative
sequences. The sequences preferably include a nucleotide triplet
(for example, AAA), and an additional nucleotide (for example C or
G). Examples of loop forming sequences include CAAA and AAAG.
[0262] The term "regulatory element" is intended to include
promoters, enhancers, internal ribosomal entry sites (IRES), and
other expression control elements (e.g. transcription termination
signals, such as polyadenylation signals and poly-U sequences).
Such regulatory elements are described, for example, in Goeddel,
GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185, Academic
Press, San Diego, Calif. (1990). Regulatory elements include those
that direct constitutive expression of a nucleotide sequence in
many types of host cell and those that direct expression of the
nucleotide sequence only in certain host cells (e.g.,
tissue-specific regulatory sequences). A tissue-specific promoter
may direct expression primarily in a desired tissue of interest,
such as muscle, neuron, bone, skin, blood, specific organs (e.g.
liver, pancreas), or particular cell types (e.g. lymphocytes).
Regulatory elements may also direct expression in a
temporal-dependent manner, such as in a cell-cycle dependent or
developmental stage-dependent manner, which may or may not also be
tissue or cell-type specific. In some embodiments, a vector
comprises one or more pol III promoter (e.g. 1, 2, 3, 4, 5, or more
pol III promoters), one or more pol II promoters (e.g. 1, 2, 3, 4,
5, or more pol II promoters), one or more pol I promoters (e.g. 1,
2, 3, 4, 5, or more pol I promoters), or combinations thereof.
Examples of pol III promoters include, but are not limited to, U6
and H1 promoters. Examples of pol II promoters include, but are not
limited to, the retroviral Rous sarcoma virus (RSV) LTR promoter
(optionally with the RSV enhancer), the cytomegalovirus (CMV)
promoter (optionally with the CMV enhancer) [see, e.g., Boshart et
al, Cell, 41:521-530 (1985)], the SV40 promoter, the dihydrofolate
reductase promoter, the .beta.-actin promoter, the phosphoglycerol
kinase (PGK) promoter, and the EF1.alpha. promoter. Also
encompassed by the term "regulatory element" are enhancer elements,
such as WPRE; CMV enhancers; the R-U5' segment in LTR of HTLV-I
(Mol. Cell. Biol., Vol. 8(1), p. 466-472, 1988); SV40 enhancer; and
the intron sequence between exons 2 and 3 of rabbit .beta.-globin
(Proc. Natl. Acad. Sci. USA., Vol. 78(3), p. 1527-31, 1981). It
will be appreciated by those skilled in the art that the design of
the expression vector can depend on such factors as the choice of
the host cell to be transformed, the level of expression desired,
etc. A vector can be introduced into host cells to thereby produce
transcripts, proteins, or peptides, including fusion proteins or
peptides, encoded by nucleic acids as described herein (e.g.,
clustered regularly interspersed short palindromic repeats (CRISPR)
transcripts, proteins, enzymes, mutant forms thereof, fusion
proteins thereof, etc.). With regards to regulatory sequences,
mention is made of U.S. patent application Ser. No. 10/491,026, the
contents of which are incorporated by reference herein in their
entirety. With regards to promoters, mention is made of PCT
publication WO 2011/028929 and U.S. application Ser. No.
12/511,940, the contents of which are incorporated by reference
herein in their entirety.
[0263] Vectors can be designed for expression of CRISPR transcripts
(e.g. nucleic acid transcripts, proteins, or enzymes) in
prokaryotic or eukaryotic cells. For example, CRISPR transcripts
can be expressed in bacterial cells such as Escherichia coli,
insect cells (using baculovirus expression vectors), yeast cells,
or mammalian cells. Suitable host cells are discussed further in
Goeddel, GENE EXPRESSION TECHNOLOGY: METHODS IN ENZYMOLOGY 185,
Academic Press, San Diego, Calif. (1990). Alternatively, the
recombinant expression vector can be transcribed and translated in
vitro, for example using T7 promoter regulatory sequences and T7
polymerase.
[0264] Vectors may be introduced and propagated in a prokaryote or
prokaryotic cell. In some embodiments, a prokaryote is used to
amplify copies of a vector to be introduced into a eukaryotic cell
or as an intermediate vector in the production of a vector to be
introduced into a eukaryotic cell (e.g. amplifying a plasmid as
part of a viral vector packaging system). In some embodiments, a
prokaryote is used to amplify copies of a vector and express one or
more nucleic acids, such as to provide a source of one or more
proteins for delivery to a host cell or host organism. Expression
of proteins in prokaryotes is most often carried out in Escherichia
coli with vectors containing constitutive or inducible promoters
directing the expression of either fusion or non-fusion proteins.
Fusion vectors add a number of amino acids to a protein encoded
therein, such as to the amino terminus of the recombinant protein.
Such fusion vectors may serve one or more purposes, such as: (i) to
increase expression of recombinant protein; (ii) to increase the
solubility of the recombinant protein; and (iii) to aid in the
purification of the recombinant protein by acting as a ligand in
affinity purification. Often, in fusion expression vectors, a
proteolytic cleavage site is introduced at the junction of the
fusion moiety and the recombinant protein to enable separation of
the recombinant protein from the fusion moiety subsequent to
purification of the fusion protein. Such enzymes, and their cognate
recognition sequences, include Factor Xa, thrombin and
enterokinase. Example fusion expression vectors include pGEX
(Pharmacia Biotech Inc; Smith and Johnson, 1988. Gene 67: 31-40),
pMAL (New England Biolabs, Beverly, Mass.) and pRIT5 (Pharmacia,
Piscataway, N.J.) that fuse glutathione S-transferase (GST),
maltose E binding protein, or protein A, respectively, to the
target recombinant protein.
[0265] Examples of suitable inducible non-fusion E. coli expression
vectors include pTrc (Amrann et al., (1988) Gene 69:301-315) and
pET 11d (Studier et al., GENE EXPRESSION TECHNOLOGY: METHODS IN
ENZYMOLOGY 185, Academic Press, San Diego, Calif. (1990)
60-89).
[0266] In some embodiments, a vector is a yeast expression vector.
Examples of vectors for expression in yeast Saccharomyces cerivisae
include pYepSec1 (Baldari, et al., 1987. EMBO J. 6: 229-234), pMFa
(Kuijan and Herskowitz, 1982. Cell 30: 933-943), pJRY88 (Schultz et
al., 1987. Gene 54: 113-123), pYES2 (Invitrogen Corporation, San
Diego, Calif.), and picZ (InVitrogen Corp, San Diego, Calif.).
[0267] In some embodiments, a vector drives protein expression in
insect cells using baculovirus expression vectors. Baculovirus
vectors available for expression of proteins in cultured insect
cells (e.g., SF9 cells) include the pAc series (Smith, et al.,
1983. Mol. Cell. Biol. 3: 2156-2165) and the pVL series (Lucklow
and Summers, 1989. Virology 170: 31-39).
[0268] In some embodiments, a vector is capable of driving
expression of one or more sequences in mammalian cells using a
mammalian expression vector. Examples of mammalian expression
vectors include pCDM8 (Seed, 1987. Nature 329: 840) and pMT2PC
(Kaufman, et al., 1987. EMBO J. 6: 187-195). When used in mammalian
cells, the expression vector's control functions are typically
provided by one or more regulatory elements. For example, commonly
used promoters are derived from polyoma, adenovirus 2,
cytomegalovirus, simian virus 40, and others disclosed herein and
known in the art. For other suitable expression systems for both
prokaryotic and eukaryotic cells see, e.g., Chapters 16 and 17 of
Sambrook, et al., MOLECULAR CLONING: A LABORATORY MANUAL. 2nd ed.,
Cold Spring Harbor Laboratory, Cold Spring Harbor Laboratory Press,
Cold Spring Harbor, N.Y., 1989.
[0269] In some embodiments, the recombinant mammalian expression
vector is capable of directing expression of the nucleic acid
preferentially in a particular cell type (e.g., tissue-specific
regulatory elements are used to express the nucleic acid).
Tissue-specific regulatory elements are known in the art.
Non-limiting examples of suitable tissue-specific promoters include
the albumin promoter (liver-specific; Pinkert, et al., 1987. Genes
Dev. 1: 268-277), lymphoid-specific promoters (Calame and Eaton,
1988. Adv. Immunol. 43: 235-275), in particular promoters of T cell
receptors (Winoto and Baltimore, 1989. EMBO J. 8: 729-733) and
immunoglobulins (Baneiji, et al., 1983. Cell 33: 729-740; Queen and
Baltimore, 1983. Cell 33: 741-748), neuron-specific promoters
(e.g., the neurofilament promoter; Byrne and Ruddle, 1989. Proc.
Natl. Acad. Sci. USA 86: 5473-5477), pancreas-specific promoters
(Edlund, et al., 1985. Science 230: 912-916), and mammary
gland-specific promoters (e.g., milk whey promoter; U.S. Pat. No.
4,873,316 and European Application Publication No. 264, 166).
Developmentally-regulated promoters are also encompassed, e.g., the
murine hox promoters (Kessel and Gruss, 1990. Science 249: 374-379)
and the .alpha.-fetoprotein promoter (Campes and Tilghman, 1989.
Genes Dev. 3: 537-546). With regards to these prokaryotic and
eukaryotic vectors, mention is made of U.S. Pat. No. 6,750,059, the
contents of which are incorporated by reference herein in their
entirety. Other embodiments of the invention may relate to the use
of viral vectors, with regards to which mention is made of U.S.
patent application Ser. No. 13/092,085, the contents of which are
incorporated by reference herein in their entirety. Tissue-specific
regulatory elements are known in the art and in this regard,
mention is made of U.S. Pat. No. 7,776,321, the contents of which
are incorporated by reference herein in their entirety.
[0270] In some embodiments, a regulatory element is operably linked
to one or more elements of a CRISPR system so as to drive
expression of the one or more elements of the CRISPR system. In
general, CRISPRs (Clustered Regularly Interspaced Short Palindromic
Repeats), also known as SPIDRs (SPacer Interspersed Direct
Repeats), constitute a family of DNA loci that are usually specific
to a particular bacterial species. The CRISPR locus comprises a
distinct class of interspersed short sequence repeats (SSRs) that
were recognized in E. coli (Ishino et al., J. Bacteriol.,
169:5429-5433 [1987]; and Nakata et al., J. Bacteriol.,
171:3553-3556 [1989]), and associated genes. Similar interspersed
SSRs have been identified in Haloferax mediterranei, Streptococcus
pyogenes, Anabaena, and Mycobacterium tuberculosis (See, Groenen et
al., Mol. Microbiol., 10:1057-1065 [1993]; Hoe et al., Emerg.
Infect. Dis., 5:254-263 [1999]; Masepohl et al., Biochim. Biophys.
Acta 1307:26-30 [1996]; and Mojica et al., Mol. Microbiol.,
17:85-93 [1995]). The CRISPR loci typically differ from other SSRs
by the structure of the repeats, which have been termed short
regularly spaced repeats (SRSRs) (Janssen et al., OMICS J. Integ.
Biol., 6:23-33 [2002]; and Mojica et al., Mol. Microbiol.,
36:244-246 [2000]). In general, the repeats are short elements that
occur in clusters that are regularly spaced by unique intervening
sequences with a substantially constant length (Mojica et al.,
[2000], supra). Although the repeat sequences are highly conserved
between strains, the number of interspersed repeats and the
sequences of the spacer regions typically differ from strain to
strain (van Embden et al., J. Bacteriol., 182:2393-2401 [2000]).
CRISPR loci have been identified in more than 40 prokaryotes (See
e.g., Jansen et al., Mol. Microbiol., 43:1565-1575 [2002]; and
Mojica et al., [2005]) including, but not limited to Aeropyrum,
Pyrobaculum, Sulfolobus, Archaeoglobus, Halocarcula,
Methanobacterium, Methanococcus, Methanosarcina, Methanopyrus,
Pyrococcus, Picrophilus, Thermoplasma, Corynebacterium,
Mycobacterium, Streptomyces, Aquifex, Porphyromonas, Chlorobium,
Thermus, Bacillus, Listeria, Staphylococcus, Clostridium,
Thermoanaerobacter, Mycoplasma, Fusobacterium, Azarcus,
Chromobacterium, Neisseria, Nitrosomonas, Desulfovibrio, Geobacter,
Myxococcus, Canmpylobacter, Wolinella, Acinetobacter, Erwinia,
Escherichia, Legionella, Methylococcus, Pasteurella,
Photobacterium, Salmonella, Xanthomonas, Yersinia, Treponema, and
Thermotoga.
[0271] In general, "CRISPR system" refers collectively to
transcripts and other elements involved in the expression of or
directing the activity of CRISPR-associated ("Cas") genes,
including sequences encoding a Cas gene, a tracr (trans-activating
CRISPR) sequence (e.g. tracrRNA or an active partial tracrRNA), a
tracr-mate sequence (encompassing a "direct repeat" and a
tracrRNA-processed partial direct repeat in the context of an
endogenous CRISPR system), a guide sequence (also referred to as a
"spacer" in the context of an endogenous CRISPR system), or other
sequences and transcripts from a CRISPR locus. In embodiments of
the invention the terms guide sequence and guide RNA are used
interchangeably. In some embodiments, one or more elements of a
CRISPR system is derived from a type I, type II, or type III CRISPR
system. In some embodiments, one or more elements of a CRISPR
system is derived from a particular organism comprising an
endogenous CRISPR system, such as Streptococcus pyogenes. In
general, a CRISPR system is characterized by elements that promote
the formation of a CRISPR complex at the site of a target sequence
(also referred to as a protospacer in the context of an endogenous
CRISPR system). In the context of formation of a CRISPR complex,
"target sequence" refers to a sequence to which a guide sequence is
designed to have complementarity, where hybridization between a
target sequence and a guide sequence promotes the formation of a
CRISPR complex. A target sequence may comprise any polynucleotide,
such as DNA or RNA polynucleotides. In some embodiments, a target
sequence is located in the nucleus or cytoplasm of a cell.
[0272] In some embodiments, direct repeats may be identified in
silico by searching for repetitive motifs that fulfill any or all
of the following criteria:
[0273] 1. found in a 2 Kb window of genomic sequence flanking the
type II CRISPR locus;
[0274] 2. span from 20 to 50 bp; and
[0275] 3. interspaced by 20 to 50 bp.
[0276] In some embodiments, 2 of these criteria may be used, for
instance 1 and 2, 2 and 3, or 1 and 3. In some embodiments, all 3
criteria may be used.
[0277] In some embodiments, candidate tracrRNA may be subsequently
predicted by sequences that fulfill any or all of the following
criteria:
[0278] 1. sequence homology to direct repeats (motif search in
Geneious with up to 18-bp mismatches);
[0279] 2. presence of a predicted Rho-independent transcriptional
terminator in direction of transcription; and
[0280] 3. stable hairpin secondary structure between tracrRNA and
direct repeat.
[0281] In some embodiments, 2 of these criteria may be used, for
instance 1 and 2, 2 and 3, or 1 and 3. In some embodiments, all 3
criteria may be used.
[0282] In some embodiments, chimeric synthetic guide RNAs (sgRNAs)
designs may incorporate at least 12 bp of duplex structure between
the direct repeat and tracrRNA.
[0283] In preferred embodiments of the invention, the CRISPR system
is a type II CRISPR system and the Cas enzyme is Cas9, which
catalyzes DNA cleavage. Enzymatic action by Cas9 derived from
Streptococcus pyogenes or any closely related Cas9 generates double
stranded breaks at target site sequences which hybridize to 20
nucleotides of the guide sequence and that have a
protospacer-adjacent motif (PAM) sequence (examples include NGG/NRG
or a PAM that can be determined as described herein) following the
20 nucleotides of the target sequence. CRISPR activity through Cas9
for site-specific DNA recognition and cleavage is defined by the
guide sequence, the tracr sequence that hybridizes in part to the
guide sequence and the PAM sequence. More aspects of the CRISPR
system are described in Karginov and Hannon, The CRISPR system:
small RNA-guided defense in bacteria and archaea, Mole Cell 2010,
Jan. 15; 37(1): 7.
[0284] The type II CRISPR locus from Streptococcus pyogenes SF370
contains a cluster of four genes Cas9, Cas1, Cas2, and Csn1, as
well as two non-coding RNA elements, tracrRNA and a characteristic
array of repetitive sequences (direct repeats) interspaced by short
stretches of non-repetitive sequences (spacers, about 30 bp each).
In this system, targeted DNA double-strand break (DSB) is generated
in four sequential steps (FIG. 2A). First, two non-coding RNAs, the
pre-crRNA array and tracrRNA, are transcribed from the CRISPR
locus. Second, tracrRNA hybridizes to the direct repeats of
pre-crRNA, which is then processed into mature crRNAs containing
individual spacer sequences. Third, the mature crRNA:tracrRNA
complex directs Cas9 to the DNA target consisting of the
protospacer and the corresponding PAM via heteroduplex formation
between the spacer region of the crRNA and the protospacer DNA.
Finally, Cas9 mediates cleavage of target DNA upstream of PAM to
create a DSB within the protospacer (FIG. 2A). FIG. 2B demonstrates
the nuclear localization of the codon optimized Cas9. To promote
precise transcriptional initiation, the RNA polymerase III-based U6
promoter was selected to drive the expression of tracrRNA (FIG.
2C). Similarly, a U6 promoter-based construct was developed to
express a pre-crRNA array consisting of a single spacer flanked by
two direct repeats (DRs, also encompassed by the term "tracr-mate
sequences"; FIG. 2C). The initial spacer was designed to target a
33-base-pair (bp) target site (30-bp protospacer plus a 3-bp CRISPR
motif (PAM) sequence satisfying the NGG recognition motif of Cas9)
in the human EMX1 locus (FIG. 2C), a key gene in the development of
the cerebral cortex.
[0285] Typically, in the context of an endogenous CRISPR system,
formation of a CRISPR complex (comprising a guide sequence
hybridized to a target sequence and complexed with one or more Cas
proteins) results in cleavage of one or both strands in or near
(e.g. within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 50, or more base
pairs from) the target sequence. Without wishing to be bound by
theory, the tracr sequence, which may comprise or consist of all or
a portion of a wild-type tracr sequence (e.g. about or more than
about 20, 26, 32, 45, 48, 54, 63, 67, 85, or more nucleotides of a
wild-type tracr sequence), may also form part of a CRISPR complex,
such as by hybridization along at least a portion of the tracr
sequence to all or a portion of a tracr mate sequence that is
operably linked to the guide sequence. In some embodiments, one or
more vectors driving expression of one or more elements of a CRISPR
system are introduced into a host cell such that expression of the
elements of the CRISPR system direct formation of a CRISPR complex
at one or more target sites. For example, a Cas enzyme, a guide
sequence linked to a tracr-mate sequence, and a tracr sequence
could each be operably linked to separate regulatory elements on
separate vectors. Alternatively, two or more of the elements
expressed from the same or different regulatory elements, may be
combined in a single vector, with one or more additional vectors
providing any components of the CRISPR system not included in the
first vector. CRISPR system elements that are combined in a single
vector may be arranged in any suitable orientation, such as one
element located 5' with respect to ("upstream" of) or 3' with
respect to ("downstream" of) a second element. The coding sequence
of one element may be located on the same or opposite strand of the
coding sequence of a second element, and oriented in the same or
opposite direction. In some embodiments, a single promoter drives
expression of a transcript encoding a CRISPR enzyme and one or more
of the guide sequence, tracr mate sequence (optionally operably
linked to the guide sequence), and a tracr sequence embedded within
one or more intron sequences (e.g. each in a different intron, two
or more in at least one intron, or all in a single intron). In some
embodiments, the CRISPR enzyme, guide sequence, tracr mate
sequence, and tracr sequence are operably linked to and expressed
from the same promoter.
[0286] In some embodiments, a vector comprises one or more
insertion sites, such as a restriction endonuclease recognition
sequence (also referred to as a "cloning site"). In some
embodiments, one or more insertion sites (e.g. about or more than
about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more insertion sites) are
located upstream and/or downstream of one or more sequence elements
of one or more vectors. In some embodiments, a vector comprises an
insertion site upstream of a tracr mate sequence, and optionally
downstream of a regulatory element operably linked to the tracr
mate sequence, such that following insertion of a guide sequence
into the insertion site and upon expression the guide sequence
directs sequence-specific binding of a CRISPR complex to a target
sequence in a eukaryotic cell. In some embodiments, a vector
comprises two or more insertion sites, each insertion site being
located between two tracr mate sequences so as to allow insertion
of a guide sequence at each site. In such an arrangement, the two
or more guide sequences may comprise two or more copies of a single
guide sequence, two or more different guide sequences, or
combinations of these. When multiple different guide sequences are
used, a single expression construct may be used to target CRISPR
activity to multiple different, corresponding target sequences
within a cell. For example, a single vector may comprise about or
more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more
guide sequences. In some embodiments, about or more than about 1,
2, 3, 4, 5, 6, 7, 8, 9, 10, or more such guide-sequence-containing
vectors may be provided, and optionally delivered to a cell.
[0287] In some embodiments, a vector comprises a regulatory element
operably linked to an enzyme-coding sequence encoding a CRISPR
enzyme, such as a Cas protein. Non-limiting examples of Cas
proteins include Cas1, Cas 1B, Cas2, Cas3, Cas4, Cas5, Cas6, Cas7,
Cas8, Cas9 (also known as Csn1 and Csx12), Cas10, Csy1, Csy2, Csy3,
Cse1, Cse2, Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6,
Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14,
Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4,
homologues thereof, or modified versions thereof. In some
embodiments, the unmodified CRISPR enzyme has DNA cleavage
activity, such as Cas9. In some embodiments, the CRISPR enzyme
directs cleavage of one or both strands at the location of a target
sequence, such as within the target sequence and/or within the
complement of the target sequence. In some embodiments, the CRISPR
enzyme directs cleavage of one or both strands within about 1, 2,
3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 50, 100, 200, 500, or more
base pairs from the first or last nucleotide of a target sequence.
In some embodiments, a vector encodes a CRISPR enzyme that is
mutated to with respect to a corresponding wild-type enzyme such
that the mutated CRISPR enzyme lacks the ability to cleave one or
both strands of a target polynucleotide containing a target
sequence. For example, an aspartate-to-alanine substitution (D10A)
in the RuvC I catalytic domain of Cas9 from S. pyogenes converts
Cas9 from a nuclease that cleaves both strands to a nickase
(cleaves a single strand). Other examples of mutations that render
Cas9 a nickase include, without limitation, H840A, N854A, and
N863A. As a further example, two or more catalytic domains of Cas9
(RuvC I, RuvC II, and RuvC III or the HNH domain) may be mutated to
produce a mutated Cas9 substantially lacking all DNA cleavage
activity. In some embodiments, a D10A mutation is combined with one
or more of H840A, N854A, or N863A mutations to produce a Cas9
enzyme substantially lacking all DNA cleavage activity. In some
embodiments, a CRISPR enzyme is considered to substantially lack
all DNA cleavage activity when the DNA cleavage activity of the
mutated enzyme is less than about 25%, 10%, 5%, 1%, 0.1%, 0.01%, or
lower with respect to its non-mutated form. Where the enzyme is not
SpCas9, mutations may be made at any or all residues corresponding
to positions 10, 762, 840, 854, 863 and/or 986 of SpCas9 (which may
be ascertained for instance by standard sequence comparison tools).
In particular, any or all of the following mutations are preferred
in SpCas9: D10A, E762A, H840A, N854A, N863A and/or D986A; as well
as conservative substitution for any of the replacement amino acids
is also envisaged. The same (or conservative substitutions of these
mutations) at corresponding positions in other Cas9s are also
preferred. Particularly preferred are D10 and H840 in SpCas9.
However, in other Cas9s, residues corresponding to SpCas9 D10 and
H840 are also preferred.
[0288] An aspartate-to-alanine substitution (D10A) in the RuvC I
catalytic domain of SpCas9 was engineered to convert the nuclease
into a nickase (SpCas9n) (see e.g. Sapranauskas et al., 2011,
Nucleic Acis Research, 39: 9275; Gasiunas et al., 2012. Proc. Natl.
Acad. Sci. USA, 109:E2579), such that nicked genomic DNA undergoes
the high-fidelity homology-directed repair (HDR). Surveyor assay
confirmed that SpCas9n does not generate indels at the EMX1
protospacer target. Co-expression of EMX1-targeting chimeric crRNA
(having the tracrRNA component as well) with SpCas9 produced indels
in the target site, whereas co-expression with SpCas9n did not
(n=3). Moreover, sequencing of 327 amplicons did not detect any
indels induced by SpCas9n. The same locus was selected to test
CRISPR-mediated HR by co-transfecting HEK 293FT cells with the
chimeric RNA targeting EMX1, hSpCas9 or hSpCas9n, as well as a HR
template to introduce a pair of restriction sites (HindIII and
NheI) near the protospacer.
[0289] Preferred orthologs are described herein. A Cas enzyme may
be identified as Cas9 as this can refer to the general class of
enzymes that share homology to the biggest nuclease with multiple
nuclease domains from the type II CRISPR system. Most preferably,
the Cas9 enzyme is from, or is derived from, spCas9 or saCas9. By
derived, Applicants mean that the derived enzyme is largely based,
in the sense of having a high degree of sequence homology with, a
wildtype enzyme, but that it has been mutated (modified) in some
way as described herein.
[0290] It will be appreciated that the terms Cas and CRISPR enzyme
are generally used herein interchangeably, unless otherwise
apparent. As mentioned above, many of the residue numberings used
herein refer to the Cas9 enzyme from the type II CRISPR locus in
Streptococcus pyogenes. However, it will be appreciated that this
invention includes many more Cas9s from other species of microbes,
such as SpCas9, SaCa9, St1Cas9 and so forth.
[0291] An example of a codon optimized sequence, in this instance
optimized for humans (i.e. being optimized for expression in
humans) is provided herein, see the SaCas9 human codon optimized
sequence. Whilst this is preferred, it will be appreciated that
other examples are possible and codon optimization for a host
species is known.
[0292] In some embodiments, an enzyme coding sequence encoding a
CRISPR enzyme is codon optimized for expression in particular
cells, such as eukaryotic cells. The eukaryotic cells may be those
of or derived from a particular organism, such as a mammal,
including but not limited to human, mouse, rat, rabbit, dog, or
non-human mammal or primate. In some embodiments, processes for
modifying the germ line genetic identity of human beings and/or
processes for modifying the genetic identity of animals which are
likely to cause them suffering without any substantial medical
benefit to man or animal, and also animals resulting from such
processes, may be excluded.
[0293] In general, codon optimization refers to a process of
modifying a nucleic acid sequence for enhanced expression in the
host cells of interest by replacing at least one codon (e.g. about
or more than about 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, or more
codons) of the native sequence with codons that are more frequently
or most frequently used in the genes of that host cell while
maintaining the native amino acid sequence. Various species exhibit
particular bias for certain codons of a particular amino acid.
Codon bias (differences in codon usage between organisms) often
correlates with the efficiency of translation of messenger RNA
(mRNA), which is in turn believed to be dependent on, among other
things, the properties of the codons being translated and the
availability of particular transfer RNA (tRNA) molecules. The
predominance of selected tRNAs in a cell is generally a reflection
of the codons used most frequently in peptide synthesis.
Accordingly, genes can be tailored for optimal gene expression in a
given organism based on codon optimization. Codon usage tables are
readily available, for example, at the "Codon Usage Database"
available at www.kazusa.orjp/codon/ (visited Jul. 9, 2002), and
these tables can be adapted in a number of ways. See Nakamura, Y.,
et al. "Codon usage tabulated from the international DNA sequence
databases: status for the year 2000" Nucl. Acids Res. 28:292
(2000). Computer algorithms for codon optimizing a particular
sequence for expression in a particular host cell are also
available, such as Gene Forge (Aptagen; Jacobus, Pa.), are also
available. In some embodiments, one or more codons (e.g. 1, 2, 3,
4, 5, 10, 15, 20, 25, 50, or more, or all codons) in a sequence
encoding a CRISPR enzyme correspond to the most frequently used
codon for a particular amino acid.
[0294] In some embodiments, a vector encodes a CRISPR enzyme
comprising one or more nuclear localization sequences (NLSs), such
as about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more
NLSs. In some embodiments, the CRISPR enzyme comprises about or
more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or
near the amino-terminus, about or more than about 1, 2, 3, 4, 5, 6,
7, 8, 9, 10, or more NLSs at or near the carboxy-terminus, or a
combination of these (e.g. one or more NLS at the amino-terminus
and one or more NLS at the carboxy terminus). When more than one
NLS is present, each may be selected independently of the others,
such that a single NLS may be present in more than one copy and/or
in combination with one or more other NLSs present in one or more
copies. In a preferred embodiment of the invention, the CRISPR
enzyme comprises at most 6 NLSs. In some embodiments, an NLS is
considered near the N- or C-terminus when the nearest amino acid of
the NLS is within about 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50,
or more amino acids along the polypeptide chain from the N- or
C-terminus. Non-limiting examples of NLSs include an NLS sequence
derived from: the NLS of the SV40 virus large T-antigen, having the
amino acid sequence PKKKRKV; the NLS from nucleoplasmin (e.g. the
nucleoplasmin bipartite NLS with the sequence KRPAATKKAGQAKKKK);
the c-myc NLS having the amino acid sequence PAAKRVKLD or
RQRRNELKRSP; the hRNPA1 M9 NLS having the sequence
NQSSNFGPMKGGNFGGRSSGPYGGGGQYFAKPRNQGGY; the sequence
RMRIZFKNKGKDTAELRRRRVEVSVELRKAKKDEQILKRRNV of the IBB domain from
importin-alpha; the sequences VSRKRPRP and PPKKARED of the myoma T
protein; the sequence POPKKKPL of human p53; the sequence
SALIKKKKKMAP of mouse c-abl IV; the sequences DRLRR and PKQKKRK of
the influenza virus NS1; the sequence RKLKKKIKKL of the Hepatitis
virus delta antigen; the sequence REKKKFLKRR of the mouse Mx1
protein; the sequence KRKGDEVDGVDEVAKKKSKK of the human
poly(ADP-ribose) polymerase; and the sequence RKCLQAGMNLEARKTKK of
the steroid hormone receptors (human) glucocorticoid.
[0295] In general, the one or more N LSs are of sufficient strength
to drive accumulation of the CRISPR enzyme in a detectable amount
in the nucleus of a eukaryotic cell. In general, strength of
nuclear localization activity may derive from the number of NLSs in
the CRISPR enzyme, the particular NLS(s) used, or a combination of
these factors. Detection of accumulation in the nucleus may be
performed by any suitable technique. For example, a detectable
marker may be fused to the CRISPR enzyme, such that location within
a cell may be visualized, such as in combination with a means for
detecting the location of the nucleus (e.g. a stain specific for
the nucleus such as DAPI). Cell nuclei may also be isolated from
cells, the contents of which may then be analyzed by any suitable
process for detecting protein, such as immunohistochemistry,
Western blot, or enzyme activity assay. Accumulation in the nucleus
may also be determined indirectly, such as by an assay for the
effect of CRISPR complex formation (e.g. assay for DNA cleavage or
mutation at the target sequence, or assay for altered gene
expression activity affected by CRISPR complex formation and/or
CRISPR enzyme activity), as compared to a control no exposed to the
CRISPR enzyme or complex, or exposed to a CRISPR enzyme lacking the
one or more NLSs.
[0296] In general, a guide sequence is any polynucleotide sequence
having sufficient complementarity with a target polynucleotide
sequence to hybridize with the target sequence and direct
sequence-specific binding of a CRISPR complex to the target
sequence. In some embodiments, the degree of complementarity
between a guide sequence and its corresponding target sequence,
when optimally aligned using a suitable alignment algorithm, is
about or more than about 50%, 60%, 75%, 80%, 85%, 90%, 95%, 97.5%,
99%, or more. Optimal alignment may be determined with the use of
any suitable algorithm for aligning sequences, non-limiting example
of which include the Smith-Waterman algorithm, the Needleman-Wunsch
algorithm, algorithms based on the Burrows-Wheeler Transform (e.g.
the Burrows Wheeler Aligner), ClustalW, Clustal X, BLAT, Novoalign
(Novocraft Technologies; available at www.novocraf.com), ELAND
(Illumina, San Diego, Calif.), SOAP (available at
soap.genomics.org.cn), and Maq (available at maq.sourceforge.net).
In some embodiments, a guide sequence is about or more than about
5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,
26, 27, 28, 29, 30, 35, 40, 45, 50, 75, or more nucleotides in
length. In some embodiments, a guide sequence is less than about
75, 50, 45, 40, 35, 30, 25, 20, 15, 12, or fewer nucleotides in
length. The ability of a guide sequence to direct sequence-specific
binding of a CRISPR complex to a target sequence may be assessed by
any suitable assay. For example, the components of a CRISPR system
sufficient to form a CRISPR complex, including the guide sequence
to be tested, may be provided to a host cell having the
corresponding target sequence, such as by transfection with vectors
encoding the components of the CRISPR sequence, followed by an
assessment of preferential cleavage within the target sequence,
such as by Surveyor assay as described herein. Similarly, cleavage
of a target polynucleotide sequence may be evaluated in a test tube
by providing the target sequence, components of a CRISPR complex,
including the guide sequence to be tested and a control guide
sequence different from the test guide sequence, and comparing
binding or rate of cleavage at the target sequence between the test
and control guide sequence reactions. Other assays are possible,
and will occur to those skilled in the art.
[0297] A guide sequence may be selected to target any target
sequence. In some embodiments, the target sequence is a sequence
within a genome of a cell. Exemplary target sequences include those
that are unique in the target genome. For example, for the S.
pyogenes Cas9, a unique target sequence in a genome may include a
Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXGG where
NNNNNNNNNNNNXGG (N is A, G, T, or C; and X can be anything) has a
single occurrence in the genome. A unique target sequence in a
genome may include an S. pyogenes Cas9 target site of the form
MMMMMMMMMNNNNNNNNNNNXGG where NNNNNNNNNNNXGG (N is A, G, T, or C;
and X can be anything) has a single occurrence in the genome. For
the S. thermophilus CRISPR1 Cas9, a unique target sequence in a
genome may include a Cas9 target site of the form
MMMMMMMMNNNNNNNNNNNNXXAGAAW where NNNNNNNNNNNNXXAGAAW (N is A, G,
T, or C; X can be anything; and W is A or T) has a single
occurrence in the genome. A unique target sequence in a genome may
include an S. thermophilus CRISPR1Cas9 target site of the form
MMMMMMMMMNNNNNNNNNNNXXAGAAW where NNNNNNNNNNNXXAGAAW (N is A, G, T,
or C; X can be anything; and W is A or T) has a single occurrence
in the genome. For the S. pyogenes Cas9, a unique target sequence
in a genome may include a Cas9 target site of the form
MMMMMMMMNNNNNNNNNNNNXGGXG where NNNNNNNNNNNNXGGXG (N is A, G, T, or
C; and X can be anything) has a single occurrence in the genome. A
unique target sequence in a genome may include an S. pyogenes Cas9
target site of the form MMMMMMMMMNNNNNNNNNNNXGGXG where
NNNNNNNNNNNXGGXG (N is A, G, T, or C; and X can be anything) has a
single occurrence in the genome. In each of these sequences "M" may
be A, G, T, or C, and need not be considered in identifying a
sequence as unique.
[0298] In some embodiments, a guide sequence is selected to reduce
the degree of secondary structure within the guide sequence. In
some embodiments, about or less than about 75%, 50%, 40%, 30%, 25%,
20%, 15%, 10%, 5%, 1%, or fewer of the nucleotides of the guide
sequence participate in self-complementary base pairing when
optimally folded. Optimal folding may be determined by any suitable
polynucleotide folding algorithm. Some programs are based on
calculating the minimal Gibbs free energy. An example of one such
algorithm is mFold, as described by Zuker and Stiegler (Nucleic
Acids Res. 9 (1981), 133-148). Another example folding algorithm is
the online webserver RNAfold, developed at Institute for
Theoretical Chemistry at the University of Vienna, using the
centroid structure prediction algorithm (see e.g. A. R. Gruber et
al., 2008, Cell 106(1): 23-24; and P A Carr and G M Church, 2009,
Nature Biotechnology 27(12): 1151-62).
[0299] In general, a tracr mate sequence includes any sequence that
has sufficient complementarity with a tracr sequence to promote one
or more of: (1) excision of a guide sequence flanked by tracr mate
sequences in a cell containing the corresponding tracr sequence;
and (2) formation of a CRISPR complex at a target sequence, wherein
the CRISPR complex comprises the tracr mate sequence hybridized to
the tracr sequence. In general, degree of complementarity is with
reference to the optimal alignment of the tracr mate sequence and
tracr sequence, along the length of the shorter of the two
sequences. Optimal alignment may be determined by any suitable
alignment algorithm, and may further account for secondary
structures, such as self-complementarity within either the tracr
sequence or tracr mate sequence. In some embodiments, the degree of
complementarity between the tracr sequence and tracr mate sequence
along the length of the shorter of the two when optimally aligned
is about or more than about 25%, 30%, 40%, 50%, 60%, 70%, 80%, 90%,
95%, 97.5%, 99%, or higher. In some embodiments, the tracr sequence
is about or more than about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15,
16, 17, 18, 19, 20, 25, 30, 40, 50, or more nucleotides in length.
In some embodiments, the tracr sequence and tracr mate sequence are
contained within a single transcript, such that hybridization
between the two produces a transcript having a secondary structure,
such as a hairpin. In an embodiment of the invention, the
transcript or transcribed polynucleotide sequence has at least two
or more hairpins. In preferred embodiments, the transcript has two,
three, four or five hairpins. In a further embodiment of the
invention, the transcript has at most five hairpins. In a hairpin
structure the portion of the sequence 5' of the final "N" and
upstream of the loop corresponds to the tracr mate sequence, and
the portion of the sequence 3' of the loop corresponds to the tracr
sequence Further non-limiting examples of single polynucleotides
comprising a guide sequence, a tracr mate sequence, and a tracr
sequence are as follows (listed 5' to 3'), where "N" represents a
base of a guide sequence, the first block of lower case letters
represent the tracr mate sequence, and the second block of lower
case letters represent the tracr sequence, and the final poly-T
sequence represents the transcription terminator:
TABLE-US-00004 (1) NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaagatttaGAAA
taaatcttgcagaagctacaaagataaggcttcatgccgaaatcaa
caccctgtcattttatggcagggtgttttcgttatttaaTTTTTT; (2)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaa
gctacaaagataaggcttcatgccgaaatcaacaccctgtcatttt
atggcagggtgttttcgttatttaaTTTTT; (3)
NNNNNNNNNNNNNNNNNNNNgtttttgtactctcaGAAAtgcagaa
gctacaaagataaggcttcatgccgaaatcaacaccctgtcatttt atggcagggtgtTTTTTT;
(4) NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAAtagcaagtta
aaataaggctagtccgttatcaacttgaaaaagtggcaccgagtcg gtgcTTTTT; (5)
NNNNNNNNNNNNNNNNNNNNgttttagagctaGAAATAGcaagtta
aaataaggctagtccgttatcaacttgaaaaagtgTTTTTTT; and (6)
NNNNNNNNNNNNNNNNNNNNgttttagagctagAAATAGcaagtta
aaataaggctagtccgttatcaTTTTTTTT.
[0300] In some embodiments, sequences (1) to (3) are used in
combination with Cas9 from S. thermophilus CRISPR1. In some
embodiments, sequences (4) to (6) are used in combination with Cas9
from S. pyogenes. In some embodiments, the tracr sequence is a
separate transcript from a transcript comprising the tracr mate
sequence.
[0301] In some embodiments, a recombination template is also
provided. A recombination template may be a component of another
vector as described herein, contained in a separate vector, or
provided as a separate polynucleotide. In some embodiments, a
recombination template is designed to serve as a template in
homologous recombination, such as within or near a target sequence
nicked or cleaved by a CRISPR enzyme as a part of a CRISPR complex.
A template polynucleotide may be of any suitable length, such as
about or more than about 10, 15, 20, 25, 50, 75, 100, 150, 200,
500, 1000, or more nucleotides in length. In some embodiments, the
template polynucleotide is complementary to a portion of a
polynucleotide comprising the target sequence. When optimally
aligned, a template polynucleotide might overlap with one or more
nucleotides of a target sequences (e.g. about or more than about 1,
5, 10, 15, 20, or more nucleotides). In some embodiments, when a
template sequence and a polynucleotide comprising a target sequence
are optimally aligned, the nearest nucleotide of the template
polynucleotide is within about 1, 5, 10, 15, 20, 25, 50, 75, 100,
200, 300, 400, 500, 1000, 5000, 10000, or more nucleotides from the
target sequence.
[0302] In some embodiments, the CRISPR enzyme is part of a fusion
protein comprising one or more heterologous protein domains (e.g.
about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more
domains in addition to the CRISPR enzyme). A CRISPR enzyme fusion
protein may comprise any additional protein sequence, and
optionally a linker sequence between any two domains. Examples of
protein domains that may be fused to a CRISPR enzyme include,
without limitation, epitope tags, reporter gene sequences, and
protein domains having one or more of the following activities:
methylase activity, demethylase activity, transcription activation
activity, transcription repression activity, transcription release
factor activity, histone modification activity, RNA cleavage
activity and nucleic acid binding activity. Non-limiting examples
of epitope tags include histidine (His) tags, V5 tags, FLAG tags,
influenza hemagglutinin (HA) tags, Myc tags, VSV-G tags, and
thioredoxin (Trx) tags. Examples of reporter genes include, but are
not limited to, glutathione-S-transferase (GST), horseradish
peroxidase (HRP), chloramphenicol acetyltransferase (CAT)
beta-galactosidase, beta-glucuronidase, luciferase, green
fluorescent protein (GFP), HcRed, DsRed, cyan fluorescent protein
(CFP), yellow fluorescent protein (YFP), and autofluorescent
proteins including blue fluorescent protein (BFP). A CRISPR enzyme
may be fused to a gene sequence encoding a protein or a fragment of
a protein that bind DNA molecules or bind other cellular molecules,
including but not limited to maltose binding protein (MBP), S-tag,
Lex A DNA binding domain (DBD) fusions, GAL4A DNA binding domain
fusions, and herpes simplex virus (HSV) BP16 protein fusions.
Additional domains that may form part of a fusion protein
comprising a CRISPR enzyme are described in US20110059502,
incorporated herein by reference. In some embodiments, a tagged
CRISPR enzyme is used to identify the location of a target
sequence.
[0303] In some embodiments, a CRISPR enzyme may form a component of
an inducible system. The inducible nature of the system would allow
for spatiotemporal control of gene editing or gene expression using
a form of energy. The form of energy may include but is not limited
to electromagnetic radiation, sound energy, chemical energy and
thermal energy. Examples of inducible system include tetracycline
inducible promoters (Tet-On or Tet-Off), small molecule two-hybrid
transcription activations systems (FKBP, ABA, etc), or light
inducible systems (Phytochrome, LOV domains, or cryptochrome). In
one embodiment, the CRISPR enzyme may be a part of a Light
Inducible Transcriptional Effector (LITE) to direct changes in
transcriptional activity in a sequence-specific manner. The
components of a light may include a CRISPR enzyme, a
light-responsive cytochrome heterodimer (e.g. from Arabidopsis
thaliana), and a transcriptional activation/repression domain.
Further examples of inducible DNA binding proteins and methods for
their use are provided in U.S. 61/736,465 and U.S. 61/721,283,
which is hereby incorporated by reference in its entirety.
[0304] In some aspects, the invention provides methods comprising
delivering one or more polynucleotides, such as or one or more
vectors as described herein, one or more transcripts thereof,
and/or one or proteins transcribed therefrom, to a host cell. In
some aspects, the invention further provides cells produced by such
methods, and animals comprising or produced from such cells. In
some embodiments, a CRISPR enzyme in combination with (and
optionally complexed with) a guide sequence is delivered to a cell.
Conventional viral and non-viral based gene transfer methods can be
used to introduce nucleic acids in mammalian cells or target
tissues. Such methods can be used to administer nucleic acids
encoding components of a CRISPR system to cells in culture, or in a
host organism. Non-viral vector delivery systems include DNA
plasmids, RNA (e.g. a transcript of a vector described herein),
naked nucleic acid, and nucleic acid complexed with a delivery
vehicle, such as a liposome. Viral vector delivery systems include
DNA and RNA viruses, which have either episomal or integrated
genomes after delivery to the cell. For a review of gene therapy
procedures, see Anderson, Science 256:808-813 (1992); Nabel &
Felgner, TIBTECH 11:211-217 (1993); Mitani & Caskey, TIBTECH
11:162-166 (1993); Dillon, TIBTECH 11:167-175 (1993); Miller,
Nature 357:455-460 (1992); Van Brunt, Biotechnology 6(10):1149-1154
(1988); Vigne, Restorative Neurology and Neuroscience 8:35-36
(1995); Kremer & Perricaudet, British Medical Bulletin
51(1):31-44 (1995); Haddada et al., in Current Topics in
Microbiology and Immunology Doerfler and Bohm (eds) (1995); and Yu
et al., Gene Therapy 1:13-26 (1994).
[0305] Methods of non-viral delivery of nucleic acids include
lipofection, microinjection, biolistics, virosomes, liposomes,
immunoliposomes, polycation or lipid:nucleic acid conjugates, naked
DNA, artificial virions, and agent-enhanced uptake of DNA.
Lipofection is described in e.g., U.S. Pat. Nos. 5,049,386,
4,946,787; and 4,897,355) and lipofection reagents are sold
commercially (e.g., Transfectam.TM. and Lipofectin.TM.). Cationic
and neutral lipids that are suitable for efficient
receptor-recognition lipofection of polynucleotides include those
of Felgner, WO 91/17424; WO 91/16024. Delivery can be to cells
(e.g. in vitro or ex vivo administration) or target tissues (e.g.
in vivo administration).
[0306] The preparation of lipid:nucleic acid complexes, including
targeted liposomes such as immunolipid complexes, is well known to
one of skill in the art (see, e.g., Crystal, Science 270:404-410
(1995); Blaese et al., Cancer Gene Ther. 2:291-297 (1995); Behr et
al., Bioconjugate Chem. 5:382-389 (1994); Remy et al., Bioconjugate
Chem. 5:647-654 (1994); Gao et al., Gene Therapy 2:710-722 (1995);
Ahmad et al., Cancer Res. 52:4817-4820 (1992); U.S. Pat. Nos.
4,186,183, 4,217,344, 4,235,871, 4,261,975, 4,485,054, 4,501,728,
4,774,085, 4,837,028, and 4,946,787).
[0307] The use of RNA or DNA viral based systems for the delivery
of nucleic acids take advantage of highly evolved processes for
targeting a virus to specific cells in the body and trafficking the
viral payload to the nucleus. Viral vectors can be administered
directly to patients (in vivo) or they can be used to treat cells
in vitro, and the modified cells may optionally be administered to
patients (ex vivo). Conventional viral based systems could include
retroviral, lentivirus, adenoviral, adeno-associated and herpes
simplex virus vectors for gene transfer. Integration in the host
genome is possible with the retrovirus, lentivirus, and
adeno-associated virus gene transfer methods, often resulting in
long term expression of the inserted transgene. Additionally, high
transduction efficiencies have been observed in many different cell
types and target tissues.
[0308] The tropism of a retrovirus can be altered by incorporating
foreign envelope proteins, expanding the potential target
population of target cells. Lentiviral vectors are retroviral
vectors that are able to transduce or infect non-dividing cells and
typically produce high viral titers. Selection of a retroviral gene
transfer system would therefore depend on the target tissue.
Retroviral vectors are comprised of cis-acting long terminal
repeats with packaging capacity for up to 6-10 kb of foreign
sequence. The minimum cis-acting LTRs are sufficient for
replication and packaging of the vectors, which are then used to
integrate the therapeutic gene into the target cell to provide
permanent transgene expression. Widely used retroviral vectors
include those based upon murine leukemia virus (MuLV), gibbon ape
leukemia virus (GaLV), Simian Immuno deficiency virus (SIV), human
immuno deficiency virus (HIV), and combinations thereof (see, e.g.,
Buchscher et al., J. Virol. 66:2731-2739 (1992); Johann et al., J.
Virol. 66:1635-1640 (1992); Sommnerfelt et al., Virol. 176:58-59
(1990); Wilson et al., J. Virol. 63:2374-2378 (1989); Miller et
al., J. Virol. 65:2220-2224 (1991); PCT/US94/05700).
[0309] In another embodiment, Cocal vesiculovirus envelope
pseudotyped retroviral vector particles are contemplated (see,
e.g., US Patent Publication No. 20120164118 assigned to the Fred
Hutchinson Cancer Research Center). Cocal virus is in the
Vesiculovirus genus, and is a causative agent of vesicular
stomatitis in mammals. Cocal virus was originally isolated from
mites in Trinidad (Jonkers et al., Am. J. Vet. Res. 25:236-242
(1964)), and infections have been identified in Trinidad, Brazil,
and Argentina from insects, cattle, and horses. Many of the
vesiculoviruses that infect mammals have been isolated from
naturally infected arthropods, suggesting that they are
vector-borne. Antibodies to vesiculoviruses are common among people
living in rural areas where the viruses are endemic and
laboratory-acquired; infections in humans usually result in
influenza-like symptoms. The Cocal virus envelope glycoprotein
shares 71.5% identity at the amino acid level with VSV-G Indiana,
and phylogenetic comparison of the envelope gene of vesiculoviruses
shows that Cocal virus is serologically distinct from, but most
closely related to, VSV-G Indiana strains among the
vesiculoviruses. Jonkers et al., Am. J. Vet. Res. 25:236-242 (1964)
and Travassos da Rosa et al., Am. J. Tropical Med. & Hygiene
33:999-1006 (1984). The Cocal vesiculovirus envelope pseudotyped
retroviral vector particles may include for example, lentiviral,
alpharetroviral, betaretroviral, gammaretroviral, deltaretroviral,
and epsilonretroviral vector particles that may comprise retroviral
Gag, Pol, and/or one or more accessory protein(s) and a Cocal
vesiculovirus envelope protein. Within certain aspects of these
embodiments, the Gag, Pol, and accessory proteins are lentiviral
and/or gammaretroviral.
[0310] In applications where transient expression is preferred,
adenoviral based systems may be used. Adenoviral based vectors are
capable of very high transduction efficiency in many cell types and
do not require cell division. With such vectors, high titer and
levels of expression have been obtained. This vector can be
produced in large quantities in a relatively simple system.
Adeno-associated virus ("AAV") vectors may also be used to
transduce cells with target nucleic acids, e.g., in the in vitro
production of nucleic acids and peptides, and for in vivo and ex
vivo gene therapy procedures (see, e.g., West et al., Virology
160:38-47 (1987); U.S. Pat. No. 4,797,368; WO 93/24641; Kotin,
Human Gene Therapy 5:793-801 (1994); Muzyczka, J. Clin. Invest.
94:1351 (1994). Construction of recombinant AAV vectors are
described in a number of publications, including U.S. Pat. No.
5,173,414; Tratschin et al., Mol. Cell. Biol. 5:3251-3260 (1985);
Tratschin, et al., Mol. Cell. Biol. 4:2072-2081 (1984); Hermonat
& Muzyczka, PNAS 81:6466-6470 (1984); and Samulski et al., J.
Virol. 63:03822-3828 (1989).
[0311] Packaging cells are typically used to form virus particles
that are capable of infecting a host cell. Such cells include 293
cells, which package adenovirus, and .psi.2 cells or PA317 cells,
which package retrovirus. Viral vectors used in gene therapy are
usually generated by producer a cell line that packages a nucleic
acid vector into a viral particle. The vectors typically contain
the minimal viral sequences required for packaging and subsequent
integration into a host, other viral sequences being replaced by an
expression cassette for the polynucleotide(s) to be expressed. The
missing viral functions are typically supplied in trans by the
packaging cell line. For example, AAV vectors used in gene therapy
typically only possess ITR sequences from the AAV genome which are
required for packaging and integration into the host genome. Viral
DNA is packaged in a cell line, which contains a helper plasmid
encoding the other AAV genes, namely rep and cap, but lacking ITR
sequences. The cell line may also infected with adenovirus as a
helper. The helper virus promotes replication of the AAV vector and
expression of AAV genes from the helper plasmid. The helper plasmid
is not packaged in significant amounts due to a lack of ITR
sequences. Contamination with adenovirus can be reduced by, e.g.,
heat treatment to which adenovirus is more sensitive than AAV.
[0312] Accordingly, AAV is considered an ideal candidate for use as
a transducing vector. Such AAV transducing vectors can comprise
sufficient cis-acting functions to replicate in the presence of
adenovirus or herpesvirus or poxvirus (e.g., vaccinia virus) helper
functions provided in trans. Recombinant AAV (rAAV) can be used to
carry exogenous genes into cells of a variety of lineages. In these
vectors, the AAV cap and/or rep genes are deleted from the viral
genome and replaced with a DNA segment of choice. Current AAV
vectors may accommodate up to 4300 bases of inserted DNA.
[0313] There are a number of ways to produce rAAV, and the
invention provides rAAV and methods for preparing rAAV. For
example, plasmid(s) containing or consisting essentially of the
desired viral construct are transfected into AAV-infected cells. In
addition, a second or additional helper plasmid is cotransfected
into these cells to provide the AAV rep and/or cap genes which are
obligatory for replication and packaging of the recombinant viral
construct. Under these conditions, the rep and/or cap proteins of
AAV act in trans to stimulate replication and packaging of the rAAV
construct. Two to Three days after transfection, rAAV is harvested.
Traditionally rAAV is harvested from the cells along with
adenovirus. The contaminating adenovirus is then inactivated by
heat treatment. In the instant invention, rAAV is advantageously
harvested not from the cells themselves, but from cell supernatant.
Accordingly, in an initial aspect the invention provides for
preparing rAAV, and in addition to the foregoing, rAAV can be
prepared by a method that comprises or consists essentially of:
infecting susceptible cells with a rAAV containing exogenous DNA
including DNA for expression, and helper virus (e.g., adenovirus,
herpesvirus, poxvirus such as vaccinia virus) wherein the rAAV
lacks functioning cap and/or rep (and the helper virus (e.g.,
adenovirus, herpesvirus, poxvirus such as vaccinia virus) provides
the cap and/or rev function that the rAAV lacks); or infecting
susceptible cells with a rAAV containing exogenous DNA including
DNA for expression, wherein the recombinant lacks functioning cap
and/or rep, and transfecting said cells with a plasmid supplying
cap and/or rep function that the rAAV lacks; or infecting
susceptible cells with a rAAV containing exogenous DNA including
DNA for expression, wherein the recombinant lacks functioning cap
and/or rep, wherein said cells supply cap and/or rep function that
the recombinant lacks; or transfecting the susceptible cells with
an AAV lacking functioning cap and/or rep and plasmids for
inserting exogenous DNA into the recombinant so that the exogenous
DNA is expressed by the recombinant and for supplying rep and/or
cap functions whereby transfection results in an rAAV containing
the exogenous DNA including DNA for expression that lacks
functioning cap and/or rep.
[0314] The rAAV can be from an AAV as herein described, and
advantageously can be an rAAV1, rAAV2, AAV5 or rAAV having hybrid
or capsid which may comprise AAV1, AAV2, AAV5 or any combination
thereof. One can select the AAV of the rAAV with regard to the
cells to be targeted by the rAAV; e.g., one can select AAV
serotypes 1, 2, 5 or a hybrid or capsid AAV1, AAV2, AAV5 or any
combination thereof for targeting brain or neuronal cells; and one
can select AAV4 for targeting cardiac tissue.
[0315] In addition to 293 cells, other cells that can be used in
the practice of the invention and the relative infectivity of
certain AAV serotypes in vitro as to these cells (see Grimm. D. et
al, J. Virol. 82: 5887-5911 (2008)) are as follows:
TABLE-US-00005 Cell Line AAV-1 AAV-2 AAV-3 AAV-4 AAV-5 AAV-6 AAV-8
AAV-9 Huh-7 13 100 2.5 0.0 0.1 10 0.7 0.0 HEK293 25 100 2.5 0.1 0.1
5 0.7 0.1 HeLa 3 100 2.0 0.1 6.7 1 0.2 0.1 HepG2 3 100 16.7 0.3 1.7
5 0.3 ND Hep1A 20 100 0.2 1.0 0.1 1 0.2 0.0 911 17 100 11 0.2 0.1
17 0.1 ND CHO 100 100 14 1.4 333 50 10 1.0 COS 33 100 33 3.3 5.0 14
2.0 0.5 MeWo 10 100 20 0.3 6.7 10 1.0 0.2 NIH3T3 10 100 2.9 2.9 0.3
10 0.3 ND A549 14 100 20 ND 0.5 10 0.5 0.1 HT1180 20 100 10 0.1 0.3
33 0.5 0.1 Monocytes 1111 100 ND ND 125 1429 ND ND Immature DC 2500
100 ND ND 222 2857 ND ND Mature DC 2222 100 ND ND 333 3333 ND
ND
[0316] The invention provides rAAV that contains or consists
essentially of an exogenous nucleic acid molecule encoding a CRISPR
(Clustered Regularly Interspaced Short Palindromic Repeats) system,
e.g., a plurality of cassettes comprising or consisting a first
cassette comprising or consisting essentially of a promoter, a
nucleic acid molecule encoding a CRISPR-associated (Cas) protein
(putative nuclease or helicase proteins), e.g., Cas9 and a
terminator, and a two, or more, advantageously up to the packaging
size limit of the vector, e.g., in total (including the first
cassette) five, cassettes comprising or consisting essentially of a
promoter, nucleic acid molecule encoding guide RNA (gRNA) and a
terminator (e.g., each cassette schematically represented as
Promoter-gRNA1-terminator, Promoter-gRNA2-terminator . . .
Promoter-gRNA(N)-terminator (where N is a number that can be
inserted that is at an upper limit of the packaging size limit of
the vector), or two or more individual rAAVs, each containing one
or more than one cassette of a CRISPR system, e.g., a first rAAV
containing the first cassette comprising or consisting essentially
of a promoter, a nucleic acid molecule encoding Cas, e.g., Cas9 and
a terminator, and a second rAAV containing a plurality, four,
cassettes comprising or consisting essentially of a promoter,
nucleic acid molecule encoding guide RNA (gRNA) and a terminator
(e.g., each cassette schematically represented as
Promoter-gRNA1-terminator, Promoter-gRNA2-terminator . . .
Promoter-gRNA(N)-terminator (where N is a number that can be
inserted that is at an upper limit of the packaging size limit of
the vector). As rAAV is a DNA virus, the nucleic acid molecules in
the herein discussion concerning AAV or rAAV are advantageously
DNA. The promoter is in some embodiments advantageously human
Synapsin I promoter (hSyn).
[0317] Additional methods for the delivery of nucleic acids to
cells are known to those skilled in the art. See, for example,
US20030087817, incorporated herein by reference.
[0318] In some embodiments, a host cell is transiently or
non-transiently transfected with one or more vectors described
herein. In some embodiments, a cell is transfected as it naturally
occurs in a subject. In some embodiments, a cell that is
transfected is taken from a subject. In some embodiments, the cell
is derived from cells taken from a subject, such as a cell line. A
wide variety of cell lines for tissue culture are known in the art.
Examples of cell lines include, but are not limited to, C8161,
CCRF-CEM, MOLT, mIMCD-3, NHDF, HeLa-S3, Huh1, Huh4, Huh7, HUVEC,
HASMC, HEKn, HEKa, MiaPaCell, Pane1, PC-3, TF1, CTLL-2, C1R, Rat6,
CV1, RPTE, A10, T24, J82, A375, ARH-77, Calu1, SW480, SW620, SKOV3,
SK-UT, CaCo2, P388D1, SEM-K2, WEHI-231, HB56, TIB55, Jurkat,
J45.01, LRMB, Bcl-1, BC-3, IC21, DLD2, Raw264.7, NRK, NRK-52E,
MRC5, MEF, Hep G2, HeLa B, HeLa T4, COS, COS-1, COS-6, COS-M6A,
BS-C-1 monkey kidney epithelial, BALB/3T3 mouse embryo fibroblast,
3T3 Swiss, 3T3-L1, 132-d5 human fetal fibroblasts; 10.1 mouse
fibroblasts, 293-T, 3T3, 721, 9L, A2780, A2780ADR, A2780cis, A172,
A20, A253, A431, A-549, ALC, B16, B35, BCP-1 cells, BEAS-2B,
bEnd.3, BHK-21, BR 293, BxPC3, C3H-10T1/2, C6/36, Cal-27, CHO,
CHO-7, CHO-IR, CHO-K1, CHO-K2, CHO-T, CHO Dhfr -/-, COR-L23,
COR-L23/CPR, COR-L23/5010, COR-L23/R23, COS-7, COV-434, CML T1,
CMT, CT26, D17, DH82, DU145, DuCaP, EL4, EM2, EM3, EMT6/AR1,
EMT6/AR10.0, FM3, H1299, H69, HB54, HB55, HCA2, HEK-293, HeLa,
Hepa1c1c7, HL-60, HMEC, HT-29, Jurkat, JY cells, K562 cells, Ku812,
KCL22, KG1, KYO1, LNCap, Ma-Me1 1-48, MC-38, MCF-7, MCF-10A,
MDA-MB-231, MDA-MB-468, MDA-MB-435, MDCK II, MDCK II, MOR/0.2R,
MONO-MAC 6, MTD-1A, MyEnd, NCI-H69/CPR, NCI-H69/LX10, NCI-H69/LX20,
NCI-H69/LX4, NIH-3T3, NALM-1, NW-145, OPCN/OPCT cell lines, Peer,
PNT-1A/PNT 2, RenCa, RIN-5F, RMA/RMAS, Saos-2 cells, Sf-9, SkBr3,
T2, T-47D, T84, THP1 cell line, U373, U87, U937, VCaP, Vero cells,
WM39, WT-49, X63, YAC-1, YAR, and transgenic varieties thereof.
Cell lines are available from a variety of sources known to those
with skill in the art (see, e.g., the American Type Culture
Collection (ATCC) (Manassus, Va.)). In some embodiments, a cell
transfected with one or more vectors described herein is used to
establish a new cell line comprising one or more vector-derived
sequences. In some embodiments, a cell transiently transfected with
the components of a CRISPR system as described herein (such as by
transient transfection of one or more vectors, or transfection with
RNA), and modified through the activity of a CRISPR complex, is
used to establish a new cell line comprising cells containing the
modification but lacking any other exogenous sequence. In some
embodiments, cells transiently or non-transiently transfected with
one or more vectors described herein, or cell lines derived from
such cells are used in assessing one or more test compounds.
[0319] In some embodiments, one or more vectors described herein
are used to produce a non-human transgenic animal or transgenic
plant. In some embodiments, the transgenic animal is a mammal, such
as a mouse, rat, or rabbit. Methods for producing transgenic
animals and plants are known in the art, and generally begin with a
method of cell transfection, such as described herein.
[0320] In another embodiment, a fluid delivery device with an array
of needles (see, e.g., US Patent Publication No. 20110230839
assigned to the Fred Hutchinson Cancer Research Center) may be
contemplated for delivery of CRISPR Cas to solid tissue. A device
of US Patent Publication No. 20110230839 for delivery of a fluid to
a solid tissue may comprise a plurality of needles arranged in an
array; a plurality of reservoirs, each in fluid communication with
a respective one of the plurality of needles; and a plurality of
actuators operatively coupled to respective ones of the plurality
of reservoirs and configured to control a fluid pressure within the
reservoir. In certain embodiments each of the plurality of
actuators may comprise one of a plurality of plungers, a first end
of each of the plurality of plungers being received in a respective
one of the plurality of reservoirs, and in certain further
embodiments the plungers of the plurality of plungers are
operatively coupled together at respective second ends so as to be
simultaneously depressable. Certain still further embodiments may
comprise a plunger driver configured to depress all of the
plurality of plungers at a selectively variable rate. In other
embodiments each of the plurality of actuators may comprise one of
a plurality of fluid transmission lines having first and second
ends, a first end of each of the plurality of fluid transmission
lines being coupled to a respective one of the plurality of
reservoirs. In other embodiments the device may comprise a fluid
pressure source, and each of the plurality of actuators comprises a
fluid coupling between the fluid pressure source and a respective
one of the plurality of reservoirs. In further embodiments the
fluid pressure source may comprise at least one of a compressor, a
vacuum accumulator, a peristaltic pump, a master cylinder, a
microfluidic pump, and a valve. In another embodiment, each of the
plurality of needles may comprise a plurality of ports distributed
along its length.
[0321] In one aspect, the invention provides for methods of
modifying a target polynucleotide in a eukaryotic cell, which may
be in vivo, ex vivo or in vitro. In some embodiments, the method
comprises sampling a cell or population of cells from a human or
non-human animal, or a plant, and modifying the cell or cells.
Culturing may occur at any stage ex vivo. The cell or cells may
even be re-introduced into the non-human animal or plant. For
re-introduced cells it is particularly preferred that the cells are
stem cells.
[0322] In some embodiments, the method comprises allowing a CRISPR
complex to bind to the target polynucleotide to effect cleavage of
said target polynucleotide thereby modifying the target
polynucleotide, wherein the CRISPR complex comprises a CRISPR
enzyme complexed with a guide sequence hybridized to a target
sequence within said target polynucleotide, wherein said guide
sequence is linked to a tracr mate sequence which in turn
hybridizes to a tracr sequence.
[0323] In one aspect, the invention provides a method of modifying
expression of a polynucleotide in a eukaryotic cell. In some
embodiments, the method comprises allowing a CRISPR complex to bind
to the polynucleotide such that said binding results in increased
or decreased expression of said polynucleotide; wherein the CRISPR
complex comprises a CRISPR enzyme complexed with a guide sequence
hybridized to a target sequence within said polynucleotide, wherein
said guide sequence is linked to a tracr mate sequence which in
turn hybridizes to a tracr sequence. Similar considerations and
conditions apply as above for methods of modifying a target
polynucleotide. In fact, these sampling, culturing and
re-introduction options apply across the aspects of the present
invention.
[0324] Indeed, in any aspect of the invention, the CRISPR complex
may comprise a CRISPR enzyme complexed with a guide sequence
hybridized to a target sequence, wherein said guide sequence may be
linked to a tracr mate sequence which in turn may hybridize to a
tracr sequence. Similar considerations and conditions apply as
above for methods of modifying a target polynucleotide.
[0325] In one aspect, the invention provides kits containing any
one or more of the elements disclosed in the above methods and
compositions. Elements may be provided individually or in
combinations, and may be provided in any suitable container, such
as a vial, a bottle, or a tube. In some embodiments, the kit
includes instructions in one or more languages, for example in more
than one language.
[0326] In some embodiments, a kit comprises one or more reagents
for use in a process utilizing one or more of the elements
described herein. Reagents may be provided in any suitable
container. For example, a kit may provide one or more reaction or
storage buffers. Reagents may be provided in a form that is usable
in a particular assay, or in a form that requires addition of one
or more other components before use (e.g. in concentrate or
lyophilized form). A buffer can be any buffer, including but not
limited to a sodium carbonate buffer, a sodium bicarbonate buffer,
a borate buffer, a Tris buffer, a MOPS buffer, a HEPES buffer, and
combinations thereof. In some embodiments, the buffer is alkaline.
In some embodiments, the buffer has a pH from about 7 to about 10.
In some embodiments, the kit comprises one or more oligonucleotides
corresponding to a guide sequence for insertion into a vector so as
to operably link the guide sequence and a regulatory element. In
some embodiments, the kit comprises a homologous recombination
template polynucleotide. In some embodiments, the kit comprises one
or more of the vectors and/or one or more of the polynucleotides
described herein. The kit may advantageously allows to provide all
elements of the systems of the invention.
[0327] In one aspect, the invention provides methods for using one
or more elements of a CRISPR system. The CRISPR complex of the
invention provides an effective means for modifying a target
polynucleotide. The CRISPR complex of the invention has a wide
variety of utility including modifying (e.g., deleting, inserting,
translocating, inactivating, activating) a target polynucleotide in
a multiplicity of cell types. As such the CRISPR complex of the
invention has a broad spectrum of applications in, e.g., gene
therapy, drug screening, disease diagnosis, and prognosis. An
exemplary CRISPR complex comprises a CRISPR enzyme complexed with a
guide sequence hybridized to a target sequence within the target
polynucleotide. The guide sequence is linked to a tracr mate
sequence, which in turn hybridizes to a tracr sequence.
[0328] In one embodiment, this invention provides a method of
cleaving a target polynucleotide. The method comprises modifying a
target polynucleotide using a CRISPR complex that binds to the
target polynucleotide and effect cleavage of said target
polynucleotide. Typically, the CRISPR complex of the invention,
when introduced into a cell, creates a break (e.g., a single or a
double strand break) in the genome sequence. For example, the
method can be used to cleave a disease gene in a cell.
[0329] The break created by the CRISPR complex can be repaired by a
repair processes such as the error prone non-homologous end joining
(NHEJ) pathway or the high fidelity homology-directed repair (HDR)
(FIG. 29). During these repair process, an exogenous polynucleotide
template can be introduced into the genome sequence. In some
methods, the HDR process is used to modify the genome sequence. For
example, an exogenous polynucleotide template comprising a sequence
to be integrated flanked by an upstream sequence and a downstream
sequence is introduced into a cell. The upstream and downstream
sequences share sequence similarity with either side of the site of
integration in the chromosome.
[0330] Where desired, a donor polynucleotide can be DNA, e.g., a
DNA plasmid, a bacterial artificial chromosome (BAC), a yeast
artificial chromosome (YAC), a viral vector, a linear piece of DNA,
a PCR fragment, a naked nucleic acid, or a nucleic acid complexed
with a delivery vehicle such as a liposome or poloxamer.
[0331] The exogenous polynucleotide template comprises a sequence
to be integrated (e.g., a mutated gene). The sequence for
integration may be a sequence endogenous or exogenous to the cell.
Examples of a sequence to be integrated include polynucleotides
encoding a protein or a non-coding RNA (e.g., a microRNA). Thus,
the sequence for integration may be operably linked to an
appropriate control sequence or sequences. Alternatively, the
sequence to be integrated may provide a regulatory function.
[0332] The upstream and downstream sequences in the exogenous
polynucleotide template are selected to promote recombination
between the chromosomal sequence of interest and the donor
polynucleotide. The upstream sequence is a nucleic acid sequence
that shares sequence similarity with the genome sequence upstream
of the targeted site for integration. Similarly, the downstream
sequence is a nucleic acid sequence that shares sequence similarity
with the chromosomal sequence downstream of the targeted site of
integration. The upstream and downstream sequences in the exogenous
polynucleotide template can have 75%, 80%, 85%, 90%, 95%, or 100%
sequence identity with the targeted genome sequence. Preferably,
the upstream and downstream sequences in the exogenous
polynucleotide template have about 95%, 96%, 97%, 98%, 99%, or 100%
sequence identity with the targeted genome sequence. In some
methods, the upstream and downstream sequences in the exogenous
polynucleotide template have about 99% or 100% sequence identity
with the targeted genome sequence.
[0333] An upstream or downstream sequence may comprise from about
20 bp to about 2500 bp, for example, about 50, 100, 200, 300, 400,
500, 600, 700, 800, 900, 1000, 1100, 1200, 1300, 1400, 1500, 1600,
1700, 1800, 1900, 2000, 2100, 2200, 2300, 2400, or 2500 bp. In some
methods, the exemplary upstream or downstream sequence have about
200 bp to about 2000 bp, about 600 bp to about 1000 bp, or more
particularly about 700 bp to about 1000 bp.
[0334] In some methods, the exogenous polynucleotide template may
further comprise a marker. Such a marker may make it easy to screen
for targeted integrations. Examples of suitable markers include
restriction sites, fluorescent proteins, or selectable markers. The
exogenous polynucleotide template of the invention can be
constructed using recombinant techniques (see, for example,
Sambrook et al., 2001 and Ausubel et al., 1996).
[0335] In an exemplary method for modifying a target polynucleotide
by integrating an exogenous polynucleotide template, a double
stranded break is introduced into the genome sequence by the CRISPR
complex, the break is repaired via homologous recombination an
exogenous polynucleotide template such that the template is
integrated into the genome. The presence of a double-stranded break
facilitates integration of the template.
[0336] In other embodiments, this invention provides a method of
modifying expression of a polynucleotide in a eukaryotic cell. The
method comprises increasing or decreasing expression of a target
polynucleotide by using a CRISPR complex that binds to the
polynucleotide.
[0337] In some methods, a target polynucleotide can be inactivated
to effect the modification of the expression in a cell. For
example, upon the binding of a CRISPR complex to a target sequence
in a cell, the target polynucleotide is inactivated such that the
sequence is not transcribed, the coded protein is not produced, or
the sequence does not function as the wild-type sequence does. For
example, a protein or microRNA coding sequence may be inactivated
such that the protein is not produced.
[0338] In some methods, a control sequence can be inactivated such
that it no longer functions as a control sequence. As used herein,
"control sequence" refers to any nucleic acid sequence that effects
the transcription, translation, or accessibility of a nucleic acid
sequence. Examples of a control sequence include, a promoter, a
transcription terminator, and an enhancer are control
sequences.
[0339] The inactivated target sequence may include a deletion
mutation (i.e., deletion of one or more nucleotides), an insertion
mutation (i.e., insertion of one or more nucleotides), or a
nonsense mutation (i.e., substitution of a single nucleotide for
another nucleotide such that a stop codon is introduced). In some
methods, the inactivation of a target sequence results in
"knock-out" of the target sequence.
[0340] A method of the invention may be used to create a plant, an
animal or cell that may be used as a disease model. As used herein,
"disease" refers to a disease, disorder, or indication in a
subject. For example, a method of the invention may be used to
create an animal or cell that comprises a modification in one or
more nucleic acid sequences associated with a disease, or a plant,
animal or cell in which the expression of one or more nucleic acid
sequences associated with a disease are altered. Such a nucleic
acid sequence may encode a disease associated protein sequence or
may be a disease associated control sequence. Accordingly, it is
understood that in embodiments of the invention, a plant, subject,
patient, organism or cell can be a non-human subject, patient,
organism or cell. Thus, the invention provides a plant, animal or
cell, produced by the present methods, or a progeny thereof. The
progeny may be a clone of the produced plant or animal, or may
result from sexual reproduction by crossing with other individuals
of the same species to introgress further desirable traits into
their offspring. The cell may be in vivo or ex vivo in the cases of
multicellular organisms, particularly animals or plants. In the
instance where the cell is in cultured, a cell line may be
established if appropriate culturing conditions are met and
preferably if the cell is suitably adapted for this purpose (for
instance a stem cell). Bacterial cell lines produced by the
invention are also envisaged. Hence, cell lines are also
envisaged.
[0341] In some methods, the disease model can be used to study the
effects of mutations on the animal or cell and development and/or
progression of the disease using measures commonly used in the
study of the disease. Alternatively, such a disease model is useful
for studying the effect of a pharmaceutically active compound on
the disease.
[0342] In some methods, the disease model can be used to assess the
efficacy of a potential gene therapy strategy. That is, a
disease-associated gene or polynucleotide can be modified such that
the disease development and/or progression is inhibited or reduced.
In particular, the method comprises modifying a disease-associated
gene or polynucleotide such that an altered protein is produced
and, as a result, the animal or cell has an altered response.
Accordingly, in some methods, a genetically modified animal may be
compared with an animal predisposed to development of the disease
such that the effect of the gene therapy event may be assessed.
[0343] In another embodiment, this invention provides a method of
developing a biologically active agent that modulates a cell
signaling event associated with a disease gene. The method
comprises contacting a test compound with a cell comprising one or
more vectors that drive expression of one or more of a CRISPR
enzyme, a guide sequence linked to a tracr mate sequence, and a
tracr sequence; and detecting a change in a readout that is
indicative of a reduction or an augmentation of a cell signaling
event associated with, e.g., a mutation in a disease gene contained
in the cell.
[0344] A cell model or animal model can be constructed in
combination with the method of the invention for screening a
cellular function change. Such a model may be used to study the
effects of a genome sequence modified by the CRISPR complex of the
invention on a cellular function of interest. For example, a
cellular function model may be used to study the effect of a
modified genome sequence on intracellular signaling or
extracellular signaling. Alternatively, a cellular function model
may be used to study the effects of a modified genome sequence on
sensory perception. In some such models, one or more genome
sequences associated with a signaling biochemical pathway in the
model are modified.
[0345] Several disease models have been specifically investigated.
These include de novo autism risk genes CHD8, KATNAL2, and SCN2A;
and the syndromic autism (Angelman Syndrome) gene UBE3A. These
genes and resulting autism models are of course preferred, but
serve to show the broad applicability of the invention across genes
and corresponding models.
[0346] An altered expression of one or more genome sequences
associated with a signaling biochemical pathway can be determined
by assaying for a difference in the mRNA levels of the
corresponding genes between the test model cell and a control cell,
when they are contacted with a candidate agent. Alternatively, the
differential expression of the sequences associated with a
signaling biochemical pathway is determined by detecting a
difference in the level of the encoded polypeptide or gene
product.
[0347] To assay for an agent-induced alteration in the level of
mRNA transcripts or corresponding polynucleotides, nucleic acid
contained in a sample is first extracted according to standard
methods in the art. For instance, mRNA can be isolated using
various lytic enzymes or chemical solutions according to the
procedures set forth in Sambrook et al. (1989), or extracted by
nucleic-acid-binding resins following the accompanying instructions
provided by the manufacturers. The mRNA contained in the extracted
nucleic acid sample is then detected by amplification procedures or
conventional hybridization assays (e.g. Northern blot analysis)
according to methods widely known in the art or based on the
methods exemplified herein.
[0348] For purpose of this invention, amplification means any
method employing a primer and a polymerase capable of replicating a
target sequence with reasonable fidelity. Amplification may be
carried out by natural or recombinant DNA polymerases such as
TaqGold.TM., T7 DNA polymerase, Klenow fragment of E. coli DNA
polymerase, and reverse transcriptase. A preferred amplification
method is PCR. In particular, the isolated RNA can be subjected to
a reverse transcription assay that is coupled with a quantitative
polymerase chain reaction (RT-PCR) in order to quantify the
expression level of a sequence associated with a signaling
biochemical pathway.
[0349] Detection of the gene expression level can be conducted in
real time in an amplification assay. In one aspect, the amplified
products can be directly visualized with fluorescent DNA-binding
agents including but not limited to DNA intercalators and DNA
groove binders. Because the amount of the intercalators
incorporated into the double-stranded DNA molecules is typically
proportional to the amount of the amplified DNA products, one can
conveniently determine the amount of the amplified products by
quantifying the fluorescence of the intercalated dye using
conventional optical systems in the art. DNA-binding dye suitable
for this application include SYBR green, SYBR blue, DAPI, propidium
iodine, Hoeste, SYBR gold, ethidium bromide, acridines, proflavine,
acridine orange, acriflavine, fluorcoumanin, ellipticine,
daunomycin, chloroquine, distamycin D, chromomycin, homidium,
mithramycin, ruthenium polypyridyls, anthramycin, and the like.
[0350] In another aspect, other fluorescent labels such as sequence
specific probes can be employed in the amplification reaction to
facilitate the detection and quantification of the amplified
products. Probe-based quantitative amplification relies on the
sequence-specific detection of a desired amplified product. It
utilizes fluorescent, target-specific probes (e.g., TaqMan.RTM.
probes) resulting in increased specificity and sensitivity. Methods
for performing probe-based quantitative amplification are well
established in the art and are taught in U.S. Pat. No.
5,210,015.
[0351] In yet another aspect, conventional hybridization assays
using hybridization probes that share sequence homology with
sequences associated with a signaling biochemical pathway can be
performed. Typically, probes are allowed to form stable complexes
with the sequences associated with a signaling biochemical pathway
contained within the biological sample derived from the test
subject in a hybridization reaction. It will be appreciated by one
of skill in the art that where antisense is used as the probe
nucleic acid, the target polynucleotides provided in the sample are
chosen to be complementary to sequences of the antisense nucleic
acids. Conversely, where the nucleotide probe is a sense nucleic
acid, the target polynucleotide is selected to be complementary to
sequences of the sense nucleic acid.
[0352] Hybridization can be performed under conditions of various
stringency. Suitable hybridization conditions for the practice of
the present invention are such that the recognition interaction
between the probe and sequences associated with a signaling
biochemical pathway is both sufficiently specific and sufficiently
stable. Conditions that increase the stringency of a hybridization
reaction are widely known and published in the art. See, for
example, (Sambrook, et al., (1989); Nonradioactive In Situ
Hybridization Application Manual, Boehringer Mannheim, second
edition). The hybridization assay can be formed using probes
immobilized on any solid support, including but are not limited to
nitrocellulose, glass, silicon, and a variety of gene arrays. A
preferred hybridization assay is conducted on high-density gene
chips as described in U.S. Pat. No. 5,445,934.
[0353] For a convenient detection of the probe-target complexes
formed during the hybridization assay, the nucleotide probes are
conjugated to a detectable label. Detectable labels suitable for
use in the present invention include any composition detectable by
photochemical, biochemical, spectroscopic, immunochemical,
electrical, optical or chemical means. A wide variety of
appropriate detectable labels are known in the art, which include
fluorescent or chemiluminescent labels, radioactive isotope labels,
enzymatic or other ligands. In preferred embodiments, one will
likely desire to employ a fluorescent label or an enzyme tag, such
as digoxigenin, .beta.-galactosidase, urease, alkaline phosphatase
or peroxidase, avidin/biotin complex.
[0354] The detection methods used to detect or quantify the
hybridization intensity will typically depend upon the label
selected above. For example, radiolabels may be detected using
photographic film or a phosphoimager. Fluorescent markers may be
detected and quantified using a photodetector to detect emitted
light. Enzymatic labels are typically detected by providing the
enzyme with a substrate and measuring the reaction product produced
by the action of the enzyme on the substrate; and finally
colorimetric labels are detected by simply visualizing the colored
label.
[0355] An agent-induced change in expression of sequences
associated with a signaling biochemical pathway can also be
determined by examining the corresponding gene products.
Determining the protein level typically involves a) contacting the
protein contained in a biological sample with an agent that
specifically bind to a protein associated with a signaling
biochemical pathway; and (b) identifying any agent:protein complex
so formed. In one aspect of this embodiment, the agent that
specifically binds a protein associated with a signaling
biochemical pathway is an antibody, preferably a monoclonal
antibody.
[0356] The reaction is performed by contacting the agent with a
sample of the proteins associated with a signaling biochemical
pathway derived from the test samples under conditions that will
allow a complex to form between the agent and the proteins
associated with a signaling biochemical pathway. The formation of
the complex can be detected directly or indirectly according to
standard procedures in the art. In the direct detection method, the
agents are supplied with a detectable label and unreacted agents
may be removed from the complex; the amount of remaining label
thereby indicating the amount of complex formed. For such method,
it is preferable to select labels that remain attached to the
agents even during stringent washing conditions. It is preferable
that the label does not interfere with the binding reaction. In the
alternative, an indirect detection procedure may use an agent that
contains a label introduced either chemically or enzymatically. A
desirable label generally does not interfere with binding or the
stability of the resulting agent:polypeptide complex. However, the
label is typically designed to be accessible to an antibody for an
effective binding and hence generating a detectable signal.
[0357] A wide variety of labels suitable for detecting protein
levels are known in the art. Non-limiting examples include
radioisotopes, enzymes, colloidal metals, fluorescent compounds,
bioluminescent compounds, and chemiluminescent compounds.
[0358] The amount of agent:polypeptide complexes formed during the
binding reaction can be quantified by standard quantitative assays.
As illustrated above, the formation of agent:polypeptide complex
can be measured directly by the amount of label remained at the
site of binding. In an alternative, the protein associated with a
signaling biochemical pathway is tested for its ability to compete
with a labeled analog for binding sites on the specific agent. In
this competitive assay, the amount of label captured is inversely
proportional to the amount of protein sequences associated with a
signaling biochemical pathway present in a test sample.
[0359] A number of techniques for protein analysis based on the
general principles outlined above are available in the art. They
include but are not limited to radioimmunoassays, ELISA (enzyme
linked immunoradiometric assays), "sandwich" immunoassays,
immunoradiometric assays, in situ immunoassays (using e.g.,
colloidal gold, enzyme or radioisotope labels), western blot
analysis, immunoprecipitation assays, immunofluorescent assays, and
SDS-PAGE.
[0360] Antibodies that specifically recognize or bind to proteins
associated with a signaling biochemical pathway are preferable for
conducting the aforementioned protein analyses. Where desired,
antibodies that recognize a specific type of post-translational
modifications (e.g., signaling biochemical pathway inducible
modifications) can be used. Post-translational modifications
include but are not limited to glycosylation, lipidation,
acetylation, and phosphorylation. These antibodies may be purchased
from commercial vendors. For example, anti-phosphotyrosine
antibodies that specifically recognize tyrosine-phosphorylated
proteins are available from a number of vendors including
Invitrogen and Perkin Elmer. Anti-phosphotyrosine antibodies are
particularly useful in detecting proteins that are differentially
phosphorylated on their tyrosine residues in response to an ER
stress. Such proteins include but are not limited to eukaryotic
translation initiation factor 2 alpha (eIF-2.alpha.).
Alternatively, these antibodies can be generated using conventional
polyclonal or monoclonal antibody technologies by immunizing a host
animal or an antibody-producing cell with a target protein that
exhibits the desired post-translational modification.
[0361] In practicing the subject method, it may be desirable to
discern the expression pattern of an protein associated with a
signaling biochemical pathway in different bodily tissue, in
different cell types, and/or in different subcellular structures.
These studies can be performed with the use of tissue-specific,
cell-specific or subcellular structure specific antibodies capable
of binding to protein markers that are preferentially expressed in
certain tissues, cell types, or subcellular structures.
[0362] An altered expression of a gene associated with a signaling
biochemical pathway can also be determined by examining a change in
activity of the gene product relative to a control cell. The assay
for an agent-induced change in the activity of a protein associated
with a signaling biochemical pathway will dependent on the
biological activity and/or the signal transduction pathway that is
under investigation. For example, where the protein is a kinase, a
change in its ability to phosphorylate the downstream substrate(s)
can be determined by a variety of assays known in the art.
Representative assays include but are not limited to immunoblotting
and immunoprecipitation with antibodies such as
anti-phosphotyrosine antibodies that recognize phosphorylated
proteins. In addition, kinase activity can be detected by high
throughput chemiluminescent assays such as AlphaScreen.TM.
(available from Perkin Elmer) and eTag.TM. assay (Chan-Hui, et al.
(2003) Clinical Immunology 111: 162-174).
[0363] Where the protein associated with a signaling biochemical
pathway is part of a signaling cascade leading to a fluctuation of
intracellular pH condition, pH sensitive molecules such as
fluorescent pH dyes can be used as the reporter molecules. In
another example where the protein associated with a signaling
biochemical pathway is an ion channel, fluctuations in membrane
potential and/or intracellular ion concentration can be monitored.
A number of commercial kits and high-throughput devices are
particularly suited for a rapid and robust screening for modulators
of ion channels. Representative instruments include FLIPR.TM.
(Molecular Devices, Inc.) and VIPR (Aurora Biosciences). These
instruments are capable of detecting reactions in over 1000 sample
wells of a microplate simultaneously, and providing real-time
measurement and functional data within a second or even a
minisecond.
[0364] In practicing any of the methods disclosed herein, a
suitable vector can be introduced to a cell or an embryo via one or
more methods known in the art, including without limitation,
microinjection, electroporation, sonoporation, biolistics, calcium
phosphate-mediated transfection, cationic transfection, liposome
transfection, dendrimer transfection, heat shock transfection,
nucleofection transfection, magnetofection, lipofection,
impalefection, optical transfection, proprietary agent-enhanced
uptake of nucleic acids, and delivery via liposomes,
immunoliposomes, virosomes, or artificial virions. In some methods,
the vector is introduced into an embryo by microinjection. The
vector or vectors may be microinjected into the nucleus or the
cytoplasm of the embryo. In some methods, the vector or vectors may
be introduced into a cell by nucleofection.
[0365] The target polynucleotide of a CRISPR complex can be any
polynucleotide endogenous or exogenous to the eukaryotic cell. For
example, the target polynucleotide can be a polynucleotide residing
in the nucleus of the eukaryotic cell. The target polynucleotide
can be a sequence coding a gene product (e.g., a protein) or a
non-coding sequence (e.g., a regulatory polynucleotide or a junk
DNA).
[0366] Examples of target polynucleotides include a sequence
associated with a signaling biochemical pathway, e.g., a signaling
biochemical pathway-associated gene or polynucleotide. Examples of
target polynucleotides include a disease associated gene or
polynucleotide. A "disease-associated" gene or polynucleotide
refers to any gene or polynucleotide which is yielding
transcription or translation products at an abnormal level or in an
abnormal form in cells derived from a disease-affected tissues
compared with tissues or cells of a non disease control. It may be
a gene that becomes expressed at an abnormally high level; it may
be a gene that becomes expressed at an abnormally low level, where
the altered expression correlates with the occurrence and/or
progression of the disease. A disease-associated gene also refers
to a gene possessing mutation(s) or genetic variation that is
directly responsible or is in linkage disequilibrium with a gene(s)
that is responsible for the etiology of a disease. The transcribed
or translated products may be known or unknown, and may be at a
normal or abnormal level.
[0367] The target polynucleotide of a CRISPR complex can be any
polynucleotide endogenous or exogenous to the eukaryotic cell. For
example, the target polynucleotide can be a polynucleotide residing
in the nucleus of the eukaryotic cell. The target polynucleotide
can be a sequence coding a gene product (e.g., a protein) or a
non-coding sequence (e.g., a regulatory polynucleotide or a junk
DNA). Without wishing to be bound by theory, it is believed that
the target sequence should be associated with a PAM (protospacer
adjacent motif); that is, a short sequence recognized by the CRISPR
complex. The precise sequence and length requirements for the PAM
differ depending on the CRISPR enzyme used, but PAMs are typically
2-5 base pair sequences adjacent the protospacer (that is, the
target sequence) Examples of PAM sequences are given in the
examples section below, and the skilled person will be able to
identify further PAM sequences for use with a given CRISPR
enzyme.
[0368] The target polynucleotide of a CRISPR complex may include a
number of disease-associated genes and polynucleotides as well as
signaling biochemical pathway-associated genes and polynucleotides
as listed in U.S. provisional patent applications 61/736,527 and
61/748,427 having Broad reference BI-2011/008/WSGR Docket No.
44063-701.101 and BI-2011/008/WSGR Docket No. 44063-701.102
respectively, both entitled SYSTEMS METHODS AND COMPOSITIONS FOR
SEQUENCE MANIPULATION filed on Dec. 12, 2012 and Jan. 2, 2013,
respectively, the contents of all of which are herein incorporated
by reference in their entirety.
[0369] Examples of target polynucleotides include a sequence
associated with a signaling biochemical pathway, e.g., a signaling
biochemical pathway-associated gene or polynucleotide. Examples of
target polynucleotides include a disease associated gene or
polynucleotide. A "disease-associated" gene or polynucleotide
refers to any gene or polynucleotide which is yielding
transcription or translation products at an abnormal level or in an
abnormal form in cells derived from a disease-affected tissues
compared with tissues or cells of a non disease control. It may be
a gene that becomes expressed at an abnormally high level; it may
be a gene that becomes expressed at an abnormally low level, where
the altered expression correlates with the occurrence and/or
progression of the disease. A disease-associated gene also refers
to a gene possessing mutation(s) or genetic variation that is
directly responsible or is in linkage disequilibrium with a gene(s)
that is responsible for the etiology of a disease. The transcribed
or translated products may be known or unknown, and may be at a
normal or abnormal level.
[0370] Examples of disease-associated genes and polynucleotides are
listed in Tables A and B. Disease specific information is available
from McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins
University (Baltimore, Md.) and National Center for Biotechnology
Information, National Library of Medicine (Bethesda, Md.),
available on the World Wide Web. Examples of signaling biochemical
pathway-associated genes and polynucleotides are listed in Table
C.
[0371] Mutations in these genes and pathways can result in
production of improper proteins or proteins in improper amounts
which affect function. Further examples of genes, diseases and
proteins are hereby incorporated by reference from U.S. Provisional
applications 61/736,527 filed Dec. 12, 2012 and 61/748,427 filed on
Jan. 2, 2013. Such genes, proteins and pathways may be the target
polynucleotide of a CRISPR complex.
TABLE-US-00006 TABLE A DISEASE/DISORDERS GENE(S) Neoplasia PTEN;
ATM; ATR; EGFR; ERBB2; ERBB3; ERBB4; Notch1; Notch2; Notch3;
Notch4; AKT; AKT2; AKT3; HIF; HIF1a; HIF3a; Met; HRG; Bcl2; PPAR
alpha; PPAR gamma; WT1 (Wilms Tumor); FGF Receptor Family members
(5 members: 1, 2, 3, 4, 5); CDKN2a; APC; RB (retinoblastoma); MEN1;
VHL; BRCA1; BRCA2; AR (Androgen Receptor); TSG101; IGF; IGF
Receptor; Igf1(4 variants); Igf2 (3 variants); Igf 1 Receptor; Igf
2 Receptor; Bax; Bcl2; caspases family (9 members: 1, 2, 3, 4, 6,
7, 8, 9, 12); Kras; Apc Age-related Macular Abcr; Ccl2; Cc2; cp
(ceruloplasmin); Timp3; cathepsinD; Degeneration Vldlr; Ccr2
Schizophrenia Neuregulin1 (Nrg1); Erb4 (receptor for Neuregulin);
Complexin1 (Cplx1); Tph1 Tryptophan hydroxylase; Tph2 Tryptophan
hydroxylase 2; Neurexin 1; GSK3; GSK3a; GSK3b Disorders 5-HTT
(Slc6a4); COMT; DRD (Drd1a); SLC6A3; DAOA; DTNBP1; Dao (Dao1)
Trinucleotide Repeat HTT (Huntington's Dx); SBMA/SMAX1/AR
(Kennedy's Disorders Dx); FXN/X25 (Friedrich's Ataxia); ATX3
(Machado- Joseph's Dx); ATXN1 and ATXN2 (spinocerebellar ataxias);
DMPK (myotonic dystrophy); Atrophin-1 and Atn1 (DRPLA Dx); CBP
(Creb-BP-global instability); VLDLR (Alzheimer's); Atxn7; Atxn10
Fragile X Syndrome FMR2; FXR1; FXR2; mGLUR5 Secretase Related APH-1
(alpha and beta); Presenilin (Psen1); nicastrin Disorders (Ncstn);
PEN-2 Others Nos1; Parp1; Nat1; Nat2 Prion-related disorders Prp
ALS SOD1; ALS2; STEX; FUS; TARDBP; VEGF (VEGF-a; VEGF-b; -VEGF-c)
Drug addiction Prkce (alcohol); Drd2; Drd4; ABAT (alcohol); GRIA2;
Grm5; Grin1; Htr1b; Grin2a; Drd3; Pdyn; Gria1 (alcohol) Autism
Mecp2; BZRAP1; MDGA2; Sema5A; Neurexin 1; Fragile X (FMR2 (AFF2);
FXR1; FXR2; Mglur5) Alzheimer's Disease E1; CHIP; UCH; UBB; Tau;
LRP; PICALM; Clusterin; PS1; SORL1; CR1; Vldlr; Uba1; Uba3; CHIP28
(Aqp1, Aquaporin 1); Uchl1; Urhl3; APP Inflammation IL-10; IL-1
(IL-1a; IL-1b); IL-13; IL-17 (IL-17a (CTLA8); IL- 17b; IL-17c;
IL-17d; IL-17f); II-23; Cx3cr1; ptpn22; TNFa; NOD2/CARD15 for IBD;
IL-6; IL-12 (IL-12a; IL-12b): CTLA4; Cx3cl1 Parkinson's Disease
x-Synuclein; DJ-1; LRRK2; Parkin; PINK1
TABLE-US-00007 TABLE B Blood and Anemia (CDAN1, CDA1, RPS19, DBA,
PKLR, PK1, NT5C3, UMPH1, coagulation diseases PSN1, RHAG, RH50A,
NRAMP2, SPTB, ALAS2, ANH1, ASB, and disorders ABCB7, ABC7, ASAT);
Bare lymphocyte syndrome (TAPBP, TPSN, TAP2, ABCB3, PSF2, RING11,
MHC2TA, C2TA, RFX5, RFXAP, RFX5), Bleeding disorders (TBXA2R,
P2RX1, P2X1); Factor H and factor H-like 1 (HF1, CFH, HUS); Factor
V and factor VIII (MCFD2); Factor VII deficiency (F7); Factor X
deficiency (F10); Factor XI deficiency (F11); Factor XII deficiency
(F12, HAF); Factor XIIIA deficiency (F13A1, F13A); Factor XIIIB
deficiency (F13B); Fanconi anemia (FANCA, FACA, FA1, FA, FAA,
FAAP95, FAAP90, FLJ34064, FANCB, FANCC, FACC, BRCA2, FANCD1,
FANCD2, FANCD, FACD, FAD, FANCE, FACE, FANCF, XRCC9, FANCG, BRIP1,
BACH1, FANCJ, PHF9, FANCL, FANCM, KIAA1596); Hemophagocytic
lymphohistiocytosis disorders (PRF1, HPLH2, UNC13D, MUNC13-4,
HPLH3, HLH3, FHL3); Hemophilia A (F8, F8C, HEMA); Hemophilia B (F9,
HEMB), Hemorrhagic disorders (PI, ATT, F5); Leukocyde deficiencies
and disorders (ITGB2, CD18, LCAMB, LAD, EIF2B1, EIF2BA, EIF2B2,
EIF2B3, EIF2B5, LVWM, CACH, CLE, EIF2B4); Sickle cell anemia (HBB);
Thalassemia (HBA2, HBB, HBD, LCRB, HBA1). Cell dysregulation B-cell
non-Hodgkin lymphoma (BCL7A, BCL7); Leukemia, (TAL1, and oncology
TCL5, SCL, TAL2, FLT3, NBS1, NBS, ZNFN1A1, IK1, LYF1, diseases and
disorders HOXD4, HOX4B, BCR, CML, PHL, ALL, ARNT, KRAS2, RASK2,
GMPS, AF10, ARHGEF12, LARG, KIAA0382, CALM, CLTH, CEBPA, CEBP,
CHIC2, BTL, FLT3, KIT, PBT, LPP, NPM1, NUP214, D9S46E, CAN, CAIN,
RUNX1, CBFA2, AML1, WHSC1L1, NSD3, FLT3, AF1Q, NPM1, NUMA1, ZNF145,
PLZF, PML, MYL, STAT5B, AF10, CALM, CLTH, ARL11, ARLTS1, P2RX7,
P2X7, BCR, CML, PHL, ALL, GRAF, NF1, VRNF, WSS, NFNS, PTPN11,
PTP2C, SHP2, NS1, BCL2, CCND1, PRAD1, BCL1, TCRA, GATA1, GF1,
ERYF1, NFE1, ABL1, NQO1, DIA4, NMOR1, NUP214, D9S46E, CAN, CAIN).
Inflammation and AIDS (KIR3DL1, NKAT3, NKB1, AMB11, KIR3DS1, IFNG,
CXCL12, immune related SDF1); Autoimmune lymphoproliferative
syndrome (TNFRSF6, APT1, diseases and disorders FAS, CD95, ALPS1A);
Combined immunodeficiency, (IL2RG, SCIDX1, SCIDX, IMD4); HIV-1
(CCL5, SCYA5, D17S136E, TCP228), HIV susceptibility or infection
(IL10, CSIF, CMKBR2, CCR2, CMKBR5, CCCKR5 (CCR5));
Immunodeficiencies (CD3E, CD3G, AICDA, AID, HIGM2, TNFRSF5, CD40,
UNG, DGU, HIGM4, TNFSF5, CD40LG, HIGM1, IGM, FOXP3, IPEX, AIID,
XPID, PIDX, TNFRSF14B, TACI); Inflammation (IL-10, IL-1 (IL-1a,
IL-1b), IL-13, IL-17 (IL-17a (CTLA8), IL-17b, IL-17c, IL-17d,
IL-17F), II-23, Cx3cr1, ptpn22, TNFa, NOD2/CARD15 for IBD, IL-6,
IL-12 (IL-12a, IL-12b), CTLA4, Cx3cl1); Severe combined
immunodeficiencies (SCIDs)(JAK3, JAKL, DCLRE1C, ARTEMIS, SCIDA,
RAG1, RAG2, ADA, PTPRC, CD45, LCA, IL7R, CD3D, T3D, IL2RG, SCIDX1,
SCIDX, IMD4). Metabolic, liver, Amyloid neuropathy (TTR, PALB);
Amyloidosis (APOA1, APP, AAA, kidney and protein CVAP, AD1, GSN,
FGA, LYZ, TTR, PALB); Cirrhosis (KRT18, KRT8, diseases and
disorders CIRH1A, NAIC, TEX292, KIAA1988); Cystic fibrosis (CFTR,
ABCC7, CF, MRP7); Glycogen storage diseases (SLC2A2, GLUT2, G6PC,
G6PT, G6PT1 , GAA, LAMP2, LAMPB, AGL, GDE, GBE1, GYS2, PYGL, PFKM);
Hepatic adenoma, 142330 (TCF1, HNF1A, MODY3), Hepatic failure,
early onset, and neurologic disorder (SCOD1, SCO1), Hepatic lipase
deficiency (LIPC), Hepatoblastoma, cancer and carcinomas (CTNNB1,
PDGFRL, PDGRL, PRLTS, AXIN1, AXIN, CTNNB1, TP53, P53, LFS1, IGF2R,
MPRI, MET, CASP8, MCH5; Medullary cystic kidney disease (UMOD,
HNFJ, FJHN, MCKD2, ADMCKD2); Phenylketonuria (PAH, PKU1, QDPR,
DHPR, PTS); Polycystic kidney and hepatic disease (FCYT, PKHD1,
ARPKD, PKD1, PKD2, PKD4, PKDTS, PRKCSH, G19P1, PCLD, SEC63).
Muscular/Skeletal Becker muscular dystrophy (DMD, BMD, MYF6),
Duchenne Muscular diseases and disorders Dystrophy (DMD, BMD);
Emery-Dreifuss muscular dystrophy (LMNA, LMN1, EMD2, FPLD, CMD1A,
HGPS, LGMD1B, LMNA, LMN1, EMD2, FPLD, CMD1A); Facioscapulohumeral
muscular dystrophy (FSHM1A, FSHD1A); Muscular dystrophy (FKRP,
MDC1C, LUMD2I, LAMA2, LAMM, LARGE, KIAA0609, MDC1D, FCMD TTID,
MYOT, CAPN3, CANP3, DYSF, LGMD2B, SGCG, LGMD2C, DMDA1, SCG3, SGCA,
ADL, DAG2, LGMD2D, DMDA2, SGCB, LGMD2E, SGCD, SGD, LGMD2F, CMD1L,
TCAP, LGMD2G, CMD1N, TRIM32, HT2A, LGMD2H, FKRP, MDC1C, LGMD2I,
TTN, CMD1G, TMD, LGMD2J, POMT1, CAV3, LGMD1C, SEPN1, SELN, RSMD1,
PLEC1, PLTN, EBS1); Osteopetrosis (LRP5, BMND1, LRP7, LR3, OPPG,
VBCH2, CLCN7, CLC7, OPTA2, OSTM1, GL, TCIRG1, TIRC7, OC116, OPTB1);
Muscular atrophy (VAPB, VAPC, ALS8, SMN1, SMA1, SMA2, SMA3, SMA4,
BSCL2, SPG17, GARS, SMAD1, CMT2D, HEXB, IGHMBP2, SMUBP2, CATF1,
SMARD1). Neurological and ALS (SOD1, ALS2, STEX, FUS, TARDBP, VEGF
(VEGF-a, VEGF-b, neuronal diseases and VEGF-c); Alzheimer disease
(APP, AAA, CVAP, AD1, APOE, AD2, disorders PSEN2, AD4, STM2, APBB2,
FE65L1, NOS3, PLAU, URK, ACE, DCP1, ACE1, MPO, PACIP1, PAXIP1L,
PTIP, A2M, BLMH, BMH, PSEN1, AD3); Autism (Mecp2, BZRAP1, MDGA2,
Sema5A, Neurexin 1, GLO1, MECP2, RTT, PPMX, MRX16, MRX79, NLGN3,
NLGN4, KIAA1260, AUTSX2); Fragile X Syndrome (FMR2, FXR1, FXR2,
mGLUR5); Huntington's disease and disease like disorders (HD, IT15,
PRNP, PRIP, JPH3, JP3, HDL2, TBP, SCA17); Parkinson disease (NR4A2,
NURR1, NOT, TINUR, SNCAIP, TBP, SCA17, SNCA, NACP, PARK1, PARK4,
DJ1, PARK7, LRRK2, PARK8, PINK1, PARK6, UCHL1, PARK5, SNCA, NACP,
PARK1, PARK4, PRKN, PARK2, PDJ, DBH, NDUFV2); Rett syndrome (MECP2,
RTT, PPMX, MRX16, MRX79, CDKL5, STK9, MECP2, RTT, PPMX, MRX16,
MRX79, x-Synuclein, DJ-1); Schizophrenia (Neuregulin1 (Nrg1), Erb4
(receptor for Neuregulin), Complexin1 (Cplx1), Tph1 Tryptophan
hydroxylase, Tph2, Tryptophan hydroxylase 2, Neurexin 1, GSK3,
GSK3a, GSK3b, 5-HTT (Slc6a4), COMT, DRD (Drd1a), SLC6A3, DAOA,
DTNBP1, Dao (Dao1)); Secretase Related Disorders (APH-1 (alpha and
beta), Presenilin (Psen1), nicastrin, (Ncstn), PEN-2, Nos1, Parp1,
Nat1, Nat2); Trinucleotide Repeat Disorders (HTT (Huntington's Dx),
SBMA/SMAX1/AR (Kennedy's Dx), FXN/X25 (Friedrich's Ataxia), ATX3
(Machado-Joseph's Dx), ATXN1 and ATXN2 (spinocerebellar ataxias),
DIVITK (myotonic dystrophy), Atrophin-1 and Atn1 (DRPLA Dx), CBP
(Crete-BP--global instability), VLDLR (Alzheimer's), Atxn7,
Atxn10). Occular diseases and Age-related macular degeneration
(Abcr, Ccl2, Cc2, cp ceruloplasmin), disorders Timp3, cathepsinD,
Vldlr, Ccr2); Cataract (CRYAA, CRYA1, CRYBB2, CRYB2, PITX3, BFSP2,
CP49, CP47, CRYAA, CRYA1, PAX6, AN2, MGDA, CRYBA1, CRYB1, CRYGC,
CRYG3, CCL, LIM2, MP19, CRYGD, CRYG4, BFSP2, CP49, CP47, HSF4, CTM,
HSF4, CTM, MIP, AQP0, CRYAB, CRYA2, CTPP2, CRYBB1, CRYGD, CRYG4,
CRYBB2, CRYB2, CRYGC, CRYG3, CCL, CRYAA, CRYA1, GJA8, CX50, CAE1,
GJA3, CX46, CZP3, CAE3, CCM1, CAM, KRIT1); Corneal clouding and
dystrophy (APOA1, TGFBI, CSD2, CDGG1, CSD, BIGH3, CDG2, TACSTD2,
TROP2, M1S1, VSX1, RINX, PPCD PPD, KTCN, COL8A2, FECD, PPCD2,
PIP5K3, CFD); Cornea plana congenital (KERA, CNA2); Glaucoma (MYOC,
TIGR, GLC1A, JOAG, GPOA, OPTN, GLC1E, FIP2, HYPL, NRP, CYP1B1,
GLC3A, OPA1, NTG, NPG, CYP1B1, GLC3A); Leber congenital amaurosis
(CRB1, RP12, CRX, CORD2, CRD, RPGRIP1, LCA6, CORD9, RPE65, RP20,
AIPL1, LCA4, GUCY2D, GUC2D, LCA1, CORD6, RDH12, LCA3); Macular
dystrophy (ELOVL4, ADMD, STGD2, STGD3, RDS, RP7, PRPH2, PRPH, AVMD,
AOFMD, VMD2).
TABLE-US-00008 TABLE C CELLULAR FUNCTION GENES PI3K/AKT Signaling
PRKCE; ITGAM; ITGA5; IRAK1; PRKAA2; EIF2AK2; PTEN; EIF4E; PRKCZ;
GRK6; MAPK1; TSC1; PLK1; AKT2; IKBKB; PIK3CA; CDK8; CDKN1B; NFKB2;
BCL2; PIK3CB; PPP2R1A; MAPK8; BCL2L1; MAPK3; TSC2; ITGA1; KRAS;
EIF4EBP1; RELA; PRKCD; NOS3; PRKAA1; MAPK9; CDK2; PPP2CA; PIM1;
ITGB7; YWHAZ; ILK; TP53; RAF1; IKBKG; RELB; DYRK1A; CDKN1A; ITGB1;
MAP2K2; JAK1; AKT1; JAK2; PIK3R1; CHUK; PDPK1; PPP2R5C; CTNNB1;
MAP2K1; NFKB1; PAK3; ITGB3; CCND1; GSK3A; FRAP1; SFN; ITGA2; TTK;
CSNK1A1; BRAF; GSK3B; AKT3; FOXO1; SGK; HSP90AA1; RPS6KB1 ERK/MAPK
Signaling PRKCE; ITGAM; ITGA5; HSPB1; IRAK1; PRKAA2; EIF2AK2; RAC1;
RAP1A; TLN1; EIF4E; ELK1; GRK6; MAPK1; RAC2; PLK1; AKT2; PIK3CA;
CDK8; CREB1; PRKCI; PTK2; FOS; RPS6KA4; PIK3CB; PPP2R1A; PIK3C3;
MAPK8; MAPK3; ITGA1; ETS1; KRAS; MYCN; EIF4EBP1; PPARG; PRKCD;
PRKAA1; MAPK9; SRC; CDK2; PPP2CA; PIM1; PIK3C2A; ITGB7; YWHAZ;
PPP1CC; KSR1; PXN; RAF1; FYN; DYRK1A; ITGB1; MAP2K2; PAK4; PIK3R1;
STAT3; PPP2R5C; MAP2K1; PAK3; ITGB3; ESR1; ITGA2; MYC; TTK;
CSNK1A1; CRKL; BRAF; ATF4; PRKCA; SRF; STAT1; SGK Glucocorticoid
Receptor RAC1; TAF4B; EP300; SMAD2; TRAF6; PCAF; ELK1; Signaling
MAPK1; SMAD3; AKT2; IKBKB; NCOR2; UBE2I; PIK3CA; CREB1; FOS; HSPA5;
NFKB2; BCL2; MAP3K14; STAT5B; PIK3CB; PIK3C3; MAPK8; BCL2L1; MAPK3;
TSC22D3; MAPK10; NRIP1; KRAS; MAPK13; RELA; STAT5A; MAPK9; NOS2A;
PBX1; NR3C1; PIK3C2A; CDKN1C; TRAF2; SERPINE1; NCOA3; MAPK14; TNF;
RAF1; IKBKG; MAP3K7; CREBBP; CDKN1A; MAP2K2; JAK1; IL8; NCOA2;
AKT1; JAK2; PIK3R1; CHUK; STAT3; MAP2K1; NFKB1; TGFBR1; ESR1;
SMAD4; CEBPB; JUN; AR; AKT3; CCL2; MMP1; STAT1; IL6; HSP90AA1
Axonal Guidance PRKCE; ITGAM; ROCK1; ITGA5; CXCR4; ADAM12;
Signaling IGF1; RAC1; RAP1A; EIF4E; PRKCZ; NRP1; NTRK2; ARHGEF7;
SMO; ROCK2; MAPK1; PGF; RAC2; PTPN11; GNAS; AKT2; PIK3CA; ERBB2;
PRKCI; PTK2; CFL1; GNAQ; PIK3CB; CXCL12; PIK3C3; WNT11; PRKD1;
GNB2L1; ABL1; MAPK3; ITGA1; KRAS; RHOA; PRKCD; PIK3C2A; ITGB7;
GLI2; PXN; VASP; RAF1; FYN; ITGB1; MAP2K2; PAK4; ADAM17; AKT1;
PIK3R1; GLI1; WNT5A; ADAM10; MAP2K1; PAK3; ITGB3; CDC42; VEGFA;
ITGA2; EPHA8; CRKL; RND1; GSK3B; AKT3; PRKCA Ephrin Receptor PRKCE;
ITGAM; ROCK1; ITGA5; CXCR4; IRAK1; Signaling PRKAA2; EIF2AK2; RAC1
; RAP1A; GRK6; ROCK2; MAPK1; PGF; RAC2; PTPN11; GNAS; PLK1; AKT2;
DOK1; CDK8; CREB1; PTK2; CFL1; GNAQ; MAP3K14; CXCL12; MAPK8;
GNB2L1; ABL1; MAPK3; ITGA1; KRAS; RHOA; PRKCD; PRKAA1; MAPK9; SRC;
CDK2; PIM1; ITGB7; PXN; RAF1; FYN; DYRK1A; ITGB1; MAP2K2; PAK4;
AKT1; JAK2; STAT3; ADAM10; MAP2K1; PAK3; ITGB3; CDC42; VEGFA;
ITGA2; EPHA8; TTK; CSNK1A1; CRKL; BRAF; PTPN13; A1F4; AKT3; SGK
Actin Cytoskeleton ACTN4; PRKCE; ITGAM; ROCK1; ITGA5; IRAK1;
Signaling PRKAA2; EIF2AK2; RAC1; INS; ARHGEF7; GRK6; ROCK2; MAPK1;
RAC2; PLK1; AKT2; PIK3CA; CDK8; PTK2; CFL1; PIK3CB; MYH9; DIAPH1;
PIK3C3; MAPK8; F2R; MAPK3; SLC9A1; ITGA1; KRAS; RHOA; PRKCD;
PRKAA1; MAPK9; CDK2; PIM1; PIK3C2A; ITGB7; PPP1CC; PXN; VIL2; RAF1;
GSN; DYRK1A; ITGB1 MAP2K2; PAK4; PIP5K1A; PIK3R1; MAP2K1; PAK3;
ITGB3; CDC42; APC; ITGA2; TTK; CSNK1A1; CRKL; BRAF; VAV3; SGK
Huntington's Disease PRKCE; IGF1; EP300; RCOR1; PRKCZ; HDAC4; TGM2;
Signaling MAPK1; CAPNS1; AKT2; EGFR; NCOR2; SP1; CAPN2; PIK3CA;
HDAC5; CREB1; PRKCI; HSPA5; REST; GNAQ; PIK3CB; PIK3C3; MAPK8;
IGF1R; PRKD1; GNB2L1; BCL2L1; CAPN1; MAPK3; CASP8; HDAC2; HDAC7A;
PRKCD; HDAC11; MAPK9; HDAC9; PIK3C2A; HDAC3; TP53; CASP9; CREBBP;
AKT1; PIK3R1; PDPK1; CASP1; APAF1; FRAP1; CASP2; JUN; BAX; ATF4;
AKT3; PRKCA; CLTC; SGK; HDAC6; CASP3 Apoptosis Signaling PRKCE;
ROCK1; BID; IRAK1; PRKAA2; EIF2AK2; BAK1; BIRC4; GRK6; MAPK1;
CAPNS1; PLK1; AKT2; IKBKB; CAPN2; CDK8; FAS; NFKB2; BCL2; MAP3K14;
MAPK8; BCL2L1; CAPN1; MAPK3; CASP8; KRAS; RELA; PRKCD; PRKAA1;
MAPK9; CDK2; PIM1; TP53; TNF; RAF1; IKBKG; RFLB; CASP9; DYRK1A;
MAP2K2; CHUK; APAF1; MAP2K1; NFKB1; PAK3; LMNA; CASP2; BIRC2; TTK;
CSNK1A1; BRAF; BAX; PRKCA; SGK; CASP3; BIRC3; PARP1 B Cell Receptor
RAC1; PTEN; LYN; ELK1; MAPK1; RAC2; PTPN11; Signaling AKT2; IKBKB;
PIK3CA; CREB1; SYK; NFKB2; CAMK2A; MAP3K14; PIK3CB; PIK3C3; MAPK8;
BCL2L1; ABL1; MAPK3; ETS1; KRAS; MAPK13; RELA; PTPN6; MAPK9; EGR1;
PIK3C2A; BTK; MAPK14; RAF1; IKBKG; RELB; MAP3K7; MAP2K2; AKT1;
PIK3R1; CHUK; MAP2K1; NFKB1; CDC42; GSK3A; FRAP1; BCL6; BCL10; JUN;
GSK3B; ATF4; AKT3; VAV3; RPS6KB1 Leukocyte Extravasation ACTN4;
CD44; PRKCE; ITGAM; ROCK1; CXCR4; CYBA; Signaling RAC1; RAP1A;
PRKCZ; ROCK2; RAC2; PTPN11; MMP14; PIK3CA; PRKCI; PTK2; PIK3CB;
CXCL12; PIK3C3; MAPK8; PRKD1; ABL1; MAPK10; CYBB; MAPK13; RHOA;
PRKCD; MAPK9; SRC; PIK3C2A; BTK; MAPK14; NOX1; PXN; VIL2; VASP;
ITGB1; MAP2K2; CTNND1; PIK3R1; CTNNB1; CLDN1; CDC42; F11R; ITK;
CRKL; VAV3; CTTN; PRKCA; MMP1; MMP9 Integrin Signaling ACTN4;
ITGAM; ROCK1; ITGA5; RAC1; PTEN; RAP1A; TLN1; ARHGEF7; MAPK1; RAC2;
CAPNS1; AKT2; CAPN2; PIK3CA; PTK2; PIK3CB; PIK3C3; MAPK8; CAV1;
CAPN1; ABL1; MAPK3; ITGA1; KRAS; RHOA; SRC; PIK3C2A; ITGB7; PPP1CC;
ILK; PXN; VASP; RAF1; FYN; ITGB1; MAP2K2; PAK4; AKT1; PIK3R1; TNK2;
MAP2K1; PAK3; ITGB3; CDC42; RND3; ITGA2; CRKL; BRAF; GSK3B; AKT3
Acute Phase Response IRAK1; SOD2; MYD88; TRAF6; ELK1; MAPK1;
PTPN11; Signaling AKT2; IKBKB; PIK3CA; FOS; NFKB2; MAP3K14; PIK3CB;
MAPK8; RIPK1; MAPK3; IL6ST; KRAS; MAPK13; IL6R; RELA; SOCS1; MAPK9;
FTL; NR3C1; TRAF2; SERPINE1; MAPK14; TNF; RAF1; PDK1; IKBKG; RELB;
MAP3K7; MAP2K2; AKT1; JAK2; PIK3R1; CHUK; STAT3; MAP2K1; NFKB1;
FRAP1; CEBPB; JUN; AKT3; IL1R1; IL6 PTEN Signaling ITGAM; ITGA5;
RAC1; PTEN; PRKCZ; BCL2L11; MAPK1; RAC2; AKT2; EGFR; IKBKB; CBL;
PIK3CA; CDKN1B; PTK2; NFKB2; BCL2; PIK3CB; BCL2L1; MAPK3; ITGA1;
KRAS; ITGB7; ILK; PDGFRB; INSR; RAF1; IKBKG; CASP9; CDKN1A; ITGB1;
MAP2K2; AKT1; PIK3R1; CHUK; PDGFRA; PDPK1; MAP2K1; NFKB1; ITGB3;
CDC42; CCND1; GSK3A; ITGA2; GSK3B; AKT3; FOXO1; CASP3; RPS6KB1 p53
Signaling PTEN; EP300; BBC3; PCAF; FASN; BRCA1; GADD45A; BIRC5;
AKT2; PIK3CA; CHEK1; TP53INP1; BCL2; PIK3CB; PIK3C3; MAPK8; THBS1;
ATR; BCL2L1; E2F1; PMAIP1; CHEK2; TNFRSF10B; TP73; RB1; HDAC9;
CDK2; PIK3C2A; MAPK14; TP53; LRDD; CDKN1A; HIPK2; AKT1; PIK3R1;
RRM2B; APAF1; CTNNB1; SIRT1; CCND1; PRKDC; ATM; SFN; CDKN2A; JUN;
SNAI2; GSK3B; BAX; AKT3 Aryl Hydrocarbon HSPB1; EP300; FASN; TGM2;
RXRA; MAPK1; NQO1; Receptor Signaling NCOR2; SP1; ARNT; CDKN1B;
FOS; CHEK1; SMARCA4; NFKB2; MAPK8; ALDH1A1; ATR; E2F1; MAPK3;
NRIP1; CHEK2; RELA; TP73; GSTP1; RB1; SRC; CDK2; AHR; NFE2L2;
NCOA3; TP53; TNF; CDKN1A; NCOA2; APAF1; NFKB1; CCND1; ATM; ESR1;
CDKN2A; MYC; JUN; ESR2; BAX; IL6; CYP1B1; HSP90AA1 Xenobiotic
Metabolism PRKCE; EP300; PRKCZ; RXRA; MAPK1; NQO1; Signaling NCOR2;
PIK3CA; ARNT; PRKCI; NFKB2; CAMK2A; PIK3CB; PPP2R1A; PIK3C3; MAPK8;
PRKD1; ALDH1A1; MAPK3; NRIP1; KRAS; MAPK13; PRKCD; GSTP1; MAPK9;
NOS2A; ABCB1; AHR; PPP2CA; FTL; NFE2L2; PIK3C2A; PPARGC1A; MAPK14;
TNF; RAF1; CREBBP; MAP2K2; PIK3R1; PPP2R5C; MAP2K1; NFKB1; KEAP1;
PRKCA; EIF2AK3; IL6; CYP1B1; HSP90AA1 SAPK/JNK Signaling PRKCE;
IRAK1; PRKAA2; EIF2AK2; RAC1; ELK1; GRK6; MAPK1; GADD45A; RAC2;
PLK1; AKT2; PIK3CA; FADD; CDK8; PIK3CB; PIK3C3; MAPK8; RIPK1;
GNB2L1 ; IRS1; MAPK3; MAPK10; DAXX; KRAS; PRKCD; PRKAA1; MAPK9;
CDK2; PIM1; PIK3C2A; TRAF2; TP53; LCK; MAP3K7; DYRK1A; MAP2K2;
PIK3R1; MAP2K1; PAK3; CDC42; JUN; TTK; CSNK1A1 ; CRKL; BRAF; SGK
PPAr/RXR Signaling PRKAA2; EP300; INS; SMAD2; TRAF6; PPARA; FASN;
RXRA; MAPK1; SMAD3; GNAS; IKBKB; NCOR2; ABCA1; GNAQ; NFKB2;
MAP3K14; STAT5B; MAPK8; IRS1; MAPK3; KRAS; RELA; PRKAA1; PPARGC1A;
NCOA3; MAPK14; INSR; RAF1; IKBKG; RELB; MAP3K7; CREBBP; MAP2K2;
JAK2; CHUK; MAP2K1; NFKB1; TGFBR1; SMAD4; JUN; IL1R1; PRKCA; IL6;
HSP90AA1; ADIPOQ NF-KB Signaling IRAK1; EIF2AK2; EP300; INS; MYD88;
PRKCZ; TRAF6; TBK1; AKT2; EGFR; IKBKB; PIK3CA; BTRC; NFKB2;
MAP3K14; PIK3CB; PIK3C3; MAPK8; RIPK1; HDAC2; KRAS; RELA; PIK3C2A;
TRAF2; TLR4; PDGRB; TNF; INSR; LCK; IKBKG; RELB; MAP3K7; CREBBP;
AKT1; PIK3R1; CHUK; PDGFRA; NFKB1; TLR2; BCL10; GSK3B; AKT3;
TNFAIP3; IL1R1 Neuregulin Signaling ERBB4; PRKCE; ITGAM; ITGA5;
PTEN; PRKCZ; ELK1; MAPK1; PTPN11; AKT2; EGFR; ERBB2; PRKCI; CDKN1B;
STAT5B; PRKD1; MAPK3; ITGA1; KRAS; PRKCD, STAT5A, SRC; ITGB7; RAF1;
ITGB1; MAP2K2; ADAM17; AKT1; PIK3R1; PDPK1; MAP2K1; ITGB3; EREG;
FRAP1; PSEN1; ITGA2; MYC; NRG1; CRKL; AKT3; PRKCA; HSP90AA1;
RPS6KB1 Wnt & Beta catenin CD44; EP300; LRP6; DVL3; CSNK1E;
GJA1; SMO; Signaling AKT2, PIN1; CDH1; BTRC; GNAQ; MARK2; PPP2R1A
WNT11; SRC; DKK1; PPP2CA; SOX6; SFRP2; ILK; LEF1; SOX9; TP53;
MAP3K7; CREBBP; TCF7L2; AKT1 PPP2R5C; WNT5A; LRP5; CTNNB1; TGFBR1;
CCND1; GSK3A; DVL1; APC; CDKN2A; MYC; CSNK1A1; GSK3B AKT3; SOX2
Insulin Receptor PTEN; INS; EIF4E; PTPN1; PRKCZ; MAPK1; TSC1;
Signaling PTPN11; AKT2; CBL; PIK3CA; PRKCI; PIK3CB; PIK3C3; MAPK8;
IRS1; MAPK3; TSC2; KRAS; EIF4EBP1; SLC2A4; PIK3C2A; PPP1CC; INSR;
RAF1; MAP2K1; GSK3A; FRAP1; CRKL; GSK3B; AKT3; FOXO1; SGK; RPS6KB1
IL-6 Signaling HSPB1; TRAF6; MAPKAPK2; ELK1; MAPK1; PTPN11; IKBKB;
FOS; NFKB2; MAP3K14; MAPK8; MAPK3; MAPK10; IL6ST; KRAS; MAPK13;
IL6R; RELA; SOCS1; MAPK9; ABCB1; TRAF2; MAPK14; TNF; RAF1; IKBKG;
RELB; MAP3K7; MAP2K2; IL8; JAK2; CHUK; STAT3; MAP2K1; NFKB1; CEBPB;
JUN; IL1R1; SRF; IL6 Hepatic Cholestasis PRKCE; IRAK1; INS; MYD88;
PRKCZ; TRAF6; PPARA; RXRA; IKBKB; PRKCI; NFKB2; MAP3K14; MAPK8;
PRKD1; MAPK10; RELA; PRKCD; MAPK9; ABCB1; TRAF2; TLR4; TNF; INSR;
IKBKG; RELB; MAP3K7; IL8; CHUK; NR1H2; TJP2; NFKB1; ESR1; SREBF1;
FGFR4; JUN; IL1R1; PRKCA; IL6 IGF-1 Signaling IGF1; PRKCZ; ELK1;
MAPK1; PTPN11; NEDD4; AKT2; PIK3CA; PRKCI; PTK2; FOS; PIK3CB;
PIK3C3; MAPK8; IGF1R; IRS1; MAPK3; IGFBP7; FRAS; PIK3C2A; YWHAZ;
PXN; RAF1; CASP9; MAP2K2; AKT1; PIK3R1; PDPK1; MAP2K1; IGFBP2; SFN;
JUN; CYR61; AKT3; FOXO1; SRF; CTGF; RPS6KB1 NRF2-mediated PRKCE;
EP300; SOD2; PRKCZ; MAPK1; SQSTM1; Oxidative NQO1; PIK3CA; PRKCI;
FOS; PIK3CB; PIK3C3; MAPK8; Stress Response PRKD1; MAPK3; KRAS;
PRKCD; GSTP1; MAPK9; FTL; NFE2L2; PIK3C2A; MAPK14; RAF1; MAP3K7;
CREBBP; MAP2K2; AKT1; PIK3R1; MAP2K1; PPIB; JUN; KEAP1; GSK3B;
ATF4; PRKCA; EIF2AK3; HSP90AA1 Hepatic Fibrosis/Hepatic EDN1; IGF1;
KDR; FLT1; SMAD2; FGFR1; MET; PGF; Stellate Cell Activation SMAD3;
EGFR; FAS; CSF1; NFKB2; BCL2; MYH9; IGF1R; IL6R; RELA; TLR4;
PDGFRB; TNF; RELB; IL8; PDGFRA; NFKB1; TGFBR1; SMAD4; VEGFA; BAX;
IL1R1; CCL2; HGF; MMP1; STAT1; IL6; CTGF; MMP9 PPAR Signaling
EP300; INS; TRAF6; PPARA; RXRA; MAPK1; IKBKB; NCOR2; FOS; NFKB2;
MAP3K14; STAT5B; MAPK3; NRIP1; KRAS; PPARG; RELA; STAT5A; TRAF2;
PPARGC1A; PDGFRB; TNF; INSR; RAF1; IKBKG; RELB; MAP3K7; CREBBP;
MAP2K2; CHUK; PDGFRA; MAP2K1; NFKB1; JUN; IL1R1; HSP90AA1 Fc
Epsilon RI Signaling PRKCE; RAC1; PRKCZ; LYN; MAPK1; RAC2; PTPN11;
AKT2; PIK3CA; SYK; PRKCI; PIK3CB; PIK3C3; MAPK8; PRKD1; MAPK3;
MAPK10; KRAS; MAPK13; PRKCD; MAPK9; PIK3C2A; BTK; MAPK14; TNF;
RAF1; FYN; MAP2K2; AKT1; PIK3R1; PDPK1; MAP2K1; AKT3; VAV3; PRKCA
G-Protein Coupled PRKCE; RAP1A; RGS16; MAPK1; GNAS; AKT2; IKBKB;
Receptor Signaling PIK3CA; CREB1; GNAQ; NFKB2; CAMK2A; PIK3CB;
PIK3C3: MAPK3; KRAS; RELA; SRC; PIK3C2A; RAF1; IKBKG; RELB; FYN;
MAP2K2; AKT1; PIK3R1; CHUK; PDPK1; STAT3; MAP2K1; NFKB1; BRAF;
ATF4; AKT3; PRKCA Inositol Phosphate PRKCE; IRAK1; PRKAA2; EIF2AK2;
PTEN; GRK6; Metabolism MAPK1; PLK1; AKT2; PIK3CA; CDK8; PIK3CB;
PIK3C3; MAPK8; MAPK3; PRKCD; PRKAA1; MAPK9; CDK2; PIM1; PIK3C2A;
DYRK1A; MAP2K2; PIP5K1A; PIK3R1; MAP2K1; PAK3; ATM; TTK; CSNK1A1;
BRAF; SGK PDGF Signaling EIF2AK2; ELK1; ABL2; MAPK1; PIK3CA; FOS;
PIK3CB;
PIK3C3; MAPK8; CAV1; ABL1; MAPK3; KRAS; SRC; PIK3C2A; PDGFRB; RAF1;
MAP2K2; JAK1; JAK2; PIK3R1; PDGFRA; STAT3; SPHK1; MAP2K1; MYC; JUN;
CRKL; PRKCA; SRF; STAT1; SPHK2 VEGF Signaling ACTN4; ROCK1; KDR;
FLT1; ROCK2; MAPK1; PGF; AKT2; PIK3CA; ARNT; PTK2; BCL2; PIK3CB;
PIK3C3; BCL2L1; MAPK3; KRAS; HIF1A; NOS3; PIK3C2A; PXN; RAF1;
MAP2K2; ELAVL1; AKT1; PIK3R1; MAP2K1; SFN; VEGFA; AKT3; FOXO1;
PRKCA Natural Killer Cell PRKCE; RAC1; PRKCZ; MAPK1; RAC2; PTPN11;
Signaling KIR2DL3; AKT2; PIK3CA; SYK; PRKCI; PIK3CB; PIK3C3; PRKD1;
MAPK3; KRAS; PRKCD; PTPN6; PIK3C2A; LCK; RAF1; FYN; MAP2K2; PAK4;
AKT1; PIK3R1; MAP2K1; PAK3; AKT3; VAV3; PRKCA Cell Cycle: Gl/S
HDAC4; SMAD3; SUV39H1; HDAC5; CDKN1B; BTRC; Checkpoint Regulation
ATR; ABL1; E2F1; HDAC2; HDAC7A; RB1; HDAC11; HDAC9; CDK2; E2F2;
HDAC3; TP53; CDKN1A; CCND1; E2F4; ATM; RBL2; SMAD4; CDKN2A; MYC;
NRG1; GSK3B; RBL1; HDAC6 T Cell Receptor RAC1; ELK1; MAPK1; IKBKB;
CBL; PIK3CA; FOS; Signaling NFKB2; PIK3GB; PIK3C3; MAPK8; MAPK3;
KRAS; RELA; PIK3C2A; BTK; LCK; RAF1; IKBKG; RELB; FYN; MAP2K2;
PIK3R1; CHUK; MAP2K1; NFKBI; ITK; BCL10; JUN; VAV3 Death Receptor
Signaling CRADD; HSPB1; BID; BIRC4; TBK1; IKBKB; FADD; FAS; NFKB2;
BCL2; MAP3K14; MAPK8; RIPK1; CASP8; DAXX; TNFRSF10B; RELA; TRAF2;
TNF; IKBKG; RELB; CASP9; CHUK; APAF1; NFKB1; CASP2; BIRC2; CASP3;
BIRC3 FGF Signaling RAC1; FGFR1; MET; MAPKAPK2; MAPK1; PTPN11;
AKT2; PIK3CA; CREB1; PIK3CB; PIK3C3; MAPK8; MAPK3; MAPK13; PTPN6;
PIK3C2A; MAPK14; RAF1; AKT1; PIK3R1; STAT3; MAP2K1; FGFR4; CRKL;
ATF4; AKT3; PRKCA; HGF GM-CSF Signaling LYN; ELK1; MAPK1; PTPN11;
AKT2; PIK3CA; CAMK2A; STAT5B; PIK3CB; PIK3C3; GNB2L1; BCL2L1;
MAPK3; ETS1; KRAS; RUNX1; PIM1; PIK3C2A; RAF1; MAP2K2; AKT1; JAK2;
PIK3R1; STAT3; MAP2K1; CCND1; AKT3; STAT1 Amyotrophic Lateral BID;
IGF1; RAC1; BIRC4; PGF; CAPNS1; CAPN2; Sclerosis Signaling PIK3CA;
BCL2; PIK3CB; PIK3C3; BCL2L1; CAPN1; PIK3C2A; TP53; CASP9; PIK3R1;
RAB5A; CASP1; APAF1; VEGFA; BIRC2; BAX; AKT3; CASP3; BIRC3 JAK/Stat
Signaling PTPN1; MAPK1; PTPN11; AKT2; PIK3CA; STAT5B; PIK3CB;
PIK3C3; MAPK3; KRAS; SOCS1; STAT5A; PTPN6; PIK3C2A; RAF1; CDKN1A;
MAP2K2; JAK1; AKT1; JAK2; PIK3R1; STAT3; MAP2K1; FRAP1; AKT3; STAT1
Nicotinate and PRKCE; IRAK1; PRKAA2; EIF2AK2; GRK6; MAPK1;
Nicotinamide PLK1; AKT2; CDK8; MAPK8; MAPK3; PRKCD; PRKAA1;
Metabolism PBEF1; MAPK9; CDK2; PIM1; DYRK1A; MAP2K2; MAP2K1; PAK3;
NT5E; TTK; CSNK1A1; BRAF; SGK Chemokine Signaling CXCR4; ROCK2;
MAPK1; PTK2; FOS; CFL1; GNAQ; CAMK2A; CXCL12; MAPK8; MAPK3; KRAS;
MAPK13; RHOA; CCR3; SRC; PPP1CC; MAPK14; NOX1; RAF1; MAP2K2;
MAP2K1; JUN; CCL2; PRKCA IL-2 Signaling ELK1; MAPK1; PTPN11; AKT2;
PIK3CA; SYK; FOS; STAT5B; PIK3CB; PIK3C3; MAPK8; MAPK3; KRAS;
SOCS1; STAT5A; PIK3C2A; LCK; RAF1; MAP2K2; JAK1; AKT1; PIK3R1;
MAP2K1; JUN; AKT3 Synaptic Long Term PRKCE; IGF1; PRKCZ; PRDX6;
LYN; MAPK1; GNAS; Depression PRKCI; GNAQ; PPP2R1A; IGF1R; PRKD1;
MAPK3; KRAS; GRN; PRKCD; NOS3; NOS2A; PPP2CA; YWHAZ; RAF1; MAP2K2;
PPP2R5C; MAP2K1; PRKCA Estrogen Receptor TAF4B; EP300; CARM1; PCAF;
MAPK1; NCOR2; Signaling SMARCA4; MAPK3; NRIP1; KRAS; SRC; NR3C1;
HDAC3; PPARGC1A; RBM9; NCOA3; RAF1; CREBBP; MAP2K2; NCOA2; MAP2K1;
PRKDC; ESR1; ESR2 Protein Ubiquitination TRAF6; SMURF1; BIRC4;
BRCA1; UCHL1; NEDD4; Pathway CBL; UBE21; BTRC; HSPA5; USP7; USP10;
FBXW7; USP9X; STUB1; USP22; B2M; BIRC2; PARK2; USP8; USP1; VHL;
HSP90AA1; BIRC3 IL-10 Signaling TRAF6; CCR1; ELK1; IKBKB; SP1; FOS;
NFKB2; MAP3K14; MAPK8; MAPK13; RELA; MAPK14; TNF; IKBKG; RELB;
MAP3K7; JAK1; CHUK; STAT3; NFKB1; JUN; IL1R1; IL6 VDR/RXR
Activation PRKCE; EP300; PRKCZ; RXRA; GADD45A; HES1; NCOR2; SP1;
PRKCI; CDKN1B; PRKD1, PRKCD; RUNX2; KLF4; YY1; NCOA3; CDKN1A;
NCOA2; SPP1; LRP5; CEBPB; FOXO1; PRKCA TGF-beta Signaling EP300;
SMAD2; SMURE1; MAPK1; SMAD3; SMAD1; FOS; MAPK8; MAPK3; KRAS; MAPK9;
RUNX2; SERPINE1; RAF1; MAP3K7; CREBBP; MAP2K2; MAP2K1; TGFBRI;
SMAD4; JUN; SMAD5 Toll-like Receptor IRAK1; EIF2AK2; MYD88; TRAF6;
PPARA; ELK1; Signaling IKBKB; FOS; NFKB2; MAP3K14; MAPK8; MAPK13;
RELA; TLR4; MAPK14; IKBKG; RELB; MAP3K7; CHUK; NFKB1; TLR2; JUN p38
MAPK Signaling HSPB1; IRAK1; TRAF6; MAPKAPK2; ELK1; FADD; FAS;
CREB1; DDIT3; RPS6KA4; DAXX; MAPK13; TRAF2; MAPK14; TNF; MAP3K7;
TGFBR1; MYC; ATF4; IL1R1; SRF; STAT1 Neurotrophin/TRK NTRK2; MAPK1;
PTPN11; PIK3CA; CREB1; FOS; Signaling PIK3CB; PIK3C3; MAPK8; MAPK3;
KRAS; PIK3C2A; RAF1; MAP2K2; AKT1; PIK3R1; PDPK1; MAP2K1; CDC42;
JUN; ATF4 FXR/RXR Activation INS; PPARA; FASN; RXRA; AKT2; SDC1;
MAPK8; APOB; MAPK10; PPARG; MTTP; MAPK9; PPARGC1A; TNF; CREBBP;
AKT1; SREBF1; FGFR4; AKT3; FOXO1 Synaptic Long Term PRKCE; RAP1A;
EP300; PRKCZ; MAPK1; CREB1; Potentiation PRKCI; GNAQ; CAMK2A;
PRKD1; MAPK3; KRAS; PRKCD; PPP1CC; RAF1; CREBBP; MAP2K2; MAP2K1;
ATF4; PRKCA Calcium Signaling RAP1A; EP300; HDAC4; MAPK1; HDAC5;
CREB1; CAMK2A; MYH9; MAPK3; HDAC2; HDAC7A; HDAC11; HDAC9; HDAC3;
CREBBP; CALR; CAMKK2; ATF4; HDAC6 EGF Signaling ELK1; MAPK1; EGFR;
PIK3CA; FOS; PIK3CB; PIK3C3; MAPK8; MAPK3; PIK3C2A; RAF1; JAK1;
PIK3R1; STAT3; MAP2K1; JUN; PRKCA; SRF; STAT1 Hypoxia Signaling in
the EDN1; PTEN; EP300; NQO1; UBE2I; CREB1; ARNT; Cardiovascular
System HIF1A; SLC2A4; NOS3; TP53; LDHA; AKTI ; ATM; VEGFA; JUN;
ATF4; VHL; HSP90AA1 LPS/IL-1 Mediated IRAK1; MYD88; TRAF6; PPARA;
RXRA; ABCA1; Inhibition of RXR MAPK8; ALDH1A1; GSTP1; MAPK9; ABCB1;
TRAF2; Function TLR4; TNF; MAP3K7; NR1H2; SREBF1; JUN; IL1R1
LXRIRXR Activation FASN; RXRA; NCOR2; ABCA1; NFKB2; IRF3; RELA;
NOS2A; TLR4; TNF; RELB; LDLR; NR1H2; NFKB1; SREBF1; IL1R1; CCL2;
IL6; MMP9 Amyloid Processing PRKCE; CSNK1E; MAPK1; CAPNS1; AKT2;
CAPN2; CAPN1; MAPK3; MAPK13; MAPT; MAPK14; AKT1; PSEN1; CSNK1A1;
GSK3B; AKT3; APP IL-4 Signaling AKT2; PIK3CA; PIK3CB; PIK3C3; IRS1;
KRAS; SOCS1; PTPN6; NR3C1; PIK3C2A; JAK1; AKT1; JAK2; PIK3R1;
FRAP1; AKT3; RPS6KB1 Cell Cycle: G2/M DNA EP300; PCAF; BRCA1;
GADD45A; PLK1; BTRC; Damage Checkpoint CHEK1; ATR; CHEK2; YWHAZ;
TP53; CDKN1A; Regulation PRKDC; ATM; SFN; CDKN2A Nitric Oxide
Signaling KDR; FLT1; PGF; AKT2; PIK3CA; PIK3CB; PIK3C3; in the
Cardiovascular CAV1; PRKCD; NOS3; PIK3C2A; AKT1; PIK3R1; System
VEGFA; AKT3; HSP90AA1 Purine Metabolism NME2; SMARCA4; MYH9; RRM2;
ADAR; EIF2AK4; PKM2; ENTPD1; RAD51; RRM2B; TJP2; RAD51C; NT5E;
POLD1; NME1 cAMP-Mediated RAP1A; MAPK1; GNAS; CREB1; CAMK2A; MAPK3;
Signaling SRC; RAF1; MAP2K2; STAT3; MAP2K1; BRAF; ATF4
Mitochondrial SOD2; MAPK8; CASP8; MAPK10; MAPK9; CASP9; Dysfunction
PARK7; PSEN1; PARK2; APP; CASP3 Notch Signaling HES1; JAG1; NUMB;
NOTCH4; ADAM17; NOTCH2; PSEN1; NOTCH3; NOTCH1; DLL4 Endoplasmic
Reticulum HSPA5; MAPK8; XBP1; TRAF2; ATF6; CASP9; ATF4; Stress
Pathway EIF2AK3; CASP3 Pyrimidine Metabolism NME2; AICDA; RRM2;
EIF2AK4; ENTPD1; RRM2B; NT5E; POLD1; NME1 Parkinson's Signaling
UCHL1; MAPK8; MAPK13; MAPK14; CASP9; PARK7; PARK2; CASP3 Cardiac
& Beta GNAS; GNAQ; PPP2R1A; GNB2L1; PPP2CA; PPP1CC; Adrenergic
Signaling PPP2R5C Glycolysis/Gluconeo- HK2; GCK; GPI; ALDH1A1;
PKM2; LDHA; HK1 genesis Interferon IFR1; SOCS1; JAK1; JAK2; IFITM1;
STAT1; IFIT3 Signaling Sonic Hedgehog ARRB2; SMO; GLI2; DYRK1A;
GLI1; GSK3B; DYRK1B Signaling Glycerophospholipid PLD1; GRN; GPAM;
YWHAZ; SPHK1; SPHK2 Metabolism Phospholipid PRDX6; PLD1; GRN;
YWHAZ; SPHK1; SPHK2 Degradation Tryptophan Metabolism SIAH2; PRMT5;
NEDD4; ALDH1A1; CYP1B1; SIAH1 Lysine Degradation SUV39H1; EHMT2;
NSD1; SETD7; PPP2R5C Nucleotide Excision ERCC5; ERCC4; XPA; XPC;
ERCC1 Repair Pathway Starch and Sucrose UCHL1; HK2; GCK; GPI; HK1
Metabolism Aminosugars Metabolism NQO1; HK2; GCK; HK1 Arachidonic
Acid PRDX6; GRN; YWHAZ; CYP1B1 Metabolism Circadian Rhythm CSNK1E;
CREB1; ATF4; NR1D1 Signaling Coagulation System BDKRB1; F2R;
SERPINE1; F3 Dopamine Receptor PPP2R1A; PPP2CA; PPP1CC; PPP2R5C
Signaling Glutathione Metabolism IDH2; GSTP1; ANPEP; IDH1
Glycerolipid Metabolism ALDH1A1; GPAM; SPHK1; SPHK2 Linoleic Acid
PRDX6; GRN; YWHAZ; CYP1B1 Metabolism Methionine Metabolism DNMT1;
DNMT3B; AHCY; DNMT3A Pyruvate Metabolism GLO1; ALDR1A1; PKM2; LDHA
Arginine and Proline ALDH1A1; NOS3; NOS2A Metabolism Eicosanoid
Signaling PRDX6; GRN; YWHAZ Fructose and Mannose HK2; GCK; HK1
Metabolism Galactose Metabolism HK2; GCK; HK1 Stilbene, Cournarine
and PRDX6; PRDX1; TYR Lignin Biosynthesis Antigen Presentation
CALR; B2M Pathway Biosynthesis of Steroids NQO1; DFICR7 Butanoate
Metabolism ALDH1A1; NLGN1 Citrate Cycle IDH2; IDH1 Fatty Acid
Metabolism ALDH1A1; CYP1B1 G ycerophospholipid PRDX6; CHKA
Metabolism Histidine Metabolism PRMT5; ALDH1A1 inositol Metabolism
ERO1L; APEX1 Metabolism of GSTP1; CYP1B1 Xenobiotics by Cytochrome
p450 Methane Metabolism PRDX6; PRDX1 Phenylalanine PRDX6; PRDX1
Metabolism Propanoate Metabolism ALDHI1A1; LDHA Selenoamino Acid
PRMT5; AHCY Metabolism Sphingolipid Metabolism SPHK1; SPFIK2
Aminophosphonate PRMT5 Metabolism Androgen and Estrogen PRMT5
Metabolism Ascorbate and Aldarate ALDH1A1 Metabolism Bile Acid
Biosynthesis ALDH1A1 Cysteine Metabolism LDHA Fatty Acid
Biosynthesis FASN Glutamate Receptor GNB2L1 Signaling NRF2-mediated
PRDX1 Oxidative Stress Response Pentose Phosphate GPI Pathway
Pentose and Glucuronate UCHL1 Interconversions Retinol Metabolism
ALDH1A1 Riboflavin Metabolism TYR Tyrosine Metabolism PRMT5, TYR
Ubiquinone Biosynthesis PRMT5 Valine, Leucine and ALDH1A1
Isoleucine Degradation Glycine, Serine and CHKA Threonine
Metabolism Lysine Degradation ALDH1A1 Pain/Taste TRPM5; TRPA1 Pain
TRPM7; TRPC5; TRPC6; TRPC1; Cnrl; cnr2; Grk2; Trpa1; Pomc; Cgrp;
Crf; Pka; Era; Nr2b; TRPM5; Prkaca; Prkacb; Prkar1a; Prkar2a
Mitochondrial Function AIF; CytC; SMAC (Diablo); Aifm-1; Aifm-2
Developmental BMP-4; Chordin (Chrd); Noggin (Nog); WNT (Wnt2;
Neurology Wnt2b; Wnt3a; Wnt4; Wnt5a; Wnt6; Wnt7b; Wnt8b; Wnt9a;
Wnt9b; Wnt10a; Wnt10b; Wnt16); beta-catenin; Dkk-1; Frizzled
related proteins; Otx-2; Gbx2; FGF-8; Reelin; Dab1; unc-86 (Pou4fl
or Brn3a); Numb; Reln
[0372] Embodiments of the invention also relate to methods and
compositions related to knocking out genes, amplifying genes and
repairing particular mutations associated with DNA repeat
instability and neurological disorders (Robert D. Wells, Tetsuo
Ashizawa, Genetic Instabilities and Neurological Diseases, Second
Edition, Academic Press, Oct. 13, 2011--Medical). Specific aspects
of tandem repeat sequences have been found to be responsible for
more than twenty human diseases (New insights into repeat
instability: role of RNA*DNA hybrids. Mclvor E I, Polak U.
Napierala M. RNA Biol. 2010 September-October; 7(5):551-8). The
CRISPR-Cas system may be harnessed to correct these defects of
genomic instability.
[0373] A further aspect of the invention relates to utilizing the
CRISPR-Cas system for correcting defects in the EMP2A and EMP2B
genes that have been identified to be associated with Lafora
disease. Lafora disease is an autosomal recessive condition which
is characterized by progressive myoclonus epilepsy which may start
as epileptic seizures in adolescence. A few cases of the disease
may be caused by mutations in genes yet to be identified. The
disease causes seizures, muscle spasms, difficulty walking,
dementia, and eventually death. There is currently no therapy that
has proven effective against disease progression. Other genetic
abnormalities associated with epilepsy may also be targeted by the
CRISPR-Cas system and the underlying genetics is further described
in Genetics of Epilepsy and Genetic Epilepsies, edited by Giuliano
Avanzini, Jeffrey L. Noebels, Mariani Foundation Paediatric
Neurology: 20; 2009).
[0374] The methods of US Patent Publication No. 20110158957
assigned to Sangamo BioSciences, Inc. involved in inactivating T
cell receptor (TCR) genes may also be modified to the CRISPR Cas
system of the present invention. In another example, the methods of
US Patent Publication No. 20100311124 assigned to Sangamo
BioSciences. Inc. and US Patent Publication No. 20110225664
assigned to Cellectis, which are both involved in inactivating
glutamine synthetase gene expression genes may also be modified to
the CRISPR Cas system of the present invention.
[0375] Several further aspects of the invention relate to
correcting defects associated with a wide range of genetic diseases
which are further described on the website of the National
Institutes of Health under the topic subsection Genetic Disorders
(website at health.nih.gov/topic/GeneticDisorders). The genetic
brain diseases may include but are not limited to
Adrenoleukodystrophy, Agenesis of the Corpus Callosum, Aicardi
Syndrome, Alpers' Disease, Alzheimer's Disease, Barth Syndrome,
Batten Disease, CADASIL, Cerebellar Degeneration, Fabry's Disease,
Gerstmann-Straussler-Scheinker Disease, Huntington's Disease and
other Triplet Repeat Disorders, Leigh's Disease, Lesch-Nyhan
Syndrome, Menkes Disease, Mitochondrial Myopathies and NINDS
Colpocephaly. These diseases are further described on the website
of the National Institutes of Health under the subsection Genetic
Brain Disorders.
[0376] In some embodiments, the condition may be neoplasia. In some
embodiments, where the condition is neoplasia, the genes to be
targeted are any of those listed in Table A (in this case PTEN and
so forth). In some embodiments, the condition may be Age-related
Macular Degeneration. In some embodiments, the condition may be a
Schizophrenic Disorder. In some embodiments, the condition may be a
Trinucleotide Repeat Disorder. In some embodiments, the condition
may be Fragile X Syndrome. In some embodiments, the condition may
be a Secretase Related Disorder. In some embodiments, the condition
may be a Prion-related disorder. In some embodiments, the condition
may be ALS. In some embodiments, the condition may be a drug
addiction. In some embodiments, the condition may be Autism. In
some embodiments, the condition may be Alzheimer's Disease. In some
embodiments, the condition may be inflammation. In some
embodiments, the condition may be Parkinson's Disease.
[0377] For example, US Patent Publication No. 20110023145,
describes use of zinc finger nucleases to genetically modify cells,
animals and proteins associated with autism spectrum disorders
(ASD). Autism spectrum disorders (ASDs) are a group of disorders
characterized by qualitative impairment in social interaction and
communication, and restricted repetitive and stereotyped patterns
of behavior, interests, and activities. The three disorders,
autism, Asperger syndrome (AS) and pervasive developmental
disorder-not otherwise specified (PDD-NOS) are a continuum of the
same disorder with varying degrees of severity, associated
intellectual functioning and medical conditions. ASDs are
predominantly genetically determined disorders with a heritability
of around 90%.
[0378] US Patent Publication No. 20110023145 comprises editing of
any chromosomal sequences that encode proteins associated with ASD
which may be applied to the CRISPR Cas system of the present
invention. The proteins associated with ASD are typically selected
based on an experimental association of the protein associated with
ASD to an incidence or indication of an ASD. For example, the
production rate or circulating concentration of a protein
associated with ASD may be elevated or depressed in a population
having an ASD relative to a population lacking the ASD. Differences
in protein levels may be assessed using proteomic techniques
including but not limited to Western blot, immunohistochemical
staining, enzyme linked immunosorbent assay (ELISA), and mass
spectrometry. Alternatively, the proteins associated with ASD may
be identified by obtaining gene expression profiles of the genes
encoding the proteins using genomic techniques including but not
limited to DNA microarray analysis, serial analysis of gene
expression (SAGE), and quantitative real-time polymerase chain
reaction (Q-PCR).
[0379] Non limiting examples of disease states or disorders that
may be associated with proteins associated with ASD include autism,
Asperger syndrome (AS), pervasive developmental disorder-not
otherwise specified (PDD-NOS), Rett's syndrome, tuberous sclerosis,
phenylketonuria, Smith-Lemli-Opitz syndrome and fragile X syndrome.
By way of non-limiting example, proteins associated with ASD
include but are not limited to the following proteins: ATP10C
aminophospholipid-MET MET receptor transporting ATPase tyrosine
kinase (ATP10C) BZRAP1 MGLUR5 (GRM5) Metabotropic glutamate
receptor 5 (MGLUR5) CDH10 Cadherin-10 MGLUR6 (GRM6) Metabotropic
glutamate receptor 6 (MGLUR6) CDH9 Cadherin-9 NLGN1 Neuroligin-1
CNTN4 Contactin-4 NLGN2 Neuroligin-2 CNTNAP2 Contactin-associated
SEMA5A Neuroligin-3 protein-like 2 (CNTNAP2) DHCR7
7-dehydrocholesterol NLGN4X Neuroligin-4X-reductase (DHCR7) linked
DOC2A Double C2-like domain--NLGN4Y Neuroligin-4 Y--containing
protein alpha linked DPP6 Dipeptidyl NLGN5 Neuroligin-5
aminopeptidase-like protein 6 EN2 engrailed 2 (EN2) NRCAM Neuronal
cell adhesion molecule (NRCAM) MDGA2 fragile X mental retardation
NRXN1 Neurexin-1 1 (MDGA2) FMR2 (AFF2) AF4/FMR2 family member
20R4M2 Olfactory receptor (AFF2) 4M2 FOXP2 Forkhead box protein P2
OR4N4 Olfactory receptor (FOXP2) 4N4 FXR1Fragile X mental OXTR
oxytocin receptor retardation, autosomal (OXTR) homolog 1 (FXR1)
FXR2 Fragile X mental PAH phenylalanine retardation, autosomal
hydroxylase (PAH) homolog 2 (FXR2) GABRA1 Gamma-aminobutyric acid
PTEN Phosphatase and receptor subunit alpha-1 tensin homologue
(GABRA1) (PTEN) GABRA5 GABAA (.gamma.-aminobutyric PTPRZ1
Receptor-type acid) receptor alpha 5 tyrosine-protein subunit
(GABRAS) phosphatase zeta (PTPRZ1) GABRB1 Gamma-aminobutyric acid
RELN Reelin receptor subunit beta-1 (GABRB1) GABRB3 GABAA
(.gamma.-aminobutyric RPL10 60S ribosomal acid) receptor .beta.3
subunit protein L10 (GABRB3) GABRG1 Gamma-aminobutyric acid SEMA5A
Semaphorin-5A receptor subunit gamma-1 (SEMA5A) (GABRG1) HIRIP3
HIRA-interacting protein 3 SEZ6L2 seizure related 6 homolog
(mouse)-like 2 HOXA1 Homeobox protein Hox-A1 SHANK3 SH3 and
multiple (HOXA1) ankyrin repeat domains 3 (SHANK3) IL6
Interleukin-6 SHBZRAP1 SH3 and multiple ankyrin repeat domains 3
(SHBZRAP1) LAMB1 Laminin subunit beta-1 SLC6A4 Serotonin (LAMB1)
transporter (SERT) MAPK3 Mitogen-activated protein TAS2R1Taste
receptor kinase 3 type 2 member 1 TAS2R1 MAZ Myc-associated zinc
finger TSC1 Tuberous sclerosis protein protein 1 MDGA2 MAM domain
containing TSC2 Tuberous sclerosis glycosylphosphatidylinositol
protein 2 anchor 2 (MDGA2) MECP2 Methyl CpG binding UBE3A Ubiquitin
protein protein 2 (MECP2) ligase E3A (UBE3A) MECP2 methyl CpG
binding WNT2 Wingless-type protein 2 (MECP2) MMTV integration site
family, member 2 (WNT2)
[0380] The identity of the protein associated with ASD whose
chromosomal sequence is edited can and will vary. In preferred
embodiments, the proteins associated with ASD whose chromosomal
sequence is edited may be the benzodiazapine receptor (peripheral)
associated protein 1 (BZRAP1) encoded by the BZRAP1 gene, the
AF4/FMR2 family member 2 protein (AFF2) encoded by the AFF2 gene
(also termed MFR2), the fragile X mental retardation autosomal
homolog 1 protein (FXR1) encoded by the FXR1 gene, the fragile X
mental retardation autosomal homolog 2 protein (FXR2) encoded by
the FXR2 gene, the MAM domain containing
glycosylphosphatidylinositol anchor 2 protein (MDGA2) encoded by
the MDGA2 gene, the methyl CpG binding protein 2 (MECP2) encoded by
the MECP2 gene, the metabotropic glutamate receptor 5 (MGLURS)
encoded by the MGLUR5-1 gene (also termed GRM5), the neurexin 1
protein encoded by the NRXN1 gene, or the semaphorin-5A protein
(SEMA5A) encoded by the SEMA5A gene. In an exemplary embodiment,
the genetically modified animal is a rat, and the edited
chromosomal sequence encoding the protein associated with ASD is as
listed below: BZRAP1 benzodiazapine receptor XM.sub.--002727789,
(peripheral) associated XM.sub.--213427, protein 1 (BZRAP1)
XM.sub.--002724533, XM.sub.--001081125 AFF2 (FMR2) AF4/FMR2 family
member 2 XM.sub.--219832, (AFF2) XM.sub.--001054673 FXR1Fragile X
mental NM.sub.--001012179 retardation, autosomal homolog 1 (FXR1)
FXR2Fragile X mental NM.sub.--001100647 retardation, autosomal
homolog 2 (FXR2) MDGA2 MAM domain containing NM.sub.--199269
glycosylphosphatidylinositol anchor 2 (MDGA2) MECP2 Methyl CpG
binding NM.sub.--022673 protein 2 (MECP2) MGLUR5Metabotropic
glutamate NM.sub.--017012 (GRM5) receptor 5 (MGLUR5) NRXN1
Neurexin-1 NM.sub.--021767 SEMA5A Semaphorin-5A (SEMA5A)
NM.sub.--001107659
[0381] Exemplary animals or cells may comprise one, two, three,
four, five, six, seven, eight, or nine or more inactivated
chromosomal sequences encoding a protein associated with ASD, and
zero, one, two, three, four, five, six, seven, eight, nine or more
chromosomally integrated sequences encoding proteins associated
with ASD. The edited or integrated chromosomal sequence may be
modified to encode an altered protein associated with ASD.
Non-limiting examples of mutations in proteins associated with ASD
include the L18Q mutation in neurexin 1 where the leucine at
position 18 is replaced with a glutamine, the R451c mutation in
neuroligin 3 where the arginine at position 451 is replaced with a
cysteine, the R87W mutation in neuroligin 4 where the arginine at
position 87 is replaced with a tryptophan, and the I425V mutation
in serotonin transporter where the isoleucine at position 425 is
replaced with a valine. A number of other mutations and chromosomal
rearrangements in ASD-related chromosomal sequences have been
associated with ASD and are known in the art. See, for example,
Freitag et al. (2010) Eur. Child. Adolesc. Psychiatry 19:169-178,
and Bucan et al. (2009) PLoS Genetics 5: e1000536, the disclosure
of which is incorporated by reference herein in its entirety.
[0382] Examples of proteins associated with Parkinson's disease
include but are not limited to .alpha.-synuclein, DJ-1, LRRK2,
PINK1, Parkin, UCHL1, Synphilin-1, and NURR1.
[0383] Examples of addiction-related proteins may include ABAT for
example.
[0384] Examples of inflammation-related proteins may include the
monocyte chemoattractant protein-1 (MCP1) encoded by the Ccr2 gene,
the C-C chemokine receptor type 5 (CCR5) encoded by the Ccr5 gene,
the IgG receptor IIB (FCGR2b, also termed CD32) encoded by the
Fcgr2b gene, or the Fc epsilon R1g (FCER1g) protein encoded by the
Fcer1g gene, for example.
[0385] Examples of cardiovascular diseases associated proteins may
include IL1B (interleukin 1, beta), XDH (xanthine dehydrogenase),
TP53 (tumor protein p53), PTGIS (prostaglandin 12 (prostacyclin)
synthase). MB (myoglobin), IL4 (interleukin 4), ANGPT1
(angiopoietin 1), ABCG8 (ATP-binding cassette, sub-family G
(WHITE), member 8), or CTSK (cathepsin K), for example.
[0386] For example, US Patent Publication No. 20110023153,
describes use of zinc finger nucleases to genetically modify cells,
animals and proteins associated with Alzheimer's Disease. Once
modified cells and animals may be further tested using known
methods to study the effects of the targeted mutations on the
development and/or progression of AD using measures commonly used
in the study of AD--such as, without limitation, learning and
memory, anxiety, depression, addiction, and sensory motor functions
as well as assays that measure behavioral, functional,
pathological, metaboloic and biochemical function.
[0387] The present disclosure comprises editing of any chromosomal
sequences that encode proteins associated with AD. The AD-related
proteins are typically selected based on an experimental
association of the AD-related protein to an AD disorder. For
example, the production rate or circulating concentration of an
AD-related protein may be elevated or depressed in a population
having an AD disorder relative to a population lacking the AD
disorder. Differences in protein levels may be assessed using
proteomic techniques including but not limited to Western blot,
immunohistochemical staining, enzyme linked immunosorbent assay
(ELISA), and mass spectrometry. Alternatively, the AD-related
proteins may be identified by obtaining gene expression profiles of
the genes encoding the proteins using genomic techniques including
but not limited to DNA microarray analysis, serial analysis of gene
expression (SAGE), and quantitative real-time polymerase chain
reaction (Q-PCR).
[0388] Examples of Alzheimer's disease associated proteins may
include the very low density lipoprotein receptor protein (VLDLR)
encoded by the VLDLR gene, the ubiquitin-like modifier activating
enzyme 1 (UBA1) encoded by the UBA1 gene, or the NEDD8-activating
enzyme E1 catalytic subunit protein (UBE1C) encoded by the UBA3
gene, for example.
[0389] By way of non-limiting example, proteins associated with AD
include but are not limited to the proteins listed as follows:
Chromosomal Sequence Encoded Protein ALAS2 Delta-aminolevulinate
synthase 2 (ALAS2) ABCA1 ATP-binding cassette transporter (ABCA1)
ACE Angiotensin 1-converting enzyme (ACE) APOE Apolipoprotein E
precursor (APOE) APP amyloid precursor protein (APP) AQP1 aquaporin
1 protein (AQP1) BIN1 Myc box-dependent-interacting protein 1 or
bridging integrator 1 protein (BIN1) BDNF brain-derived
neurotrophic factor (BDNF) BTNL8 Butyrophilin-like protein 8
(BTNL8) C1ORF49 chromosome 1 open reading frame 49 CDH4 Cadherin-4
CHRNB2 Neuronal acetylcholine receptor subunit beta-2 CKLFSF2
CKLF-like MARVEL transmembrane domain-containing protein 2
(CKLFSF2) CLEC4E C-type lectin domain family 4, member e (CLEC4E)
CLU clusterin protein (also known as apoplipoprotein J) CR1
Erythrocyte complement receptor 1 (CR1, also known as CD35, C3b/C4b
receptor and immune adherence receptor) CR1L Erythrocyte complement
receptor 1 (CR1L) CSF3R granulocyte colony-stimulating factor 3
receptor (CSF3R) CST3 Cystatin C or cystatin 3 CYP2C Cytochrome
P450 2C DAPK1 Death-associated protein kinase 1 (DAPK1) ESR1
Estrogen receptor 1 FCAR Fc fragment of IgA receptor (FCAR, also
known as CD89) FCGR3B Fc fragment of IgG, low affinity IIIb,
receptor (FCGR3B or CD16b) FFA2 Free fatty acid receptor 2 (FFA2)
FGA Fibrinogen (Factor I) GAB2 GRB2-associated-binding protein 2
(GAB2) GAB2 GRB2-associated-binding protein 2 (GAB2) GALP
Galanin-like peptide GAPDHS Glyceraldehyde-3-phosphate
dehydrogenase, spermatogenic (GAPDHS) GMPB GMBP HP Haptoglobin (HP)
HTR75-hydroxytryptamine (serotonin) receptor 7 (adenylate
cyclase-coupled) IDE Insulin degrading enzyme IF127 IF127 IF16
Interferon, alpha-inducible protein 6 (IF16) IFIT2
Interferon-induced protein with tetratricopeptide repeats 2 (IFIT2)
IL1RN interleukin-1 receptor antagonist (IL-RA) IL8RA Interleukin 8
receptor, alpha (IL8RA or CD181) IL8RB Interleukin 8 receptor, beta
(IL8RB) JAG1 Jagged 1 (JAG1) KCNJ15 Potassium inwardly-rectifying
channel, subfamily J, member 15 (KCNJ15) LRP6 Low-density
lipoprotein receptor-related protein 6 (LRP6) MAPT
microtubule-associated protein tau (MAPT) MARK4 MAP/microtubule
affinity-regulating kinase 4 (MARK4) MPHOSPH1 M-phase
phosphoprotein 1 MTHFR 5,10-methylenetetrahydrofolate reductase MX2
Interferon-induced GTP-binding protein Mx2 NBN Nibrin, also known
as NBN NCSTN Nicastrin NIACR2 Niacin receptor 2 (NIACR2, also known
as GPR109B) NMNAT3 nicotinamide nucleotide adenylyltransferase 3
NTM Neurotrimin (or HNT) ORM1 Orosmucoid 1 (ORM1) or Alpha-1-acid
glycoprotein 1 P2RY13 P2Y purinoceptor 13 (P2RY13) PBEF1
Nicotinamide phosphoribosyltransferase (NAmPRTase or Nampt) also
known as pre-B-cell colony-enhancing factor 1 (PBEF1) or visfatin
PCK1 Phosphoenolpyruvate carboxykinase PICALM phosphatidylinositol
binding clathrin assembly protein (PICALM) PLAU Urokinase-type
plasminogen activator (PLAU) PLXNC1 Plexin C1 (PLXNC1) PRNP Prion
protein PSEN1 presenilin 1 protein (PSEN1) PSEN2 presenilin 2
protein (PSEN2) PTPRA protein tyrosine phosphatase receptor type A
protein (PTPRA) RALGPS2 RAl GEF with PH domain and SH3 binding
motif 2 (RALGPS2) RGSL2 regulator of G-protein signaling like 2
(RGSL2) SELENBP1 Selenium binding protein 1 (SELNBP1) SLC25A37
Mitoferrin-1 SORL1 sortilin-related receptor L(DLR class) A
repeats-containing protein (SORL1) TF Transferrin TFAM
Mitochondrial transcription factor A TNF Tumor necrosis factor
TNFRSF10C Tumor necrosis factor receptor superfamily member 10C
(TNFRSF10C) TNFSF10 Tumor necrosis factor receptor superfamily,
(TRAIL) member 10a (TNFSF10) UBA1 ubiquitin-like modifier
activating enzyme 1 (UBA1) UBA3 NEDD8-activating enzyme E1
catalytic subunit protein (UBE1C) UBB ubiquitin B protein (UBB)
UBQLN1 Ubiquilin-1 UCHL1 ubiquitin carboxyl-terminal esterase L1
protein (UCHL1) UCHL3 ubiquitin carboxyl-terminal hydrolase isozyme
L3 protein (UCHL3) VLDLR very low density lipoprotein receptor
protein (VLDLR)
[0390] In exemplary embodiments, the proteins associated with AD
whose chromosomal sequence is edited may be the very low density
lipoprotein receptor protein (VLDLR) encoded by the VLDLR gene, the
ubiquitin-like modifier activating enzyme 1 (UBA1) encoded by the
UBA1 gene, the NEDD8-activating enzyme E1 catalytic subunit protein
(UBE1C) encoded by the UBA3 gene, the aquaporin 1 protein (AQP1)
encoded by the AQP1 gene, the ubiquitin carboxyl-terminal esterase
L1 protein (UCHL1) encoded by the UCHL1 gene, the ubiquitin
carboxyl-terminal hydrolase isozyme L3 protein (UCHL3) encoded by
the UCHL3 gene, the ubiquitin B protein (UBB) encoded by the UBB
gene, the microtubule-associated protein tau (MAPT) encoded by the
MAPT gene, the protein tyrosine phosphatase receptor type A protein
(PTPRA) encoded by the PTPRA gene, the phosphatidylinositol binding
clathrin assembly protein (PICALM) encoded by the PICALM gene, the
clusterin protein (also known as apoplipoprotein J) encoded by the
CLU gene, the presenilin 1 protein encoded by the PSEN1 gene, the
presenilin 2 protein encoded by the PSEN2 gene, the
sortilin-related receptor L(DLR class) A repeats-containing protein
(SORL1) protein encoded by the SORL1 gene, the amyloid precursor
protein (APP) encoded by the APP gene, the Apolipoprotein E
precursor (APOE) encoded by the APOE gene, or the brain-derived
neurotrophic factor (BDNF) encoded by the BDNF gene. In an
exemplary embodiment, the genetically modified animal is a rat, and
the edited chromosomal sequence encoding the protein associated
with AD is as as follows: APP amyloid precursor protein (APP)
NM.sub.--019288 AQP1 aquaporin 1 protein (AQP1) NM.sub.--012778
BDNF Brain-derived neurotrophic factor NM.sub.--012513 CLU
clusterin protein (also known as NM.sub.--053021 apoplipoprotein J)
MAPT microtubule-associated protein NM.sub.--017212 tau (MAPT)
PICALM phosphatidylinositol binding NM.sub.--053554 clathrin
assembly protein (PICALM) PSEN1 presenilin 1 protein (PSEN1)
NM.sub.--019163 PSEN2 presenilin 2 protein (PSEN2) NM.sub.--031087
PTPRA protein tyrosine phosphatase NM.sub.--012763 receptor type A
protein (PTPRA) SOR1 sortilin-related receptor L(DLR
NM.sub.--053519, class) A repeats-containing XM.sub.--001065506,
protein (SORL1) XM.sub.--217115 UBA1 ubiquitin-like modifier
activating NM.sub.--001014080 enzyme 1 (UBA1) UBA3 NEDD8-activating
enzyme E1 NM.sub.--057205 catalytic subunit protein (UBE1C) UBB
ubiquitin B protein (UBB) NM.sub.--138895 UCHL1 ubiquitin
carboxyl-terminal NM.sub.--017237 esterase L1 protein (UCHL1) UCHL3
ubiquitin carboxyl-terminal NM.sub.--001110165 hydrolase isozyme L3
protein (UCHL3) VLDLR very low density lipoprotein NM.sub.--013155
receptor protein (VLDLR)
[0391] The animal or cell may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15 or more disrupted chromosomal sequences
encoding a protein associated with AD and zero, 1, 2, 3, 4, 5, 6,
7, 8, 9, 10, 11, 12, 13, 14, 15 or more chromosomally integrated
sequences encoding a protein associated with AD.
[0392] The edited or integrated chromosomal sequence may be
modified to encode an altered protein associated with AD. A number
of mutations in AD-related chromosomal sequences have been
associated with AD. For instance, the V7171 (i.e. valine at
position 717 is changed to isoleucine) missense mutation in APP
causes familial AD. Multiple mutations in the presenilin-1 protein,
such as H163R (i.e. histidine at position 163 is changed to
arginine), A246E (i.e. alanine at position 246 is changed to
glutamate), L286V (i.e. leucine at position 286 is changed to
valine) and C410Y (i.e. cysteine at position 410 is changed to
tyrosine) cause familial Alzheimer's type 3. Mutations in the
presenilin-2 protein, such as N141 I (i.e. asparagine at position
141 is changed to isoleucine), M239V (i.e. methionine at position
239 is changed to valine), and D439A (i.e. aspartate at position
439 is changed to alanine) cause familial Alzheimer's type 4. Other
associations of genetic variants in AD-associated genes and disease
are known in the art. See, for example, Waring et al. (2008) Arch.
Neurol. 65:329-334, the disclosure of which is incorporated by
reference herein in its entirety.
[0393] Examples of proteins associated Autism Spectrum Disorder may
include the benzodiazapine receptor (peripheral) associated protein
1 (BZRAP1) encoded by the BZRAP1 gene, the AF4/FMR2 family member 2
protein (AFF2) encoded by the AFF2 gene (also termed MFR2), the
fragile X mental retardation autosomal homolog 1 protein (FXR1)
encoded by the FXR1 gene, or the fragile X mental retardation
autosomal homolog 2 protein (FXR2) encoded by the FXR2 gene, for
example.
[0394] Examples of proteins associated Macular Degeneration may
include the ATP-binding cassette, sub-family A (ABC1) member 4
protein (ABCA4) encoded by the ABCR gene, the apolipoprotein E
protein (APOE) encoded by the APOE gene, or the chemokine (C-C
motif) Ligand 2 protein (CCL2) encoded by the CCL2 gene, for
example.
[0395] Examples of proteins associated Schizophrenia may include
NRG1, ErbB4, CPLX1, TPH1, TPH2, NRXN1, GSK3A, BDNF, DISC1, GSK3B,
and combinations thereof.
[0396] Examples of proteins involved in tumor suppression may
include ATM (ataxia telangiectasia mutated), ATR (ataxia
telangiectasia and Rad3 related), EGFR (epidermal growth factor
receptor), ERBB2 (v-erb-b2 erythroblastic leukemia viral oncogene
homolog 2), ERBB3 (v-erb-b2 erythroblastic leukemia viral oncogene
homolog 3), ERBB4 (v-erb-b2 erythroblastic leukemia viral oncogene
homolog 4), Notch 1, Notch2, Notch 3, or Notch 4, for example.
[0397] Examples of proteins associated with a secretase disorder
may include PSENEN (presenilin enhancer 2 homolog (C. elegans)),
CTSB (cathepsin B), PSEN1 (presenilin 1), APP (amyloid beta (A4)
precursor protein), APH1B (anterior pharynx defective I homolog B
(C. elegans)), PSEN2 (presenilin 2 (Alzheimer disease 4)), or BACE
(beta-site APP-cleaving enzyme 1), for example.
[0398] For example, US Patent Publication No. 20110023146,
describes use of zinc finger nucleases to genetically modify cells,
animals and proteins associated with secretase-associated
disorders. Secretases are essential for processing pre-proteins
into their biologically active forms. Defects in various components
of the secretase pathways contribute to many disorders,
particularly those with hallmark amyloidogenesis or amyloid
plaques, such as Alzheimer's disease (AD).
[0399] A secretase disorder and the proteins associated with these
disorders are a diverse set of proteins that effect susceptibility
for numerous disorders, the presence of the disorder, the severity
of the disorder, or any combination thereof. The present disclosure
comprises editing of any chromosomal sequences that encode proteins
associated with a secretase disorder. The proteins associated with
a secretase disorder are typically selected based on an
experimental association of the secretase-related proteins with the
development of a secretase disorder. For example, the production
rate or circulating concentration of a protein associated with a
secretase disorder may be elevated or depressed in a population
with a secretase disorder relative to a population without a
secretase disorder. Differences in protein levels may be assessed
using proteomic techniques including but not limited to Western
blot, immunohistochemical staining, enzyme linked immunosorbent
assay (ELISA), and mass spectrometry. Alternatively, the protein
associated with a secretase disorder may be identified by obtaining
gene expression profiles of the genes encoding the proteins using
genomic techniques including but not limited to DNA microarray
analysis, serial analysis of gene expression (SAGE), and
quantitative real-time polymerase chain reaction (Q-PCR).
[0400] By way of non-limiting example, proteins associated with a
secretase disorder include PSENEN (presenilin enhancer 2 homolog
(C. elegans)), CTSB (cathepsin B), PSEN1 (presenilin 1), APP
(amyloid beta (A4) precursor protein), APH1B (anterior pharynx
defective 1 homolog B (C. elegans)), PSEN2 (presenilin 2 (Alzheimer
disease 4)), BACE1 (beta-site APP-cleaving enzyme 1), ITM2B
(integral membrane protein 2B), CTSD (cathepsin D), NOTCH1 (Notch
homolog 1, translocation-associated (Drosophila)), TNF (tumor
necrosis factor (TNF superfamily, member 2)), INS (insulin), DYT10
(dystonia 10), ADAM17 (ADAM metallopeptidase domain 17), APOE
(apolipoprotein E), ACE (angiotensin I converting enzyme
(peptidyl-dipeptidase A) 1), STN (statin), TP53 (tumor protein
p53), IL6 (interleukin 6 (interferon, beta 2)), NGFR (nerve growth
factor receptor (TNFR superfamily, member 16)), IL1B (interleukin
1, beta), ACHE (acetylcholinesterase (Yt blood group)), CTNNB1
(catenin (cadherin-associated protein), beta 1, 88 kDa), IGF1
(insulin-like growth factor 1 (somatomedin C)), IFNG (interferon,
gamma), NRG1 (neuregulin 1), CASP3 (caspase 3, apoptosis-related
cysteine peptidase), MAPK1 (mitogen-activated protein kinase 1),
CDH1 (cadherin 1, type 1, E-cadherin (epithelial)), APBB1 (amyloid
beta (A4) precursor protein-binding, family B, member 1 (Fe65)),
HMGCR (3-hydroxy-3-methylglutaryl-Coenzyme A reductase). CREB1
(cAMP responsive element binding protein 1), PTGS2
(prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase
and cyclooxygenase)), HES1 (hairy and enhancer of split 1,
(Drosophila)), CAT (catalase), TGFB1 (transforming growth factor,
beta 1), ENO2 (enolase 2 (gamma, neuronal)), ERBB4 (v-erb-a
erythroblastic leukemia viral oncogene homolog 4 (avian)), TRAPPC10
(trafficking protein particle complex 10), MAOB (monoamine oxidase
B), NGF (nerve growth factor (beta polypeptide)), MMP12 (matrix
metallopeptidase 12 (macrophage elastase)), JAG1 (jagged 1
(Alagille syndrome)), CD40LG (CD40 ligand), PPARG (peroxisome
proliferator-activated receptor gamma), FGF2 (fibroblast growth
factor 2 (basic)), IL3 (interleukin 3 (colony-stimulating factor,
multiple)), LRP1 (low density lipoprotein receptor-related protein
1), NOTCH4 (Notch homolog 4 (Drosophila)), MAPK8 (mitogen-activated
protein kinase 8), PREP (prolyl endopeptidase), NOTCH3 (Notch
homolog 3 (Drosophila)), PRNP (prion protein), CTSG (cathepsin G),
EGF (epidermal growth factor (beta-urogastrone)), REN (renin), CD44
(CD44 molecule (Indian blood group)), SELP (selectin P (granule
membrane protein 140 kDa, antigen CD62)), GHR (growth hormone
receptor), ADCYAP1 (adenylate cyclase activating polypeptide 1
(pituitary)), INSR (insulin receptor), GFAP (glial fibrillary
acidic protein), MMP3 (matrix metallopeptidase 3 (stromelysin 1,
progelatinase)), MAPK10 (mitogen-activated protein kinase 10), SP
(Sp 1 transcription factor), MYC (v-myc myelocytomatosis viral
oncogene homolog (avian)), CTSE (cathepsin E), PPARA (peroxisome
proliferator-activated receptor alpha), JUN (jun oncogene), TIMP1
(TIMP metallopeptidase inhibitor 1), IL5 (interleukin 5
(colony-stimulating factor, eosinophil)), IL1A (interleukin 1,
alpha), MMP9 (matrix metallopeptidase 9 (gelatinase B, 92 kDa
gelatinase, 92 kDa type IV collagenase)), HTR4 (5-hydroxytryptamine
(serotonin) receptor 4), HSPG2 (heparan sulfate proteoglycan 2),
KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog), CYCS
(cytochrome c, somatic), SMG1 (SMG1 homolog, phosphatidylinositol
3-kinase-related kinase (C. elegans)), IL1R1 (interleukin 1
receptor, type 1), PROK1 (prokineticin 1), MAPK3 (mitogen-activated
protein kinase 3), NTRK1 (neurotrophic tyrosine kinase, receptor,
type 1), IL13 (interleukin 13), MME (membrane
metallo-endopeptidase), TKT (transketolase), CXCR2 (chemokine
(C-X-C motif) receptor 2), IGF1R (insulin-like growth factor 1
receptor), RARA (retinoic acid receptor, alpha), CREBBP (CREB
binding protein), PTGS1 (prostaglandin-endoperoxide synthase 1
(prostaglandin G/H synthase and cyclooxygenase)), GALT
(galactose-1-phosphate uridylyltransferase), CHRM1 (cholinergic
receptor, muscarinic 1), ATXN1 (ataxin 1), PAWR (PRKC, apoptosis,
WT1, regulator), NOTCH2 (Notch homolog 2 (Drosophila)), M6PR
(mannose-6-phosphate receptor (cation dependent)), CYP46A1
(cytochrome P450, family 46, subfamily A, polypeptide 1), CSNK1 D
(casein kinase 1, delta), MAPK14 (mitogen-activated protein kinase
14), PRG2 (proteoglycan 2, bone marrow (natural killer cell
activator, eosinophil granule major basic protein)), PRKCA (protein
kinase C, alpha), L1 CAM (L1 cell adhesion molecule), CD40 (CD40
molecule, TNF receptor superfamily member 5), NR1I2 (nuclear
receptor subfamily 1, group I, member 2), JAG2 (jagged 2), CTNND1
(catenin (cadherin-associated protein), delta 1), CDH2 (cadherin 2,
type 1, N-cadherin (neuronal)), CMA1 (chymase 1, mast cell), SORT1
(sortilin 1), DLK1 (delta-like 1 homolog (Drosophila)), THEM4
(thioesterase superfamily member 4), JUP (junction plakoglobin),
CD46 (CD46 molecule, complement regulatory protein), CCL11
(chemokine (C-C motif) ligand 11), CAV3 (caveolin 3), RNASE3
(ribonuclease, RNase A family, 3 (eosinophil cationic protein)),
HSPA8 (heat shock 70 kDa protein 8), CASP9 (caspase 9,
apoptosis-related cysteine peptidase), CYP3A4 (cytochrome P450,
family 3, subfamily A, polypeptide 4), CCR3 (chemokine (C-C motif)
receptor 3), TFAP2A (transcription factor AP-2 alpha (activating
enhancer binding protein 2 alpha)), SCP2 (sterol carrier protein
2), CDK4 (cyclin-dependent kinase 4), HIF1A (hypoxia inducible
factor 1, alpha subunit (basic helix-loop-helix transcription
factor)), TCF7L2 (transcription factor 7-like 2 (T-cell specific,
HMG-box)), IL1R2 (interleukin 1 receptor, type II), B3GALTL (beta
1,3-galactosyltransferase-like), MDM2 (Mdm2 p53 binding protein
homolog (mouse)), RELA (v-rel reticuloendotheliosis viral oncogene
homolog A (avian)), CASP7 (caspase 7, apoptosis-related cysteine
peptidase), IDE (insulin-degrading enzyme), FABP4 (fatty acid
binding protein 4, adipocyte), CASK (calcium/calmodulin-dependent
serine protein kinase (MAGUK family)), ADCYAP1R1 (adenylate cyclase
activating polypeptide 1 (pituitary) receptor type I), ATF4
(activating transcription factor 4 (tax-responsive enhancer element
B67)), PDGFA (platelet-derived growth factor alpha polypeptide),
C21 or f33 (chromosome 21 open reading frame 33), SCG5
(secretogranin V (7B2 protein)), RNF123 (ring finger protein 123),
NFKB1 (nuclear factor of kappa light polypeptide gene enhancer in
B-cells 1), ERBB2 (v-erb-b2 erythroblastic leukemia viral oncogene
homolog 2, neuro/glioblastoma derived oncogene homolog (avian)),
CAV1 (caveolin 1, caveolae protein, 22 kDa), MMP7 (matrix
metallopeptidase 7 (matrilysin, uterine)), TGFA (transforming
growth factor, alpha), RXRA (retinoid X receptor, alpha), STX1A
(syntaxin 1A (brain)), PSMC4 (proteasome (prosome, macropain) 26S
subunit, ATPase, 4), P2RY2 (purinergic receptor P2Y, G-protein
coupled, 2), TNFRSF21 (tumor necrosis factor receptor superfamily,
member 21). DLG1 (discs, large homolog 1 (Drosophila)), NUMBL (numb
homolog (Drosophila)-like), SPN (sialophorin), PLSCR1 (phospholipid
scramblase 1), UBQLN2 (ubiquilin 2), UBQLN1 (ubiquilin 1), PCSK7
(proprotein convertase subtilisin/kexin type 7), SPON1 (spondin 1,
extracellular matrix protein), SILV (silver homolog (mouse)), QPCT
(glutaminyl-peptide cyclotransferase), HESS (hairy and enhancer of
split 5 (Drosophila)), GCC1 (GRIP and coiled-coil domain containing
1), and any combination thereof.
[0401] The genetically modified animal or cell may comprise 1, 2,
3, 4, 5, 6, 7, 8, 9, 10 or more disrupted chromosomal sequences
encoding a protein associated with a secretase disorder and zero,
1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more chromosomally integrated
sequences encoding a disrupted protein associated with a secretase
disorder.
[0402] Examples of proteins associated with Amyotrophic Lateral
Sclerosis may include SOD1 (superoxide dismutase 1), ALS2
(amyotrophic lateral sclerosis 2), FUS (fused in sarcoma), TARDBP
(TAR DNA binding protein), VAGFA (vascular endothelial growth
factor A), VAGFB (vascular endothelial growth factor B), and VAGFC
(vascular endothelial growth factor C), and any combination
thereof.
[0403] For example, US Patent Publication No. 20110023144,
describes use of zinc finger nucleases to genetically modify cells,
animals and proteins associated with amyotrophyic lateral sclerosis
(ALS) disease. ALS is characterized by the gradual steady
degeneration of certain nerve cells in the brain cortex, brain
stem, and spinal cord involved in voluntary movement.
[0404] Motor neuron disorders and the proteins associated with
these disorders are a diverse set of proteins that effect
susceptibility for developing a motor neuron disorder, the presence
of the motor neuron disorder, the severity of the motor neuron
disorder or any combination thereof. The present disclosure
comprises editing of any chromosomal sequences that encode proteins
associated with ALS disease, a specific motor neuron disorder. The
proteins associated with ALS are typically selected based on an
experimental association of ALS-related proteins to ALS. For
example, the production rate or circulating concentration of a
protein associated with ALS may be elevated or depressed in a
population with ALS relative to a population without ALS.
Differences in protein levels may be assessed using proteomic
techniques including but not limited to Western blot,
immunohistochemical staining, enzyme linked immunosorbent assay
(ELISA), and mass spectrometry. Alternatively, the proteins
associated with ALS may be identified by obtaining gene expression
profiles of the genes encoding the proteins using genomic
techniques including but not limited to DNA microarray analysis,
serial analysis of gene expression (SAGE), and quantitative
real-time polymerase chain reaction (Q-PCR).
[0405] By way of non-limiting example, proteins associated with ALS
include but are not limited to the following proteins: SOD1
superoxide dismutase 1, ALS3 amyotrophic lateral soluble sclerosis
3 SETX senataxin ALS5 amyotrophic lateral sclerosis 5 FUS fused in
sarcoma ALS7 amyotrophic lateral sclerosis 7 ALS2 amyotrophic
lateral DPP6 Dipeptidyl-peptidase 6 sclerosis 2 NEFH neurofilament,
heavy PTGS1 prostaglandin-polypeptide endoperoxide synthase 1
SLC1A2 solute carrier family 1 TNFRSF10B tumor necrosis factor
(glial high affinity receptor superfamily, glutamate transporter),
member 10b member 2 PRPH peripherin HSP90AA1 heat shock protein 90
kDa alpha (cytosolic), class A member 1 GRIA2 glutamate receptor,
IFNG interferon, gamma ionotropic, AMPA 2 S100B S100 calcium
binding FGF2 fibroblast growth factor 2 protein B AOX1 aldehyde
oxidase 1 CS citrate synthase TARDBP TAR DNA binding protein TXN
thioredoxin RAPH1 Ras association MAP3K5 mitogen-activated protein
(RaIGDS/AF-6) and kinase 5 pleckstrin homology domains 1 NBEAL1
neurobeachin-like 1 GPX1 glutathione peroxidase 1 ICA1L islet cell
autoantigen RAC1 ras-related C3 botulinum 1.69 kDa-like toxin
substrate 1 MAPT microtubule-associated ITPR2 inositol
1,4,5-protein tau triphosphate receptor, type 2 ALS2CR4 amyotrophic
lateral GLS glutaminase sclerosis 2 (juvenile) chromosome region,
candidate 4 ALS2CR8 amyotrophic lateral CNTFR ciliary neurotrophic
factor sclerosis 2 (juvenile) receptor chromosome region, candidate
8 ALS2CR11 amyotrophic lateral FOLH1 folate hydrolase 1 sclerosis 2
(juvenile) chromosome region, candidate 11 FAM117B family with
sequence P4HB prolyl 4-hydroxylase, similarity 117, member B beta
polypeptide CNTF ciliary neurotrophic factor SQSTM1 sequestosome 1
STRADB STE20-related kinase NAIP NLR family, apoptosis adaptor beta
inhibitory protein YWHAQ tyrosine 3-SLC33A1 solute carrier family
33 monooxygenase/tryptoph (acetyl-CoA transporter), an
5-monooxygenase member 1 activation protein, theta polypeptide
TRAK2 trafficking protein, FIG. 4 FIG. 4 homolog, SAC1 kinesin
binding 2 lipid phosphatase domain containing NIF3L1 NIF3 NGG1
interacting INA internexin neuronal factor 3-like 1 intermediate
filament protein, alpha PARD3B par-3 partitioning COX8A cytochrome
c oxidase defective 3 homolog B subunit VIIIA CDK15
cyclin-dependent kinase HECW1 HECT, C2 and WW 15 domain containing
E3 ubiquitin protein ligase 1 NOS1 nitric oxide synthase 1 MET met
proto-oncogene SOD2 superoxide dismutase 2, HSPB1 heat shock 27 kDa
mitochondrial protein 1 NEFL neurofilament, light CTSB cathepsin B
polypeptide ANG angiogenin, HSPA8 heat shock 70 kDa ribonuclease,
RNase A protein 8 family, 5 VAPB VAMP (vesicle-ESR1 estrogen
receptor 1 associated membrane protein)-associated protein B and C
SNCA synuclein, alpha HGF hepatocyte growth factor CAT catalase
ACTB actin, beta NEFM neurofilament, medium TH tyrosine hydroxylase
polypeptide BCL2 B-cell CLL/lymphoma 2 FAS Fas (TNF receptor
superfamily, member 6) CASP3 caspase 3, apoptosis-CLU clusterin
related cysteine peptidase SMN1 survival of motor neuron G6PD
glucose-6-phosphate 1, telomeric dehydrogenase BAX BCL2-associated
X HSF1 heat shock transcription protein factor 1 RNF19A ring finger
protein 19A JUN jun oncogene ALS2CR12 amyotrophic lateral HSPA5
heat shock 70 kDa sclerosis 2 (juvenile) protein 5 chromosome
region, candidate 12 MAPK14 mitogen-activated protein IL10
interleukin 10 kinase 14 APEX1 APEX nuclease TXNRD1 thioredoxin
reductase 1 (multifunctional DNA repair enzyme) 1 NOS2 nitric oxide
synthase 2, TIMP1 TIMP metallopeptidase inducible inhibitor 1 CASP9
caspase 9, apoptosis-XIAP X-linked inhibitor of related cysteine
apoptosis peptidase GLG1 golgi glycoprotein 1 EPO erythropoietin
VEGFA vascular endothelial ELN elastin growth factor A GDNF glial
cell derived NFE2L2 nuclear factor (erythroid-neurotrophic factor
derived 2)-like 2 SLC6A3 solute carrier family 6 HSPA4 heat shock
70 kDa (neurotransmitter protein 4 transporter, dopamine), member 3
APOE apolipoprotein E PSMB8 proteasome (prosome, macropain)
subunit, beta type, 8 DCTN1 dynactin 1 TIMP3 TIMP metallopeptidase
inhibitor 3 KIFAP3 kinesin-associated SLC1A1 solute carrier family
1 protein 3 (neuronal/epithelial high affinity glutamate
transporter, system Xag), member 1 SMN2 survival of motor neuron
CCNC cyclin C 2, centromeric MPP4 membrane protein, STUB1 STIP1
homology and U-palmitoylated 4 box containing protein 1 ALS2
amyloid beta (A4) PRDX6 peroxiredoxin 6 precursor protein SYP
synaptophysin CABIN1 calcineurin binding protein 1 CASP1 caspase 1,
apoptosis-GART phosphoribosylglycinami related cysteine de
formyltransferase, peptidase phosphoribosylglycinami de synthetase,
phosphoribosylaminoimidazole synthetase CDK5 cyclin-dependent
kinase 5 ATXN3 ataxin 3 RTN4 reticulon 4 C1QB complement component
1, q subcomponent, B chain VEGFC nerve growth factor HTT huntingtin
receptor PARK7 Parkinson disease 7 XDH xanthine dehydrogenase GFAP
glial fibrillary acidic MAP2 microtubule-associated protein protein
2 CYCS cytochrome c, somatic FCGR3B Fc fragment of IgG, low
affinity IIIb, CCS copper chaperone for UBL5 ubiquitin-like 5
superoxide dismutase MMP9 matrix metallopeptidase SLC18A3 solute
carrier family 18 9 ((vesicular acetylcholine), member 3 TRPM7
transient receptor HSPB2 heat shock 27 kDa potential cation
channel, protein 2 subfamily M, member 7 AKT1 v-akt murine thymoma
DERL1 Der1-like domain family, viral oncogene homolog 1 member 1
CCL2 chemokine (C-C motif) NGRN neugrin, neurite ligand 2 outgrowth
associated GSR glutathione reductase TPPP3 tubulin
polymerization-promoting protein family member 3 APAF1 apoptotic
peptidase BTBD10 BTB (POZ) domain activating factor 1 containing 10
GLUD1 glutamate CXCR4 chemokine (C-X-C motif) dehydrogenase 1
receptor 4 SLCIA3 solute carrier family 1 FLT1 fms-related tyrosine
(glial high affinity glutamate transporter), member 3 kinase 1 PON1
paraoxonase 1 AR androgen receptor LIF leukemia inhibitory factor
ERBB3 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3
LGALS1 lectin, galactoside-CD44 CD44 molecule binding, soluble, 1
TP53 tumor protein p53 TLR3 toll-like receptor 3 GRIA1 glutamate
receptor, GAPDH glyceraldehyde-3-ionotropic, AMPA 1 phosphate
dehydrogenase GRIK1 glutamate receptor, DES desmin ionotropic,
kainate 1 CHAT choline acetyltransferase FLT4 fins-related tyrosine
kinase 4 CHMP2B chromatin modifying BAG1 BCL2-associated protein 2B
athanogene MT3 metallothionein 3 CHRNA4 cholinergic receptor,
nicotinic, alpha 4 GSS glutathione synthetase BAK1
BCL2-antagonist/killer 1 KDR kinase insert domain GSTP1 glutathione
S-transferase receptor (a type III pi 1 receptor tyrosine kinase)
OGG1 8-oxoguanine DNA IL6 interleukin 6 (interferon, glycosylase
beta 2).
[0406] The animal or cell may comprise 1, 2, 3, 4, 5, 6, 7, 8, 9,
10 or more disrupted chromosomal sequences encoding a protein
associated with ALS and zero, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more
chromosomally integrated sequences encoding the disrupted protein
associated with ALS. Preferred proteins associated with ALS include
SOD1 (superoxide dismutase 1), ALS2 (amyotrophic lateral sclerosis
2), FUS (fused in sarcoma), TARDBP (TAR DNA binding protein), VAGFA
(vascular endothelial growth factor A), VAGFB (vascular endothelial
growth factor B), and VAGFC (vascular endothelial growth factor C),
and any combination thereof.
[0407] Examples of proteins associated with prion diseases may
include SOD1 (superoxide dismutase 1), ALS2 (amyotrophic lateral
sclerosis 2), FUS (fused in sarcoma), TARDBP (TAR DNA binding
protein), VAGFA (vascular endothelial growth factor A), VAGFB
(vascular endothelial growth factor B), and VAGFC (vascular
endothelial growth factor C), and any combination thereof.
[0408] Examples of proteins related to neurodegenerative conditions
in prion disorders may include A2M (Alpha-2-Macroglobulin), AATF
(Apoptosis antagonizing transcription factor), ACPP (Acid
phosphatase prostate), ACTA2 (Actin alpha 2 smooth muscle aorta),
ADAM22 (ADAM metallopeptidase domain), ADORA3 (Adenosine A3
receptor), or ADRA1D (Alpha-1D adrenergic receptor for Alpha-1D
adrenoreceptor), for example.
[0409] Examples of proteins associated with Immunodeficiency may
include A2M [alpha-2-macroglobulin]; AANAT [arylalkylamine
N-acetyltransferase]; ABCA1 [ATP-binding cassette, sub-family A
(ABC1), member 1]; ABCA2 [ATP-binding cassette, sub-family A
(ABC1), member 2]; or ABCA3 [ATP-binding cassette, sub-family A
(ABC1), member 3]; for example.
[0410] Examples of proteins associated with Trinucleotide Repeat
Disorders include AR (androgen receptor), FMR1 (fragile X mental
retardation 1), HTT (huntingtin), or DMPK (dystrophia
myotonica-protein kinase), FXN (frataxin), ATXN2 (ataxin 2), for
example.
[0411] Examples of proteins associated with Neurotransmission
Disorders include SST (somatostatin), NOS1 (nitric oxide synthase 1
(neuronal)), ADRA2A (adrenergic, alpha-2A-, receptor), ADRA2C
(adrenergic, alpha-2C-, receptor), TACR1 (tachykinin receptor 1),
or HTR2c (5-hydroxytryptamine (serotonin) receptor 2C), for
example.
[0412] Examples of neurodevelopmental-associated sequences include
A2BP1 [ataxin 2-binding protein 1], AADAT [aminoadipate
aminotransferase], AANAT [arylalkylamine N-acetyltransferase], ABAT
[4-aminobutyrate aminotransferase], ABCA1 [ATP-binding cassette,
sub-family A (ABC1), member 1], or ABCA13 [ATP-binding cassette,
sub-family A (ABC1), member 13], for example.
[0413] Further examples of preferred conditions treatable with the
present system include may be selected from: Aicardi-Goutieres
Syndrome; Alexander Disease; Allan-Herndon-Dudley Syndrome;
POLG-Related Disorders; Alpha-Mannosidosis (Type II and III);
Alstrom Syndrome; Angelman; Syndrome; Ataxia-Telangiectasia;
Neuronal Ceroid-Lipofuscinoses; Beta-Thalassemia; Bilateral Optic
Atrophy and (Infantile) Optic Atrophy Type 1; Retinoblastoma
(bilateral); Canavan Disease; Cerebrooculofacioskeletal Syndrome 1
[COFS1]; Cerebrotendinous Xanthomatosis; Cornelia de Lange
Syndrome; MAPT-Related Disorders; Genetic Prion Diseases; Dravet
Syndrome; Early-Onset Familial Alzheimer Disease; Friedreich Ataxia
[FRDA]; Fryns Syndrome; Fucosidosis; Fukuyama Congenital Muscular
Dystrophy; Galactosialidosis; Gaucher Disease; Organic Acidemias;
Hemophagocytic Lymphohistiocytosis; Hutchinson-Gilford Progeria
Syndrome; Mucolipidosis II; Infantile Free Sialic Acid Storage
Disease; PLA2G6-Associated Neurodegeneration; Jervell and
Lange-Nielsen Syndrome; Junctional Epidermolysis Bullosa;
Huntington Disease; Krabbe Disease (Infantile); Mitochondrial
DNA-Associated Leigh Syndrome and NARP; Lesch-Nyhan Syndrome;
LIS1-Associated Lissencephaly; Lowe Syndrome; Maple Syrup Urine
Disease; MECP2 Duplication Syndrome; ATP7A-Related Copper Transport
Disorders: LAMA2-Related Muscular Dystrophy; Arylsulfatase A
Deficiency; Mucopolysaccharidosis Types I, II or III; Peroxisome
Biogenesis Disorders, Zellweger Syndrome Spectrum;
Neurodegeneration with Brain Iron Accumulation Disorders; Acid
Sphingomyelinase Deficiency; Niemann-Pick Disease Type C; Glycine
Encephalopathy; ARX-Related Disorders; Urea Cycle Disorders;
COL1A1/2-Related Osteogenesis Imperfecta; Mitochondrial DNA
Deletion Syndromes; PLP1-Related Disorders; Perry Syndrome;
Phelan-McDermid Syndrome; Glycogen Storage Disease Type II (Pompe
Disease) (Infantile); MAPT-Related Disorders; MECP2-Related
Disorders; Rhizomelic Chondrodysplasia Punctata Type 1; Roberts
Syndrome; Sandhoff Disease; Schindler Disease--Type 1; Adenosine
Deaminase Deficiency; Smith-Lemli-Opitz Syndrome; Spinal Muscular
Atrophy; Infantile-Onset Spinocerebellar Ataxia; Hexosaminidase A
Deficiency; Thanatophoric Dysplasia Type 1; Collagen Type
VI-Related Disorders; Usher Syndrome Type I; Congenital Muscular
Dystrophy; Wolf-Hirschhorn Syndrome; Lysosomal Acid Lipase
Deficiency; and Xeroderma Pigmentosum.
[0414] As will be apparent, it is envisaged that the present system
can be used to target any polynucleotide sequence of interest. Some
examples of conditions or diseases that might be usefully treated
using the present system are included in the Tables above and
examples of genes currently associated with those conditions are
also provided there. However, the genes exemplified are not
exhaustive.
[0415] For example, "wild type StCas9" refers to wild type Cas9
from S. thermophilus, the protein sequence of which is given in the
SwissProt database under accession number G3ECR1. Similarly, S.
pyogenes Cas9 is included in SwissProt under accession number
Q99ZW2.
[0416] The ability to use CRISPR-Cas systems to perform efficient
and cost effective gene editing and manipulation will allow the
rapid selection and comparison of single and multiplexed genetic
manipulations to transform such genomes for improved production and
enhanced traits. In this regard reference is made to US patents and
publications: U.S. Pat. No. 6,603,061--Agrobacterium-Mediated Plant
Transformation Method; U.S. Pat. No. 7,868,149-Plant Genome
Sequences and Uses Thereof and US 2009/0100536--Transgenic Plants
with Enhanced Agronomic Traits, all the contents and disclosure of
each of which are herein incorporated by reference in their
entirety. In the practice of the invention, the contents and
disclosure of Morrell et al "Crop genomics: advances and
applications" Nat Rev Genet. 2011 Dec. 29; 13(2):85-96 are also
herein incorporated by reference in their entirety.
EXAMPLES
[0417] The following examples are given for the purpose of
illustrating various embodiments of the invention and are not meant
to limit the present invention in any fashion. The present
examples, along with the methods described herein are presently
representative of preferred embodiments, are exemplary, and are not
intended as limitations on the scope of the invention. Changes
therein and other uses which are encompassed within the spirit of
the invention as defined by the scope of the claims will occur to
those skilled in the art.
Example 1
CRISPR Complex Activity in the Nucleus of a Eukaryotic Cell
[0418] An example type II CRISPR system is the type II CRISPR locus
from Streptococcus pyogenes SF370, which contains a cluster of four
genes Cas9, Cas1, Cas2, and Csn1, as well as two non-coding RNA
elements, tracrRNA and a characteristic array of repetitive
sequences (direct repeats) interspaced by short stretches of
non-repetitive sequences (spacers, about 30 bp each). In this
system, targeted DNA double-strand break (DSB) is generated in four
sequential steps (FIG. 2A). First, two non-coding RNAs, the
pre-crRNA array and tracrRNA, are transcribed from the CRISPR
locus. Second, tracrRNA hybridizes to the direct repeats of
pre-crRNA, which is then processed into mature crRNAs containing
individual spacer sequences. Third, the mature crRNA:tracrRNA
complex directs Cas9 to the DNA target consisting of the
protospacer and the corresponding PAM via heteroduplex formation
between the spacer region of the crRNA and the protospacer DNA.
Finally, Cas9 mediates cleavage of target DNA upstream of PAM to
create a DSB within the protospacer (FIG. 2A). This example
describes an example process for adapting this RNA-programmable
nuclease system to direct CRISPR complex activity in the nuclei of
eukaryotic cells.
[0419] Cell Culture and Transfection
[0420] Human embryonic kidney (HEK) cell line HEK 293FT (Life
Technologies) was maintained in Dulbecco's modified Eagle's Medium
(DMEM) supplemented with 10% fetal bovine serum (HyClone), 2 mM
GlutaMAX (Life Technologies), 100 U/mL penicillin, and 100 .mu.g/mL
streptomycin at 37.degree. C. with 5% CO.sub.2 incubation. Mouse
neuro2A (N2A) cell line (ATCC) was maintained with DMEM
supplemented with 5% fetal bovine serum (HyClone), 2 mM GlutaMAX
(Life Technologies), 100 U/mL penicillin, and 100 .mu.g/mL
streptomycin at 37.degree. C. with 5% CO.sub.2.
[0421] HEK 293FT or N2A cells were seeded into 24-well plates
(Corning) one day prior to transfection at a density of 200,000
cells per well. Cells were transfected using Lipofectamine 2000
(Life Technologies) following the manufacturer's recommended
protocol. For each well of a 24-well plate a total of 800 ng of
plasmids were used.
[0422] Surveyor Assay and Sequencing Analysis for Genome
Modification
[0423] HEK 293FT or N2A cells were transfected with plasmid DNA as
described above. After transfection, the cells were incubated at
37.degree. C. for 72 hours before genomic DNA extraction. Genomic
DNA was extracted using the QuickExtract DNA extraction kit
(Epicentre) following the manufacturer's protocol. Briefly, cells
were resuspended in QuickExtract solution and incubated at
65.degree. C. for 15 minutes and 98.degree. C. for 10 minutes.
Extracted genomic DNA was immediately processed or stored at
-20.degree. C.
[0424] The genomic region surrounding a CRISPR target site for each
gene was PCR amplified, and products were purified using QiaQuick
Spin Column (Qiagen) following manufacturer's protocol. A total of
400 ng of the purified PCR products were mixed with 2 .mu.l
10.times. Taq polymerase PCR buffer (Enzymatics) and ultrapure
water to a final volume of 20 .mu.l, and subjected to a
re-annealing process to enable heteroduplex formation: 95.degree.
C. for 10 min, 95.degree. C. to 85.degree. C. ramping at -2.degree.
C./s, 85.degree. C. to 25.degree. C. at -0.25.degree. C./s, and
25.degree. C. hold for 1 minute. After re-annealing, products were
treated with Surveyor nuclease and Surveyor enhancer S
(Transgenomics) following the manufacturer's recommended protocol,
and analyzed on 4-20% Novex TBE poly-acrylamide gels (Life
Technologies). Gels were stained with SYBR Gold DNA stain (Life
Technologies) for 30 minutes and imaged with a Gel Doc gel imaging
system (Bio-rad). Quantification was based on relative band
intensities, as a measure of the fraction of cleaved DNA. FIG. 7
provides a schematic illustration of this Surveyor assay.
[0425] Restriction fragment length polymorphism assay for detection
of homologous recombination.
[0426] HEK 293FT and N2A cells were transfected with plasmid DNA,
and incubated at 37.degree. C. for 72 hours before genomic DNA
extraction as described above. The target genomic region was PCR
amplified using primers outside the homology arms of the homologous
recombination (HR) template. PCR products were separated on a 1%
agarose gel and extracted with MinElute GelExtraction Kit (Qiagen).
Purified products were digested with HindIII (Fermentas) and
analyzed on a 6% Novex TBE poly-acrylamide gel (Life
Technologies).
[0427] RNA Secondary Structure Prediction and Analysis
[0428] RNA secondary structure prediction was performed using the
online webserver RNAfold developed at Institute for Theoretical
Chemistry at the University of Vienna, using the centroid structure
prediction algorithm (see e.g. A. R. Gruber et al., 2008, Cell
106(1): 23-24; and P A Carr and G M Church, 2009, Nature
Biotechnology 27(12): 1151-62).
[0429] RNA Purification
[0430] HEK 293FT cells were maintained and transfected as stated
above. Cells were harvested by trypsinization followed by washing
in phosphate buffered saline (PBS). Total cell RNA was extracted
with TRI reagent (Sigma) following manufacturer's protocol.
Extracted total RNA was quantified using Naonodrop (Thermo
Scientific) and normalized to same concentration.
[0431] Northern Blot Analysis of crRNA and tracrRNA Expression in
Mammalian Cells
[0432] RNAs were mixed with equal volumes of 2.times. loading
buffer (Ambion), heated to 95.degree. C. for 5 min, chilled on ice
for 1 min, and then loaded onto 8% denaturing polyacrylamide gels
(SequaGel, National Diagnostics) after pre-running the gel for at
least 30 minutes. The samples were electrophoresed for 1.5 hours at
40 W limit. Afterwards, the RNA was transferred to Hybond N+
membrane (GE Healthcare) at 300 mA in a semi-dry transfer apparatus
(Bio-rad) at room temperature for 1.5 hours. The RNA was
crosslinked to the membrane using autocrosslink button on
Stratagene UV Crosslinker the Stratalinker (Stratagene). The
membrane was pre-hybridized in ULTRAhyb-Oligo Hybridization Buffer
(Ambion) for 30 min with rotation at 42.degree. C., and probes were
then added and hybridized overnight. Probes were ordered from IDT
and labeled with [gamma-.sup.32P] ATP (Perkin Elmer) with T4
polynucleotide kinase (New England Biolabs). The membrane was
washed once with pre-warmed (42.degree. C.) 2.times.SSC, 0.5% SDS
for 1 min followed by two 30 minute washes at 42.degree. C. The
membrane was exposed to a phosphor screen for one hour or overnight
at room temperature and then scanned with a phosphorimager
(Typhoon).
[0433] Bacterial CRISPR System Construction and Evaluation
[0434] CRISPR locus elements, including tracrRNA, Cas9, and leader
were PCR amplified from Streptococcus pyogenes SF370 genomic DNA
with flanking homology arms for Gibson Assembly. Two BsaI type IIS
sites were introduced in between two direct repeats to facilitate
easy insertion of spacers (FIG. 8). PCR products were cloned into
EcoRV-digested pACYC184 downstream of the tet promoter using Gibson
Assembly Master Mix (NEB). Other endogenous CRISPR system elements
were omitted, with the exception of the last 50 bp of Csn2. Oligos
(Integrated DNA Technology) encoding spacers with complimentary
overhangs were cloned into the BsaI-digested vector pDC000 (NEB)
and then ligated with T7 ligase (Enzymatics) to generate pCRISPR
plasmids. Challenge plasmids containing spacers with PAM
[0435] expression in mammalian cells (expression constructs
illustrated in FIG. 6A, with functionality as determined by results
of the Surveyor assay shown in FIG. 6B). Transcription start sites
are marked as +1, and transcription terminator and the sequence
probed by northern blot are also indicated. Expression of processed
tracrRNA was also confirmed by Northern blot. FIG. 6C shows results
of a Northern blot analysis of total RNA extracted from 293FT cells
transfected with U6 expression constructs carrying long or short
tracrRNA, as well as SpCas9 and DR-EMX1(1)-DR. Left and right
panels are from 293FT cells transfected without or with SpRNase
III, respectively. U6 indicate loading control blotted with a probe
targeting human U6 snRNA. Transfection of the short tracrRNA
expression construct led to abundant levels of the processed form
of tracrRNA (.about.75 bp). Very low amounts of long tracrRNA are
detected on the Northern blot.
[0436] To promote precise transcriptional initiation, the RNA
polymerase III-based U6 promoter was selected to drive the
expression of tracrRNA (FIG. 2C). Similarly, a U6 promoter-based
construct was developed to express a pre-crRNA array consisting of
a single spacer flanked by two direct repeats (DRs, also
encompassed by the term "tracr-mate sequences"; FIG. 2C). The
initial spacer was designed to target a 33-base-pair (bp) target
site (30-bp protospacer plus a 3-bp CRISPR motif (PAM) sequence
satisfying the NGG recognition motif of Cas9) in the human EMX1
locus (FIG. 2C), a key gene in the development of the cerebral
cortex.
[0437] To test whether heterologous expression of the CRISPR system
(SpCas9, SpRNase III, tracrRNA, and pre-crRNA) in mammalian cells
can achieve targeted cleavage of mammalian chromosomes, HEK 293FT
cells were transfected with combinations of CRISPR components.
Since DSBs in mammalian nuclei are partially repaired by the
non-homologous end joining (NHEJ) pathway, which leads to the
formation of indels, the Surveyor assay was used to detect
potential cleavage activity at the target EMX1 locus (FIG. 7) (see
e.g. Guschin et al., 2010, Methods Mol Biol 649: 247).
Co-transfection of all four CRISPR components was able to induce up
to 5.0% cleavage in the protospacer (see FIG. 2D). Co-transfection
of all CRISPR components minus SpRNase III also induced up to 4.7%
indel in the protospacer, suggesting that there may be endogenous
mammalian RNases that are capable of assisting with crRNA
maturation, such as for example the related Dicer and Drosha
enzymes. Removing any of the remaining three components abolished
the genome cleavage activity of the CRISPR system (FIG. 2D). Sanger
sequencing of amplicons containing the target locus verified the
cleavage activity: in 43 sequenced clones, 5 mutated alleles
(11.6%) were found. Similar experiments using a variety of guide
sequences produced indel percentages as high as 29% (see FIGS. 3-6,
10, and 11). These results define a three-component system for
efficient CRISPR-mediated genome modification in mammalian cells.
To optimize the cleavage efficiency, Applicants also tested whether
different isoforms of tracrRNA affected the cleavage efficiency and
found that, in this example system, only the short (89-bp)
transcript form was able to mediate cleavage of the human EMX1
genomic locus (FIG. 6B).
[0438] FIG. 12 provides an additional Northern blot analysis of
crRNA processing in mammalian cells. FIG. 12A illustrates a
schematic showing the expression vector for a single spacer flanked
by two direct repeats (DR-EMX1(1)-DR). The 30 bp spacer targeting
the human EMX1 locus protospacer 1 (see FIG. 6) and the direct
repeat sequences are shown in the sequence beneath FIG. 12A. The
line indicates the region whose reverse-complement sequence was
used to generate Northern blot probes for EMX1(1) crRNA detection.
FIG. 12B shows a Northern blot analysis of total RNA extracted from
293FT cells transfected with U6 expression constructs carrying
DR-EMX1(1)-DR. Left and right panels are from 293FT cells
transfected without or with SpRNase III respectively. DR-EMX1(1)-DR
was processed into mature crRNAs only in the presence of SpCas9 and
short tracrRNA and was not dependent on the presence of SpRNase
III. The mature crRNA detected from transfected 293FT total RNA is
-33 bp and is shorter than the 39-42 bp mature crRNA from S.
pyogenes. These results demonstrate that a CRISPR system can be
transplanted into eukaryotic cells and reprogrammed to facilitate
cleavage of endogenous mammalian target polynucleotides.
[0439] FIG. 2 illustrates the bacterial CRISPR system described in
this example. FIG. 2A illustrates a schematic showing the CRISPR
locus 1 from Streptococcus pyogenes SF370 and a proposed mechanism
of CRISPR-mediated DNA cleavage by this system. Mature crRNA
processed from the direct repeat-spacer array directs Cas9 to
genomic targets consisting of complimentary protospacers and a
protospacer-adjacent motif (PAM). Upon target-spacer base pairing,
Cas9 mediates a double-strand break in the target DNA. FIG. 2B
illustrates engineering of S. pyogenes Cas9 (SpCas9) and RNase III
(SpRNase III) with nuclear localization signals (NLSs) to enable
import into the mammalian nucleus. FIG. 2C illustrates mammalian
expression of SpCas9 and SpRNase III driven by the constitutive
EF1a promoter and tracrRNA and pre-crRNA array (DR-Spacer-DR)
driven by the RNA Pol3 promoter U6 to promote precise transcription
initiation and termination. A protospacer from the human EMX1 locus
with a satisfactory PAM sequence is used as the spacer in the
pre-crRNA array. FIG. 2D illustrates surveyor nuclease assay for
SpCas9-mediated minor insertions and deletions. SpCas9 was
expressed with and without SpRNase III, tracrRNA, and a pre-crRNA
array carrying the EMX1-target spacer. FIG. 2E illustrates a
schematic representation of base pairing between target locus and
EMX1-targeting crRNA, as well as an example chromatogram showing a
micro deletion adjacent to the SpCas9 cleavage site. FIG. 2F
illustrates mutated alleles identified from sequencing analysis of
43 clonal amplicons showing a variety of micro insertions and
deletions. Dashes indicate deleted bases, and non-aligned or
mismatched bases indicate insertions or mutations. Scale bar=10
.mu.m.
[0440] To further simplify the three-component system, a chimeric
crRNA-tracrRNA hybrid design was adapted, where a mature crRNA
(comprising a guide sequence) may be fused to a partial tracrRNA
via a stem-loop to mimic the natural crRNA:tracrRNA duplex. To
increase co-delivery efficiency, a bicistronic expression vector
was created to drive co-expression of a chimeric RNA and SpCas9 in
transfected cells. In parallel, the bicistronic vectors were used
to express a pre-crRNA (DR-guide sequence-DR) with SpCas9, to
induce processing into crRNA with a separately expressed tracrRNA
(compare FIG. 11B top and bottom). FIG. 8 provides schematic
illustrations of bicistronic expression vectors for pre-crRNA array
(FIG. 8A) or chimeric crRNA (represented by the short line
downstream of the guide sequence insertion site and upstream of the
EF1.alpha. promoter in FIG. 8B) with hSpCas9, showing location of
various elements and the point of guide sequence insertion. The
expanded sequence around the location of the guide sequence
insertion site in FIG. 8B also shows a partial DR sequence
(GTTTAGAGCTA) and a partial tracrRNA sequence
(TAGCAAGTTAAAATAAGGCTAGTCCGTTTTT). Guide sequences can be inserted
between BbsI sites using annealed oligonucleotides. Sequence design
for the oligonucleotides are shown below the schematic
illustrations in FIG. 8, with appropriate ligation adapters
indicated. WPRE represents the Woodchuck hepatitis virus
post-transcriptional regulatory element. The efficiency of chimeric
RNA-mediated cleavage was tested by targeting the same EMX1 locus
described above. Using both Surveyor assay and Sanger sequencing of
amplicons, Applicants confirmed that the chimeric RNA design
facilitates cleavage of human EMX1 locus with approximately a 4.7%
modification rate (FIG. 3).
[0441] Generalizability of CRISPR-mediated cleavage in eukaryotic
cells was tested by targeting additional genomic loci in both human
and mouse cells by designing chimeric RNA targeting multiple sites
in the human EMX1 and PVALB, as well as the mouse Th loci. FIG. 13
illustrates the selection of some additional targeted protospacers
in human PVALB (FIG. 13A) and mouse Th (FIG. 13B) loci. Schematics
of the gene loci and the location of three protospacers within the
last exon of each are provided. The underlined sequences include 30
bp of protospacer sequence and 3 bp at the 3' end corresponding to
the PAM sequences. Protospacers on the sense and anti-sense strands
are indicated above and below the DNA sequences, respectively. A
modification rate of 6.3% and 0.75% was achieved for the human
PVALB and mouse Th loci respectively, demonstrating the broad
applicability of the CRISPR system in modifying different loci
across multiple organisms (FIG. 5). While cleavage was only
detected with one out of three spacers for each locus using the
chimeric constructs, all target sequences were cleaved with
efficiency of indel production reaching 27% when using the
co-expressed pre-crRNA arrangement (FIGS. 6 and 13).
[0442] FIG. 11 provides a further illustration that SpCas9 can be
reprogrammed to target multiple genomic loci in mammalian cells.
FIG. 11A provides a schematic of the human EMX1 locus showing the
location of five protospacers, indicated by the underlined
sequences. FIG. 11B provides a schematic of the pre-crRNA/trcrRNA
complex showing hybridization between the direct repeat region of
the pre-crRNA and tracrRNA (top), and a schematic of a chimeric RNA
design comprising a 20 bp guide sequence, and tracr mate and tracr
sequences consisting of partial direct repeat and tracrRNA
sequences hybridized in a hairpin structure (bottom). Results of a
Surveyor assay comparing the efficacy of Cas9-mediated cleavage at
five protospacers in the human EMX1 locus is illustrated in FIG.
11C. Each protospacer is targeted using either processed
pre-crRNA/tracrRNA complex (crRNA) or chimeric RNA (chiRNA).
[0443] Since the secondary structure of RNA can be crucial for
intermolecular interactions, a structure prediction algorithm based
on minimum free energy and Boltzmann-weighted structure ensemble
was used to compare the putative secondary structure of all guide
sequences used in the genome targeting experiment (see e.g. Gruber
et al., 2008, Nucleic Acids Research, 36: W70). Analysis revealed
that in most cases, the effective guide sequences in the chimeric
crRNA context were substantially free of secondary structure
motifs, whereas the ineffective guide sequences were more likely to
form internal secondary structures that could prevent base pairing
with the target protospacer DNA. It is thus possible that
variability in the spacer secondary structure might impact the
efficiency of CRISPR-mediated interference when using a chimeric
crRNA.
[0444] Further vector designs for SpCas9 are shown in FIG. 22,
which illustrates single expression vectors incorporating a U6
promoter linked to an insertion site for a guide oligo, and a Cbh
promoter linked to SpCas9 coding sequence. The vector shown in FIG.
22b includes a tracrRNA coding sequence linked to an H1
promoter.
[0445] In the bacterial assay, all spacers facilitated efficient
CRISPR interference (FIG. 3C). These results suggest that there may
be additional factors affecting the efficiency of CRISPR activity
in mammalian cells.
[0446] To investigate the specificity of CRISPR-mediated cleavage,
the effect of single-nucleotide mutations in the guide sequence on
protospacer cleavage in the mammalian genome was analyzed using a
series of EMX1-targeting chimeric crRNAs with single point
mutations (FIG. 3A). FIG. 3B illustrates results of a Surveyor
nuclease assay comparing the cleavage efficiency of Cas9 when
paired with different mutant chimeric RNAs. Single-base mismatch up
to 12-bp 5' of the PAM substantially abrogated genomic cleavage by
SpCas9, whereas spacers with mutations at farther upstream
positions retained activity against the original protospacer target
(FIG. 3B). In addition to the PAM, SpCas9 has single-base
specificity within the last 12-bp of the spacer. Furthermore,
CRISPR is able to mediate genomic cleavage as efficiently as a pair
of TALE nucleases (TALEN) targeting the same EMX1 protospacer. FIG.
3C provides a schematic showing the design of TALENs targeting
EMX1, and FIG. 3D shows a Surveyor gel comparing the efficiency of
TALEN and Cas9 (n=3).
[0447] Having established a set of components for achieving
CRISPR-mediated gene editing in mammalian cells through the
error-prone NHEJ mechanism, the ability of CRISPR to stimulate
homologous recombination (HR), a high fidelity gene repair pathway
for making precise edits in the genome, was tested. The wild type
SpCas9 is able to mediate site-specific DSBs, which can be repaired
through both NHEJ and HR. In addition, an aspartate-to-alanine
substitution (D10A) in the RuvC I catalytic domain of SpCas9 was
engineered to convert the nuclease into a nickase (SpCas9n;
illustrated in FIG. 4A) (see e.g. Sapranausaks et al., 2011,
Nucleic Acids Resch, 39: 9275; Gasiunas et al., 2012, Proc. Natl.
Acad. Sci. USA, 109:E2579), such that nicked genomic DNA undergoes
the high-fidelity homology-directed repair (HDR). Surveyor assay
confirmed that SpCas9n does not generate indels at the EMX1
protospacer target. As illustrated in FIG. 4B, co-expression of
EMX1-targeting chimeric crRNA with SpCas9 produced indels in the
target site, whereas co-expression with SpCas9n did not (n=3).
Moreover, sequencing of 327 amplicons did not detect any indels
induced by SpCas9n. The same locus was selected to test
CRISPR-mediated HR by co-transfecting HEK 293FT cells with the
chimeric RNA targeting EMX1, hSpCas9 or hSpCas9n, as well as a HR
template to introduce a pair of restriction sites (HindIII and
NheI) near the protospacer. FIG. 4C provides a schematic
illustration of the HR strategy, with relative locations of
recombination points and primer annealing sequences (arrows).
SpCas9 and SpCas9n indeed catalyzed integration of the HR template
into the EMX1 locus. PCR amplification of the target region
followed by restriction digest with HindIII revealed cleavage
products corresponding to expected fragment sizes (arrows in
restriction fragment length polymorphism gel analysis shown in FIG.
4D), with SpCas9 and SpCas9n mediating similar levels of HR
efficiencies. Applicants further verified HR using Sanger
sequencing of genomic amplicons (FIG. 4E). These results
demonstrate the utility of CRISPR for facilitating targeted gene
insertion in the mammalian genome. Given the 14-bp (12-bp from the
spacer and 2-bp from the PAM) target specificity of the wild type
SpCas9, the availability of a nickase can significantly reduce the
likelihood of off-target modifications, since single strand breaks
are not substrates for the error-prone NHEJ pathway.
[0448] Expression constructs mimicking the natural architecture of
CRISPR loci with arrayed spacers (FIG. 2A) were constructed to test
the possibility of multiplexed sequence targeting. Using a single
CRISPR array encoding a pair of EMX1- and PVALB-targeting spacers,
efficient cleavage at both loci was detected (FIG. 4F, showing both
a schematic design of the crRNA array and a Surveyor blot showing
efficient mediation of cleavage). Targeted deletion of larger
genomic regions through concurrent DSBs using spacers against two
targets within EMX1 spaced by 119 bp was also tested, and a 1.6%
deletion efficacy (3 out of 182 amplicons; FIG. 4G) was detected.
This demonstrates that the CRISPR system can mediate multiplexed
editing within a single genome.
Example 2
CRISPR System Modifications and Alternatives
[0449] The ability to use RNA to program sequence-specific DNA
cleavage defines a new class of genome engineering tools for a
variety of research and industrial applications. Several aspects of
the CRISPR system can be further improved to increase the
efficiency and versatility of CRISPR targeting. Optimal Cas9
activity may depend on the availability of free Mg.sup.2+ at levels
higher than that present in the mammalian nucleus (see e.g. Jinek
et al., 2012, Science, 337:816), and the preference for an NGG
motif immediately downstream of the protospacer restricts the
ability to target on average every 12-bp in the human genome (FIG.
9, evaluating both plus and minus strands of human chromosomal
sequences). Some of these constraints can be overcome by exploring
the diversity of CRISPR loci across the microbial metagenome (see
e.g. Makarova et al., 2011, Nat Rev Microbiol, 9:467). Other CRISPR
loci may be transplanted into the mammalian cellular milieu by a
process similar to that described in Example 1. For example, FIG.
10 illustrates adaptation of the Type II CRISPR system from CRISPR
1 of Streptococcus thermophilus LMD-9 for heterologous expression
in mammalian cells to achieve CRISPR-mediated genome editing. FIG.
10A provides a Schematic illustration of CRISPR 1 from S.
thermophilus LMD-9. FIG. 10B illustrates the design of an
expression system for the S. thermophilus CRISPR system. Human
codon-optimized hStCas9 is expressed using a constitutive
EF1.alpha. promoter. Mature versions of tracrRNA and crRNA are
expressed using the U6 promoter to promote precise transcription
initiation. Sequences from the mature crRNA and tracrRNA are
illustrated. A single base indicated by the lower case "a" in the
crRNA sequence is used to remove the polyU sequence, which serves
as a RNA polIII transcriptional terminator. FIG. 10C provides a
schematic showing guide sequences targeting the human EMX1 locus.
FIG. 10D shows the results of hStCas9-mediated cleavage in the
target locus using the Surveyor assay. RNA guide spacers 1 and 2
induced 14% and 6.4%, respectively. Statistical analysis of
cleavage activity across biological replica at these two
protospacer sites is also provided in FIG. 5. FIG. 14 provides a
schematic of additional protospacer and corresponding PAM sequence
targets of the S. thermophilus CRISPR system in the human EMX1
locus. Two protospacer sequences are highlighted and their
corresponding PAM sequences satisfying NNAGAAW motif are indicated
by underlining 3' with respect to the corresponding highlighted
sequence. Both protospacers target the anti-sense strand.
Example 3
Sample Target Sequence Selection Algorithm
[0450] A software program is designed to identify candidate CRISPR
target sequences on both strands of an input DNA sequence based on
desired guide sequence length and a CRISPR motif sequence (PAM) for
a specified CRISPR enzyme. For example, target sites for Cas9 from
S. pyogenes, with PAM sequences NGG, may be identified by searching
for 5'-N.sub.x-NGG-3' both on the input sequence and on the
reverse-complement of the input. Likewise, target sites for Cas9 of
S. thermophilus CRISPR1, with PAM sequence NNAGAAW, may be
identified by searching for 5'-N.sub.x-NNAGAAW-3' both on the input
sequence and on the reverse-complement of the input. Likewise,
target sites for Cas9 of S. thermophilus CRISPR3, with PAM sequence
NGGNG, may be identified by searching for 5'-N.sub.x-NGGNG-3' both
on the input sequence and on the reverse-complement of the input.
The value "x" in N.sub.x may be fixed by the program or specified
by the user, such as 20.
[0451] Since multiple occurrences in the genome of the DNA target
site may lead to nonspecific genome editing, after identifying all
potential sites, the program filters out sequences based on the
number of times they appear in the relevant reference genome. For
those CRISPR enzymes for which sequence specificity is determined
by a `seed` sequence, such as the 11-12 bp 5' from the PAM
sequence, including the PAM sequence itself, the filtering step may
be based on the seed sequence. Thus, to avoid editing at additional
genomic loci, results are filtered based on the number of
occurrences of the seed:PAM sequence in the relevant genome. The
user may be allowed to choose the length of the seed sequence. The
user may also be allowed to specify the number of occurrences of
the seed:PAM sequence in a genome for purposes of passing the
filter. The default is to screen for unique sequences. Filtration
level is altered by changing both the length of the seed sequence
and the number of occurrences of the sequence in the genome. The
program may in addition or alternatively provide the sequence of a
guide sequence complementary to the reported target sequence(s) by
providing the reverse complement of the identified target
sequence(s). An example visualization of some target sites in the
human genome is provided in FIG. 18.
[0452] Further details of methods and algorithms to optimize
sequence selection can be found in U.S. application Ser. No.
61/064,798 (Attorney docket 44790.11.2022; Broad Reference
BI-2012/084); incorporated herein by reference.
Example 4
Evaluation of Multiple Chimeric crRNA-tracrRNA Hybrids
[0453] This example describes results obtained for chimeric RNAs
(chiRNAs; comprising a guide sequence, a tracr mate sequence, and a
tracr sequence in a single transcript) having tracr sequences that
incorporate different lengths of wild-type tracrRNA sequence. FIG.
16a illustrates a schematic of a bicistronic expression vector for
chimeric RNA and Cas9. Cas9 is driven by the CBh promoter and the
chimeric RNA is driven by a U6 promoter. The chimeric guide RNA
consists of a 20 bp guide sequence (Ns) joined to the tracr
sequence (running from the first "U" of the lower strand to the end
of the transcript), which is truncated at various positions as
indicated. The guide and tracr sequences are separated by the
tracr-mate sequence GUUUUAGAGCUA followed by the loop sequence
GAAA. Results of SURVEYOR assays for Cas9-mediated indels at the
human EMX1 and PVALB loci are illustrated in FIGS. 16b and 16c,
respectively. Arrows indicate the expected SURVEYOR fragments.
ChiRNAs are indicated by their "+n" designation, and crRNA refers
to a hybrid RNA where guide and tracr sequences are expressed as
separate transcripts. Quantification of these results, performed in
triplicate, are illustrated by histogram in FIGS. 17a and 17b,
corresponding to FIGS. 16b and 16c, respectively ("N.D." indicates
no indels detected). Protospacer IDs and their corresponding
genomic target, protospacer sequence, PAM sequence, and strand
location are provided in Table D. Guide sequences were designed to
be complementary to the entire protospacer sequence in the case of
separate transcripts in the hybrid system, or only to the
underlined portion in the case of chimeric RNAs.
TABLE-US-00009 TABLE D protospacer genomic ID target protospacer
sequence (5' to 3') PAM strand 1 EMX1
GGACATCGATGTCACCTCCAATGACTAGCG TGG + 2 EMX1
CATTGGAGGTGACATCGATGTCCTCCCCAT TGG - 3 EMX1
GGAAGGGCCTGAGTCCGAGCAGAAGAAGAA GGG + 4 PVALB
GGTGGCGAGAGGGGCCGAGATTGGGTGTTC AGG + 5 PVALB
ATGCAGGAGGGTGGCGAGAGGGGCCGAGAT TGG +
[0454] Further details to optimize guide sequences can be found in
U.S. application Ser. No. 61/836,127 (Attorney docket
44790.08.2022; Broad Reference BI-2013/004G); incorporated herein
by reference.
[0455] Initially, three sites within the EMX1 locus in human HEK
293FT cells were targeted. Genome modification efficiency of each
chiRNA was assessed using the SURVEYOR nuclease assay, which
detects mutations resulting from DNA double-strand breaks (DSBs)
and their subsequent repair by the non-homologous end joining
(NHEJ) DNA damage repair pathway. Constructs designated chiRNA(+n)
indicate that up to the +n nucleotide of wild-type tracrRNA is
included in the chimeric RNA construct, with values of 48, 54, 67,
and 85 used for n. Chimeric RNAs containing longer fragments of
wild-type tracrRNA (chiRNA(+67) and chiRNA(+85)) mediated DNA
cleavage at all three EMX1 target sites, with chiRNA(+85) in
particular demonstrating significantly higher levels of DNA
cleavage than the corresponding crRNA/tracrRNA hybrids that
expressed guide and tracr sequences in separate transcripts (FIGS.
16b and 17a). Two sites in the PVALB locus that yielded no
detectable cleavage using the hybrid system (guide sequence and
tracr sequence expressed as separate transcripts) were also
targeted using chiRNAs. chiRNA(+67) and chiRNA(+85) were able to
mediate significant cleavage at the two PVALB protospacers (FIGS.
16c and 17b).
[0456] For all five targets in the EMX1 and PVALB loci, a
consistent increase in genome modification efficiency with
increasing tracr sequence length was observed. Without wishing to
be bound by any theory, the secondary structure formed by the 3'
end of the tracrRNA may play a role in enhancing the rate of CRISPR
complex formation.
Example 5
Cas9 Diversity
[0457] The CRISPR-Cas system is an adaptive immune mechanism
against invading exogenous DNA employed by diverse species across
bacteria and archaea. The type II CRISPR-Cas9 system consists of a
set of genes encoding proteins responsible for the "acquisition" of
foreign DNA into the CRISPR locus, as well as a set of genes
encoding the "execution" of the DNA cleavage mechanism; these
include the DNA nuclease (Cas9), a non-coding transactivating
cr-RNA (tracrRNA), and an array of foreign DNA-derived spacers
flanked by direct repeats (crRNAs). Upon maturation by Cas9, the
tracRNA and crRNA duplex guide the Cas9 nuclease to a target DNA
sequence specified by the spacer guide sequences, and mediates
double-stranded breaks in the DNA near a short sequence motif in
the target DNA that is required for cleavage and specific to each
CRISPR-Cas system. The type II CRISPR-Cas systems are found
throughout the bacterial kingdom and highly diverse in in Cas9
protein sequence and size, tracrRNA and crRNA direct repeat
sequence, genome organization of these elements, and the motif
requirement for target cleavage. One species may have multiple
distinct CRISPR-Cas systems.
[0458] Applicants evaluated 207 putative Cas9s from bacterial
species identified based on sequence homology to known Cas9s and
structures orthologous to known subdomains, including the HNH
endonuclease domain and the RuvC endonuclease domains [information
from the Eugene Koonin and Kira Makarova]. Phylogenetic analysis
based on the protein sequence conservation of this set revealed
five families of Cas9s, including three groups of large Cas9s
(.about.1400 amino acids) and two of small Cas9s (.about.1100 amino
acids) (see FIGS. 19 and 20A-F).
[0459] Further details of Cas9s and mutations of the Cas9 enzyme to
convert into a nickase or DNA binding protein and use of same with
altered functionality can be found in U.S. application Ser. Nos.
61/836,101 and 61/835,936 (Attorney docket 44790.09.2022 and
4790.07.2022 and Broad Reference BI-2013/004E and BI-2013/004F
respectively) incorporated herein by reference.
Example 6
Cas9 Orthologs
[0460] Applicants analyzed Cas9 orthologs to identify the relevant
PAM sequences and the corresponding chimeric guide RNA. Having an
expanded set of PAMs provides broader targeting across the genome
and also significantly increases the number of unique target sites
and provides potential for identifying novel Cas9s with increased
levels of specificity in the genome.
[0461] The specificity of Cas9 orthologs can be evaluated by
testing the ability of each Cas9 to tolerate mismatches between the
guide RNA and its DNA target. For example, the specificity of
SpCas9 has been characterized by testing the effect of mutations in
the guide RNA on cleavage efficiency. Libraries of guide RNAs were
made with single or multiple mismatches between the guide sequence
and the target DNA. Based on these findings, target sites for
SpCas9 can be selected based on the following guidelines:
[0462] To maximize SpCas9 specificity for editing a particular
gene, one should choose a target site within the locus of interest
such that potential `off-target` genomic sequences abide by the
following four constraints: First and foremost, they should not be
followed by a PAM with either 5'-NGG or NAG sequences. Second,
their global sequence similarity to the target sequence should be
minimized. Third, a maximal number of mismatches should lie within
the PAM-proximal region of the off-target site. Finally, a maximal
number of mismatches should be consecutive or spaced less than four
bases apart.
[0463] Similar methods can be used to evaluate the specificity of
other Cas9 orthologs and to establish criteria for the selection of
specific target sites within the genomes of target species. As
mentioned previously phylogenetic analysis based on the protein
sequence conservation of this set revealed five families of Cas9s,
including three groups of large Cas9s (.about.1400 amino acids) and
two of small Cas9s (.about.1100 amino acids) (see FIGS. 19 and
20A-F). Further details on Cas orthologs can be found in U.S.
application Ser. Nos. 61/836,101 and 61/835,936 (Attorney docket
44790.09.2022 and 4790.07.2022 and Broad Reference BI-2013/004E and
BI-2013/004F respectively) incorporated herein by reference.
Example 7
Methodological Improvement to Simplify Cloning and Delivery
[0464] Rather than encoding the U6-promoter and guide RNA on a
plasmid, Applicants amplified the U6 promoter with a DNA oligo to
add on the guide RNA. The resulting PCR product may be transfected
into cells to drive expression of the guide RNA.
[0465] Example primer pair that allows the generation a PCR product
consisting of U6-promoter::guideRNA targeting human Emx1 locus:
[0466] Forward Primer: AAACTCTAGAgagggcctatttcccatgattc
[0467] Reverse Primer (carrying the guide RNA, which is
underlined):
TABLE-US-00010 acctctagAAAAAAAGCACCGACTCGGTGCCACTTTTTCAAGTT
GATAACGGACTAGCATTTTAACTTGCTATGCCTTTGTTTTGTTT
CCAAAACAGCATAGCTCTAAAACCCCTAGTCATTGGAGGTGACG
GTGTTTCGTCCTTTCCACaag
Example 8
Methodological Improvement to Improve Activity
[0468] Rather than use pol3 promoters, in particular RNA polymerase
III (e.g. U6 or H1 promoters), to express guide RNAs in eukaryotic
cells, Applicants express the T7 polymerase in eukaryotic cells to
drive expression of guide RNAs using the T7 promoter.
[0469] One example of this system may involve introduction of three
pieces of DNA:
[0470] 1. expression vector for Cas9
[0471] 2. expression vector for T7 polymerase
[0472] 3. expression vector containing guideRNA fused to the T7
promoter
Example 9
Methodological Improvement to Reduce Toxicity of Cas9: Delivery of
Cas9 in the Form of mRNA
[0473] Delivery of Cas9 in the form of mRNA enables transient
expression of Cas9 in cells, to reduce toxicity. For example,
humanized SpCas9 may be amplified using the following primer
pair:
[0474] Forward Primer (to add on T7 promoter for in vitro
transcription):
TABLE-US-00011 TAATACGACTCACTATAGGAAGTGCGCCACCATGGC
CCCAAAGAAGAAGCGG
[0475] Reverse Primer (to add on polyA tail):
TABLE-US-00012 GGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTttcttaCT
TTTTCTTTTTTGCCTGGCCG
[0476] Applicants transfect the Cas9 mRNA into cells with either
guide RNA in the form of RNA or DNA cassettes to drive guide RNA
expression in eukaryotic cells.
Example 10
Methodological Improvement to Reduce Toxicity of Cas9: Use of an
Inducible Promoter
[0477] Applicants transiently turn on Cas9 expression only when it
is needed for carrying out genome modification. Examples of
inducible system include tetracycline inducible promoters (Tet-On
or Tet-Off), small molecule two-hybrid transcription activations
systems (FKBP, ABA, etc), or light inducible systems (Phytochrome,
LOV domains, or cryptochrome).
Example 11
Improvement of the Cas9 System for In Vivo Application
[0478] Applicants conducted a Metagenomic search for a Cas9 with
small molecular weight. Most Cas9 homologs are fairly large. For
example the SpCas9 is around 1368aa long, which is too large to be
easily packaged into viral vectors for delivery. A graph
representing the length distribution of Cas9 homologs is generated
from sequences deposited in GenBank (FIG. 23). Some of the
sequences may have been mis-annotated and therefore the exact
frequency for each length may not necessarily be accurate.
Nevertheless it provides a glimpse at distribution of Cas9 proteins
and suggest that there are shorter Cas9 homologs.
[0479] Through computational analysis, Applicants found that in the
bacterial strain Campylobacter, there are two Cas9 proteins with
less than 1000 amino acids. The sequence for one Cas9 from
Campylobacter jejuni is presented below. At this length, CjCas9 can
be easily packaged into AAV, lentiviruses, Adenoviruses, and other
viral vectors for robust delivery into primary cells and in vivo in
animal models. In a preferred embodiment of the invention, the Cas9
protein from S. aureus is used.
TABLE-US-00013 >Campylobacter jejuni Cas9 (CjCas9)
MARILAFDIGISSIGWAFSENDELKDCGVRIFTKVENPKTGES
LALPRRLARSARKRLARRKARLNHLKHLIANEFKLNYEDYQSF
DESLAKAYKGSLISPYELRFRALNELLSKQDFARVILHIAKRR
GYDDIKNSDDKEKGMLKAIKQNEEKLANYQSVGEYLYKEYFQK
FKENSKEFTNVRNKKESYERCIAQSFLKDELKIAFKKQREFGF
SFSKKFEEEVLSVAFYKRALKDFSHINGNCSFFTDEKRAPKNS
PLAFMFVALTRIINLINNLKNTEGILYTKDDLNALLNEVLKNG
TUFYKQTKKLLGLSDDYEFKGEKGTYHEFKKYKEFIKALGEHN
LSQDDLNEIAKDITLIKDEIKLKKALAKYDLNQNQIDSLSKLE
FKUHLNISFKALKLNTPLMLEGKKYDEACNELNLKVAIINEDK
KDFLPAFNETYYKDEVTNPVVLRAIIKEYRKVLNALLKKYGKV
MINIEIAREVGKNFISQRAKIEKEQNENYKAKKDAELECEKLG
LKINSKNILKLRLFKEQKEFCAYSGEKIKISDLQDEKMLEIDH
IYPYSRSFDDSYMNKVINFTKQNQEKLNQTPFEAFGNDSAKWQ
KIEVLAKNLPTKKQKRILDKNYKDKEQKNFKDRNLNDTRYIAR
LVLNYTKDYLDFITLSDDENTKLNDTQKGSKVHVEAKSCIMLT
SALRHTWGFSAICDRNNHLHHAIDAVIIAYANNSIVKAFSDFK
KEQESNSAELYAKKISTLDYKNKRKFTEPFSGERQKVIDKIDE
IFVSKPERKKPSCIALFIEETFRKEEEFYQSYGGKEGVLKALE
LGKIRKVNGKIVKNGDMFRVDIFKEIKKTNKFYAVPIYTMDFA
LKVLPNKAVARSKKGEIKDWILMDENYEFCFSLYKDSLILIQT
KDMQEPEFVYYNAFTSSTVSLIVSKIADNKFETLSKNQKILFK
NANEKEVIAKSIGIQNLKVFEKYWSALGEVTKAEFRQREDFKK
[0480] The putative tracrRNA element for this CjCas9 is:
TABLE-US-00014 TATAATCTCATAAGAAATTTAAAAAGGGACTAAAATAAAGAGTTTG
CGGGACTCTGCGGGGTTACAATCCCCTAAAACCGCTTTTAAAATT
[0481] The Direct Repeat sequence is:
TABLE-US-00015 ATTTTACCATAAAGAAATTTAAAAAGGGACTAAAAC
[0482] An example of a chimeric guideRNA for CjCas9 is:
TABLE-US-00016 NNNNNNNNNNNNNNNNNNNNGUUUUAGUCCCGAAAGGGACUAAAAU
AAAGAGUUUGCGGGACUCUGCGGGGUUACAAUCCCCUAAAACCGCU UUU
Example 12
Cas9 Optimization
[0483] For enhanced function or to develop new functions,
Applicants generate chimeric Cas9 proteins by combining fragments
from different Cas9 homologs. For example, two example chimeric
Cas9 proteins:
[0484] For example, Applicants fused the N-term of St1Cas9
(fragment from this protein is in bold) with C-term of SpCas9
(fragment from this protein is underlined).
TABLE-US-00017 >St1(N)Sp(C)Cas9
MSDLVLGLDIGIGSVGVGIILNKVTGEHHKNSRIFPAAQAENNLVRRTN
RQGRRLARRKKHRRVRLNRLFEESGLITDVIKISINLNPYQLRVKGLID
ELSNEELHALKNININKTIRGISYLDDASDDGNSSVGDYAQIWKENSKQ
LETKTPGIMLERYQTYGQLRGDFTVEKDGKKHRLINVFPTSAYRSEALR
ILQTQQEFNPQITDEHNRYLEILTGKRKYYHGPGNEKSRTDYGRYRTSG
ETLDNIFGILIGKCTFYPDEFRAAKASYTAQEFNLLNDLNNLTVPTETK
KLSKEQKNQIINYVKNEKAMGPAKLFKYIAKILLSCDVADIKGYRIDKS
GKAMITFEAYRKMKTILETLDIEQMDRETIDKLAYNTLTLNTEREGIQE
ALEHEFADGSFSQKQVDELVQFRKANSSIFGKGWHNFSVKLMMEIWELY
ETSKEQMTELTRILGKQKTTSSSNKTKYIDEKLLTEEIYNPVVAKSVRO
AIKIVINAAIKEYGDFDNIVIEMARENQTTQKGOKNSRERNIKRIEEGI
NKELGSQILKEHPVETQLIONEKINLYYLQNGRDMYVDQELDINRISDY
DVDIIIVPQSFIXDDSIDNKVILTRSDKNRGKSDNVPSEEVVKKMKNYW
RQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKEIV
AQIIDSMNTKIDENDKLIREVKVITIKSKINSDRKDIFQFYKYREINNY
HHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIG
KATAKYFFYSNIMNFFICTEITLANGEIRKRPLIETNGETGEIVWDKGR
DFATVRKVLSMPQVMVKKTEVQTGGFSKESILPKRINSDKIIARKKDWD
PKKYGGFDSPTVAYSVINVAKVEKGKSICKLKSVKELLGITIMERSSFE
KNPIDFLEAKGYKEVKKDLIIKLPKYSIFELENGRKRMILASAGELQKG
NEALPSKYVNFLYLASIIYEKLKGSPEDNEQKQLEVEQHKHYLDEIIEQ
ISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAP
AAFKYFDTTIDRKRYTSTKEVLDATLIFIQSITGLYETRIDLSQLGGD
>Sp(N)St1(C)Cas9
MDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGA
LLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHR
LEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKAD
LRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKITIQINQTYNQUEENPI
NASGVDAKAIISARISKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPN
FKSNFDLAEDAKLOLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAIL
LSDILRVNTEETKAPLSASMIKRYDEHFIQDLTLLKALVRQQLPEKYKEI
FFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLR
KQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPY
YVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDK
NLPNEKVLPKHSLLYEYFTVYNELTKYKYVTEGMRKRAFLSGFKKAIVDL
IFKTNRKVINKKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKD
KDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKR
RRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQUHDDSEKE
DIQKAQVSGQGDSUIEFTIANLAGSPAIKKGILQTVKVVDEINKVMGRHK
PENIVIEMARETNEDDEKKMQMQKANKDEKDAAMLKAANQYNGKAELPHS
VFHGHKQLATKIRLWHQQGERCLYTGKTISIHDLINNSNQFEVDHILPLS
ITFDDSLANKVINYATANQEKGQRTPWALDSMDDAWSFRELKAFVRESKT
LSNKKKENLLTEEDISKHARKKFIERNLVDTRYASIZVVLNALQERFRAR
KIDTKVSVVRGQFTSQLRRHWGIEKTRIYIYHHHAVDALIINASSQLNLW
KKQKNTLVSYSEDQLLLDIETGELISDDEYKESVFKAPYQHFVDTLKSKE
FEDSILFSYQVDSKFNRKISDATIYATRQAKVGKDKADETYYLGKIKDIY
TQDGYDAFMKIYKKDKSKFLMYRHDPQTFEKVIEFILENYPNKQINEKGK
EVPCNPFLKYKEEHIGYIRKYSKKGNGPEIKSLKYYDSKLGNIIIDFIPI
KDSNNKVAILQSVSPWRADVYFNKTTGKYEILGLKYADLQFEKGTCTYKI
SQEKYNDIKKKEGVDSDSEFKFTLYKNDLLLVKDTETKEQQLFRFLSRTM
PKQKHYVELKPYDKQKFEGGEALIKVLGNVANSGQCKKGLCKSNISIYIK
VRTDVLGNQIIIIKNEGDKPKLDF
[0485] The benefit of making chimeric Cas9 include:
[0486] reduce toxicity
[0487] improve expression in eukaryotic cells
[0488] enhance specificity
[0489] reduce molecular weight of protein, make protein smaller by
combining the smallest domains from different Cas9 homologs.
[0490] Altering the PAM sequence requirement
Example 13
Utilization of Cas9 as a Generic DNA Binding Protein
[0491] Applicants used Cas9 as a generic DNA binding protein by
mutating the two catalytic domains (D10 and H840) responsible for
cleaving both strands of the DNA target. In order to upregulate
gene transcription at a target locus Applicants fused the
transcriptional activation domain (VP64) to Cas9. Applicants
hypothesized that it would be important to see strong nuclear
localization of the Cas9-VP64 fusion protein because transcription
factor activation strength is a function of time spent at the
target. Therefore, Applicants cloned a set of Cas9-VP64-GFP
constructs, transfected them into 293 cells and assessed their
localization under a fluorescent microscope 12 hours
post-transfection.
[0492] The same constructs were cloned as a 2A-GFP rather than a
direct fusion in order to functionally test the constructs without
a bulky GFP present to interfere. Applicants elected to target the
Sox2 locus with the Cas9 transactivator because it could be useful
for cellular reprogram and the locus has already been validated as
a target for TALE-TF mediated transcriptional activation. For the
Sox2 locus Applicants chose eight targets near the transcriptional
start site (TSS). Each target was 20 bp long with a neighboring NGG
protospacer adjacent motif (PAM). Each Cas9-VP64 construct was
co-transfected with each PCR generated chimeric crispr RNA (chiRNA)
in 293 cells. 72 hours post transfection the transcriptional
activation was assessed using RT-qPCR.
[0493] To further optimize the transcriptional activator,
Applicants titrated the ratio of chiRNA (Sox2.1 and Sox2.5) to Cas9
(NLS-VP64-NLS-hSpCas9-NLS-VP64-NLS), transfected into 293 cells,
and quantified using RT-qPCR. These results indicate that Cas9 can
be used as a generic DNA binding domain to upregulate gene
transcription at a target locus.
[0494] Applicants designed a second generation of constructs.
(Table below).
TABLE-US-00018 pLenti-EF1a-GFP-2A-6xHis-NLS-VP64-NLS-hSpCsn1(D10A,
H840A)-NLS pLenti-EF1a-GFP-2A-6xHis-NLS-VP64-NLS-hSpCsn1(D10A,
H840A) pLenti-EF1a-GFP-2A-6xHis-NLS-VP64-NLS-NLS-hSpCsn1(D10A,
H840A) pLenti-EF1a-GFP-2A-6xHis-NLS-hSpCsn1(D10A, H840A)-NLS
pLenti-EF1a-GFP-2A-6xHis-NLS-hSpCsn1(D10A, H840A)
pLenti-EF1a-GFP-2A-6xHis-NLS-NLS-hSpCsn1(D10A, H840A)
[0495] Applicants use these constructs to assess transcriptional
activation (VP64 fused constructs) and repression (Cas9 only) by
RT-qPCR. Applicants assess the cellular localization of each
construct using anti-His antibody, nuclease activity using a
Surveyor nuclease assay, and DNA binding affinity using a gel shift
assay. In a preferred embodiment of the invention, the gel shift
assay is an EMSA gel shift assay.
Example 14
Cas9 Transgenic and Knock in Mice
[0496] To generate a mouse that expresses the Cas9 nuclease
Applicants submit two general strategies, transgenic and knock in.
These strategies may be applied to generate any other model
organism of interest, for e.g. Rat. For each of the general
strategies Applicants made a constitutively active Cas9 and a Cas9
that is conditionally expressed (Cre recombinase dependent). The
constitutively active Cas9 nuclease is expressed in the following
context: pCAG-NLS-Cas9-NLS-P2A-EGFP-WPRE-bGHpolyA. pCAG is the
promoter, NLS is a nuclear localization signal, P2A is the peptide
cleavage sequence, EGFP is enhanced green fluorescent protein, WPRE
is the woodchuck hepatitis virus posttranscriptional regulatory
element, and bGHpolyA is the bovine growth hormone poly-A signal
sequence (FIGS. 25A-B). The conditional version has one additional
stop cassette element, loxP-SV40 polyA x3-loxP, after the promoter
and before NLS-Cas9-NLS (i.e.
pCAG-loxP-SV40polyAx3-loxP-NLS-Cas9-NLS-P2A-EGFP-WPRE-bGHpolyA).
The important expression elements can be visualized as in FIG. 26.
The constitutive construct should be expressed in all cell types
throughout development, whereas, the conditional construct will
only allow Cas9 expression when the same cell is expressing the Cre
recombinase. This latter version will allow for tissue specific
expression of Cas9 when Cre is under the expression of a tissue
specific promoter. Moreover, Cas9 expression could be induced in
adult mice by putting Cre under the expression of an inducible
promoter such as the TET on or off system.
[0497] Validation of Cas9 constructs: Each plasmid was functionally
validated in three ways: 1) transient transfection in 293 cells
followed by confirmation of GFP expression; 2) transient
transfection in 293 cells followed by immunofluorescence using an
antibody recognizing the P2A sequence; and 3) transient
transfection followed by Surveyor nuclease assay. The 293 cells may
be 293FT or 293 T cells depending on the cells that are of
interest. In a preferred embodiment the cells are 293FT cells. The
results of the Surveyor were run out on the top and bottom row of
the gel for the conditional and constitutive constructs,
respectively. Each was tested in the presence and absence of
chimeric RNA targeted to the hEMX1 locus (chimeric RNA hEMX1.1).
The results indicate that the construct can successfully target the
hEMX1 locus only in the presence of chimeric RNA (and Cre in the
conditional case). The gel was quantified and the results are
presented as average cutting efficiency and standard deviation for
three samples.
[0498] Transgenic Cas9 mouse: To generate transgenic mice with
constructs, Applicants inject pure, linear DNA into the pronucleus
of a zygote from a pseudo pregnant CB56 female. Founders are
identified, genotyped, and backcrossed to CB57 mice. The constructs
were successfully cloned and verified by Sanger sequencing.
[0499] Knock in Cas9 mouse: To generate Cas9 knock in mice
Applicants target the same constitutive and conditional constructs
to the Rosa26 locus. Applicants did this by cloning each into a
Rosa26 targeting vector with the following elements: Rosa26 short
homology arm--constitutive/conditional Cas9 expression
cassette--pPGK-Neo-Rosa26 long homology arm--pPGK-DTA. pPGK is the
promoter for the positive selection marker Neo, which confers
resistance to neomycin, a 1 kb short arm, a 4.3 kb long arm, and a
negative selection diphtheria toxin (DTA) driven by PGK.
[0500] The two constructs were electroporated into R1 mESCs and
allowed to grow for 2 days before neomycin selection was applied.
Individual colonies that had survived by days 5-7 were picked and
grown in individual wells. 5-7 days later the colonies were
harvested, half were frozen and the other half were used for
genotyping. Genotyping was done by genomic PCR, where one primer
annealed within the donor plasmid (AttpF) and the other outside of
the short homology arm (Rosa26-R) Of the 22 colonies harvested for
the conditional case, 7 were positive (Left). Of the 27 colonies
harvested for the constitutive case, zero were positive (Right). It
is likely that Cas9 causes some level of toxicity in the mESC and
for this reason there were no positive clones. To test this
Applicants introduced a Cre expression plasmid into correctly
targeted conditional Cas9 cells and found very low toxicity after
many days in culture. The reduced copy number of Cas9 in correctly
targeted conditional Cas9 cells (1-2 copies per cell) is enough to
allow stable expression and relatively no cytotoxicity. Moreover,
this data indicates that the Cas9 copy number determines toxicity.
After electroporation each cell should get several copies of Cas9
and this is likely why no positive colonies were found in the case
of the constitutive Cas9 construct. This provides strong evidence
that utilizing a conditional, Cre-dependent strategy should show
reduced toxicity. Applicants inject correctly targeted cells into a
blastocyst and implant into a female mouse. Chimerics are
identified and backcrossed. Founders are identified and
genotyped.
[0501] Utility of the conditional Cas9 mouse: Applicants have shown
in 293 cells that the Cas9 conditional expression construct can be
activated by co-expression with Cre. Applicants also show that the
correctly targeted R1 mESCs can have active Cas9 when Cre is
expressed. Because Cas9 is followed by the P2A peptide cleavage
sequence and then EGFP Applicants identify successful expression by
observing EGFP. This same concept is what makes the conditional
Cas9 mouse so useful. Applicants may cross their conditional Cas9
mouse with a mouse that ubiquitously expresses Cre (ACTB-Cre line)
and may arrive at a mouse that expresses Cas9 in every cell. It
should only take the delivery of chimeric RNA to induce genome
editing in embryonic or adult mice. Interestingly, if the
conditional Cas9 mouse is crossed with a mouse expressing Cre under
a tissue specific promoter, there should only be Cas9 in the
tissues that also express Cre. This approach may be used to edit
the genome in only precise tissues by delivering chimeric RNA to
the same tissue.
Example 15
Cas9 Diversity and Chimeric RNAs
[0502] The CRISPR-Cas system is an adaptive immune mechanism
against invading exogenous DNA employed by diverse species across
bacteria and archaea. The type II CRISPR-Cas system consists of a
set of genes encoding proteins responsible for the "acquisition" of
foreign DNA into the CRISPR locus, as well as a set of genes
encoding the "execution" of the DNA cleavage mechanism; these
include the DNA nuclease (Cas9), a non-coding transactivating
cr-RNA (tracrRNA), and an array of foreign DNA-derived spacers
flanked by direct repeats (crRNAs). Upon maturation by Cas9, the
tracrRNA and crRNA duplex guide the Cas9 nuclease to a target DNA
sequence specified by the spacer guide sequences, and mediates
double-stranded breaks in the DNA near a short sequence motif in
the target DNA that is required for cleavage and specific to each
CRISPR-Cas system. The type II CRISPR-Cas systems are found
throughout the bacterial kingdom and highly diverse in in Cas9
protein sequence and size, tracrRNA and crRNA direct repeat
sequence, genome organization of these elements, and the motif
requirement for target cleavage. One species may have multiple
distinct CRISPR-Cas systems.
[0503] Applicants evaluated 207 putative Cas9s from bacterial
species identified based on sequence homology to known Cas9s and
structures orthologous to known subdomains, including the HNH
endonuclease domain and the RuvC endonuclease domains [information
from the Eugene Koonin and Kira Makarova]. Phylogenetic analysis
based on the protein sequence conservation of this set revealed
five families of Cas9s, including three groups of large Cas9s
(.about.1400 amino acids) and two of small Cas9s (.about.1100 amino
acids) (FIGS. 19A-D and 20A-F).
[0504] Applicants have also optimized Cas9 guide RNA using in vitro
methods.
Example 16
Cas9 Mutations
[0505] In this example, Applicants show that the following
mutations can convert SpCas9 into a nicking enzyme: D10A, E762A,
H840A, N854A, N863A, D986A.
[0506] Applicants provide sequences showing where the mutation
points are located within the SpCas9 gene (FIG. 24A-M). Applicants
also show that the nickases are still able to mediate homologous
recombination. Furthermore, Applicants show that SpCas9 with these
mutations (individually) do not induce double strand break.
[0507] Cas9 orthologs all share the general organization of 3-4
RuvC domains and a HNH domain. The 5' most RuvC domain cleaves the
non-complementary strand, and the HNH domain cleaves the
complementary strand. All notations are in reference to the guide
sequence.
[0508] The catalytic residue in the 5' RuvC domain is identified
through homology comparison of the Cas9 of interest with other Cas9
orthologs (from S. pyogenes type II CRISPR locus, S. thermophilus
CRISPR locus 1, S. thermophilus CRISPR locus 3, and Franciscilla
novicida type II CRISPR locus), and the conserved Asp residue is
mutated to alanine to convert Cas9 into a complementary-strand
nicking enzyme. Similarly, the conserved His and Asn residues in
the HNH domains are mutated to Alanine to convert Cas9 into a
non-complementary-strand nicking enzyme.
Example 17
Cas9 Transcriptional Activation and Cas9 Repressor
[0509] Cas9 Transcriptional Activation
[0510] A second generation of constructs were designed and tested
(Table 1). These constructs are used to assess transcriptional
activation (VP64 fused constructs) and repression (Cas9 only) by
RT-qPCR. Applicants assess the cellular localization of each
construct using anti-H is antibody, nuclease activity using a
Surveyor nuclease assay, and DNA binding affinity using a gel shift
assay.
[0511] Cas Repressor
[0512] It has been shown previously that dCas9 can be used as a
generic DNA binding domain to repress gene expression. Applicants
report an improved dCas9 design as well as dCas9 fusions to the
repressor domains KRAB and SID4x. From the plasmid library created
for modulating transcription using Cas9 in Table 1, the following
repressor plasmids were functionally characterized by qPCR: pXRP27,
pXRP28, pXRP29, pXRP48, pXRP49, pXRP50, pXRP51, pXRP52, pXRP53,
pXRP56, pXRP58, pXRP59, pXRP61, and pXRP62.
[0513] Each dCas9 repressor plasmid was co-transfected with two
guide RNAs targeted to the coding strand of the beta-catenin gene.
RNA was isolated 72 hours after transfection and gene expression
was quantified by RT-qPCR. The endogenous control gene was GAPDH.
Two validated shRNAs were used as positive controls. Negative
controls were certain plasmids transfected without gRNA, these are
denoted as "pXRP## control". The plasmids pXRP28, pXRP29, pXRP48,
and pXRP49 could repress the beta-catenin gene when using the
specified targeting strategy. These plasmids correspond to dCas9
without a functional domain (pXRP28 and pXRP28) and dCas9 fused to
SID4x (pXRP48 and pXRP49).
[0514] Further work investigates: repeating the above experiment,
targeting different genes, utilizing other gRNAs to determine the
optimal targeting position, and multiplexed repression.
TABLE-US-00019 TABLE 1
pXRP024-pLenti2-EF1a-VP64-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP025-pLenti2-EF1a-VP64-NLS-GGGGS.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP026-pLenti2-EF1a-VP64-NLS-EAAAK.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP027-pLenti2-EF1a-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP028-pLenti2-EF1a-NLS-GGGGS.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP029-pLenti2-EF1a-NLS-EAAAK.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP030-pLenti2-pSV40-VP64-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP031-pLenti2-pPGK-VP64-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP032-pLenti2-LTR-VP64-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP033-pLenti2-pSV40-VP64-NLS-GGGGS.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPR-
E
pXRP034-pLenti2-pPGK-VP64-NLS-GGGGS.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP035-pLenti2-LTR-VP64-NLS-GGGGS.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP036-pLenti2-pSV40-VP64-NLS-EAAAK.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPR-
E
pXRP037-pLenti2-pPGK-VP64-NLS-EAAAK.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP038-pLenti2-LTR-VP64-NLS-EAAAK.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP048-pLenti2-EF1a-SID4x-NLS-FLAG-Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP049-pLenti2-EF1a-SID4X-NLS-GGGGS.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPR-
E
pXRP050-pLenti2-EF1a-SID4X-NLS-EAAAK.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPR-
E
pXRP051-pLenti2-EF1a-KRAR-NLS-FLAG-Liniker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP052-pLenti2-EF1a-KRAB-NLS-GGGGS.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP053-pLenti2-EF1a-KRAB-NLS-EAAAK.sub.3Linker-dCas9-NLS-gLuc-2A-GFP-WPRE
pXRP054-pLenti2-EF1a-dCas9-Liniker-FLAG-NLS-VP64-gLuc-2A-GFP-WPRE
pXRP055-pLenti2-EF1a-dCas9-Linker-FLAG-NLS-SID4X-gLuc-2A-GFP-WPRE
pXRP056-pLenti2-EF1a-dCas9-Linker-FLAG-NLS-KRAB-gLuc-2A-GFP-WPRE
pXRP057-pLenti2-EF1a-dCas9-GGGGGS.sub.3-NLS-VP64-gLuc-2A-GFP-WPRE
pXRP058-pLenti2-EF1a-dCas9-GGGGGS.sub.3-NLS-SID4X-gLuc-2A-GFP-WPRE
pXRP059-pLenti2-EF1a-dCas9-GGGGGS.sub.3-NLS-KRAB-gLuc-2A-GFP-WPRE
pXRP060-pLenti2-EF1a-dCas9-EAAAK.sub.3-NLS-VP64-gLuc-2A-GFP-WPRE
pXRP061-pLenti2-EF1a-dCas9-EAAAK.sub.3-NLS-SID4X-gLuc-2A-GFP-WPRE
pXRP062-pLenti2-EF1a-dCas9-EAAAK.sub.3-NLS-KRAB-gLuc-2A-GFP-WPRE
pXRP024-pLenti2-EF1a-VP64-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP025-pLenti2-EF1a-VP64-NLS-GGGGS.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP026-pLenti2-EF1a-VP64-NLS-EAAAK.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP027-pLenti2-EF1a-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP028-pLenti2-EF1a-NLS-GGGGS.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP029-pLenti2-EF1a-NLS-EAAAK.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP030-pLenti2-pSV40-VP64-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP031-pLenti2-pPGK-VP64-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP032-pLenti2-ETR-VP64-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP033-pLenti2-pSV40-VP64-NLS-GGGGS.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP034-pLenti2-pPGK-VP64-NLS-GGGGS.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP035-pLenti2-LTR-VP64-NLS-GUGGS.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP036-pLenti2-pSV40-VP64-NLS-EAAAK.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP037-pLenti2-pPGK-VP64-NLS-EAAAK.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP038-pLenti2-LTR-VP64-NLS-EAAAK.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP048-pLenti2-EF1a-SID4x-NLS-FEAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP049-pLenti2-EF1a-SID4X-NLS-GGGGS.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP050-pLenti2-EF1a-SID4X-NLS-EAAAK.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP051-pLenti2-EF1a-KRAB-NLS-FLAG-Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP052-pLenti2-EF1a-KRAB-NLS-GGGGS.sub.3Linker-Cas9-NLS-gLuc-2A-GEP-WPRE
pXRP053-pLenti2-FF1a-KRAB-NLS-EAAAK.sub.3Linker-Cas9-NLS-gLuc-2A-GFP-WPRE
pXRP054-pLenti2-EF1a-Cas9-Linker-FLAG-NLS-VP64-gLuc-2A-GFP-WPRE
pXRP055-pLenti2-EF1a-Cas9-Linker-FLAG-NLS-SID4X-gLuc-2A-GFP-WPRE
pXRP056-pLenti2-EF1a-Cas9-Linker-FLAG-NLS-KRAB-gLuc-2A-GFP-WPRE
pXRP057-pLenti2-EF1a-Cas9-GGGGGS.sub.3-NLS-VP64-gLuc-2A-GFP-WPRE
pXRP058-pLenti2-EF1a-Cas9-GGGGGS.sub.3-NLS-SID4X-gLuc-2A-GFP-WPRE
pXRP059-pLenti2-EF1a-Cas9-GGGGGS.sub.3-NLS-KRAB-gLuc-2A-GFP-WPRE
pXRP060-pLenti2-FF1a-Cas9-EAAAK.sub.3-NES-VP64-gLuc-2A-GFP-WPRE
pXRP061-pLenti2-EF1a-Cas9-EAAAK.sub.3-NES-SID4X-gLuc-2A-GFP-WPRE
pXRP062-pLenti2-EF1a-Cas9-EAAAK.sub.3-NES-KRAB-gLuc-2A-GFP-WPRE
Example 18
Targeted Deletion of Genes Involved in Cholesterol Biosynthesis,
Fatty Acid Biosynthesis, and Other Metabolic Disorders, Genes
Encoding Mis-Folded Proteins Involved in Amyloid and Other
Diseases, Oncogenes Leading to Cellular Transformation, Latent
Viral Genes, and Genes Leading to Dominant-Negative Disorders,
Amongst Other Disorders
[0515] Applicants demonstrate gene delivery of a CRISPR-Cas system
in the liver, brain, ocular, epithelial, hematopoetic, or another
tissue of a subject or a patient in need thereof, suffering from
metabolic disorders, amyloidosis and protein-aggregation related
diseases, cellular transformation arising from genetic mutations
and translocations, dominant negative effects of gene mutations,
latent viral infections, and other related symptoms, using either
viral or nanoparticle delivery system.
[0516] Study Design:
[0517] Subjects or patients in need thereof suffering from
metabolic disorders, amyloidosis and protein aggregation related
disease which include but are not limited to human, non-primate
human, canine, feline, bovine, equine, other domestic animals and
related mammals. The CRISPR-Cas system is guided by a chimeric
guide RNA and targets a specific site of the human genomic loci to
be cleaved. After cleavage and non-homologous end-joining mediated
repair, frame-shift mutation results in knock out of genes.
[0518] Applicants select guide-RNAs targeting genes involved in
above-mentioned disorders to be specific to endogenous loci with
minimal off-target activity. Two or more guide RNAs may be encoded
into a single CRISPR array to induce simultaneous double-stranded
breaks in DNA leading to micro-deletions of affected genes or
chromosomal regions.
[0519] Identification and Design of Gene Targets
[0520] For each candidate disease gene, Applicants select DNA
sequences of interest include protein-coding exons, sequences
including and flanking known dominant negative mutation sites,
sequences including and flanking pathological repetitive sequences.
For gene-knockout approaches, early coding exons closest to the
start codon offer best options for achieving complete knockout and
minimize possibility of truncated protein products retaining
partial function.
[0521] Applicants analyze sequences of interest for all possible
targetable 20-bp sequences immediately 5' to a NGG motif (for
SpCas9 system) or a NNAGAAW (for St1Cas9 system). Applicants choose
sequences for unique, single RNA-guided Cas9 recognition in the
genome to minimize off-target effects based on computational
algorithm to determine specificity.
[0522] Cloning of Guide Sequences into a Delivery System
[0523] Guide sequences are synthesized as double-stranded 20-24 bp
oligonucleotides. After 5'-phosphorylation treatment of oligos and
annealing to form duplexes, oligos are ligated into suitable vector
depending on the delivery method:
[0524] Virus-Based Delivery Methods
[0525] AAV-based vectors (PX260, 330, 334, 335) have been described
elsewhere
[0526] Lentiviral-based vectors use a similar cloning strategy of
directly ligating guide sequences into a single vector carrying a
U6 promoter-driven chimeric RNA scaffold and a EF1a promoter-driven
Cas9 or Cas9 nickase.
[0527] Virus production is described elsewhere.
[0528] Nanoparticle-Based RNA Delivery Methods
[0529] 1. Guide sequences are synthesized as an oligonucleotide
duplex encoding T7 promoter-guide sequence-chimeric RNA. A T7
promoter is added 5' of Cas9 by PCR method.
[0530] 2. T7-driven Cas9 and guide-chimeric RNAs are transcribed in
vitro, and Cas9 mRNA is further capped and A-tailed using
commercial kits. RNA products are purified per kit
instructions.
[0531] Hydrodynamic Tail Vein Delivery Methods (for Mouse)
[0532] Guide sequences are cloned into AAV plasmids as described
above and elsewhere in this application.
[0533] In Vitro Validation on Cell Lines
[0534] Transfection
[0535] 1. DNA Plasmid Transfection
[0536] Plasmids carrying guide sequences are transfected into human
embryonic kidney (HEK293T) or human embryonic stem (hES) cells,
other relevant cell types using lipid-, chemical-, or
electroporation-based methods. For a 24-well transfection of
HEK293T cells (.about.260,000 cells), 500 ng of total DNA is
transfected into each single well using Lipofectamine 2000. For a
12-well transfection of hES cells, 1 ug of total DNA is transfected
into a single well using Fugene HD.
[0537] 2. RNA Transfection
[0538] Purified RNA described above is used for transfection into
HEK293T cells. 1-2 ug of RNA may be transfected into .about.260,000
using Lipofectamine 2000 per manufacturer's instruction. RNA
delivery of Cas9 and chimeric RNA is shown in FIG. 28.
[0539] Assay of Indel Formation In Vitro
[0540] Cells are harvested 72-hours post-transfection and assayed
for indel formation as an indication of double-stranded breaks.
[0541] Briefly, genomic region around target sequence is PCR
amplified (.about.400-600 bp amplicon size) using high-fidelity
polymerase. Products are purified, normalized to equal
concentration, and slowly annealed from 95.degree. C. to 4.degree.
C. to allow formation of DNA heteroduplexes. Post annealing, the
Cel-I enzyme is used to cleave heteroduplexes, and resulting
products are separated on a polyacrylamide gel and indel efficiency
calculated.
[0542] In Vivo Proof of Principle in Animal
[0543] Delivery Mechanisms
[0544] AAV or Lentivirus production is described elsewhere.
[0545] Nanoparticle Formulation: RNA Mixed into Nanoparticle
Formulation
[0546] Hydrodynamic tail vein injections with DNA plasmids in mice
are conducted using a commercial kit
[0547] Cas9 and guide sequences are delivered as virus,
nanoparticle-coated RNA mixture, or DNA plasmids, and injected into
subject animals. A parallel set of control animals is injected with
sterile saline, Cas9 and GFP, or guide sequence and GFP alone.
[0548] Three weeks after injection, animals are tested for
amelioration of symptoms and sacrificed. Relevant organ systems
analyzed for indel formation. Phenotypic assays include blood
levels of HDL, LDL, lipids,
[0549] Assay for Indel Formation
[0550] DNA is extracted from tissue using commercial kits; indel
assay will be performed as described for in vitro
demonstration.
[0551] Therapeutic applications of the CRISPR-Cas system are
amenable for achieving tissue-specific and temporally controlled
targeted deletion of candidate disease genes. Examples include
genes involved in cholesterol and fatty acid metabolism, amyloid
diseases, dominant negative diseases, latent viral infections,
among other disorders.
[0552] Examples of a single guide-RNA to introduce targeted indels
at a gene locus
TABLE-US-00020 Disease GENE SPACER PAM Mechanism References
Hypercholes- HMG- GCCAAATTG CGG Knockout Fluvastatin: a review of
its terolemia CR GACGACCCT pharmacology and use in the CG
management of hypercholesterolaemia.(Plosker GL et al. Drugs 1996,
51(3): 433-459) Hypercholes- SQLE CGAGGAGAC TGG Knockout Potential
role of nonstatin terolemia CCCCGTTTC cholesterol lowering agents
GG (Trapani et al. IUBMB Life, Volume 63, Issue 11, pages 964- 971,
November 2011) Hyperlipid- DGAT1 CCCGCCGCC AGG Knockout DGAT1
inhibitors as anti-obesity emia GCCGTGGCT and anti-diabetic agents.
(Birch CG AM et al. Current Opinion in Drug Discovery &
Development Leukemia BCR- TGAGCTCTA AGG Knockout Killing of
leukemic cells with a ABL CGAGATCCA BCR/ABL fusion gene by RNA CA
interference (RNAi.).( Fuchs et al. Oncogene 2002, 21(37):
5716-5724)
[0553] Examples of a pair of guide-RNA to introduce chromosomal
microdeletion at a gene locus
TABLE-US-00021 Disease GENE SPACER PAM Mechanism References
Hyperlipid- PLIN2 CTCAAAATT TGG Micro- Perilipin-2 Null Mice are
emia guide1 CATACCGGT deletion Protected Against Diet-Induced TG
Obesity, Adipose Inflammation Hyperlipid- PLIN2 CGTTAAACA TGG
Micro- and Fatty Liver Disease emia guide2 ACAACCGGA deletion
(McManaman JL et al. The CT Journal of Lipid Research, jlr.M035063.
First Published on Feb. 12, 2013) Hyperlipid- SREBP TTCACCCCCG ggg
Micro- Inhibition of SREBP by a Small emia guide1 CGGCGCTGA
deletion Molecule, Betulin, Improves AT Hyperlipidemia and Insulin
Hyperlipid- SREBP ACCACTACC agg Micro- Resistance and Reduces emia
guide2 AGTCCGTCC deletion Atherosclerotic Plaques (Tang J et AC al.
Cell Metabolism, Volume 13, issue 1, 44-56, 5 Jan. 2011)
Example 19
Targeted Integration of Repair for Genes Carrying Disease-Causing
Mutations; Reconstitution of Enzyme Deficiencies and Other Related
Diseases
[0554] Study Design
[0555] I. Identification and Design of Gene Targets [0556]
Described in Example 22
[0557] II. Cloning of Guide Sequences and Repair Templates into a
Delivery System [0558] Described above in Example 22 [0559]
Applicants clone DNA repair templates to include homology arms with
diseased allele as well a wild-type repair template
[0560] III. In Vitro Validation on Cell Lines [0561] a.
Transfection is described above in Example 22; Cas9, guide RNAs,
and repair template are co-transfected into relevant cell types.
[0562] b. Assay for repair in vitro [0563] i. Applicants harvest
cells 72-hours post-transfection and assay for repair [0564] ii.
Briefly, Applicants amplify genomic region around repair template
PCR using high-fidelity polymerase. Applicants sequence products
for decreased incidence of mutant allele.
[0565] IV. In Vivo Proof of Principle in Animal [0566] a. Delivery
mechanisms are described above Examples 22 and 34. [0567] b. Assay
for repair in vivo [0568] i. Applicants perform the repair assay as
described in the in vitro demonstration.
[0569] V. Therapeutic Applications [0570] The CRISPR-Cas system is
amenable for achieving tissue-specific and temporally controlled
targeted deletion of candidate disease genes. Examples include
genes involved in cholesterol and fatty acid metabolism, amyloid
diseases, dominant negative diseases, latent viral infections,
among other disorders.
[0571] Example of one single missense mutation with repair
template:
TABLE-US-00022 Disease GENE SPACER PAM Mechanism Reference Familial
TTR AGCCTTTCTGA CGG V30M Transthyretin mutations in health amyloid
ACACATGCA repair and disease (Joao et al. Human Mutation,
polyneuropathy Volume 5, Issue 3, pages 191-196, 1995) V30M
CCTGCCATCAATGTGGCCATGCATGTGTTCAGAAAGGCT allele
CCTGCCATCAATGTGGCCGTGCATGTGTTCAGAAAGGCT WT allele
Example 20
Therapeutic Application of the CRISPR-Cas System in Glaucoma,
Amyloidosis, and Huntington's Disease
[0572] Glaucoma: Applicants design guide RNAs to target the first
exon of the mycilin (MYOC) gene. Applicants use adenovirus vectors
(Ad5) to package both Cas9 as well as a guide RNA targeting the
MYOC gene. Applicants inject adenoviral vectors into the trabecular
meshwork where cells have been implicated in the pathophysiology of
glaucoma. Applicants initially test this out in mouse models
carrying the mutated MYOC gene to see whether they improve visual
acuity and decrease pressure in the eyes. Therapeutic application
in humans employ a similar strategy.
[0573] Amyloidosis: Applicants design guide RNAs to target the
first exon of the transthyretin (TTR) gene in the liver. Applicants
use AAV8 to package Cas9 as well as guide RNA targeting the first
exon of the TTR gene. AAV8 has been shown to have efficient
targeting of the liver and will be administered intravenously. Cas9
can be driven either using liver specific promoters such as the
albumin promoter, or using a constitutive promoter. A pol3 promoter
drives the guide RNA.
[0574] Alternatively, Applicants utilize hydrodynamic delivery of
plasmid DNA to knockout the TTR gene. Applicants deliver a plasmid
encoding Cas9 and the guideRNA targeting Exon1 of TTR.
[0575] As a further alternative approach, Applicants administer a
combination of RNA (mRNA for Cas9, and guide RNA). RNA can be
packaged using liposomes such as Invivofectamine from Life
Technologies and delivered intravenously. To reduce RNA-induced
immunogenicity, increase the level of Cas9 expression and guide RNA
stability, Applicants modify the Cas9 mRNA using 5' capping.
Applicants also incorporate modified RNA nucleotides into Cas9 mRNA
and guide RNA to increase their stability and reduce immunogenicity
(e.g. activation of TLR). To increase efficiency, Applicants
administer multiple doses of the virus, DNA, or RNA.
[0576] Huntington's Disease: Applicants design guide RNA based on
allele specific mutations in the HTT gene of patients. For example,
in a patient who is heterozygous for HTT with expanded CAG repeat,
Applicants identify nucleotide sequences unique to the mutant HTT
allele and use it to design guideRNA. Applicants ensure that the
mutant base is located within the last 9 bp of the guide RNA (which
Applicants have ascertained has the ability to discriminate between
single DNA base mismatches between the target size and the guide
RNA).
[0577] Applicants package the mutant HTT allele specific guide RNA
and Cas9 into AAV9 and deliver into the striatum of Huntington's
patients. Virus is injected into the striatum stereotactically via
a craniotomy. AAV9 is known to transduce neurons efficiently.
Applicants drive Cas9 using a neuron specific promoter such as
human Synapsin 1.
Example 21
Therapeutic Application of the CRISPR-Cas System in HIV
[0578] Chronic viral infection is a source of significant morbidity
and mortality. While there exists for many of these viruses
conventional antiviral therapies that effectively target various
aspects of viral replication, current therapeutic modalities are
usually non-curative in nature due to "viral latency." By its
nature, viral latency is characterized by a dormant phase in the
viral life cycle without active viral production. During this
period, the virus is largely able to evade both immune surveillance
and conventional therapeutics allowing for it to establish
long-standing viral reservoirs within the host from which
subsequent re-activation can permit continued propagation and
transmission of virus. Key to viral latency is the ability to
stably maintain the viral genome, accomplished either through
episomal or proviral latency, which stores the viral genome in the
cytoplasm or integrates it into the host genome, respectively. In
the absence of effective vaccinations which would prevent primary
infection, chronic viral infections characterized by latent
reservoirs and episodes of lytic activity can have significant
consequences: human papilloma virus (HPV) can result in cervical
cancer, hepatitis C virus (HCV) predisposes to hepatocellular
carcinoma, and human immunodeficiency virus eventually destroys the
host immune system resulting in susceptibility to opportunistic
infections. As such, these infections require life-long use of
currently available antiviral therapeutics. Further complicating
matters is the high mutability of many of these viral genomes which
lead to the evolution of resistant strains for which there exists
no effective therapy.
[0579] The CRISPR-Cas system is a bacterial adaptive immune system
able to induce double-stranded DNA breaks (DSB) in a
multiplex-able, sequence-specific manner and has been recently
re-constituted within mammalian cell systems. It has been shown
that targeting DNA with one or numerous guide-RNAs can result in
both indels and deletions of the intervening sequences,
respectively. As such, this new technology represents a means by
which targeted and multiplexed DNA mutagenesis can be accomplished
within a single cell with high efficiency and specificity.
Consequently, delivery of the CRISPR-Cas system directed against
viral DNA sequences could allow for targeted disruption and
deletion of latent viral genomes even in the absence of ongoing
viral production.
[0580] As an example, chronic infection by HIV-1 represents a
global health issue with 33 million individuals infected and an
annual incidence of 2.6 million infections. The use of the
multimodal highly active antiretroviral therapy (HAART), which
simultaneously targets multiple aspects of viral replication, has
allowed HIV infection to be largely managed as a chronic, not
terminal, illness. Without treatment, progression of HIV to AIDS
occurs usually within 9-10 years resulting in depletion of the host
immune system and occurrence of opportunistic infections usually
leading to death soon thereafter. Secondary to viral latency,
discontinuation of HAART invariably leads to viral rebound.
Moreover, even temporary disruptions in therapy can select for
resistant strains of HIV uncontrollable by available means.
Additionally, the costs of HAART therapy are significant: within
the US $10,000-15,0000 per person per year. As such, treatment
approaches directly targeting the HIV genome rather than the
process of viral replication represents a means by which
eradication of latent reservoirs could allow for a curative
therapeutic option.
[0581] Development and delivery of an HIV-1 targeted CRISPR-Cas
system represents a unique approach differentiable from existing
means of targeted DNA mutagenesis, i.e. ZFN and TALENs, with
numerous therapeutic implications. Targeted disruption and deletion
of the HIV-1 genome by CRISPR-mediated DSB and indels in
conjunction with HAART could allow for simultaneous prevention of
active viral production as well as depletion of latent viral
reservoirs within the host.
[0582] Once integrated within the host immune system, the
CRISPR-Cas system allows for generation of a HIV-1 resistant
sub-population that, even in the absence of complete viral
eradication, could allow for maintenance and re-constitution of
host immune activity. This could potentially prevent primary
infection by disruption of the viral genome preventing viral
production and integration, representing a means to "vaccination".
Multiplexed nature of the CRISPR-Cas system allows targeting of
multiple aspects of the genome simultaneously within individual
cells.
[0583] As in HAART, viral escape by mutagenesis is minimized by
requiring acquisition of multiple adaptive mutations concurrently.
Multiple strains of HIV-1 can be targeted simultaneously which
minimizes the chance of super-infection and prevents subsequent
creation of new recombinants strains. Nucleotide, rather than
protein, mediated sequence-specificity of the CRISPR-Cas system
allows for rapid generation of therapeutics without need for
significantly altering delivery mechanism.
[0584] In order to accomplish this, Applicants generate CRISPR-Cas
guide RNAs that target the vast majority of the HIV-1 genome while
taking into account HIV-1 strain variants for maximal coverage and
effectiveness. Sequence analyses of genomic conservation between
HIV-1 subtypes and variants should allow for targeting of flanking
conserved regions of the genome with the aims of deleting
intervening viral sequences or induction of frame-shift mutations
which would disrupt viral gene functions.
[0585] Applicants accomplish delivery of the CRISPR-Cas system by
conventional adenoviral or lentiviral-mediated infection of the
host immune system. Depending on approach, host immune cells could
be a) isolated, transduced with CRISPR-Cas, selected, and
re-introduced in to the host or b) transduced in vivo by systemic
delivery of the CRISPR-Cas system. The first approach allows for
generation of a resistant immune population whereas the second is
more likely to target latent viral reservoirs within the host.
TABLE-US-00023 Examples of potential HIV-1 targeted spacers adapted
from Mcintyre et al, which generated shRNAs against HIV-1 optimized
for maximal coverage of HIV-1 variants. CACTGCTTAAGCCTCGCTCGAGG
TCACCAGCAATATTCGCTCGAGG CACCAGCAATATTCCGCTCGAGG
TAGCAACAGACATACGCTCGAGG GGGCAGTAGTAATACGCTCGAGG
CCAATTCCCATACATTATTGTAC
Example 22
Targeted Correction of deltaF508 or Other Mutations in Cystic
Fibrosis
[0586] An aspect of the invention provides for a pharmaceutical
composition that may comprise an CRISPR-Cas gene therapy particle
and a biocompatible pharmaceutical carrier. According to another
aspect, a method of gene therapy for the treatment of a subject
having a mutation in the CFTR gene comprises administering a
therapeutically effective amount of a CRISPR-Cas gene therapy
particle to the cells of a subject.
[0587] This Example demonstrates gene transfer or gene delivery of
a CRISPR-Cas system in airways of subject or a patient in need
thereof, suffering from cystic fibrosis or from cystic fibrosis
related symptoms, using adeno-associated virus (AAV) particles.
[0588] Study Design: Subjects or patients in need there of: Human,
non-primate human, canine, feline, bovine, equine and other
domestic animals, related. This study tests efficacy of gene
transfer of a CRISPR-Cas system by a AAV vector. Applicants
determine transgene levels sufficient for gene expression and
utilize a CRISPR-Cas system comprising a Cas9 enzyme to target
deltaF508 or other CFTR-inducing mutations.
[0589] The treated subjects receive pharmaceutically effective
amount of aerosolized AAV vector system per lung endobronchially
delivered while spontaneously breathing. The control subjects
receive equivalent amount of a pseudotyped AAV vector system with
an internal control gene. The vector system may be delivered along
with a pharmaceutically acceptable or biocompatible pharmaceutical
carrier. Three weeks or an appropriate time interval following
vector administration, treated subjects are tested for amelioration
of cystic fibrosis related symptoms.
[0590] Applicants use an adenovirus or an AAV particle.
[0591] Applicants clone the following gene constructs, each
operably linked to one or more regulatory sequences (Cbh or EF1a
promoter for Cas9, U6 or H1 promoter for chimeric guide RNA), into
one or more adenovirus or AAV vectors or any other compatible
vector: A CFTRdelta508 targeting chimeric guide RNA (FIG. 31B), a
repair template for deltaF508 mutation (FIG. 31C) and a codon
optimized Cas9 enzyme with optionally one or more nuclear
localization signal or sequence(s) (NLS(s)), e.g., two (2)
NLSs.
[0592] Identification of Cas9 Target Site
[0593] Applicants analyzed the human CFTR genomic locus and
identified the Cas9 target site (FIG. 31A). (PAM may contain a NGG
or a NNAGAAW motif).
[0594] Gene Repair Strategy
[0595] Applicants introduce an adenovirus/AAV vector system
comprising a Cas9 (or Cas9 nickase) and the guide RNA along with a
adenovirus/AAV vector system comprising the homology repair
template containing the F508 residue into the subject via one of
the methods of delivery discussed earlier. The CRISPR-Cas system is
guided by the CFTRdelta 508 chimeric guide RNA and targets a
specific site of the CFTR genomic locus to be nicked or cleaved.
After cleavage, the repair template is inserted into the cleavage
site via homologous recombination correcting the deletion that
results in cystic fibrosis or causes cystic fibrosis related
symptoms. This strategy to direct delivery and provide systemic
introduction of CRISPR systems with appropriate guide RNAs can be
employed to target genetic mutations to edit or otherwise
manipulate genes that cause metabolic, liver, kidney and protein
diseases and disorders such as those in Table B.
Example 23
Generation of Gene Knockout Cell Library
[0596] This example demonstrates how to generate a library of cells
where each cell has a single gene knocked out:
[0597] Applicants make a library of ES cells where each cell has a
single gene knocked out, and the entire library of ES cells will
have every single gene knocked out. This library is useful for the
screening of gene function in cellular processes as well as
diseases.
[0598] To make this cell library, Applicants integrate Cas9 driven
by an inducible promoter (e.g. doxycycline inducible promoter) into
the ES cell. In addition, Applicants integrate a single guide RNA
targeting a specific gene in the ES cell. To make the ES cell
library, Applicants simply mix ES cells with a library of genes
encoding guide RNAs targeting each gene in the human genome.
Applicants first introduce a single BxB1 attB site into the AAVS1
locus of the human ES cell. Then Applicants use the BxB1 integrase
to facilitate the integration of individual guide RNA genes into
the BxB1 attB site in AAVS1 locus. To facilitate integration, each
guide RNA gene is contained on a plasmid that carries of a single
attP site. This way BxB1 will recombine the attB site in the genome
with the attP site on the guide RNA containing plasmid.
[0599] To generate the cell library, Applicants take the library of
cells that have single guide RNAs integrated and induce Cas9
expression. After induction, Cas9 mediates double strand break at
sites specified by the guide RNA. To verify the diversity of this
cell library, Applicants carry out whole exome sequencing to ensure
that Applicants are able to observe mutations in every single
targeted gene. This cell library can be used for a variety of
applications, including whole library-based screens, or can be
sorted into individual cell clones to facilitate rapid generation
of clonal cell lines with individual human genes knocked out.
Example 24
Engineering of Microalgae Using Cas9
[0600] Methods of Delivering Cas9
[0601] Method 1: Applicants deliver Cas9 and guide RNA using a
vector that expresses Cas9 under the control of a constitutive
promoter such as Hsp70A-Rbc S2 or Beta2-tubulin.
[0602] Method 2: Applicants deliver Cas9 and T7 polymerase using
vectors that expresses Cas9 and T7 polymerase under the control of
a constitutive promoter such as Hsp70A-Rbc S2 or Beta2-tubulin.
Guide RNA will be delivered using a vector containing T7 promoter
driving the guide RNA.
[0603] Method 3: Applicants deliver Cas9 mRNA and in vitro
transcribed guide RNA to algae cells. RNA can be in vitro
transcribed. Cas9 mRNA will consist of the coding region for Cas9
as well as 3'UTR from Cop1 to ensure stabilization of the Cas9
mRNA.
[0604] For Homologous recombination, Applicants provide an
additional homology directed repair template.
[0605] Sequence for a cassette driving the expression of Cas9 under
the control of beta-2 tubulin promoter, followed by the 3' UTR of
Cop1.
TABLE-US-00024 TCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTAGGGCGGGCTGCGA
GACGGCTTCCCGGCGCTGCATGCAACACCGATGATGCTTCGACCCCCCGA
AGCTCCTTCGGGGCTGCATGGGCGCTCCGATGCCGCTCCAGGGCGAGCGC
TGTTTAAATAGCCAGGCCCCCGATTGCAAAGACATTATAGCGAGCTACCA
AAGCCATATTCAAACACCTAGATCACTACCACTTCTACACAGGCCACTCG
AGCTTGTGATCGCACTCCGCTAAGGGGGCGCCTCTTCCTCTTCGTTTCAG
TCACAACCCGCAAACATGTACCCATACGATGTTCCAGATTACGCTTCGCC
GAAGAAAAAGCGCAAGGTCGAAGCGTCCGACAAGAAGTACAGCATCGGCC
TGGACATCGGCACCAACTCTGTGGGCTGGGCCGTGATCACCGACGAGTAC
AAGGTGCCCAGCAAGAAATTCAAGGTGCTGGGCAACACCGACCGGCACAG
CATCAAGAAGAACCTGATCGGAGCCCTGCTGTTCGACAGCGGCGAAACAG
CCGAGGCCACCCGGCTGAAGAGAACCGCCAGAAGAAGATACACCAGACGG
AAGAACCGGATCTGCTATCTGCAAGAGATCTTCAGCAACGAGATGGCCAA
GGTGGACGACAGCTTCTTCCACAGACTGGAAGAGTCCTTCCTGGTGGAAG
AGGATAAGAAGCACGAGCGGCACCCCATCTTCGGCAACATCGTGGACGAG
GTGGCCTACCACGAGAAGTACCCCACCATCTACCACCTGAGAAAGAAACT
GGTGGACAGCACCGACAAGGCCGACCTGCGGCTGATCTATCTGGCCCTGG
CCCACATGATCAAGTTCCGGGGCCACTTCCTGATCGAGGGCGACCTGAAC
CCCGACAACAGCGACGTGGACAAGCTGTTCATCCAGCTGGTGCAGACCTA
CAACCAGCTGTTCGAGGAAAACCCCATCAACGCCAGCGGCGTGGACGCCA
AGGCCATCCTGTCTGCCAGACTGAGCAAGAGCAGACGGCTGGAAAATCTG
ATCGCCCAGCTGCCCGGCGAGAAGAAGAATGGCCTGTTCGGCAACCTGAT
TGCCCTGAGCCTGGGCCTGACCCCCAACTTCAAGAGCAACTTCGACCTGG
CCGAGGATGCCAAACTGCAGCTGAGCAAGGACACCTACGACGACGACCTG
GACAACCTGCTGGCCCAGATCGGCGACCAGTACGCCGACCTGTTTCTGGC
CGCCAAGAACCTGTCCGACGCCATCCTGCTGAGCGACATCCTGAGAGTGA
ACACCGAGATCACCAAGGCCCCCCTGAGCGCCTCTATGATCAAGAGATAC
GACGAGCACCACCAGGACCTGACCCTGCTGAAAGCTCTCGTGCGGCAGCA
GCTGCCTGAGAAGTACAAAGAGATTTTCTTCGACCAGAGCAAGAACGGCT
ACGCCGGCTACATTGACGGCGGAGCCAGCCAGGAAGAGTTCTACAAGTTC
ATCAAGCCCATCCTGGAAAAGATGGACGGCACCGAGGAACTGCTCGTGAA
GCTGAACAGAGAGGACCTGCTGCGGAAGCAGCGGACCTTCGACAACGGCA
GCATCCCCCACCAGATCCACCTGGGAGAGCTGCACGCCATTCTGCGGCGG
CAGGAAGATTTTTACCCATTCCTGAAGGACAACCGGGAAAAGATCGAGAA
GATCCTGACCTTCCGCATCCCCTACTACGTGGGCCCTCTGGCCAGGGGAA
ACAGCAGATTCGCCTGGATGACCAGAAAGAGCGAGGAAACCATCACCCCC
TGGAACTTCGAGGAAGTGGTGGACAAGGGCGCTTCCGCCCAGAGCTTCAT
CGAGCGGATGACCAACTTCGATAAGAACCTGCCCAACGAGAAGGTGCTGC
CCAAGCACAGCCTGCTGTACGAGTACTTCACCGTGTATAACGAGCTGACC
AAAGTGAAATACGTGACCGAGGGAATGAGAAAGCCCGCCTTCCTGAGCGG
CGAGCAGAAAAAGGCCATCGTGGACCTGCTGTTCAAGACCAACCGGAAAG
TGACCGTGAAGCAGCTGAAAGAGGACTACTTCAAGAAAATCGAGTGCTTC
GACTCCGTGGAAATCTCCGGCGTGGAAGATCGGTTCAACGCCTCCCTGGG
CACATACCACGATCTGCTGAAAATTATCAAGGACAAGGACTTCCTGGACA
ATGAGGAAAACGAGGACATTCTGGAAGATATCGTGCTGACCCTGACACTG
TTTGAGGACAGAGAGATGATCGAGGAACGGCTGAAAACCTATGCCCACCT
GTTCGACGACAAAGTGATGAAGCAGCTGAAGCGGCGGAGATACACCGGCT
GGGGCAGGCTGAGCCGGAAGCTGATCAACGGCATCCGGGACAAGCAGTCC
GGCAAGACAATCCTGGATTTCCTGAAGTCCGACGGCTTCGCCAACAGAAA
CTTCATGCAGCTGATCCACGACGACAGCCTGACCTTTAAAGAGGACATCC
AGAAAGCCCAGGTGTCCGGCCAGGGCGATAGCCTGCACGAGCACATTGCC
AATCTGGCCGGCAGCCCCGCCATTAAGAAGGGCATCCTGCAGACAGTGAA
GGTGGTGGACGAGCTCGTGAAAGTGATGGGCCGGCACAAGCCCGAGAACA
TCGTGATCGAAATGGCCAGAGAGAACCAGACCACCCAGAAGGGACAGAAG
AACAGCCGCGAGAGAATGAAGCGGATCGAAGAGGGCATCAAAGAGCTGGG
CAGCCAGATCCTGAAAGAACACCCCGTGGAAAACACCCAGCTGCAGAACG
AGAAGCTGTACCTGTACTACCTGCAGAATGGGCGGGATATGTACGTGGAC
CAGGAACTGGACATCAACCGGCTGTCCGACTACGATGTGGACCATATCGT
GCCTCAGAGCTTTCTGAAGGACGACTCCATCGACAACAAGGTGCTGACCA
GAAGCGACAAGAACCGGGGCAAGAGCGACAACGTGCCCTCCGAAGAGGTC
GTGAAGAAGATGAAGAACTACTGGCGGCAGCTGCTGAACGCCAAGCTGAT
TACCCAGAGAAAGTTCGACAATCTGACCAAGGCCGAGAGAGGCGGCCTGA
GCGAACTGGATAAGGCCGGCTTCATCAAGAGACAGCTGGTGGAAACCCGG
CAGATCACAAAGCACGTGGCACAGATCCTGGACTCCCGGATGAACACTAA
GTACGACGAGAATGACAAGCTGATCCGGGAAGTGAAAGTGATCACCCTGA
AGTCCAAGCTGGTGTCCGATTTCCGGAAGGATTTCCAGTTTTACAAAGTG
CGCGAGATCAACAACTACCACCACGCCCACGACGCCTACCTGAACGCCGT
CGTGGGAACCGCCCTGATCAAAAAGTACCCTAAGCTGGAAAGCGAGTTCG
TGTACGGCGACTACAAGGTGTACGACGTGCGGAAGATGATCGCCAAGAGC
GAGCAGGAAATCGGCAAGGCTACCGCCAAGTACTTCTTCTACAGCAACAT
CATGAACTTTTTCAAGACCGAGATTACCCTGGCCAACGGCGAGATCCGGA
AGCGGCCTCTGATCGAGACAAACGGCGAAACCGGGGAGATCGTGTGGGAT
AAGGGCCGGGATTTTGCCACCGTGCGGAAAGTGCTGAGCATGCCCCAAGT
GAATATCGTGAAAAAGACCGAGGTGCAGACAGGCGGCTTCAGCAAAGAGT
CTATCCTGCCCAAGAGGAACAGCGATAAGCTGATCGCCAGAAAGAAGGAC
TGGGACCCTAAGAAGTACGGCGGCTTCGACAGCCCCACCGTGGCCTATTC
TGTGCTGGTGGTGGCCAAAGTGGAAAAGGGCAAGTCCAAGAAACTGAAGA
GTGTGAAAGAGCTGCTGGGGATCACCATCATGGAAAGAAGCAGCTTCGAG
AAGAATCCCATGCTGCCTAAGTACTCCCTGTTCGAGCTGGAAAACGGCCG
GAAGAGAATGCTGGCCTCTGCCGGCGAACTGCAGAAGGGAAACGAACTGG
CCCTGCCCTCCAAATATGTGAACTTCCTGTACCTGGCCAGCCACTATGAG
AAGCTGAAGGGCTCCCCCGAGGATAATGAGCAGAAACAGCTGTTTGTGGA
ACAGCACAAGCACTACCTGGACGAGATCATCGAGCAGATCAGCGAGTTCT
CCAAGAGAGTGATCCTGGCCGACGCTAATCTGGACAAAGTGCTGTCCGCC
TACAACAAGCACCGGGATAAGCCCATCAGAGAGCAGGCCGAGAATATCAT
CCACCTGTTTACCCTGACCAATCTGGGAGCCCCTGCCGCCTTCAAGTACT
TTGACACCACCATCGACCGGAAGAGGTACACCAGCACCAAAGAGGTGCTG
GACGCCACCCTGATCCACCAGAGCATCACCGGCCTGTACGAGACACGGAT
CGACCTGTCTCAGCTGGGAGGCGACAGCCCCAAGAAGAAGAGAAAGGTGG
AGGCCAGCTAAGGATCCGGCAAGACTGGCCCCGCTTGGCAACGCAACAGT
GAGCCCCTCCCTAGTGTGTTTGGGGATGTGACTATGTATTCGTGTGTTGG
CCAACGGGTCAACCCGAACAGATTGATACCCGCCTTGGCATTTCCTGTCA
GAATGTAACGTCAGTTGATGGTACT
[0606] Sequence for a cassette driving the expression of T7
polymerase under the control of beta-2 tubulin promoter, followed
by the 3' UTR of Cop1:
TABLE-US-00025 TCTTTCTTGCGCTATGACACTTCCAGCAAAAGGTAGGGCGGGCTGCGA
GACGGCTTCCCGGCGCTGCATGCAACACCGATGATGCTTCGACCCCCCGA
AGCTCCTTCGGGGCTGCATGGGCGCTCCGATGCCGCTCCAGGGCGAGCGC
TGTTTAAATAGCCAGGCCCCCGATTGCAAAGACATTATAGCGAGCTACCA
AAGCCATATTCAAACACCTAGATCACTACCACTTCTACACAGGCCACTCG
AGCTTGTGATCGCACTCCGCTAAGGGGGCGCCTCTTCCTCTTCGTTTCAG
TCACAACCCGCAAACatgcctaagaagaagaggaaggttaacacgattaa
catcgctaagaacgacttctctgacatcgaactggctgctatcccgttca
acactctggctgaccattacggtgagcgtttagctcgcgaacagttggcc
cttgagcatgagtcttacgagatgggtgaagcacgcttccgcaagatgta
gagcgtcaacttaaagctggtgaggttgcggataacgctgccgccaagcc
tctcatcactaccctactccctaagatgattgcacgcatcaacgactggt
ttgaggaagtgaaagctaagcgcggcaagcgcccgacagccttccagttc
ctgcaagaaatcaagccggaagccgtagcgtacatcaccattaagaccac
tctggcttgcctaaccagtgctgacaatacaaccgttcaggctgtagcaa
gcgcaatcggtcgggccattgaggacgaggctcgcttcggtcgtatccgt
gaccttgaagctaagcacttcaagaaaaacgttgaggaacaactcaacaa
gcgcgtagggcacgtctacaagaaagcatttatgcaagttgtcgaggctg
acatgctctctaagggtctactcggtggcgaggcgtggtcttcgtggcat
aaggaagactctattcatgtaggagtacgcgcatcgagatgctcattgag
tcaaccggaatggttagcttacaccgccaaaatgctggcgtagtaggtca
agactctgagactatcgaactcgcacctgaatacgctgaggctatcgcaa
cccgtgcaggtgcgctggctggcatctctccgatgttccaaccttgcgta
gttcctcctaagccgtggactggcattactggtggtggctattgggctaa
cggtcgtcgtcctctggcgctggtgcgtactcacagtaagaaagcactga
tgcgctacgaagacgtttacatgcctgaggtgtacaaagcgattaacatt
gcgcaaaacaccgcatggaaaatcaacaagaaagtcctagcggtcgccaa
cgtaatcaccaagtggaagcattgtccggtcgaggacatccctgcgattg
agcgtgaagaactcccgatgaaaccggaagacatcgacatgaatcctgag
gctctcaccgcgtggaaacgtgctgccgctgctgtgtaccgcaaggacaa
ggctcgcaagtctcgccgtatcagccttgagttcatgcttgagcaagcca
ataagtttgctaaccataaggccatctggttcccttacaacatggactgg
cgcggtcgtgtttacgctgtgtcaatgttcaacccgcaaggtaacgatat
gaccaaaggactgcttacgctggcgaaaggtaaaccaatcggtaaggaag
gttactactggctgaaaatccacggtgcaaactgtgcgggtgtcgacaag
gttccgttccctgagcgcatcaagttcattgaggaaaaccacgagaacat
catggcttgcgctaagtctccactggagaacacttggtgggctgagcaag
attctccgttctgcttccttgcgttctgctttgagtacgctggggtacag
caccacggcctgagctataactgctcccttccgctggcgtttgacgggtc
ttgctctggcatccagcacttctccgcgatgctccgagatgaggtaggtg
gtcgcgcggttaacttgcttcctagtgaaaccgttcaggacatctacggg
attgttgctaagaaagtcaacgagattctacaagcagacgcaatcaatgg
gaccgataacgaagtagttaccgtgaccgatgagaacactggtgaaatct
ctgagaaagtcaagctgggcactaaggcactggctggtcaatggctggct
tacggtgttactcgcagtgtgactaagcgttcagtcatgacgctggctta
cgggtccaaagagttcggcttccgtcaacaagtgctggaagataccattc
agccagctattgattccggcaagggtctgatgttcactcagccgaatcag
gctgctggatacatggctaagctgatttgggaatctgtgagcgtgacggt
ggtagctgcggttgaagcaatgaactggcttaagtctgctgctaagctgc
tggctgctgaggtcaaagataagaagactggagagattcttcgcaagcgt
tgcgctgtgcattgggtaactcctgatggtttccctgtgtggcaggaata
caagaagcctattcagacgcgcttgaacctgatgttcctcggtcagttcc
gcttacagcctaccattaacaccaacaaagatagcgagattgatgcacac
aaacaggagtctggtatcgctcctaactttgtacacagccaagacggtag
ccaccttcgtaagactgtagtgtgggcacacgagaagtacggaatcgaat
cttttgcactgattcacgactccttcggtacgattccggctgacgctgcg
aacctgttcaaagcagtgcgcgaaactatggttgacacatatgagtcttg
tgatgtactggctgatttctacgaccagttcgctgaccagttgcacgagt
ctcaattggacaaaatgccagcacttccggctaaaggtaacttgaacctc
cgtgacatcttagagtcggacttcgcgttcgcgtaaGGATCCGGCAAGAC
TGGCCCCGCTTGGCAACGCAACAGTGAGCCCCTCCCTAGTGTGTTTGGGG
ATGTGACTATGTATTCGTGTGTTGGCCAACGGGTCAACCCGAACAGATTG
ATACCCGCCTTGGCATTTCCTGTCAGAATGTAACGTCAGTTGATGGTACT
[0607] Sequence of guide RNA driven by the T7 promoter (T7
promoter, Ns represent targeting sequence):
TABLE-US-00026 gaaatTAATACGACTCACTATANNNNNNNNNNNNNNNNNNNNgttttaga
gctaGAAAtagcaagttaaaataaggctagtccgttatcaacttgaaaaa
gtggcaccgagtcggtgcttttttt
[0608] Gene Delivery:
[0609] Chlamydomonas reinhardtii strain CC-124 and CC-125 from the
Chlamydomonas Resource Center will be used for electroporation.
Electroporation protocol follows standard recommended protocol from
the GeneArt Chlamydomonas Engineering kit.
[0610] Also, Applicants generate a line of Chlamydomonas
reinhardtii that expresses Cas9 constitutively. This can be done by
using pChlamy1 (linearized using PvuI) and selecting for hygromycin
resistant colonies. Sequence for pChlamy1 containing Cas9 is below.
In this way to achieve gene knockout one simply needs to deliver
RNA for the guideRNA. For homologous recombination Applicants
deliver guideRNA as well as a linearized homologous recombination
template.
[0611] pChlamy1-Cas9:
TABLE-US-00027 TGCGGTATTTCACACCGCATCAGGTGGCACTTTTCGGGGAAATGTGC
GCGGAACCCCTATTTGTTTATTTTTCTAAATACATTCAAATATGTATCCG
CTCATGAGATTATCAAAAAGGATCTTCACCTAGATCCTTTTAAATTAAAA
ATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACA
GTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTT
CGTTCATCCATAGTTGCCTGACTCCCCGTCGTGTAGATAACTACGATACG
GGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCAC
GCTCACCGGCTCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCC
GAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCCAGTCTATTAA
TTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCA
ACGTTGTTGCCATTGCTACAGGCATCGTGGTGTCACGCTCGTCGTTTGGT
ATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATC
CCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATCGTTG
TCAGAAGTAAGTTGGCCGCAGTGTTATCACTCATGGTTATGGCAGCACTG
CATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGG
TGAGTACTCAACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTT
GCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACATAGCAGAACT
TTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAG
GATCTTACCGCTGTTGAGATCCAGTTCGATGTAACCCACTCGTGCACCCA
ACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAA
ACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATG
TTGAATACTCATACTCTTCCTTTTTCAATATTATTGAAGCATTTATCAGG
GTTATTGTCTCATGACCAAAATCCCTTAACGTGAGTTTTCGTTCCACTGA
GCGTCAGACCCCGTAGAAAAGATCAAAGGATCTTCTTGAGATCCTTTTTT
TCTGCGCGTAATCTGCTGCTTGCAAACAAAAAAACCACCGCTACCAGCGG
TGGTTTGTTTGCCGGATCAAGAGCTACCAACTCTTTTTCCGAAGGTAACT
GGCTTCAGCAGAGCGCAGATACCAAATACTGTTCTTCTAGTGTAGCCGTA
GTTAGGCCACCACTTCAAGAACTCTGTAGCACCGCCTACATACCTCGCTC
TGCTAATCCTGTTACCAGTGGCTGTTGCCAGTGGCGATAAGTCGTGTCTT
ACCGGGTTGGACTCAAGACGATAGTTACCGGATAAGGCGCAGCGGTCGGG
CTGAACGGGGGGTTCGTGCACACAGCCCAGCTTGGAGCGAACGACCTACA
CCGAACTGAGATACCTACAGCGTGAGCTATGAGAAAGCGCCACGCTTCCC
GAAGGGAGAAAGGCGGACAGGTATCCGGTAAGCGGCAGGGTCGGAACAGG
AGAGCGCACGAGGGAGCTTCCAGGGGGAAACGCCTGGTATCTTTATAGTC
CTGTCGGGTTTCGCCACCTCTGACTTGAGCGTCGATTTTTGTGATGCTCG
TCAGGGGGGCGGAGCCTATGGAAAAACGCCAGCAACGCGGCCTTTTTACG
GTTCCTGGCCTTTTGCTGGCCTTTTGCTCACATGTTCTTTCCTGCGTTAT
CCCCTGATTCTGTGGATAACCGTATTACCGCCTTTGAGTGAGCTGATACC
GCTCGCCGCAGCCGAACGACCGAGCGCAGCGAGTCAGTGAGCGAGGAAGC
GGTCGCTGAGGCTTGACATGATTGGTGCGTATGTTTGTATGAAGCTACAG
GACTGATTTGGCGGGCTATGAGGGCGGGGGAAGCTCTGGAAGGGCCGCGA
TGGGGCGCGCGGCGTCCAGAAGGCGCCATACGGCCCGCTGGCGGCACCCA
TCCGGTATAAAAGCCCGCGACCCCGAACGGTGACCTCCACTTTCAGCGAC
AAACGAGCACTTATACATACGCGACTATTCTGCCGCTATACATAACCACT
CAGCTAGCTTAAGATCCCATCAAGCTTGCATGCCGGGCGCGCCAGAAGGA
GCGCAGCCAAACCAGGATGATGTTTGATGGGGTATTTGAGCACTTGCAAC
CCTTATCCGGAAGCCCCCTGGCCCACAAAGGCTAGGCGCCAATGCAAGCA
GTTCGCATGCAGCCCCTGGAGCGGTGCCCTCCTGATAAACCGGCCAGGGG
GCCTATGTTCTTTACTTTTTTACAAGAGAAGTCACTCAACATCTTAAAAT
GGCCAGGTGAGTCGACGAGCAAGCCCGGCGGATCAGGCAGCGTGCTTGCA
GATTTGACTTGCAACGCCCGCATTGTGTCGACGAAGGCTTTTGGCTCCTC
TGTCGCTGTCTCAAGCAGCATCTAACCCTGCGTCGCCGTTTCCATTTGCA
GGAGATTCGAGGTACCATGTACCCATACGATGTTCCAGATTACGCTTCGC
CGAAGAAAAAGCGCAAGGTCGAAGCGTCCGACAAGAAGTACAGCATCGGC
CTGGACATCGGCACCAACTCTGTGGGCTGGGCCGTGATCACCGACGAGTA
CAAGGTGCCCAGCAAGAAATTCAAGGTGCTGGGCAACACCGACCGGCACA
GCATCAAGAAGAACCTGATCGGAGCCCTGCTGTTCGACAGCGGCGAAACA
GCCGAGGCCACCCGGCTGAAGAGAACCGCCAGAAGAAGATACACCAGACG
GAAGAACCGGATCTGCTATCTGCAAGAGATCTTCAGCAACGAGATGGCCA
AGGTGGACGACAGCTTCTTCCACAGACTGGAAGAGTCCTTCCTGGTGGAA
GAGGATAAGAAGCACGAGCGGCACCCCATCTTCGGCAACATCGTGGACGA
GGTGGCCTACCACGAGAAGTACCCCACCATCTACCACCTGAGAAAGAAAC
TGGTGGACAGCACCGACAAGGCCGACCTGCGGCTGATCTATCTGGCCCTG
GCCCACATGATCAAGTTCCGGGGCCACTTCCTGATCGAGGGCGACCTGAA
CCCCGACAACAGCGACGTGGACAAGCTGTTCATCCAGCTGGTGCAGACCT
ACAACCAGCTGTTCGAGGAAAACCCCATCAACGCCAGCGGCGTGGACGCC
AAGGCCATCCTGTCTGCCAGACTGAGCAAGAGCAGACGGCTGGAAAATCG
ATCGCCCAGCTGCCCGGCGAGAAGAAGAATGGCCTGTTCGGCAACCTGAT
TGCCCTGAGCCTGGGCCTGACCCCCAACTTCAAGAGCAACTTCGACCTGG
CCGAGGATGCCAAACTGCAGCTGAGCAAGGACACCTACGACGACGACCTG
GACAACCTGCTGGCCCAGATCGGCGACCAGTACGCCGACCTGTTTCTGGC
CGCCAAGAACCTGTCCGACGCCATCCTGCTGAGCGACATCCTGAGAGTGA
ACACCGAGATCACCAAGGCCCCCCTGAGCGCCTCTATGATCAAGAGATAC
GACGAGCACCACCAGGACCTGACCCTGCTGAAAGCTCTCGTGCGGCAGCA
GCTGCCTGAGAAGTACAAAGAGATTTTCTTCGACCAGAGCAAGAACGGCT
ACGCCGGCTACATTGACGGCGGAGCCAGCCAGGAAGAGTTCTACAAGTTC
ATCAAGCCCATCCTGGAAAAGATGGACGGCACCGAGGAACTGCTCGTGAA
GCTGAACAGAGAGGACCTGCTGCGGAAGCAGCGGACCTTCGACAACGGCA
GCATCCCCCACCAGATCCACCTGGGAGAGCTGCACGCCATTCTGCGGCGG
CAGGAAGATTTTTACCCATTCCTGAAGGACAACCGGGAAAAGATCGAGAA
GATCCTGACCTTCCGCATCCCCTACTACGTGGGCCCTCTGGCCAGGGGAA
ACAGCAGATTCGCCTGGATGACCAGAAAGAGCGAGGAAACCATCACCCCC
TGGAACTTCGAGGAAGTGGTGGACAAGGGCGCTTCCGCCCAGAGCTTCAT
CGAGCGGATGACCAACTTCGATAAGAACCTGCCCAACGAGAAGGTGCTGC
CCAAGCACAGCCTGCTGTACGAGTACTTCACCGTGTATAACGAGCTGACC
AAAGTGAAATACGTGACCGAGGGAATGAGAAAGCCCGCCTTCCTGAGCGG
CGAGCAGAAAAAGGCCATCGTGGACCTGCTGTTCAAGACCAACCGGAAAG
TGACCGTGAAGCAGCTGAAAGAGGACTACTTCAAGAAAATCGAGTGCTTC
GACTCCGTGGAAATCTCCGGCGTGGAAGATCGGTTCAACGCCTCCCTGGG
CACATACCACGATCTGCTGAAAATTATCAAGGACAAGGACTTCCTGGACA
ATGAGGAAAACGAGGACATTCTGGAAGATATCGTGCTGACCCTGACACTG
TTTGAGGACAGAGAGATGATCGAGGAACGGCTGAAAACCTATGCCCACCT
GTTCGACGACAAAGTGATGAAGCAGCTGAAGCGGCGGAGATACACCGGCT
GGGGCAGGCTGAGCCGGAAGCTGATCAACGGCATCCGGGACAAGCAGTCC
GGCAAGACAATCCTGGATTTCCTGAAGTCCGACGGCTTCGCCAACAGAAA
CTTCATGCAGCTGATCCACGACGACAGCCTGACCTTTAAAGAGGACATCC
AGAAAGCCCAGGTGTCCGGCCAGGGCGATAGCCTGCACGAGCACATTGCC
AATCTGGCCGGCAGCCCCGCCATTAAGAAGGGCATCCTGCAGACAGTGAA
GGTGGTGGACGAGCTCGTGAAAGTGATGGGCCGGCACAAGCCCGAGAACA
TCGTGATCGAAATGGCCAGAGAGAACCAGACCACCCAGAAGGGACAGAAG
AACAGCCGCGAGAGAATGAAGCGGATCGAAGAGGGCATCAAAGAGCTGGG
CAGCCAGATCCTGAAAGAACACCCCGTGGAAAACACCCAGCTGCAGAACG
AGAAGCTGTACCTGTACTACCTGCAGAATGGGCGGGATATGTACGTGGAC
CAGGAACTGGACATCAACCGGCTGTCCGACTACGATGTGGACCATATCGT
GCCTCAGAGCTTTCTGAAGGACGACTCCATCGACAACAAGGTGCTGACCA
GAAGCGACAAGAACCGGGGCAAGAGCGACAACGTGCCCTCCGAAGAGGTC
GTGAAGAAGATGAAGAACTACTGGCGGCAGCTGCTGAACGCCAAGCTGAT
TACCCAGAGAAAGTTCGACAATCTGACCAAGGCCGAGAGAGGCGGCCTGA
GCGAACTGGATAAGGCCGGCTTCATCAAGAGACAGCTGGTGGAAACCCGG
CAGATCACAAAGCACGTGGCACAGATCCTGGACTCCCGGATGAACACTAA
GTACGACGAGAATGACAAGCTGATCCGGGAAGTGAAAGTGATCACCCTGA
AGTCCAAGCTGGTGTCCGATTTCCGGAAGGATTTCCAGTTTTACAAAGTG
CGCGAGATCAACAACTACCACCACGCCCACGACGCCTACCTGAACGCCGT
CGTGGGAACCGCCCTGATCAAAAAGTACCCTAAGCTGGAAAGCGAGTTCG
TGTACGGCGACTACAAGGTGTACGACGTGCGGAAGATGATCGCCAAGAGC
GAGCAGGAAATCGGCAAGGCTACCGCCAAGTACTTCTTCTACAGCAACAT
CATGAACTTTTTCAAGACCGAGATTACCCTGGCCAACGGCGAGATCCGGA
AGCGGCCTCTGATCGAGACAAACGGCGAAACCGGGGAGATCGTGTGGGAT
AAGGGCCGGGATTTTGCCACCGTGCGGAAAGTGCTGAGCATGCCCCAAGT
GAATATCGTGAAAAAGACCGAGGTGCAGACAGGCGGCTTCAGCAAAGAGT
CTATCCTGCCCAAGAGGAACAGCGATAAGCTGATCGCCAGAAAGAAGGAC
TGGGACCCTAAGAAGTACGGCGGCTTCGACAGCCCCACCGTGGCCTATTC
TGTGCTGGTGGTGGCCAAAGTGGAAAAGGGCAAGTCCAAGAAACTGAAGA
GTGTGAAAGAGCTGCTGGGGATCACCATCATGGAAAGAAGCAGCTTCGAG
AAGAATCCCATCGACTTTCTGGAAGCCAAGGGCTACAAAGAAGTGAAAAA
GGACCTGATCATCAAGCTGCCTAAGTACTCCCTGTTCGAGCTGGAAAACG
GCCGGAAGAGAATGCTGGCCTCTGCCGGCGAACTGCAGAAGGGAAACGAA
CTGGCCCTGCCCTCCAAATATGTGAACTTCCTGTACCTGGCCAGCCACTA
TGAGAAGCTGAAGGGCTCCCCCGAGGATAATGAGCAGAAACAGCTGTTTG
TGGAACAGCACAAGCACTACCTGGACGAGATCATCGAGCAGATCAGCGAG
TTCTCCAAGAGAGTGATCCTGGCCGACGCTAATCTGGACAAAGTGCTGTC
CGCCTACAACAAGCACCGGGATAAGCCCATCAGAGAGCAGGCCGAGAATA
TCATCCACCTGTTTACCCTGACCAATCTGGGAGCCCCTGCCGCCTTCAAG
TACTTTGACACCACCATCGACCGGAAGAGGTACACCAGCACCAAAGAGGT
GCTGGACGCCACCCTGATCCACCAGAGCATCACCGGCCTGTACGAGACAC
GGATCGACCTGTCTCAGCTGGGAGGCGACAGCCCCAAGAAGAAGAGAAAG
GTGGAGGCCAGCTAACATATGATTCGAATGTCTTTCTTGCGCTATGACAC
TTCCAGCAAAAGGTAGGGCGGGCTGCGAGACGGCTTCCCGGCGCTGCATG
CAACACCGATGATGCTTCGACCCCCCGAAGCTCCTTCGGGGCTGCATGGG
CGCTCCGATGCCGCTCCAGGGCGAGCGCTGTTTAAATAGCCAGGCCCCCG
ATTGCAAAGACATTATAGCGAGCTACCAAAGCCATATTCAAACACCTAGA
TCACTACCACTTCTACACAGGCCACTCGAGCTTGTGATCGCACTCCGCTA
AGGGGGCGCCTCTTCCTCTTCGTTTCAGTCACAACCCGCAAACATGACAC
AAGAATCCCTGTTACTTCTCGACCGTATTGATTCGGATGATTCCTACGCG
AGCCTGCGGAACGACCAGGAATTGTGGGAGGTGAGTCGACGAGCAAGCCC
GGCGGATCAGGCAGCGTGCTTGCAGATTTGACTTGCAACGCCCGCATTGT
GTCGACGAAGGCTTTTGGCTCCTCTGTCGCTGTCTCAAGCAGCATCTAAC
CCTGCGTCGCCGTTTCCATTTGCAGCCGCTGGCCCGCCGAGCCCTGGAGG
AGCTCGGGCTGCCGGTGCCGCCGGTGCTGCGGGTGCCCGGCGAGAGCACC
AACCCCGTACTGGTCGGCGAGCCCGGCCCGGTGATCAAGCTGTTCGGCGA
GCACTGGTGCGGTCCGGAGAGCCTCGCGTCGGAGTCGGAGGCGTACGCGG
TCCTGGCGGACGCCCCGGTGCCGGTGCCCCGCCTCCTCGGCCGCGGCGAG
CTGCGGCCCGGCACCGGAGCCTGGCCGTGGCCCTACCTGGTGATGAGCCG
GATGACCGGCACCACCTGGCGGTCCGCGATGGACGGCACGACCGACCGGA
ACGCGCTGCTCGCCCTGGCCCGCGAACTCGGCCGGGTGCTCGGCCGGCTG
CACAGGGTGCCGCTGACCGGGAACACCGTGCTCACCCCCCATTCCGAGGT
CTTCCCGGAACTGCTGCGGGAACGCCGCGCGGCGACCGTCGAGGACCACC
GCGGGTGGGGCTACCTCTCGCCCCGGCTGCTGGACCGCCTGGAGGACTGG
CTGCCGGACGTGGACACGCTGCTGGCCGGCCGCGAACCCCGGTTCGTCCA
CGGCGACCTGCACGGGACCAACATCTTCGTGGACCTGGCCGCGACCGAGG
TCACCGGGATCGTCGACTTCACCGACGTCTATGCGGGAGACTCCCGCTAC
AGCCTGGTGCAACTGCATCTCAACGCCTTCCGGGGCGACCGCGAGATCCT
GGCCGCGCTGCTCGACGGGGCGCAGTGGAAGCGGACCGAGGACTTCGCCC
GCGAACTGCTCGCCTTCACCTTCCTGCACGACTTCGAGGTGTTCGAGGAG
ACCCCGCTGGATCTCTCCGGCTTCACCGATCCGGAGGAACTGGCGCAGTT
CCTCTGGGGGCCGCCGGACACCGCCCCCGGCGCCTGATAAGGATCCGGCA
AGACTGGCCCCGCTTGGCAACGCAACAGTGAGCCCCTCCCTAGTGTGTTT
GGGGATGTGACTATGTATTCGTGTGTTGGCCAACGGGTCAACCCGAACAG
ATTGATACCCGCCTTGGCATTTCCTGTCAGAATGTAACGTCAGTTGATGG TACT
[0612] For all modified Chlamydomonas reinhardtii cells, Applicants
use PCR, SURVEYOR nuclease assay, and DNA sequencing to verify
successful modification.
Example 25
Use of Cas9 to Target a Variety of Disease Types
[0613] Diseases that involve mutations in protein coding
sequence:
[0614] Dominant disorders may be targeted by inactivating the
dominant negative allele. Applicants use Cas9 to target a unique
sequence in the dominant negative allele and introduce a mutation
via NHEJ. The NHEJ-induced indel may be able to introduce a
frame-shift mutation in the dominant negative allele and eliminate
the dominant negative protein. This may work if the gene is
haplo-sufficient (e.g. MYOC mutation induced glaucoma and
Huntington's disease).
[0615] Recessive disorders may be targeted by repairing the disease
mutation in both alleles. For dividing cells, Applicants use Cas9
to introduce double strand breaks near the mutation site and
increase the rate of homologous recombination using an exogenous
recombination template. For dividing cells, this may be achieved
using multiplexed nickase activity to catalyze the replacement of
the mutant sequence in both alleles via NHEJ-mediated ligation of
an exogenous DNA fragment carrying complementary overhangs.
[0616] Applicants also use Cas9 to introduce protective mutations
(e.g. inactivation of CCR5 to prevent HIV infection, inactivation
of PCSK9 for cholesterol reduction, or introduction of the A673T
into APP to reduce the likelihood of Alzheimer's disease).
[0617] Diseases that Involve Non-Coding Sequences
[0618] Applicants use Cas9 to disrupt non-coding sequences in the
promoter region, to alter transcription factor binding sites and
alter enhancer or repressor elements. For example, Cas9 may be used
to excise out the Klf1 enhancer EHS1 in hematopoietic stem cells to
reduce BCL11a levels and reactivate fetal globin gene expression in
differentiated erythrocytes
[0619] Applicants also use Cas9 to disrupt functional motifs in the
5' or 3' untranslated regions. For example, for the treatment of
myotonic dystrophy, Cas9 may be used to remove CTG repeat
expansions in the DMPK gene.
Example 26
Multiplexed Nickase
[0620] Aspects of optimization and the teachings of Cas9 detailed
in this application may also be used to generate Cas9 nickases.
Applicants use Cas9 nickases in combination with pairs of guide
RNAs to generate DNA double strand breaks with defined overhangs.
When two pairs of guide RNAs are used, it is possible to excise an
intervening DNA fragment. If an exogenous piece of DNA is cleaved
by the two pairs of guide RNAs to generate compatible overhangs
with the genomic DNA, then the exogenous DNA fragment may be
ligated into the genomic DNA to replace the excised fragment. For
example, this may be used to remove trinucleotide repeat expansion
in the huntintin (HTT) gene to treat Huntington's Disease.
[0621] If an exogenous DNA that bears fewer number of CAG repeats
is provided, then it may be able to generate a fragment of DNA that
bears the same overhangs and can be ligated into the HTT genomic
locus and replace the excised fragment.
TABLE-US-00028 HTT locus . . . CCGTGCCGGGCGGGAGACCGCCATGG
GGCCCGGCTGTGGCTGAGGAGC . . . with . . . GGCACGGCCCGCCCTCTGGC
TGGGCCGGGCCGACACCGACTCCTCG . . . fragment excised by Cas9 nickase
and two pairs of guide RNAs + exogenous DNA CGACCCTGGAAA . . .
reduced number of CAG repeats . . . CCCCGCCGCCACCC fragment with
GGTACCGCTGGGACCTTT . . . . . . GGGGCGGCGG fewer number of CAG
repeats also cleaved by Cas9 nic- akse and the two pairs of guide
RNAs
[0622] The ligation of the exogenous DNA fragment into the genome
does not require homologous recombination machineries and therefore
this method may be used in post-mitotic cells such as neurons.
Example 27
Delivery of CRISPR System
[0623] Cas9 and its chimeric guide RNA, or combination of tracrRNA
and crRNA, can be delivered either as DNA or RNA. Delivery of Cas9
and guide RNA both as RNA (normal or containing base or backbone
modifications) molecules can be used to reduce the amount of time
that Cas9 protein persist in the cell. This may reduce the level of
off-target cleavage activity in the target cell. Since delivery of
Cas9 as mRNA takes time to be translated into protein, it might be
advantageous to deliver the guide RNA several hours following the
delivery of Cas9 mRNA, to maximize the level of guide RNA available
for interaction with Cas9 protein.
[0624] In situations where guide RNA amount is limiting, it may be
desirable to introduce Cas9 as mRNA and guide RNA in the form of a
DNA expression cassette with a promoter driving the expression of
the guide RNA. This way the amount of guide RNA available will be
amplified via transcription.
[0625] A variety of delivery systems can be introduced to introduce
Cas9 (DNA or RNA) and guide RNA (DNA or RNA) into the host cell.
These include the use of liposomes, viral vectors, electroporation,
nanoparticles, nanowires (Shalek et al., Nano Letters, 2012),
exosomes. Molecular trojan horses liposomes (Pardridge et al., Cold
Spring Harb Protoc; 2010; doi: 10.1101/pdb.prot5407) may be used to
deliver Cas9 and guide RNA across the blood brain barrier.
Example 28
Therapeutic Strategies for Trinucleotide Repeat Disorders
[0626] As previously mentioned in the application, the target
polynucleotide of a CRISPR complex may include a number of
disease-associated genes and polynucleotides and some of these
disease associated gene may belong to a set of genetic disorders
referred to as Trinucleotide repeat disorders (referred to as also
trinucleotide repeat expansion disorders, triplet repeat expansion
disorders or codon reiteration disorders).
[0627] These diseases are caused by mutations in which the
trinucleotide repeats of certain genes exceed the normal, stable
threshold which may usually differ in a gene. The discovery of more
repeat expansion disorders has allowed for the classification of
these disorders into a number of categories based on underlying
similar characteristics. Huntington's disease (HD) and the
spinocerebellar ataxias that are caused by a CAG repeat expansion
in protein-coding portions of specific genes are included in
Category I. Diseases or disorders with expansions that tend to make
them phenotypically diverse and include expansions are usually
small in magnitude and also found in exons of genes are included in
Category II. Category III includes disorders or diseases which are
characterized by much larger repeat expansions than either Category
I or II and are generally located outside protein coding regions.
Examples of Category III diseases or disorders include but are not
limited to Fragile X syndrome, myotonic dystrophy, two of the
spinocerebellar ataxias, juvenile myoclonic epilepsy, and
Friedreich's ataxia.
[0628] Similar therapeutic strategies, like the one mentioned for
Friedreich's ataxia below may be adopted to address other
trinucleotide repeat or expansion disorders as well. For example,
another triple repeat disease that can be treated using almost
identical strategy is dystrophia myotonica 1 (DM1), where there is
an expanded CTG motif in the 3' UTR. In Friedreich's ataxia, the
disease results from expansion of GAA trinucleotides in the first
intron of frataxin (FXN). One therapeutic strategy using CRISPR is
to excise the GAA repeat from the first intron. The expanded GAA
repeat is thought to affect the DNA structure and leads to recruit
the formation of heterochrornatin which turn off the frataxin gene
(FIG. 32A).
[0629] Competitive Advantage over other therapeutic strategies are
listed below:
[0630] siRNA knockdown is not applicable in this case, as disease
is due to reduced expression of frataxin. Viral gene therapy is
currently being explored. HSV-1 based vectors were used to deliver
the frataxin gene in animal models and have shown therapeutic
effect. However, long term efficacy of virus-based frataxin
delivery suffer from several problems: First, it is difficult to
regulate the expression of frataxin to match natural levels in
health individuals, and second, long term over expression of
frataxin leads to cell death.
[0631] Nucleases may be used to excise the GAA repeat to restore
healthy genotype, but Zinc Finger Nuclease and TALEN strategies
require delivery of two pairs of high efficacy nucleases, which is
difficult for both delivery as well as nuclease engineering
(efficient excision of genomic DNA by ZFN or TALEN is difficult to
achieve).
[0632] In contrast to above strategies, the CRISPR-Cas system has
clear advantages. The Cas9 enzyme is more efficient and more
multiplexible, by which it is meant that one or more targets can be
set at the same time. So far, efficient excision of genomic DNA
>30% by Cas9 in human cells and may be as high as 30%, and may
be improved in the future. Furthermore, with regard to certain
trinucleotide repeat disorders like Huntington's disease (HD),
trinucleotide repeats in the coding region may be addressed if
there are differences between the two alleles. Specifically, if a
HD patient is heterozygous for mutant HTT and there are nucleotide
differences such as SNPs between the wt and mutant HTT alleles,
then Cas9 may be used to specifically target the mutant HTT allele.
ZFN or TALENs will not have the ability to distinguish two alleles
based on single base differences.
[0633] In adopting a strategy using the CRISPR-Cas 9 enzyme to
address Friedreich's ataxia, Applicants design a number of guide
RNAs targeting sites flanking the GAA expansion and the most
efficient and specific ones are chosen (FIG. 32B).
[0634] Applicants deliver a combination of guide RNAs targeting the
intron I of FXN along with Cas9 to mediate excision of the GAA
expansion region. AAV9 may be used to mediate efficient delivery of
Cas9 and in the spinal cord.
[0635] If the Alu element adjacent to the GAA expansion is
considered important, there may be constraints to the number of
sites that can be targeted but Applicants may adopt strategies to
avoid disrupting it.
[0636] Alternative Strategies:
[0637] Rather than modifying the genome using Cas9, Applicants may
also directly activate the FXN gene using Cas9 (nuclease activity
deficient)-based DNA binding domain to target a transcription
activation domain to the FXN gene. Applicants may have to address
the robustness of the Cas9-mediated artificial transcription
activation to ensure that it is robust enough as compared to other
methods (Tremblay et al., Transcription Activator-Like Effector
Proteins Induce the Expression of the Frataxin Gene; Human Gene
Therapy. August 2012, 23(8): 883-890.)
Example 29
Strategies for Minimizing Off Target Cleavage Using Cas9
Nickase
[0638] As previously mentioned in the application, Cas9 may be
mutated to mediate single strand cleavage via one or more of the
following mutations: D10A, E762A, and H840A.
[0639] To mediate gene knockout via NHEJ, Applicants use a nickase
version of Cas9 along with two guide RNAs. Off-target nicking by
each individual guide RNA may be primarily repaired without
mutation, double strand breaks (which can lead to mutations via
NHEJ) only occur when the target sites are adjacent to each other.
Since double strand breaks introduced by double nicking are not
blunt, co-expression of end-processing enzymes such as TREX1 will
increase the level of NHEJ activity.
[0640] The following list of targets in tabular form are for genes
involved in the following diseases:
[0641] Lafora's Disease--target GSY1 or PPP1R3C (PTG) to reduce
glycogen in neurons.
[0642] Hypercholesterolemia--target PCSK9
[0643] Target sequences are listed in pairs (L and R) with
different number of nucleotides in the spacer (0 to 3 bp). Each
spacer may also be used by itself with the wild type Cas9 to
introduce double strand break at the target locus.
TABLE-US-00029 GYS1 (human) GGCC-L ACCCTTGTTAGCCACCTCCC GGCC-R
GAACGCAGTGCTCTTCGAAG GGNCC-L CTCACGCCCTGCTCCGTGTA GGNCC-R
GGCGACAACTACTTCCTGGT GGNNCC-L CTCACGCCCTGCTCCGTGTA GGNNCC-R
GGGCGACAACTACTTCCTGG GGNNNCC-L CCTCTTCAGGGCCGGGGTGG GGNNNCC-R
GAGGACCCAGGTGGAACTGC PCSK9 (human) GGCC-L TCAGCTCCAGGCGGTCCTGG
GGCC-R AGCAGCAGCAGCAGTGGCAG GGNCC-L TGGGCACCGTCAGCTCCAGG GGNCC-R
CAGCAGTGGCAGCGGCCACC GGNNCC-L ACCTCTCCCCTGGCCCTCAT GGNNCC-R
CCAGGACCGCCTGGAGCTGA GGNNNCC-L CCGTCAGCTCCAGGCGGTCC GGNNNCC-R
AGCAGCAGCAGCAGTGGCAG PPP1R3C (PTG) GGCC-L ATGTGCCAAGCAAAGCCTCA
(human) GGCC-R TTCGGTCATGCCCGTGGATG GGNCC-L GTCGTTGAAATTCATCGTAC
GGNCC-R ACCACCTGTGAAGAGTTTCC GGNNCC-L CGTCGTTGAAATTCATCGTA GGNNCC-R
ACCACCTGTGAAGAGTTTCC Gys1 (mouse) GGCC-L GAACGCAGTGCTTTTCGAGG
GGCC-R ACCCTTGTTGGCCACCTCCC GGNCC-L GGTGACAACTACTATCTGGT GGNCC-R
CTCACACCCTGCTCCGTGTA GGNNCC-L GGGTGACAACTACTATCTGG GGNNCC-R
CTCACACCCTGCTCCGTGTA GGNNNCC-L CGAGAACGCAGTGCTTTTCG GGNNNCC-R
ACCCTTGTTGGCCACCTCCC PPP1R3C (PTG) GGCC-L ATGAGCCAAGCAAATCCTCA
(mouse) GGCC-R TTCCGTCATGCCCGTGGACA GGNCC-L CTTCGTTGAAAACCATTGTA
GGNCC-R CCACCTCTGAAGAGTTTCCT GGNNCC-L CTTCGTTGAAAACCATTGTA GGNNCC-R
ACCACCTCTGAAGAGTTTCC GGNNNCC-L CTTCCACTCACTCTGCGATT GGNNNCC-R
ACCATGTCTCAGTGTCAAGC PCSK9 (mouse) GGCC-L GGCGGCAACAGCGGCAACAG
GGCC-R ACTGCTCTGCGTGGCTGCGG GGNNCC-L CCGCAGCCACGCAGAGCAGT GGNNCC-R
GCACCTCTCCTCGCCCCGAT
[0644] Alternative Strategies for Improving Stability of Guide RNA
and Increasing Specificity
[0645] 1. Nucleotides in the 5' of the guide RNA may be linked via
thiolester linkages rather than phosphoester linkage like in
natural RNA. Thiolester linkage may prevent the guide RNA from
being digested by endogenous RNA degradation machinery.
[0646] 2. Nucleotides in the guide sequence (5' 20 bp) of the guide
RNA can use bridged nucleic acids (BNA) as the bases to improve the
binding specificity.
Example 30
CRISPR-Cas for Rapid, Multiplex Genome Editing
[0647] Aspects of the invention relate to protocols and methods by
which efficiency and specificity of gene modification may be tested
within 3-4 days after target design, and modified clonal cell lines
may be derived within 2-3 weeks.
[0648] Programmable nucleases are powerful technologies for
mediating genome alteration with high precision. The RNA-guided
Cas9 nuclease from the microbial CRISPR adaptive immune system can
be used to facilitate efficient genome editing in eukaryotic cells
by simply specifying a 20-nt targeting sequence in its guide RNA.
Applicants describe a set of protocols for applying Cas9 to
facilitate efficient genome editing in mammalian cells and generate
cell lines for downstream functional studies. Beginning with target
design, efficient and specific gene modification can be achieved
within 3-4 days, and modified clonal cell lines can be derived
within 2-3 weeks.
[0649] The ability to engineer biological systems and organisms
holds enormous potential for applications across basic science,
medicine, and biotechnology. Programmable sequence-specific
endonucleases that facilitate precise editing of endogenous genomic
loci are now enabling systematic interrogation of genetic elements
and causal genetic variations in a broad range of species,
including those that have not been genetically tractable
previously. A number of genome editing technologies have emerged in
recent years, including zinc finger nucleases (ZFNs), transcription
activator-like effector nucleases (TALENs), and the RNA-guided
CRISPR-Cas nuclease system. The first two technologies use a common
strategy of tethering endonuclease catalytic domains to modular
DNA-binding proteins for inducing targeted DNA double stranded
breaks (DSB) at specific genomic loci. By contrast, Cas9 is a
nuclease guided by small RNAs through Watson-Crick base-pairing
with target DNA, presenting a system that is easy to design,
efficient, and well-suited for high-throughput and multiplexed gene
editing for a variety of cell types and organisms. Here Applicants
describe a set of protocols for applying the recently developed
Cas9 nuclease to facilitate efficient genome editing in mammalian
cells and generate cell lines for downstream functional
studies.
[0650] Like ZFNs and TALENs, Cas9 promotes genome editing by
stimulating DSB at the target genomic loci. Upon cleavage by Cas9,
the target locus undergoes one of two major pathways for DNA damage
repair, the error-prone non-homologous end joining (NHEJ) or the
high-fidelity homology directed repair (HDR) pathway. Both pathways
may be utilized to achieve the desired editing outcome.
[0651] NHEJ: In the absence of a repair template, the NHEJ process
re-ligates DSBs, which may leave a scar in the form of indel
mutations. This process can be harnessed to achieve gene knockouts,
as indels occurring within a coding exon may lead to frameshift
mutations and a premature stop codon. Multiple DSBs may also be
exploited to mediate larger deletions in the genome.
[0652] HDR: Homology directed repair is an alternate major DNA
repair pathway to NHEJ. Although HDR typically occurs at lower
frequencies than NHEJ, it may be harnessed to generate precise,
defined modifications at a target locus in the presence of an
exogenously introduced repair template. The repair template may be
either in the form of double stranded DNA, designed similarly to
conventional DNA targeting constructs with homology arms flanking
the insertion sequence, or single-stranded DNA oligonucleotides
(ssODNs). The latter provides an effective and simple method for
making small edits in the genome, such as the introduction of
single nucleotide mutations for probing causal genetic variations.
Unlike NHEJ. HDR is generally active only in dividing cells and its
efficiency varies depending on the cell type and state.
[0653] Overview of CRISPR: The CRISPR-Cas system, by contrast, is
at minimum a two-component system consisting of the Cas9 nuclease
and a short guide RNA. Re-targeting of Cas9 to different loci or
simultaneous editing of multiple genes simply requires cloning a
different 20-bp oligonucleotide. Although specificity of the Cas9
nuclease has yet to be thoroughly elucidated, the simple
Watson-Crick base-pairing of the CRISPR-Cas system is likely more
predictable than that of ZFN or TA LEN domains.
[0654] The type II CRISPR-Cas (clustered regularly interspaced
short palindromic repeats) is a bacterial adaptive immune system
that uses Cas9, to cleave foreign genetic elements. Cas9 is guided
by a pair of non-coding RNAs, a variable crRNA and a required
auxiliary tracrRNA. The crRNA contains a 20-nt guide sequence
determines specificity by locating the target DNA via Watson-Crick
base-pairing. In the native bacterial system, multiple crRNAs are
co-transcribed to direct Cas9 against various targets. In the
CRISPR-Cas system derived from Streptococcus pyogenes, the target
DNA must immediately precede a 5'-NGG/NRG protospacer adjacent
motif (PAM), which can vary for other CRISPR systems.
[0655] CRISPR-Cas is reconstituted in mammalian cells through the
heterologous expression of human codon-optimized Cas9 and the
requisite RNA components. Furthermore, the crRNA and tracrRNA can
be fused to create a chimeric, synthetic guide RNA (sgRNA). Cas9
can thus be re-directed toward any target of interest by altering
the 20-nt guide sequence within the sgRNA.
[0656] Given its ease of implementation and multiplex capability,
Cas9 has been used to generate engineered eukaryotic cells carrying
specific mutations via both NHEJ and HDR. In addition, direct
injection of sgRNA and mRNA encoding Cas9 into embryos has enabled
the rapid generation of transgenic mice with multiple modified
alleles; these results hold promise for editing organisms that are
otherwise genetically intractable.
[0657] A mutant Cas9 carrying a disruption in one of its catalytic
domains has been engineered to nick rather than cleave DNA,
allowing for single-stranded breaks and preferential repair through
HDR, potentially ameliorating unwanted indel mutations from
off-target DSBs. Additionally, a Cas9 mutant with both DNA-cleaving
catalytic residues mutated has been adapted to enable
transcriptional regulation in E. coli, demonstrating the potential
of functionalizing Cas9 for diverse applications. Certain aspects
of the invention relate to the construction and application of Cas9
for multiplexed editing of human cells.
[0658] Applicants have provided a human codon-optimized, nuclear
localization sequence-flanked Cas9 to facilitate eukaryotic gene
editing. Applicants describe considerations for designing the 20-nt
guide sequence, protocols for rapid construction and functional
validation of sgRNAs, and finally use of the Cas9 nuclease to
mediate both NHEJ- and HDR-based genome modifications in human
embryonic kidney (HEK-293FT) and human stem cell (HUES9) lines.
This protocol can likewise be applied to other cell types and
organisms.
[0659] Target selection for sgRNA: There are two main
considerations in the selection of the 20-nt guide sequence for
gene targeting: 1) the target sequence should precede the 5'-NGG
PAM for S. pyogenes Cas9, and 2) guide sequences should be chosen
to minimize off-target activity. Applicants provided an online Cas9
targeting design tool that takes an input sequence of interest and
identifies suitable target sites. To experimentally assess
off-target modifications for each sgRNA, Applicants also provide
computationally predicted off-target sites for each intended
target, ranked according to Applicants' quantitative specificity
analysis on the effects of base-pairing mismatch identity,
position, and distribution.
[0660] The detailed information on computationally predicted
off-target sites is as follows:
[0661] Considerations for Off-target Cleavage Activities: Similar
to other nucleases, Cas9 can cleave off-target DNA targets in the
genome at reduced frequencies. The extent to which a given guide
sequence exhibit off-target activity depends on a combination of
factors including enzyme concentration, thermodynamics of the
specific guide sequence employed, and the abundance of similar
sequences in the target genome. For routine application of Cas9, it
is important to consider ways to minimize the degree of off-target
cleavage and also to be able to detect the presence of off-target
cleavage.
[0662] Minimizing off-target activity: For application in cell
lines, Applicants recommend following two steps to reduce the
degree of off-target genome modification. First, using our online
CRISPR target selection tool, it is possible to computationally
assess the likelihood of a given guide sequence to have off-target
sites. These analyses are performed through an exhaustive search in
the genome for off-target sequences that are similar sequences as
the guide sequence. Comprehensive experimental investigation of the
effect of mismatching bases between the sgRNA and its target DNA
revealed that mismatch tolerance is 1) position dependent--the 8-14
bp on the 3' end of the guide sequence are less tolerant of
mismatches than the 5' bases, 2) quantity dependent--in general
more than 3 mismatches are not tolerated, 3) guide sequence
dependent--some guide sequences are less tolerant of mismatches
than others, and 4) concentration dependent--off-target cleavage is
highly sensitive to the amount of transfected DNA. The Applicants'
target site analysis web tool (available at the website
genome-engineering.org/tools) integrates these criteria to provide
predictions for likely off-target sites in the target genome.
Second, Applicants recommend titrating the amount of Cas9 and sgRNA
expression plasmid to minimize off-target activity.
[0663] Detection of off-target activities: Using Applicants' CRISPR
targeting web tool, it is possible to generate a list of most
likely off-target sites as well as primers performing SURVEYOR or
sequencing analysis of those sites. For isogenic clones generated
using Cas9, Applicants strongly recommend sequencing these
candidate off-target sites to check for any undesired mutations. It
is worth noting that there may be off target modifications in sites
that are not included in the predicted candidate list and full
genome sequence should be performed to completely verify the
absence of off-target sites. Furthermore, in multiplex assays where
several DSBs are induced within the same genome, there may be low
rates of translocation events and can be evaluated using a variety
of techniques such as deep sequencing.
[0664] The online tool provides the sequences for all oligos and
primers necessary for 1) preparing the sgRNA constructs, 2)
assaying target modification efficiency, and 3) assessing cleavage
at potential off-target sites. It is worth noting that because the
U6 RNA polymerase III promoter used to express the sgRNA prefers a
guanine (G) nucleotide as the first base of its transcript, an
extra G is appended at the 5' of the sgRNA where the 20-nt guide
sequence does not begin with G.
[0665] Approaches for sgRNA construction and delivery: Depending on
the desired application, sgRNAs may be delivered as either 1) PCR
amplicons containing an expression cassette or 2) sgRNA-expressing
plasmids. PCR-based sgRNA delivery appends the custom sgRNA
sequence onto the reverse PCR primer used to amplify a U6 promoter
template. The resulting amplicon may be co-transfected with a
plasmid containing Cas9 (PX165). This method is optimal for rapid
screening of multiple candidate sgRNAs, as cell transfections for
functional testing can be performed mere hours after obtaining the
sgRNA-encoding primers. Because this simple method obviates the
need for plasmid-based cloning and sequence verification, it is
well suited for testing or co-transfecting a large number of sgRNAs
for generating large knockout libraries or other scale-sensitive
applications. Note that the sgRNA-encoding primers are over 100-bp,
compared to the .about.20-bp oligos required for plasmid-based
sgRNA delivery.
[0666] Construction of an expression plasmid for sgRNA is also
simple and rapid, involving a single cloning step with a pair of
partially complementary oligonucleotides. After annealing the oligo
pairs, the resulting guide sequences may be inserted into a plasmid
bearing both Cas9 and an invariant scaffold bearing the remainder
of the sgRNA sequence (PX330). The transfection plasmids may also
be modified to enable virus production for in vivo delivery.
[0667] In addition to PCR and plasmid-based delivery methods, both
Cas9 and sgRNA can be introduced into cells as RNA.
[0668] Design of repair template: Traditionally, targeted DNA
modifications have required use of plasmid-based donor repair
templates that contain homology arms flanking the site of
alteration. The homology arms on each side can vary in length, but
are typically longer than 500 bp. This method can be used to
generate large modifications, including insertion of reporter genes
such as fluorescent proteins or antibiotic resistance markers. The
design and construction of targeting plasmids has been described
elsewhere.
[0669] More recently, single-stranded DNA oligonucleotides (ssODNs)
have been used in place of targeting plasmids for short
modifications within a defined locus without cloning. To achieve
high HDR efficiencies, ssODNs contain flanking sequences of at
least 40 bp on each side that are homologous to the target region,
and can be oriented in either the sense or antisense direction
relative to the target locus.
[0670] Functional Testing
[0671] SURVEYOR nuclease assay: Applicants detected indel mutations
either by the SURVEYOR nuclease assay (or PCR amplicon sequencing.
Applicants online CRISPR target design tool provides recommended
primers for both approaches. However, SURVEYOR or sequencing
primers may also be designed manually to amplify the region of
interest from genomic DNA and to avoid non-specific amplicons using
NCBI Primer-BLAST. SURVEYOR primers should be designed to amplify
300-400 bp (for a 600-800 bp total amplicon) on either side of the
Cas9 target for allowing clear visualization of cleavage bands by
gel electrophoresis. To prevent excessive primer dimer formation,
SURVEYOR primers should be designed to be typically under 25-nt
long with melting temperatures of -60.degree. C. Applicants
recommend testing each pair of candidate primers for specific PCR
amplicons as well as for the absence of non-specific cleavage
during the SURVEYOR nuclease digestion process.
[0672] Plasmid- or ssODN-mediated HDR: HDR can be detected via
PCR-amplification and sequencing of the modified region. PCR
primers for this purpose should anneal outside the region spanned
by the homology arms to avoid false detection of residual repair
template (HDR Fwd and Rev, FIG. 30). For ssODN-mediated HDR,
SURVEYOR PCR primers can be used.
[0673] Detection of indels or HDR by sequencing: Applicants
detected targeted genome modifications by either Sanger or
next-generation deep sequencing (NGS). For the former, genomic DNA
from modified region can be amplified using either SURVEYOR or HDR
primers. Amplicons should be subcloned into a plasmid such as pUC19
for transformation; individual colonies can be sequenced to reveal
clonal genotype.
[0674] Applicants designed next-generation sequencing (NGS) primers
for shorter amplicons, typically in the 100-200 bp size range. For
detecting NHEJ mutations, it is important to design primers with at
least 10-20 bp between the priming regions and the Cas9 target site
to allow detection of longer indels. Applicants provide guidelines
for a two-step PCR method to attach barcoded adapters for multiplex
deep sequencing. Applicants recommend the Illumina platform, due to
its generally low levels of false positive indels. Off-target
analysis (described previously) can then be performed through read
alignment programs such as ClustalW, Geneious, or simple sequence
analysis scripts.
[0675] Materials and Reagents
[0676] sgRNA Preparation:
[0677] UltraPure DNaseRNase-free distilled water (Life
Technologies, cat. no. 10977-023)
[0678] Herculase II fusion polymerase (Agilent Technologies, cat.
no. 600679)
[0679] CRITICAL. Standard Taq polymerase, which lacks 3'-5'
exonuclease proofreading activity, has lower fidelity and can lead
to amplification errors. Herculase II is a high-fidelity polymerase
(equivalent fidelity to Pfu) that produces high yields of PCR
product with minimal optimization. Other high-fidelity polymerases
may be substituted.
[0680] Herculase II reaction buffer (5.times.; Agilent
Technologies, included with polymerase)
[0681] dNTP solution mix (25 mM each; Enzymatics, cat. no.
N205L)
[0682] MgCl2 (25 mM; ThermoScientific, cat. no. R0971)
[0683] QIAquick gel extraction kit (Qiagen, cat. no. 28704)
[0684] QIAprep spin miniprep kit (Qiagen, cat. no. 27106)
[0685] UltraPure TBE buffer (10.times.; Life Technologies, cat. no.
15581-028)
[0686] SeaKem LE agarose (Lonza, cat. no. 50004)
[0687] SYBR Safe DNA stain (10,000.times.; Life Technologies, cat.
no. S33102)
[0688] 1-kb Plus DNA ladder (Life Technologies, cat. no.
10787-018)
[0689] TrackIt CyanOrange loading buffer (Life Technologies, cat.
no. 10482-028)
[0690] FastDigest BbsI (BpiI) (Fermentas/ThermoScientific, cat. no.
FD1014)
[0691] Fermentas Tango Buffer (Fermentas/ThermoScientific, cat. no.
BY5)
[0692] DL-dithiothreitol (DTT; Fermentas/ThermoScientific, cat. no.
R0862)
[0693] T7 DNA ligase (Enzymatics, cat. no. L602L)
[0694] Critical: Do not substitute the more commonly used T4
ligase. T7 ligase has 1,000-fold higher activity on the sticky ends
than on the blunt ends and higher overall activity than
commercially available concentrated T4 ligases.
[0695] T7 2X Rapid Ligation Buffer (included with T7 DNA ligase,
Enzymatics, cat. no. L602L)
[0696] T4 Polynucleotide Kinase (New England Biolabs, cat. no
M0201S)
[0697] T4 DNA Ligase Reaction Buffer (10.times.; New England
Biolabs, cat. no B0202S)
[0698] Adenosine 5'-triphosphate (10 mM; New England Biolabs, cat.
no. P0756S)
[0699] PlasmidSafe ATP-dependent DNase (Epicentre, cat. no.
E3101K)
[0700] One Shot Stb13 chemically competent Escherichia coli (E.
coli) (Life Technologies, cat. no. C7373-03)
[0701] SOC medium (New England Biolabs, cat. no. B9020S)
[0702] LB medium (Sigma, cat. no. L3022)
[0703] LB agar medium (Sigma, cat. no. L2897)
[0704] Ampicillin, sterile filtered (100 mg ml-l; Sigma, cat. no.
A5354)
[0705] Mammalian Cell Culture:
[0706] HEK293FT cells (Life Technologies, cat. no. R700-07)
[0707] Dulbecco's minimum Eagle's medium (DMEM, 1.times., high
glucose; Life Technologies, cat. no. 10313-039)
[0708] Dulbecco's minimum Eagle's medium (DMEM, 1.times., high
glucose, no phenol red; Life Technologies, cat. no. 31053-028)
[0709] Dulbecco's phosphate-buffered saline (DPBS, 1.times.; Life
Technologies, cat. no. 14190-250)
[0710] Fetal bovine serum, qualified and heat inactivated (Life
Technologies, cat. no. 10438-034)
[0711] Opti-MEM I reduced-serum medium (FBS; Life Technologies,
cat. no. 11058-021)
[0712] Penicillin-streptomycin (100.times.; Life Technologies, cat.
no. 15140-163)
[0713] TrypLE.TM. Express (1.times., no Phenol Red; Life
Technologies, cat. no. 12604-013)
[0714] Lipofectamine 2000 transfection reagent (Life Technologies,
cat. no. 11668027)
[0715] Amaxa SF Cell Line 4D-Nucleofector.RTM. X Kit S (32 RCT;
Lonza, cat. no V4XC-2032)
[0716] HUES 9 cell line (HARVARD STEM CELL SCIENCE)
[0717] Geltrex LDEV-Free Reduced Growth Factor Basement Membrane
Matrix (Life Technologies, cat. no. A1413201)
[0718] mTeSR1 medium (Stemcell Technologies, cat. no. 05850)
[0719] Accutase cell detachment solution (Stemcell Technologies,
cat. no. 07920)
[0720] ROCK Inhibitor (Y-27632; Millipore, cat. no. SCM075)
[0721] Amaxa P3 Primary Cell 4D-Nucleofector.RTM. X Kit S (32 RCT;
Lonza cat. no. V4XP-3032)
[0722] Genotyping Analysis:
[0723] QuickExtract DNA extraction solution (Epicentre, cat. no.
QE09050)
[0724] PCR primers for SURVEYOR, RFLP analysis, or sequencing (see
Primer table)
[0725] Herculase II fusion polymerase (Agilent Technologies, cat.
no. 600679)
[0726] CRITICAL. As Surveyor assay is sensitive to single-base
mismatches, it is particularly important to use a high-fidelity
polymerase. Other high-fidelity polymerases may be substituted.
[0727] Herculase II reaction buffer (5.times.; Agilent
Technologies, included with polymerase)
[0728] dNTP solution mix (25 mM each; Enzymatics, cat. no.
N205L)
[0729] QIAquick gel extraction kit (Qiagen, cat. no. 28704)
[0730] Taq Buffer (10.times.; Genscript, cat. no. B0005)
[0731] SURVEYOR mutation detection kit for standard gel
electrophoresis (Transgenomic, cat. no. 706025)
[0732] UltraPure TBE buffer (10.times.; Life Technologies, cat. no.
15581-028)
[0733] SeaKem LE agarose (Lonza, cat. no. 50004)
[0734] 4-20% TBE Gels 1.0 mm, 15 Well (Life Technologies, cat. no.
EC62255BOX)
[0735] Novex.RTM. Hi-Density TBE Sample Buffer (5.times.; Life
Technologies, cat. no. LC6678)
[0736] SYBR Gold Nucleic Acid Gel Stain (10,000.times.; Life
Technologies, cat. no. S-11494)
[0737] 1-kb Plus DNA ladder (Life Technologies, cat. no.
10787-018)
[0738] TrackIt CyanOrange loading buffer (Life Technologies, cat.
no. 10482-028)
[0739] FastDigest HindIII (Fermentas/ThermoScientific, cat. no.
FD0504)
[0740] Equipment
[0741] Filtered sterile pipette tips (Corning)
[0742] Standard 1.5 ml microcentrifuge tubes (Eppendorf, cat. no.
0030 125.150)
[0743] Axygen 96-well PCR plates (VWR, cat. no. PCR-96M2-HSC)
[0744] Axygen 8-Strip PCR tubes (Fischer Scientific, cat. no.
14-222-250)
[0745] Falcon tubes, polypropylene, 15 ml (BD Falcon, cat. no.
352097)
[0746] Falcon tubes, polypropylene, 50 ml (BD Falcon, cat. no.
352070)
[0747] Round-bottom Tube with cell strainer cap. 5 ml (BD Falcon,
cat. no. 352235)
[0748] Petri dishes (60 mm.times.15 mm; BD Biosciences, cat. no.
351007)
[0749] Tissue culture plate (24 well; BD Falcon, cat. no.
353047)
[0750] Tissue culture plate (96 well, flat bottom: BD Falcon, cat.
no. 353075)
[0751] Tissue culture dish (100 mm; 131BD) Falcon, 353003)
[0752] 96-well thermocycler with programmable temperature stepping
functionality (Applied Biosystems Veriti, cat. no. 4375786).
[0753] Desktop microcentrifuges 5424, 5804 (Eppendorf)
[0754] Gel electrophoresis system (PowerPac basic power supply,
Bio-Rad, cat. no. 164-5050, and Sub-Cell GT System gel tray,
Bio-Rad, cat. no. 170-4401)
[0755] Novex XCell SureLock Mini-Cell (Life Technologies, cat. no.
EI0001)
[0756] Digital gel imaging system (GelDoc EZ, Bio-Rad, cat. no.
170-8270, and blue sample tray, Bio-Rad, cat. no. 170-8273)
[0757] Blue light transilluminator and orange filter goggles
(SafeImager 2.0; Invitrogen, cat. no. G6600)
[0758] Gel quantification software (Bio-Rad, ImageLab, included
with GelDoc EZ, or open-source ImageJ from the National Institutes
of Health, available at the website rsbweb.nih.gov/ij/) UV
spectrophotometer (NanoDrop 2000c, Thermo Scientific)
[0759] Reagent Setup
[0760] Tris-borate EDTA (TBE) electrophoresis solution Dilute TBE
buffer in distilled water to 1.times. working solution for casting
agarose gels and for use as a buffer for gel electrophoresis.
Buffer may be stored at room temperature (18-22.degree. C.) for at
least 1 year. [0761] ATP, 10 mM Divide 10 mM ATP into 50-.mu.l
aliquots and store at -20.degree. C. for up to 1 year; avoid
repeated freeze-thaw cycles. [0762] DTT, 10 mM Prepare 10 mM DTT
solution in distilled water and store in 20-.mu.l aliquots at
-70.degree. C. for up to 2 years; for each reaction, use a new
aliquot, as DTT is easily oxidized. [0763] D10 culture medium For
culture of HEK293FT cells, prepare D10 culture medium by
supplementing DMEM with 1.times. GlutaMAX and 10% (vol/vol) fetal
bovine serum. As indicated in the protocol, this medium can also be
supplemented with 1.times. penicillin-streptomycin. D10 medium can
be made in advance and stored at 4.degree. C. for up to 1 month.
[0764] mTeSR1 culture medium For culture of human embryonic stem
cells, prepare mTeSR1 medium by supplementing the 5.times.
supplement (included with mTeSR1 basal medium), and 100 ug/ml
Normocin.
[0765] Procedure
[0766] Design of Targeting Components and Use of the Online Tool
.cndot. Timing 1 d
[0767] 1| Input target genomic DNA sequence. Applicants provide an
online Cas9 targeting design tool that takes an input sequence of
interest, identifies and ranks suitable target sites, and
computationally predicts off-target sites for each intended target.
Alternatively, one can manually select guide sequence by
identifying the 20-bp sequence directly upstream of any 5'-NGG.
[0768] 2| Order necessary oligos and primers as specified by the
online tool. If the site is chosen manually, the oligos and primers
should be designed.
Preparation of sgRNA Expression Construct
[0769] 3| To generate the sgRNA expression construct, either the
PCR- or plasmid-based protocol can be used.
[0770] (A) via PCR amplification .cndot. Timing 2 h
[0771] (i) Applicants prepare diluted U6 PCR template. Applicants
recommend using PX330 as a PCR template, but any U6-containing
plasmid may likewise be used as the PCR template. Applicants
diluted template with ddH.sub.2O to a concentration of 10 ng/ul.
Note that if a plasmid or cassette already containing an U6-driven
sgRNA is used as a template, a gel extraction needs to be performed
to ensure that the product contains only the intended sgRNA and no
trace sgRNA carryover from template.
[0772] (ii) Applicants prepared diluted PCR oligos. U6-Fwd and
U6-sgRNA-Rev primers are diluted to a final concentration of 10 uM
in ddH.sub.2O (add 10 ul of 100 uM primer to 90 ul ddH.sub.2O).
[0773] (iii) U6-sgRNA PCR reaction. Applicants set up the following
reaction for each U6-sgRNA-Rev primer and mastermix as needed:
TABLE-US-00030 Component: Amount (ul) Final concentration Herculase
II PCR buffer, 5X 10 1X dNTP, 100 mM (25 mM each) 0.5 1 mM U6
template (PX330) 1 0.2 ng/ul U6-Fwd primer 1 0.2 uM U6-sgRNA-Rev
primer (variable) 1 0.2 uM Herculase II Fusion polymerase 0.5
Distilled water 36 Total 50
[0774] (iv) Applicants performed PCR reaction on the reactions from
step (iii) using the following cycling conditions:
TABLE-US-00031 Cycle number Denature Anneal Extend 1 95.degree. C.,
2 m 2-31 95.degree. C., 20 s 60.degree. C., 20 s 72.degree. C., 20
s 32 72.degree. C., 3 m
[0775] (v) After the reaction is completed, Applicants ran the
product on a gel to verify successful, single-band amplification.
Cast a 2% (wt/vol) agarose gel in 1.times.TBE buffer with 1.times.
SYBR Safe dye. Run 5 ul of the PCR product in the gel at 15 V
cm.sup.-1 for 20-30 min. Successful amplicons should yield one
single 370-bp product and the template should be invisible. It
should not be necessary to gel extract the PCR amplicon.
[0776] (vi) Applicants purified the PCR product using the QIAquick
PCR purification kit according to the manufacturer's directions.
Elute the DNA in 35 ul of Buffer EB or water. Purified PCR products
may be stored at 4.degree. C. or -20.degree. C.
[0777] (B) Cloning sgRNA into Cas9-Containing Bicistronic
Expression Vector .cndot. Timing 3 d
[0778] (i) Prepare the sgRNA oligo inserts. Applicants resuspended
the top and bottom strands of oligos for each sgRNA design to a
final concentration of 100 uM. Phosphorylate and anneal the oligo
as follows:
TABLE-US-00032 Oligo 1 (100 uM) 1 ul Oligo 2 (100 uM) 1 ul T4
Ligation Buffer, 10X 1 ul T4 PNK 1 ul ddH.sub.2O 6 ul Total 10
ul
[0779] (ii) Anneal in a thermocycler using the following
parameters:
[0780] 37.degree. C. for 30 m
[0781] 95.degree. C. for 5 m
[0782] Ramp down to 25.degree. C. at 5.degree. C. per m
[0783] (iii) Applicants diluted phosphorylated and annealed oligos
1:200 by add 1 ul of oligo to 199 ul room temperature
ddH.sub.2O.
[0784] (iv) Clone sgRNA oligo into PX330. Applicants set up Golden
Gate reaction for each sgRNA. Applicants recommend also setting up
a no-insert, PX330 only negative control.
TABLE-US-00033 PX330 (100 ng) x ul Diluted oligo duplex from step
(iii) 2 ul Tango Buffer, 10X 2 ul DTT, 10 mM 1 ul ATP, 10 mM 1 ul
FastDigest BbsI 1 ul T7 Ligase 0.5 ul ddH.sub.2O x ul Total 20
ul
[0785] (v) Incubate the Golden Gate reaction for a total of 1
h:
TABLE-US-00034 Cycle number Condition 1-6 37.degree. C. for 5 m,
21.degree. C. for 5 m
[0786] (vi) Applicants treated Golden Gate reaction with
PlasmidSafe exonuclease to digest any residual linearized DNA. This
step is optional but highly recommended.
TABLE-US-00035 Golden Gate reaction from step 4 11 ul 10X
PlasmidSafe Buffer 1.5 ul ATP, 10 mM 1.5 ul PlasmidSafe exonuclease
1 ul Total 15 ul
[0787] (vii) Applicants incubated the PlasmidSafe reaction at
37.degree. C. for 30 min, followed by inactivation at 70.degree. C.
for 30 min. Pause point: after completion, the reaction may be
frozen and continued later. The circular DNA should be stable for
at least 1 week.
[0788] (viii) Transformation. Applicants transformed the
PlasmidSafe-treated plasmid into a competent E. coli strain,
according to the protocol supplied with the cells. Applicants
recommend Stb13 for quick transformation. Briefly, Applicants added
5 ul of the product from step (vii) into 20 ul of ice-cold
chemically competent Stb13 cells. This is then incubated on ice for
10 m, heat shocked at 42.degree. C. for 30 s, returned immediately
to ice for 2 m, 100 ul of SOC medium is added, and this is plated
onto an LB plate containing 100 ug/ml ampicillin with incubation
overnight at 37.degree. C.
[0789] (ix) Day 2: Applicants inspected plates for colony growth.
Typically, there are no colonies on the negative control plates
(ligation of BbsI-digested PX330 only, no annealed sgRNA oligo),
and tens to hundreds of colonies on the PX330-sgRNA cloning
plates.
[0790] (x) From each plate, Applicants picked 2-3 colonies to check
correct insertion of sgRNA. Applicants used a sterile pipette tip
to inoculate a single colony into a 3 ml culture of LB medium with
100 ug/ml ampicillin. Incubate and shake at 37.degree. C.
overnight.
[0791] (xi) Day 3: Applicants isolated plasmid DNA from overnight
cultures using a QiAprep Spin miniprep kit according to the
manufacturer's instructions.
[0792] (xii) Sequence validate CRISPR plasmid. Applicants verified
the sequence of each colony by sequencing from the U6 promoter
using the U6-Fwd primer. Optional: sequence the Cas9 gene using
primers listed in the following Primer table.
TABLE-US-00036 Primer Sequence (5' to 3') Purpose U6-For
GAGGGCCTATTTCCCATGATTCC Amplify U6- sgRNA. U6-Rev
AAAAAAAGCACCGACTCGGTGCCA Amplify U6- CTTTTTCAAGTTGATAACGGACTA
sgRNA; N is GCCTTATTTTAACTTGCTATTTCT reverse
AGCTCTAAAACNNNNNNNNNNNNN complement NNNNNNCCGGTGTTTCGTCCTTTC of
target CACAAG sgRNA- CACCGNNNNNNNNNNNNNNNNNNN Clone sgRNA top into
PX330 sgRNA- AAACNNNNNNNNNNNNNNNNNNNC Clone sgRNA bottom into PX330
U6- AAAAAAAGCACCGACTCGGTGCCA Amplify U6- EMX1-
CTTTTTCAAGTTGATAACGGACTA EMX1 sgRNA Rev GCCTTATTTTAACTTGCTATTTCT
AGCTCTAAAACCCCTAGTCATTGG AGGTGACCGGTGTTTCGTCCTTTC CACAAG EMX1-top
CACCGTCACCTCCAATGACTAGGG Clone EMX1 sgRNA into PX330 EMX1-
AAACCCCTAGTCATTGGAGGTGAC Clone EMX1 bottom sgRNA into PX330 ssODN-
CAGAAGAAGAAGGGCTCCCATCAC EMX1 HDR sense ATCAACCGGTGGCGCATTGCCACG
(sense; AAGCAGGCCAATGGGGAGGACATC insertion GATGTCACCTCCAATGACAAGCTT
underlined) GCTAGCGGTGGGCAACCACAAACC CACGAGGGCAGAGTGCTGCTTGCT
GCTGGCCAGGCCCCTGCGTGGGCC CAAGCTGGACTCTGGCCACTCCCT ssODN-
AGGGAGTGGCCAGAGTCCAGCTTG EMX1 HDR antisense
GGCCCACGCAGGGGCCTGGCCAGC (antisense; AGCAAGCAGCACTCTGCCCTCGTG
insertion GGTTTGTGGTTGCCCACCGCTAGC underlined)
AAGCTTGTCATTGGAGGTGACATC GATGTCCTCCCCATTGGCCTGCTT
CGTGGCAATGCGCCACCGGTTGAT GTGATGGGAGCCCTTCTTCTTCTG EMX1-
CCATCCCCTTCTGTGAATGT EMX1 SURV-F SURVEYOR assay PCR, sequencing
EMX1- GGAGATTGGAGACACGGAGA EMX1 SURV-R SURVEYOR assay PCR,
sequencing EMX1- GGCTCCCTGGGTTCAAAGTA EMX1 RFLP HDR-F analysis PCR,
sequencing EMX1- AGAGGGGTCTGGATGTCGTAA EMX1 RFLP HDR-R analysis
PCR, sequencing PUC19-F CGCCAGGGTTTTCCCAGTCACGAC pUC19 multiple
cloning site F primer, for Sanger sequencing
[0793] Applicants referenced the sequencing results against the
PX330 cloning vector sequence to check that the 20 bp guide
sequence was inserted between the U6 promoter and the remainder of
the sgRNA scaffold. Details and sequence of the PX330 map in
GenBank vector map format (*.gb file) can be found at the website
crispr.genome-engineering.org.
[0794] (Optional) Design of ssODN Template .cndot. Timing 3 d
Planning Ahead
[0795] 3| Design and order ssODN. Either the sense or antisense
ssODN can be purchased directly from supplier. Applicants recommend
designing homology arms of at least 40 bp on either side and 90 bp
for optimal HDR efficiency. In Applicants' experience, antisense
oligos have slightly higher modification efficiencies.
[0796] 4| Applicants resuspended and diluted ssODN ultramers to a
final concentration of 10 uM. Do not combine or anneal the sense
and antisense ssODNs. Store at -20.degree. C.
[0797] 5| Note for HDR applications, Applicants recommend cloning
sgRNA into the PX330 plasmid.
[0798] Functional Validation of sgRNAs: Cell Culture and
Transfections .cndot. Timing 3-4 d
[0799] The CRISPR-Cas system has been used in a number of mammalian
cell lines. Conditions may vary for each cell line. The protocols
below details transfection conditions for HEK239FT cells. Note for
ssODN-mediated HDR transfections, the Amaxa SF Cell Line
Nucleofector Kit is used for optimal delivery of ssODNs. This is
described in the next section.
[0800] 7| HEK293FT maintenance. Cells are maintained according to
the manufacturer's recommendations. Briefly, Applicants cultured
cells in D10 medium (GlutaMax DMEM supplemented with 10% Fetal
Bovine Serum), at 37.degree. C. and 5% CO2.
[0801] 8| To passage, Applicants removed medium and rinsed once by
gently adding DPBS to side of vessel, so as not to dislodge cells.
Applicants added 2 ml of TrypLE to a T75 flask and incubated for 5
m at 37.degree. C. 10 ml of warm D10 medium is added to inactivate
and transferred to a 50 ml Falcon tube. Applicants dissociated
cells by triturating gently, and re-seeded new flasks as necessary.
Applicants typically passage cells every 2-3 d at a split ratio of
1:4 or 1:8, never allowing cells to reach more than 70% confluency.
Cell lines are restarted upon reaching passage number 15.
[0802] 9| Prepare cells for transfection. Applicants plated
well-dissociated cells onto 24-well plates in D10 medium without
antibiotics 16-24 h before transfection at a seeding density of
1.3.times.10.sup.5 cells per well and a seeding volume of 500 ul.
Scale up or down according to the manufacturer's manual as needed.
It is suggested to not plate more cells than recommended density as
doing so may reduce transfection efficiency.
[0803] 10| On the day of transfection, cells are optimal at 70-90%
confluency. Cells may be transfected with Lipofectamine 2000 or
Amaxa SF Cell Line Nucleofector Kit according to the manufacturers'
protocols.
[0804] (A) For sgRNAs cloned into PX330, Applicants transfected 500
ng of sequence-verified CRISPR plasmid; if transfecting more than
one plasmid, mix at equimolar ratio and no more than 500 ng
total.
[0805] (B) For sgRNA amplified by PCR, Applicants mixed the
following:
TABLE-US-00037 PX165 (Cas9 only) 200 ng sgRNA amplicon (each) 40 ng
pUC19 fill up total DNA to 500 ng
[0806] Applicants recommend transfecting in technical triplicates
for reliable quantification and including transfection controls
(e.g. GFP plasmid) to monitor transfection efficiency. In addition,
PX330 cloning plasmid and/or sgRNA amplicon may be transfected
alone as a negative control for downstream functional assays.
[0807] 11| Applicants added Lipofectamine complex to cells gently
as HEK293FT cells may detach easily from plate easily and result in
lower transfection efficiency.
[0808] 12| Applicants checked cells 24 h after transfection for
efficiency by estimating the fraction of fluorescent cells in the
control (e.g., GFP) transfection using a fluorescence microscope.
Typically cells are more than 70% transfected.
[0809] 13| Applicants supplemented the culture medium with an
additional 500 ul of warm D10 medium. Add D10 very slowly to the
side of the well and do not use cold medium, as cells can detach
easily.
[0810] 14| Cells are incubated for a total of 48-72 h
post-transfection before harvested for indel analysis. Indel
efficiency does not increase noticeably after 48 h.
[0811] (Optional) Co-Transfection of CRISPR Plasmids and ssODNs or
Targeting Plasmids for HR .cndot. Timing 3-4 d
[0812] 15| Linearize targeting plasmid. Targeting vector is
linearized if possible by cutting once at a restriction site in the
vector backbone near one of the homology arms or at the distal end
of either homology arm.
[0813] 16| Applicants ran a small amount of the linearized plasmid
alongside uncut plasmid on a 0.8-1% agarose gel to check successful
linearization. Linearized plasmid should run above the supercoiled
plasmid.
[0814] 17| Applicants purified linearized plasmid with the QIAQuick
PCR Purification kit.
[0815] 18| Prepare cells for transfection. Applicants cultured
HEK293FT in T75 or T225 flasks. Sufficient cell count before day of
transfection is planned for. For the Amaxa strip-cuvette format,
2.times.10.sup.6 cells are used per transfection.
[0816] 19| Prepare plates for transfection. Applicants added 1 ml
of warm D10 medium into each well of a 12 well plate. Plates are
placed into the incubator to keep medium warm.
[0817] 20| Nucleofection. Applicants transfected HEK293FT cells
according to the Amaxa SF Cell Line Nucleofector 4D Kit
manufacturer's instructions, adapted in the steps below.
[0818] a. For ssODN and CRISPR cotransfection, pre-mix the
following DNA in PCR tubes:
TABLE-US-00038 pCRISPR plasmid (Cas9 + sgRNA) 500 ng ssODN template
(10 uM) 1 ul
[0819] b. For HDR targeting plasmid and CRISPR cotransfection,
pre-mix the following DNA in PCR tubes:
TABLE-US-00039 CRISPR plasmid (Cas9 + sgRNA) 500 ng Linearized
targeting plasmid 500 ng
[0820] For transfection controls, see previous section. In
addition, Applicants recommend transfecting ssODN or targeting
plasmid alone as a negative control.
[0821] 21| Dissociate to single cells. Applicants removed medium
and rinsed once gently with DPBS, taking care not to dislodge
cells. 2 ml of TrypLE is added to a T75 flask and incubated for 5 m
at 37.degree. C. 10 ml of warm D10 medium is added to inactivate
and triturated gently in a 50 ml Falcon tube. It is recommended
that cells are triturated gently and dissociated to single cells.
Large clumps will reduce transfection efficiency. Applicants took a
10 ul aliquot from the suspension and diluted into 90 ul of D10
medium for counting. Applicants counted cells and calculated the
number of cells and volume of suspension needed for transfection.
Applicants typically transfected 2.times.10.sup.5 cells per
condition using the Amaxa Nucleocuvette strips, and recommend
calculating for 20% more cells than required to adjust for volume
loss in subsequent pipetting steps. The volume needed is
transferred into a new Falcon tube.
[0822] 23| Applicants spun down the new tube at 200.times.g for 5
m.
[0823] Applicants prepared the transfection solution by mixing the
SF solution and S supplement as recommended by Amaxa. For Amaxa
strip-cuvettes, a total of 20 ul of supplemented SF solution is
needed per transfection. Likewise, Applicants recommend calculating
for 20% more volume than required.
[0824] 25| Applicants removed medium completely from pelleted cells
from step 23 and gently resuspended in appropriate volume (20 ul
per 2.times.10.sup.5 cells) of S1-supplemented SF solution. Do not
leave cells in SF solution for extended period of time.
[0825] 26| 20 ul of resuspended cells is pipetted into each DNA
pre-mix from step 20. Pipette gently to mix and transfer to
Nucleocuvette strip chamber. This is repeated for each transfection
condition.
[0826] Electroporate cells using the Nucleofector 4D program
recommended by Amaxa, CM-130.
[0827] 28| Applicants gently and slowly pipetted 100 ul of warm D10
medium into each Nucleocuvette strip chamber, and transferred all
volume into the pre-warmed plate from step 19. CRITICAL. Cells are
very fragile at this stage and harsh pipetting can cause cell
death. Incubate for 24 h. At this point, transfection efficiency
can be estimated from fraction of fluorescent cells in positive
transfection control. Nucleofection typically results in greater
than 70-80% transfection efficiency. Applicants slowly added 1 ml
warm D10 medium to each well without dislodging the cells. Incubate
cells for a total of 72 h.
[0828] Human Embryonic Stem Cell (HUES 9) Culture and Transfection
.cndot. Timing 3-4 d
[0829] Maintaining hESC (HUES9) line. Applicants routinely maintain
HUES9 cell line in feeder-free conditions with mTesR1 medium.
Applicants prepared mTeSR1 medium by adding the 5.times. supplement
included with basal medium and 100 ug/ml Normocin. Applicants
prepared a 10 ml aliquot of mTeSR1 medium supplemented further with
10 uM Rock Inhibitor. Coat tissue culture plate. Dilute cold
GelTrex 1:100 in cold DMEM and coat the entire surface of a 100 mm
tissue culture plate.
[0830] Place plate in incubator for at least 30 m at 37.degree. C.
Thaw out a vial of cells at 37.degree. C. in a 15 ml Falcon tube,
add 5 ml of mTeSR1 medium, and pellet at 200.times.g for 5 m.
Aspirate off GelTrex coating and seed .about.1.times.106 cells with
10 ml mTeSR1 medium containing Rock Inhibitor. Change to normal
mTeSR1 medium 24 h after transfection and re-feed daily. Passaging
cells. Re-feed cells with fresh mTeSR1 medium daily and passage
before reaching 70% confluency. Aspirate off mTeSR1 medium and wash
cells once with DPBS. Dissociate cells by adding 2 ml Accutase and
incubating at 37.degree. C. for 3-5 m. Add 10 ml mTeSR1 medium to
detached cells, transfer to 15 ml Falcon tube and resuspend gently.
Re-plate onto GelTrex-coated plates in mTeSR1 medium with 10 uM
Rock Inhibitor. Change to normal mTeSR1 medium 24 h after
plating.
[0831] Transfection. Applicants recommend culturing cells for at
least 1 week post-thaw before transfecting using the Amaxa P3
Primary Cell 4-D Nucleofector Kit (Lonza). Re-feed log-phase
growing cells with fresh medium 2 h before transfection. Dissociate
to single cells or small clusters of no more than 10 cells with
accutase and gentle resuspension. Count the number of cells needed
for nucleofection and spin down at 200.times.g for 5 m. Remove
medium completely and resuspend in recommended volume of
S1-supplemented P3 nucleofection solution. Gently plate
electroporated cells into coated plates in presence of 1.times.
Rock Inhibitor.
[0832] Check transfection success and re-feed daily with regular
mTeSR1 medium beginning 24 h after nucleofection. Typically,
Applicants observe greater than 70% transfection efficiency with
Amaxa Nucleofection. Harvest DNA. 48-72 h post transfection,
dissociate cells using accutase and inactivate by adding 5.times.
volume of mTeSR1. Spin cells down at 200.times.g for 5 m. Pelleted
cells can be directed processed for DNA extraction with
QuickExtract solution. It is recommended to not mechanically
dissociate cells without accutase. It is recommended to not spin
cells down without inactivating accutase or above the recommended
speed; doing so may cause cells to lyse.
Isolation of Clonal Cell Lines by FACS. Timing .cndot. 2-3 h
Hands-on; 2-3 Weeks Expansion
[0833] Clonal isolation may be performed 24 h post-transfection by
FACS or by serial dilution.
[0834] 54| Prepare FACS buffer. Cells that do not need sorting
using colored fluorescence may be sorted in regular D10 medium
supplemented with 1.times. penicillin/streptinomycin. If colored
fluorescence sorting is also required, a phenol-free DMEM or DPBS
is substituted for normal DMEM. Supplement with 1.times.
penicillin/streptinomycin and filter through a 0.22 um Steriflip
filter.
[0835] 51| Prepare 96 well plates. Applicants added 100 ul of D10
media supplemented with 1.times. penicillin/streptinomycin per well
and prepared the number of plates as needed for the desired number
of clones.
[0836] 56| Prepare cells for FACS. Applicants dissociated cells by
aspirating the medium completely and adding 100 ul TrypLE per well
of a 24-well plate. Incubate for 5 m and add 400 ul warm D10
media.
[0837] 57| Resuspended cells are transferred into a 15 ml Falcon
tube and gently triturated 20 times. Recommended to check under the
microscope to ensure dissociation to single cells.
[0838] 58| Spin down cells at 200.times.g for 5 minutes.
[0839] 59| Applicants aspirated the media, and resuspended the
cells in 200 ul of FACS media.
[0840] 60| Cells are filtered through a 35 um mesh filter into
labeled FACS tubes. Applicants recommend using the BD Falcon
12.times.75 mm Tube with Cell Strainer cap. Place cells on ice
until sorting.
[0841] 61| Applicants sorted single cells into 96-well plates
prepared from step 55. Applicants recommend that in one single
designated well on each plate, sort 100 cells as a positive
control.
[0842] NOTE. The remainder of the cells may be kept and used for
genotyping at the population level to gauge overall modification
efficiency.
[0843] 62| Applicants returned cells into the incubator and allowed
them to expand for 2-3 weeks. 100 ul of warm D10 medium is added 5
d post sorting. Change 100 ul of medium every 3-5 d as
necessary.
[0844] 63| Colonies are inspected for "clonal" appearance 1 week
post sorting: rounded colonies radiating from a central point. Mark
off wells that are empty or may have been seeded with doublets or
multiplets.
[0845] 64| When cells are more than 60% confluent, Applicants
prepared a set of replica plates for passaging. 100 ul of D10
medium is added to each well in the replica plates. Applicants
dissociated cells directly by pipetting up and down vigorously 20
times. 20% of the resuspended volume was plated into the prepared
replica plates to keep the clonal lines. Change the medium every
2-3 d thereafter and passage accordingly.
[0846] 65| Use the remainder 80% of cells for DNA isolation and
genotyping.
[0847] Optional: Isolation of Clonal Cell Lines by Dilution. Timing
.cndot. 2-3 h Hands-on; 2-3 Weeks Expansion
[0848] 66| Applicants dissociated cells from 24-well plates as
described above. Make sure to dissociate to single cells. A cell
strainer can be used to prevent clumping of cells.
[0849] 67| The number of cells are counted in each condition.
Serially dilute each condition in D10 medium to a final
concentration of 0.5 cells per 100 ul. For each 96 well plate,
Applicants recommend diluting to a final count of 60 cells in 12 ml
of D10. Accurate count of cell number is recommended for
appropriate clonal dilution. Cells may be recounted at an
intermediate serial dilution stage to ensure accuracy.
[0850] 68| Multichannel pipette was used to pipette 100 ul of
diluted cells to each well of a 96 well plate.
[0851] NOTE. The remainder of the cells may be kept and used for
genotyping at the population level to gauge overall modification
efficiency.
[0852] 69| Applicants inspected colonies for "clonal" appearance
.about.1 week post plating: rounded colonies radiating from a
central point. Mark off wells that may have seeded with doublets or
multiplets.
[0853] 70| Applicants returned cells to the incubator and allowed
them to expand for 2-3 weeks. Re-feed cells as needed as detailed
in previous section.
[0854] SURVEYOR Assay for CRISPR Cleavage Efficiency. Timing
.cndot. 5-6 h
[0855] Before assaying cleavage efficiency of transfected cells,
Applicants recommend testing each new SURVEYOR primer on negative
(untransfected) control samples through the step of SURVEYOR
nuclease digestion using the protocol described below.
Occasionally, even single-band clean SURVEYOR PCR products can
yield non-specific SURVEYOR nuclease cleavage bands and potentially
interfere with accurate indel analysis.
[0856] 71| Harvest cells for DNA. Dissociate cells and spin down at
200.times.g for 5 m. NOTE. Replica plate at this stage as needed to
keep transfected cell lines.
[0857] 72| Aspirate the supernatant completely.
[0858] 73| Applicants used QuickExtract DNA extraction solution
according to the manufacturer's instructions. Applicants typically
used 50 ul of the solution for each well of a 24 well plate and 10
ul for a 96 well plate.
[0859] 74| Applicants normalized extracted DNA to a final
concentration of 100-200 ng/ul with ddH.sub.2O. Pause point:
Extracted DNA may be stored at -20.degree. C. for several
months.
[0860] 75| Set up the SURVEYOR PCR. Master mix the following using
SURVEYOR primers provided by Applicants online/computer algorithm
tool:
TABLE-US-00040 Component: Amount (ul) Final concentration Herculase
II PCR buffer, 5X 10 1X dNTP, 100 mM (25 mM each) 1 1 mM SURVEYOR
Fwd primer (10 uM) 1 0.2 uM SURVEYOR Rev primer (10 uM) 1 0.2 uM
Herculase II Fusion polymerase 1 MgCl.sub.2 (25 mM) 2 1 mM
Distilled water 33 Total 49 (for each reaction)
[0861] 76| Applicants added 100-200 ng of normalized genomic DNA
template from step 74 for each reaction.
[0862] 77| PCR reaction was performed using the following cycling
conditions, for no more than 30 amplification cycles:
TABLE-US-00041 Cycle number Denature Anneal Extend 1 95.degree. C.,
2 min 2-31 95.degree. C., 20 s 60.degree. C., 20 s 72.degree. C.,
30 s 32 72.degree. C., 3 min
[0863] 78| Applicants ran 2-5 ul of PCR product on a 1% gel to
check for single-band product. Although these PCR conditions are
designed to work with most pairs of SURVEYOR primers, some primers
may need additional optimization by adjusting the template
concentration, MgCl.sub.2 concentration, and/or the annealing
temperature.
[0864] 79| Applicants purified the PCR reactions using the QIAQuick
PCR purification kit and normalized eluant to 20 ng/ul. Pause
point: Purified PCR product may be stored at -20.degree. C.
[0865] 80| DNA heteroduplex formation. The annealing reaction was
set up as follows:
TABLE-US-00042 Taq PCR buffer, 10X 2 ul Normalized DNA (20 ng/ul)
18 ul Total volume 20 ul
[0866] 81| Anneal the reaction using the following conditions:
TABLE-US-00043 Cycle number Condition 1 95.degree. C., 10 mn 2
95.degree. C.-85.degree. C., -2.degree. C./s 3 85.degree. C., 1 min
4 85.degree. C.-75.degree. C., -0.3.degree. C./s 5 75.degree. C., 1
min 6 75.degree. C.-65.degree. C., -0.3.degree. C./s 7 65.degree.
C., 1 min 8 65.degree. C.-55.degree. C., -0.3.degree. C./s 9
55.degree. C., 1 min 10 55.degree. C.-45.degree. C., -0.3.degree.
C./s 11 45.degree. C., 1 min 12 45.degree. C.-35.degree. C.,
-0.3.degree. C./s 13 35.degree. C., 1 min 14 35.degree.
C.-25.degree. C., -0.3.degree. C./s 15 25.degree. C., 1 min
[0867] 82| SURVEYOR nuclease S digestion. Applicants prepared
master-mix and added the following components on ice to annealed
heteroduplexes from step 81 for a total final volume of 25 ul:
TABLE-US-00044 Component Amount (ul) Final Concentration MgCl.sub.2
solution, 0.15 M 2.5 15 mM ddH.sub.2O 0.5 SURVEYOR nuclease S 1 1X
SURVEYOR enhancer S 1 1X Total 5
[0868] 83| Vortex well and spin down. Incubate the reaction at
42.degree. C. for 1 h.
[0869] 84| Optional: 2 ul of the Stop Solution from the SURVEYOR
kit may be added. Pause point. The digested product may be stored
at -20.degree. C. for analysis at a later time.
[0870] 85| Visualize the SURVEYOR reaction. SURVEYOR nuclease
digestion products may be visualized on a 2% agarose gel. For
better resolution, products may be run on a 4-20% gradient
Polyacrylamide TBE gel. Applicants loaded 10 ul of product with the
recommended loading buffer and ran the gel according to
manufacturer's instructions. Typically, Applicants run until the
bromophenol blue dye has migrated to the bottom of the gel. Include
DNA ladder and negative controls on the same gel.
[0871] 86| Applicants stained the gel with 1.times.SYBR Gold dye
diluted in TBE. The gel was gently rocked for 15 m.
[0872] 87| Applicants imaged the gel using a quantitative imaging
system without overexposing the bands. The negative controls should
have only one band corresponding to the size of the PCR product,
but may have occasionally non-specific cleavage bands of other
sizes. These will not interfere with analysis if they are different
in size from target cleavage bands. The sum of target cleavage band
sizes, provided by Applicants online/computer algorithm tool,
should be equal to the size of the PCR product.
[0873] 88| Estimate the cleavage intensity. Applicants quantified
the integrated intensity of each band using ImageJ or other gel
quantification software.
[0874] 89| For each lane, Applicants calculated the fraction of the
PCR product cleaved (f.sub.cut) using the following formula:
f.sub.cut=(b+c)/(a+b+c), where a is the integrated intensity of the
undigested PCR product and b and c are the integrated intensities
of each cleavage product. 901 Cleavage efficiency may be estimated
using the following formula, based on the binomial probability
distribution of duplex formation:
91|indel (%)=100.times.(1- {square root over ((1-f.sub.cut))})
[0875] Sanger Sequencing for Assessing CRISPR Cleavage Efficiency.
Timing. 3 d
[0876] Initial steps are identical to Steps 71-79 of the SURVEYOR
assay. Note: SURVEYOR primers may be used for Sanger sequencing if
appropriate restriction sites are appended to the Forward and
Reverse primers. For cloning into the recommended pUC19 backbone,
EcoRI may be used for the Fwd primer and HindIII for the Rev
primer.
[0877] 92| Amplicon digestion. Set up the digestion reaction as
follows:
TABLE-US-00045 Component Amount (ul) Fast Digest buffer, 10X 3
FastDigest EcoRI 1 FastDigest HindIII 1 Normalized DNA (20 ng/ul)
10 ddH.sub.2O 15 Total volume 30
[0878] 93| pUC19 backbone digestion. Set up the digestion reaction
as follows:
TABLE-US-00046 Component Amount (ul) Fast Digest buffer, 10X 3
FastDigest EcoRI 1 FastDigest HindIII 1 FastAP Alkaline Phosphatase
1 pUC19 vector (200 ng/ul) 5 ddH.sub.2O 20 Total volume 30
[0879] 94| Applicants purified the digestion reactions using the
QIAQuick PCR purification kit. Pause point: Purified PCR product
may be stored at -20.degree. C.
[0880] 95| Applicants ligated the digested pUC19 backbone and
Sanger amplicons at a 1:3 vector:insert ratio as follows:
TABLE-US-00047 Component Amount (ul) Digested pUC19 x (50 ng)
Digested insert x (1:3 vector:insert molar ratio) T7 ligase 1 2X
Rapid Ligation Buffer 10 ddH.sub.2O x Total volume 20
[0881] 96| Transformation. Applicants transformed the
PlasmidSafe-treated plasmid into a competent E. coli strain,
according to the protocol supplied with the cells. Applicants
recommend Stb13 for quick transformation. Briefly, 5 ul of the
product from step 95 is added into 20 ul of ice-cold chemically
competent Stb13 cells, incubated on ice for 10 m, heat shocked at
42.degree. C. for 30 s, returned immediately to ice for 2 m, 100 ul
of SOC medium is added, and plated onto an LB plate containing 100
ug/ml ampicillin. This is incubated overnight at 37.degree. C.
[0882] 97| Day 2: Applicants inspected plates for colony growth.
Typically, there are no colonies on the negative control plates
(ligation of EcoRI-HindIII digested pUC19 only, no Sanger amplicon
insert), and tens to hundreds of colonies on the pUC19-Sanger
amplicon cloning plates.
[0883] 98| Day 3: Applicants isolated plasmid DNA from overnight
cultures using a QIAprep Spin miniprep kit according to the
manufacturer's instructions.
[0884] 99| Sanger sequencing. Applicants verified the sequence of
each colony by sequencing from the pUC19 backbone using the
pUC19-For primer. Applicants referenced the sequencing results
against the expected genomic DNA sequence to check for the presence
of Cas9-induced NHEJ mutations. % editing efficiency=(# modified
clones)/(# total clones). It is important to pick a reasonable
number of clones (>24) to generate accurate modification
efficiencies.
[0885] Genotyping for Microdeletion. Timing .cndot. 2-3 d Hands on;
2-3 Weeks Expansion
[0886] 100| Cells were transfected as described above with a pair
of sgRNAs targeting the region to be deleted.
[0887] 101| 24 h post-transfection, clonal lines are isolated by
FACS or serial dilution as described above.
[0888] 102| Cells are expanded for 2-3 weeks.
[0889] 103| Applicants harvested DNA from clonal lines as described
above using 10 ul QuickExtract solution and normalized genomic DNA
with ddH.sub.2O to a final concentration of 50-100 ng/ul.
[0890] 104| PCR Amplify the modified region. The PCR reaction is
set up as follows:
TABLE-US-00048 Final Component: Amount (ul) concentration Herculase
II PCR buffer, 5X 10 1X dNTP, 100 mM (25 mM each) 1 1 mM Out Fwd
primer (10 uM) 1 0.2 uM Out Rev primer (10 uM) 1 0.2 uM Herculase
II Fusion polymerase 1 MgCl2 (25 mM) 2 1 mM ddH.sub.2O 32 Total 48
(for each reaction)
[0891] Note: if deletion size is more than 1 kb, set up a parallel
set of PCR reactions with In-Fwd and In-Rev primers to screen for
the presence of the wt allele.
[0892] 105| To screen for inversions, a PCR reaction is set up as
follows:
TABLE-US-00049 Final Component: Amount (ul) concentration Herculase
II PCR buffer, 5X 10 1X dNTP, 100 mM (25 mM each) 1 1 mM Out Fwd or
Out-Rev primer (10 uM) 1 0.2 uM In Fwd or In-Rev primer (10 uM) 1
0.2 uM Herculase II Fusion polymerase 1 MgCl.sub.2 (25 mM) 2 1 mM
ddH.sub.2O 32 Total 48 (for each reaction)
[0893] Note: primers are paired either as Out-Fwd+In Fwd, or
Out-Rev+In-Rev.
[0894] 106| Applicants added 100-200 ng of normalized genomic DNA
template from step 103 for each reaction.
[0895] 107| PCR reaction was performed using the following cycling
conditions:
TABLE-US-00050 Cycle number Denature Anneal Extend 1 95.degree. C.,
2 min 2-31 95.degree. C., 20 s 60.degree. C., 20 s 72.degree. C.,
30 s 32 72.degree. C., 3 m
[0896] 108| Applicants run 2-5 ul of PCR product on a 1-2% gel to
check for product. Although these PCR conditions are designed to
work with most primers, some primers may need additional
optimization by adjusting the template concentration, MgCl.sub.2
concentration, and/or the annealing temperature.
[0897] Genotyping for Targeted Modifications Via HDR. Timing
.andgate. 2-3 d, 2-3 h Hands on
[0898] 109| Applicants harvested DNA as described above using
QuickExtract solution and normalized genomic DNA with TE to a final
concentration of 100-200 ng/ul.
[0899] 110| PCR Amplify the modified region. The PCR reaction is
set up as follows:
TABLE-US-00051 Component: Amount (ul) Final concentration Herculase
II PCR buffer, 5X 10 1X dNTP, 100 mM (25 mM each) 1 1 mM HDR Fwd
primer (10 uM) 1 0.2 uM HDR Rev primer (10 uM) 1 0.2 uM Herculase
II Fusion polymerase 1 MgCl.sub.2 (25 mM) 2 1 mM ddH.sub.2O 33
Total 49 (for each reaction)
[0900] 111| Applicants added 100-200 ng of genomic DNA template
from step 109 for each reaction and run the following program.
TABLE-US-00052 Cycle number Denature Anneal Extend 1 95.degree. C.,
2 min 2-31 95.degree. C., 20 s 60.degree. C., 20 s 72.degree. C.,
30-60 s per kb 32 72.degree. C., 3 min
[0901] 112| Applicants ran 5 ul of PCR product on a 0.8-1% gel to
check for single-band product. Primers may need additional
optimization by adjusting the template concentration, MgCl.sub.2
concentration, and/or the annealing temperature.
[0902] 113| Applicants purified the PCR reactions using the
QIAQuick PCR purification kit.
[0903] 114| In the HDR example, a HindIII restriction site is
inserted into the EMX1 gene. These are detected by a restriction
digest of the PCR amplicon:
TABLE-US-00053 Component Amount (ul) Purified PCR amplicon (200-300
ng) x F.D. buffer, Green 1 HindIII 0.5 ddH2O x Total 10
[0904] i. The DNA is digested for 10 m at 37.degree. C.:
[0905] ii. Applicants ran 10 ul of the digested product with
loading dye on a 4-20% gradient polyacrylamide TBE gel until the
xylene cyanol band had migrated to the bottom of the gel.
[0906] iii. Applicants stained the gel with 1.times.SYBR Gold dye
while rocking for 15 m.
[0907] iv. The cleavage products are imaged and quantified as
described above in the SURVEYOR assay section. HDR efficiency is
estimated by the formula: (b+c)/(a+b+c), where a is the integrated
intensity for the undigested HDR PCR product, and b and c are the
integrated intensities for the HindIII-cut fragments.
[0908] 115| Alternatively, purified PCR amplicons from step 113 may
be cloned and genotyped using Sanger sequencing or NGS.
[0909] Deep Sequencing and Off-Target Analysis .cndot. Timing 1-2
d
[0910] The online CRISPR target design tool generates candidate
genomic off-target sites for each identified target site.
Off-target analysis at these sites can be performed by SURVEYOR
nuclease assay, Sanger sequencing, or next-generation deep
sequencing. Given the likelihood of low or undetectable
modification rates at many of these sites, Applicants recommend
deep sequencing with the Illumina Miseq platform for high
sensitivity and accuracy. Protocols will vary with sequencing
platform; here, Applicants briefly describe a fusion PCR method for
attaching sequencing adapters.
[0911] 116| Design deep sequencing primers. Next-generation
sequencing (NGS) primers are designed for shorter amplicons,
typically in the 100-200 bp size range. Primers may be manually
designed using NCBI Primer-Blast or generated with online CRISPR
target design tools (website at genome-engineering.org/tools).
[0912] 117| Harvest genomic DNA from Cas9-targeted cells. Normalize
QuickExtract genomic DNA to 100-200 ng/ul with ddH2O.
[0913] 118| Initial library preparation PCR. Using the NGS primers
from step 116, prepare the initial library preparation PCR
TABLE-US-00054 Component: Amount (ul) Final concentration Herculase
II PCR buffer, 5X 10 1X dNTP, 100 mM (25 mM each) 1 1 mM NGS Fwd
primer (10 uM) 1 0.2 uM NGS Rev primer (10 uM) 1 0.2 uM Herculase
II Fusion polymerase 1 MgCl2 (25 mM) 2 1 mM ddH2O 33 Total 49 (for
each reaction)
[0914] 119| Add 100-200 ng of normalized genomic DNA template for
each reaction.
[0915] 120|Perform PCR reaction using the following cycling
conditions, for no more than 20 amplification cycles:
TABLE-US-00055 Cycle number Denature Anneal Extend 1 95.degree. C.,
2 min 2-21 95.degree. C., 20 s 60.degree. C., 20 s 72.degree. C.,
15 s 27 72.degree. C., 3 min
[0916] 121| Run 2-5 ul of PCR product on a 1% gel to check for
single-band product. As with all genomic DNA PCRs, NGS primers may
require additional optimization by adjusting the template
concentration, MgCl.sub.2 concentration, and/or the annealing
temperature.
[0917] 122| Purify the PCR reactions using the QIAQuick PCR
purification kit and normalize eluant to 20 ng/ul. Pause point:
Purified PCR product may be stored at -20.degree. C.
[0918] 123| Nextera AT DNA Sample Preparation Kit. Following the
manufacturer's protocol, generate Miseq sequencing-ready libraries
with unique barcodes for each sample.
[0919] 124| Analyze sequencing data. Off-target analysis may be
performed through read alignment programs such as ClustalW,
Geneious, or simple sequence analysis scripts.
[0920] Timing
[0921] Steps 1-2 Design and synthesis of sgRNA oligos and ssODNs:
1-5 d, variable depending on supplier
[0922] Steps 3-5 Construction of CRISPR plasmid or PCR expression
cassette: 2 h to 3 d
[0923] Steps 6-53 Transfection into cell lines: 3 d (1 h hands-on
time)
[0924] Steps 54-70 Optional derivation of clonal lines: 1-3 weeks,
variable depending on cell type
[0925] Steps 71-91 Functional validation of NHEJ via SURVEYOR: 5-6
h
[0926] Steps 92-124 Genotyping via Sanger or next-gen deep
sequencing: 2-3 d (3-4 h hands on time)
Addressing Situations Concerning Herein Examples
TABLE-US-00056 [0927] Situation Solution No amplification of
Titrate U6-template concentration sgRNA SURVEYOR or HDR Titrate
MgCl2; normalize and titrate PCR dirty or template concentration;
annealing no amplification temp gradient; redesign primers Unequal
amplification Set up separate PCRs to detect wildtype of alleles in
and deletion alleles; Redesign primers microdeletion PCRs with
similar sized amplicons Colonies on Increase BbsI; increase Golden
Gate reaction negative cycle number, cut PX330 separately with
control plate Antarctic Phosphate treatment No sgRNA sequences
Screen additional colonies or wrong sequences Low lipofectamine
Check cell health and density; titrate DNA; transfection efficiency
add GFP transfection control Low nucleofection Check cell health
and density; titrate DNA; transfection efficiency suspend to single
cell Clumps or no cells Filter cells before FACS; dissociate to
single after FACS cells; resuspend in appropriate density Clumps or
no cells Recount cells; dissociate to single cells and in serial
dilution filter through strainer; check serial dilution High
SURVEYOR. Redesign primers to prime from different background on
locations negative sample Dirty SURVEYOR Purify PCR product; reduce
input DNA; result on gel reduce 42.degree. C. incubation to 30 m No
Purify and normalize PCR product; SURVEYOR re-anneal with TaqB
buffer; cleavage Redesign sgRNAs; sequence verify Cas9 on px330
backbone Samples do not Supplement with MgCl2 to a final sink in
TBE concentration of 15 mM or add acrylamide gel loading buffer
containing glycerol
[0928] Discussion
[0929] CRISPR-Cas may be easily multiplexed to facilitate
simultaneous modification of several genes and mediate chromosomal
microdeletions at high efficiencies. Applicants used two sgRNAs to
demonstrate simultaneous targeting of the human GRIN2B and DYRK1A
loci at efficiencies of up to 68% in HEK293FT cells. Likewise, a
pair of sgRNAs may be used to mediate microdeletions, such as
excision of an exon, which can be genotyped by PCR on a clonal
level. Note that the precise location of exon junctions can vary.
Applicants also demonstrated the use of ssODNs and targeting vector
to mediate HDR with both wildtype and nickase mutant of Cas9 in HEK
293FT and HUES9 cells (FIG. 30). Note that Applicants have not been
able to detect HDR in HUES9 cells using the Cas9 nickase, which may
be due to low efficiency or a potential difference in repair
activities in HUES9 cells. Although these values are typical, there
is some variability in the cleavage efficiency of a given sgRNA,
and on rare occasions certain sgRNAs may not work for reasons yet
unknown. Applicants recommend designing two sgRNAs for each locus,
and testing their efficiencies in the intended cell type.
Example 31
NLSs
[0930] Cas9 Transcriptional Modulator: Applicants set out to turn
the Cas9/gRNA CRISPR system into a generalized DNA binding system
in which functions beyond DNA cleavage can be executed. For
instance, by fusing functional domain(s) onto a catalytically
inactive Cas9 Applicants have imparted novel functions, such as
transcriptional activation/repression, methylation/demethylation,
or chromatin modifications. To accomplish this goal Applicants made
a catalytically inactive Cas9 mutant by changing two residues
essential for nuclease activity, D10 and H840, to alanine. By
mutating these two residues the nuclease activity of Cas9 is
abolished while maintaining the ability to bind target DNA. The
functional domains Applicants decided to focus on to test
Applicants' hypothesis are the transcriptional activator VP64 and
the transcriptional repressors SID and KRAB.
[0931] Cas9 Nuclear localization: Applicants hypothesized that the
most effective Cas9 transcriptional modulator would be strongly
localized to the nucleus where it would have its greatest influence
on transcription. Moreover, any residual Cas9 in the cytoplasm
could have unwanted effects. Applicants determined that wild-type
Cas9 does not localize into the nucleus without including multiple
nuclear localization signals (NLSs) (although a CRISPR system need
not have one or more NLSs but advantageously has at least one or
more NLS(s)). Because multiple NLS sequences were required it was
reasoned that it is difficult to get Cas9 into the nucleus and any
additional domain that is fused to Cas9 could disrupt the nuclear
localization. Therefore, Applicants made four Cas9-VP64-GFP fusion
constructs with different NLS sequences
(pXRP02--pLenti2-EF1a-NLS-hSpCsn1 (10A,840A)-NLS-VP64-EGFP,
pXRP04--pLenti2-EF1a-NLS-hSpCsn1(10A,840A)-NLS-VP64-2A-EGFP-NLS,
pXRP06--pLenti2-EF1a-NLS-EGFP-VP64-NLS-hSpCsn1(10A,840A)-NLS,
pXRP08--pLenti2-EF1a-NLS-VP64-NLS-hSpCsn1(10A,840A)-NLS-VP64-EGFP-NLS).
These constructs were cloned into a lenti backbone under the
expression of the human EF1a promoter. The WPRE element was also
added for more robust protein expression. Each construct was
transfected into HEK 293FT cells using Lipofectame 2000 and imaged
24 hours post-transfection. The best nuclear localization is
obtained when the fusion proteins have NLS sequences on both the N-
and C-term of the fusion protein. The highest observed nuclear
localization occurred in the construct with four NLS elements.
[0932] To more robustly understand the influence of NLS elements on
Cas9 Applicants made 16 Cas9-GFP fusions by adding the same alpha
importin N LS sequence on either the N- or C-term looking at zero
to three tandem repeats. Each construct was transfected into HEK
293FT cells using Lipofectame 2000 and imaged 24 hours
post-transfection. Notably, the number of NLS elements does not
directly correlate with the extent of nuclear localization. Adding
an NLS on the C-term has a greater influence on nuclear
localization than adding on the N-term.
[0933] Cas9 Transcriptional Activator: Applicants functionally
tested the Cas9-VP64 protein by targeting the Sox2 locus and
quantifying transcriptional activation by RT-qPCR. Eight DNA target
sites were chosen to span the promoter of Sox2. Each construct was
transfected into HEK 293FT cells using Lipofectame 2000 and 72
hours post-transfection total RNA was extracted from the cells. 1
ug of RNA was reverse transcribed into cDNA (qScript Supermix) in a
40 ul reaction. 2 ul of reaction product was added into a single 20
ul TaqMan assay qPCR reaction. Each experiment was performed in
biological and technical triplicates. No RT control and no template
control reactions showed no amplification. Constructs that do not
show strong nuclear localization, pXRP02 and pXRP04, result in no
activation. For the construct that did show strong nuclear
localization, pXRP08, moderate activation was observed.
Statistically significant activation was observed in the case of
guide RNAs Sox2.4 and Sox2.5.
Example 32
In Vivo Mouse Data
[0934] Material and Reagents
Herculase II fusion polymerase (Agilent Technologies, cat. no.
600679) 10.times. NEBuffer 4 (NEB, cat. No. B7004S) BsaI HF (NEB,
cat. No. R3535S) T7 DNA ligase (Enzymatics, cat. no. L602L) Fast
Digest buffer, 10.times. (ThermoScientific, cat. No. B64)
FastDigest NotI (ThermoScientific, cat. No. FD0594) FastAP Alkaline
Phosphatase (ThermoScientific, cat. No. EF0651) Lipofectamine-2000
(Life Technologies, cat. No. 11668-019) Trypsin (Life Technologies,
cat. No. 15400054) Forceps #4 (Sigma, cat. No. Z168777-1EA) Forceps
#5 (Sigma, cat. No. F6521-1EA) 10.times. Hank's Balanced Salt
Solution (Sigma, cat. No. H4641-500M L) Penicillin/Streptomycin
solution (Life Technologies, cat. No. P4333) Neurobasal (Life
Technologies, cat. No. 21103049) B27 Supplement (Life Technologies,
cat. No. 17504044) L-glutamine (Life Technologies, cat. No.
25030081) Glutamate (Sigma, cat. No. RES5063G-A7)
.beta.-mercaptoethanol (Sigma, cat. No. M6250-100mL) HA rabbit
antibody (Cell Signaling, cat. No. 3724S) LIVE/DEAD.RTM. Cell
Imaging Kit (Life Technologies, cat. No. R37601) 30G World
Precision Instrument syringe (World Precision Instruments, cat. No.
NANOFIL) Stereotaxic apparatus (Kopf Instruments) UltraMicroPump3
(World Precision Instruments, cat. No. UMP3-4) Sucrose (Sigma, cat.
No. S7903) Calcium chloride (Sigma, cat. No. C1016) Magnesium
acetate (Sigma, cat. No. M0631)
Tris-HCl (Sigma, cat. no T5941)
[0935] EDTA (Sigma, cat. No. E6758) NP-40 (Sigma, cat. No. NP40)
Phenylmethanesulfonyl fluoride (Sigma, cat. No. 78830) Magnesium
chloride (Sigma, cat. No. M8266) Potassium chloride (Sigma, cat.
No. P9333) .beta.-glycerophosphate (Sigma, cat. No. G9422) Glycerol
(Sigma, cat. No. G9012) Vybrant.RTM. DyeCycle.TM. Ruby Stain (Life
technologies, cat. No. S4942) FACS Aria Flu-act-cell sorter (Koch
Institute of MIT, Cambridge US) DNAeasy Blood & Tissue Kit
(Qiagen, cat. No. 69504)
[0936] Procedure
[0937] Constructing gRNA Multiplexes for Using In Vivo in the
Brain
[0938] Applicants designed and PCR amplified single gRNAs targeting
mouse TET and DNMT family members (as described herein) Targeting
efficiency was assessed in N2a cell line (FIG. 33). To obtain
simultaneous modification of several genes in vivo, efficient gRNA
was multiplexed in AAV-packaging vector (FIG. 34). To facilitate
further analysis of system efficiency applicants added to the
system expression cassette consistent of GFP-KASH domain fusion
protein under control of human Synapsin I promoter (FIG. 34). This
modification allows for further analysis of system efficiency in
neuronal population (more detail procedure in section Sorting
nuclei and in vivo results).
[0939] All 4 parts of the system were PCR amplified using Herculase
II Fusion polymerase using following primers:
TABLE-US-00057 1st U6 7w:
gagggtctcgtccttgcggccgcgctagcgagggcctatttcccatgatt c 1st gRNA Rv:
ctcggtctcggtAAAAAAgcaccgactcggtgccactttttcaagttgat
aacggactagccttattttaacttgctaTTTCtagctctaaaacNNNNNN
NNNNNNNNNNNNNNGGTGTTTCGTCCTTTCCAC 2nd U6 Fw:
gagggtctaTTTaccggtgagggcctatttcccatgattcc 2nd gRNA Rv:
ctcggtctcctcAAAAAAgcaccgactcggtgccactttttcaagttgat aacggactagc
cttattttaacttgctaTTTCtagctctaaaacNNNNN
NNNNNNNNNNNNNNNGGTGTTTCGTCCTTTCCAC 3rd U6 Fw:
gagggtctcTTTgagctcgagggcctatttcccatgattc 3rd gRNA Rv:
ctcggtctcgcgtAAAAAAgcaccgactcggtgccactttttcaagttga taacggactag
ccttattttaacttgctaTTTCtagctctaaaacNNNN
NNNNNNNNNNNNNNNNGGTGTTTCGTCCTTTCCA hSyn_GFP-kash Fw:
gagggtctcTTacgcgtgtgtctagac hSyn_GFP-kash Rv:
ctcggtctcAaggaCAGGGAAGGGAGCAGTGGTTCACGCCTGTAATCCCA GCAATTTGGGA
GGCCAAGGTGGGTAGATCACCTGAGATTAGGAGTTGC
(NNNNNNNNNNNNNNNNNNNN is a reverse compliment targeted genomic
sequence)
[0940] Applicants used Golden Gate strategy to assemble all parts
(1:1 molecular ratio) of the system in a single step reaction:
TABLE-US-00058 l.sup.st U6_gRNA 18 ng 2.sup.nd U6_gRNA 18 ng
3.sup.rd U6_gRNA 18 ng Syn_GFP-kash 100 ng 10x NEBuffer 4 1.0 .mu.l
10x BSA 1.0 .mu.l 10 mM ATP 1.0 .mu.l BsaI HF 0.75 .mu.l T7 ligase
0.25 .mu.l ddH.sub.2O 10 .mu.l Cycle number Condition 1-50
37.degree. C. for 5 m, 21.degree. C. for 5 m
[0941] Golden Gate reaction product was PCR amplified using
Herculase II fusion polymerase and following primers:
TABLE-US-00059 Fw 5'cctgtccttgcggccgcgctagcgagggc Rv
5'cacgcggccgcaaggacagggaagggagcag
[0942] PCR product was cloned into AAV backbone, between ITR
sequences using NotI restriction sites:
PCR Product Digestion:
TABLE-US-00060 [0943] Fast Digest buffer, 10X 3 .mu.l FastDigest
NotI 1 .mu.l DNA 1 .mu.g ddH.sub.2O up to 30 .mu.l
AAV Backbone Digestion:
TABLE-US-00061 [0944] Fast Digest buffer, 10X 3 .mu.l FastDigest
NotI 1 .mu.l FastAP Alkaline Phosphatase 1 .mu.l AAV backbone 1
.mu.g ddH.sub.2O up to 30 .mu.l
[0945] After 20 min incubation in 37.degree. C. samples were
purified using QiAQuick PCR purification kit. Standardized samples
were ligated at a 1:3 vector:insert ratio as follows:
TABLE-US-00062 Digested pUC19 50 ng Digested insert 1:3
vector:insert molar ratio T7 ligase 1 .mu.l 2X Rapid Ligation
Buffer 5 .mu.l ddH.sub.20 up to 10 .mu.l
[0946] After transformation of bacteria with ligation reaction
product, applicants confirmed obtained clones with Sanger
sequencing.
[0947] Positive DNA clones were tested in N2a cells after
co-transfection with Cas9 construct (FIGS. 35 and 36).
[0948] Design of New Cas9 Constructs for AAV Delivery
[0949] AAV delivery system despite its unique features has packing
limitation--to successfully deliver expressing cassette in vivo it
has to be in size < then 4.7 kb. To decrease the size of SpCas9
expressing cassette and facilitate delivery applicants tested
several alteration: different promoters, shorter polyA signal and
finally a smaller version of Cas9 from Staphylococcus aureus
(SaCas9) (FIGS. 37 and 38). All tested promoters were previously
tested and published to be active in neurons, including mouse Mecp2
(Gray et al., 2011), rat Map1b and truncated rat Map1b (Liu and
Fischer, 1996). Alternative synthetic polyA sequence was previously
shown to be functional as well (Levitt et al., 1989; Gray et al.,
2011). All cloned constructs were expressed in N2a cells after
transfection with Lipofectamine 2000, and tested with Western
blotting method (FIG. 39).
[0950] Testing AAV Multiplex System in Primary Neurons
[0951] To confirm functionality of developed system in neurons,
Applicants use primary neuronal cultures in vitro. Mouse cortical
neurons was prepared according to the protocol published previously
by Banker and Goslin (Banker and Goslin, 1988).
[0952] Neuronal cells are obtained from embryonic day 16. Embryos
are extracted from the euthanized pregnant female and decapitated,
and the heads are placed in ice-cold HBSS. The brains are then
extracted from the skulls with forceps (#4 and #5) and transferred
to another change of ice-cold HBSS. Further steps are performed
with the aid of a stereoscopic microscope in a Petri dish filled
with ice-cold HBSS and #5 forceps. The hemispheres are separated
from each other and the brainstem and cleared of meninges. The
hippocampi are then very carefully dissected and placed in a 15 ml
conical tube filled with ice-cold HBSS. Cortices that remain after
hippocampal dissection can be used for further cell isolation using
an analogous protocol after removing the brain steam residuals and
olfactory bulbs. Isolated hippocampi are washed three times with 10
ml ice-cold HBSS and dissociated by 15 min incubation with trypsin
in HBSS (4 ml HBSS with the addition of 10 .mu.l 2.5% trypsin per
hippocampus) at 37.degree. C. After trypsinization, the hippocampi
are very carefully washed three times to remove any traces of
trypsin with HBSS preheated to 37.degree. C. and dissociated in
warm HBSS. Applicants usually dissociate cells obtained from 10-12
embryos in 1 ml HBSS using 1 ml pipette tips and dilute dissociated
cells up to 4 ml. Cells are plated at a density of 250 cells/mm2
and cultured at 37.degree. C. and 5% CO2 for up to 3 week
[0953] HBSS
435 ml H20
50 ml 10.times. Hank's Balanced Salt Solution
16.5 ml 0.3M HEPES pH 7.3
[0954] 5 ml penicillin-streptomycin solution Filter (0.2 .mu.m) and
store 4.degree. C.
[0955] Neuron Plating Medium (100 ml)
97 ml Neurobasal
2 ml B27 Supplement
[0956] 1 ml penicillin-streptomycin solution 250 .mu.l glutamine
125 .mu.l glutamate Neurons are transduced with concentrated AAV1/2
virus or AAV1 virus from filtered medium of HEK293FT cells, between
4-7 days in culture and keep for at least one week in culture after
transduction to allow for delivered gene expression.
[0957] AAV-Driven Expression of the System
[0958] Applicants confirmed expression of SpCas9 and SaCas9 in
neuronal cultures after AAV delivery using Western blot method
(FIG. 42). One week after transduction neurons were collected in
NuPage SDS loading buffer with .beta.-mercaptoethanol to denaturate
proteins in 95.degree. C. for 5 min. Samples were separated on SDS
PAGE gel and transferred on PVDF membrane for WB protein detection.
Cas9 proteins were detected with HA antibody.
[0959] Expression of Syn-GFP-kash from gRNA multiplex AAV was
confirmed with fluorescent microscopy (FIG. 50).
[0960] Toxicity
[0961] To assess the toxicity of AAV with CRISPR system Applicants
tested overall morphology of neurons one week after virus
transduction (FIG. 45). Additionally, Applicants tested potential
toxicity of designed system with the LIVE/DEAD.RTM. Cell Imaging
Kit, which allows to distinguish live and dead cells in culture. It
is based on the presence of intracellular esterase activity (as
determined by the enzymatic conversion of the non-fluorescent
calcein AM to the intensely green fluorescent calcein). On the
other hand, the red, cell-impermeant component of the Kit enters
cells with damaged membranes only and bind to DNA generating
fluorescence in dead cells. Both fluorophores can be easily
visualized in living cells with fluorescent microscopy. AAV-driven
expression of Cas9 proteins and multiplex gRNA constructs in the
primary cortical neurons was well tolerated and not toxic (FIGS. 43
and 44), what indicates that designed AAV system is suitable for in
vivo tests.
[0962] Virus Production
[0963] Concentrated virus was produced according to the methods
described in McClure et al., 2011. Supernatant virus production
occurred in HEK293FT cells.
[0964] Brain Surgeries
[0965] For viral vector injections 10-15 week old male C57BL/6N
mice were anesthetized with a Ketamine/Xylazine cocktail (Ketamine
dose of 100 mg/kg and Xylazine dose of 10 mg/kg) by intraperitoneal
injection. Intraperitonial administration of Buprenex was used as a
pre-emptive analgesic (1 mg/kg). Animals were immobilized in a Kopf
stereotaxic apparatus using intra-aural positioning studs and tooth
bar to maintain an immobile skull. Using a hand-held drill, a hole
(1-2 mm) at -3.0 mm posterior to Bregma and 3.5 mm lateral for
injection in the CA1 region of the hippocampus was made. Using 30G
World Precision Instrument syringe at a depth of 2.5 mm, the
solution of AAV viral particles in a total volume of 1 ul was
injected. The injection was monitored by a `World Precision
Instruments UltraMicroPump3` injection pump at a flow rate of 0.5
ul/min to prevent tissue damage. When the injection was complete,
the injection needle was removed slowly, at a rate of 0.5 mm/min.
After injection, the skin was sealed with 6-0 Ethilon sutures.
Animals were postoperatively hydrated with 1 mL lactated Ringer's
(subcutaneous) and housed in a temperature controlled (37.degree.
C.) environment until achieving an ambulatory recovery. 3 weeks
after surgery animals were euthanized by deep anesthesia followed
by tissue removal for nuclei sorting or with 4% paraformaldehyde
perfusion for immunochemistry.
[0966] Sorting Nuclei and In Vivo Results
[0967] Applicants designed a method to specifically genetically tag
the gRNA targeted neuronal cell nuclei with GFP for Fluorescent
Activated Cell Sorting (FACS) of the labeled cell nuclei and
downstream processing of DNA, RNA and nuclear proteins. To that
purpose the applicants' multiplex targeting vector was designed to
express both a fusion protein between GFP and the mouse nuclear
membrane protein domain KASH (Starr DA, 2011, Current biology) and
the 3 gRNAs to target specific gene loci of interest (FIG. 34).
GFP-KASH was expressed under the control of the human Synapsin
promoter to specifically label neurons. The amino acid of the
fusion protein GFP-KASH was:
TABLE-US-00063 MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICT
TGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIF
FKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHN
VYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNH
YLSTQSALSKDPNEKRDHMVLLEFVTAAGITLGMDELYKSGLRSREEEEE
TDSRMPHLDSPGSSQPRRSFLSRVIRAALPLQLLLLLLLLLACLLPASED
DYSCTQANNFARSFYPMLRYTNGPPPT
[0968] One week after AAV1/2 mediated delivery into the brain a
robust expression of GFP-KASH was observed. For FACS and downstream
processing of labeled nuclei, the hippocampi were dissected 3 weeks
after surgery and processed for cell nuclei purification using a
gradient centrifugation step. For that purpose the tissue was
homogenized in 320 mM Sucrose, 5 mM CaCl, 3 mM Mg(Ac)2, 10 mM Tris
pH 7.8, 0.1 mM EDTA, 0.1% NP40, 0.1 mM Phenylmethanesulfonyl
fluoride (PMSF), 1 mM 3-mercaptoethanol using 2 ml Dounce
homogenizer (Sigma) The homogenisate was centrifuged on a 25% to
29% Optiprep.RTM. gradient according to the manufacture's protocol
for 30 min at 3.500 rpm at 4.degree. C. The nuclear pellet was
resuspended in 340 mM Sucrose, 2 mM MgCl2, 25 mM KCl, 65 mM
glycerophosphate, 5% glycerol, 0.1 mM PMSF, 1 mM
.beta.-mercaptoethanol and Vybrant.RTM.; DyeCycle.TM. Ruby Stain
(Life technologies) was added to label cell nuclei (offers
near-infrared emission for DNA). The labeled and purified nuclei
were sorted by FACS using an Aria Flu-act-cell sorter and BDFACS
Diva software. The sorted GFP+ and GFP- nuclei were finally used to
purify genomic DNA using DNAeasy Blood & Tissue Kit (Qiagen)
for Surveyor assay analysis of the targeted genomic regions. The
same approach can be easily used to purify nuclear RNA or protein
from targeted cells for downstream processing. Due to the 2-vector
system (FIG. 34) the applicants using in this approach efficient
Cas9 mediated DNA cleavage was expected to occur only in a small
subset of cells in the brain (cells which were co-infected with
both the multiplex targeting vector and the Cas9 encoding vector).
The method described here enables the applicants to specifically
purify DNA, RNA and nuclear proteins from the cell population
expressing the 3 gRNAs of interest and therefore are supposed to
undergo Cas9 mediated DNA cleavage. By using this method the
applicants were able to visualize efficient DNA cleavage in vivo
occurring only in a small subset of cells.
[0969] Essentially, what Applicants have shown here is targeted in
vivo cleavage. Furthermore, Applicants used a multiple approach,
with several different sequences targeted at the same time, but
independently. Presented system can be applied for studying brain
pathologic conditions (gene knock out, e.g. Parkinson disease) and
also open a field for further development of genome editing tools
in the brain. By replacing nuclease activity with gene
transcription regulators or epigenetic regulators it will be
possible to answer whole spectrum of scientific question about role
of gene regulation and epigenetic changes in the brain in not only
in the pathologic conditions but also in physiological process as
learning and memory formation. Finally, presented technology can be
applied in more complex mammalian system as primates, what allows
to overcome current technology limitations.
Example 33
Model Data
[0970] Several disease models have been specifically investigated.
These include de novo autism risk genes CHD8, KATNAL2, and SCN2A;
and the syndromic autism (Angelman Syndrome) gene UBE3A. These
genes and resulting autism models are of course preferred, but show
that the invention may be applied to any gene and therefore any
model is possible.
[0971] Applicants have made these cells lines using Cas9 nuclease
in human embryonic stem cells (hESCs). The lines were created by
transient transfection of hESCs with Cbh-Cas9-2A-EGFP and
pU6-sgRNA. Two sgRNAs are designed for each gene targeting most
often the same exons in which patient nonsense (knock-out)
mutations have been recently described from whole exome sequencing
studies of autistic patients. The Cas9-2A-EGFP and pU6 plasmids
were created specifically for this project.
Example 34
AAV Production System or Protocol
[0972] An AAV production system or protocol that was developed for,
and works particularly well with, high through put screening uses
is provided herein, but it has broader applicability in the present
invention as well. Manipulating endogenous gene expression presents
various challenges, as the rate of expression depends on many
factors, including regulatory elements, mRNA processing, and
transcript stability. To overcome this challenge, Applicants
developed an adeno-associated virus (AAV)-based vector for the
delivery. AAV has an ssDNA-based genome and is therefore less
susceptible to recombination.
[0973] AAV1/2 (serotype AAV1/2, i.e., hybrid or mosaic AAV1/AAV2
capsid AAV) heparin purified concentrated virus protocol
[0974] Media: D10+HEPES
500 ml bottle DMEM high glucose+Glutamax (GIBCO) 50 ml Hyclone FBS
(heat-inactivated) (Thermo Fischer) 5.5 ml HEPES solution (1M,
GIBCO) Cells: low passage HEK293FT (passage <10 at time of virus
production, thaw new cells of passage 2-4 for virus production,
grow up for 3-5 passages)
[0975] Transfection Reagent: Polyethylenimine (PEI) "Max"
Dissolve 50 mg PEI "Max" in 50 ml sterile Ultrapure H20
Adjust pH to 7.1
[0976] Filter with 0.22 um fliptop filter Seal tube and wrap with
parafilm Freeze aliquots at -20.degree. C. (for storage, can also
be used immediately)
[0977] Cell Culture
Culture low passage HEK293FT in D10+HEPES Passage everyday between
1:2 and 1:2.5 Advantageously do not allow cells to reach more than
85% confluency
[0978] For T75
[0979] Warm 10 ml HBSS (--Mg2+, --Ca2+, GIBCO)+1 ml TrypLE Express
(GIBCO) per flask to 37.degree. C. (Waterbath)
Aspirate media fully
[0980] Add 10 ml warm HBSS gently (to wash out media
completely)
[0981] Add 1 ml TrypLE per Flask
[0982] Place flask in incubator (37.degree. C.) for 1 min
[0983] Rock flask to detach cells
[0984] Add 9 ml D10+HEPES media (37.degree. C.)
[0985] Pipette up and down 5 times to generate single cell
suspension
[0986] Split at 1:2-1:2.5 (12 ml media for T75) ratio (if cells are
growing more slowly, discard and thaw a new batch, they are not in
optimal growth)
[0987] transfer to T225 as soon as enough cells are present (for
ease of handling large amounts of cells)
[0988] AAV Production (5*15 Cm Dish Scale Per Construct):
Plate 10 million cells in 21.5 ml media into a 15 cm dish Incubate
for 18-22 hours at 37.degree. C. Transfection is ideal at 80%
confluence
[0989] Per Plate
Prewarm 22 ml media (D10+HEPES)
[0990] Prepare Tube with DNA Mixture (Use Endofree Maxiprep
DNA):
5.2 ug vector of interest plasmid 4.35 ug AAV 1 serotype plasmid
4.35 ug AAV 2 serotype plasmid 10.4 ug pDF6 plasmid (adenovirus
helper genes) .quadrature. Vortex to mix Add 434 uL DMEM (no
serum!) Add 130 ul PEI solution Vortex 5-10 seconds Add
DNA/DMEM/PEI mixture to prewarmed media Vortex briefly to mix
Replace media in 15 cm dish with DNA/DMEM/PEI mixture Return to
37.degree. C. incubator Incubate 48 h before harvesting (make sure
medium isn't turning too acidic)
[0991] Virus Harvest:
1. aspirate media carefully from 15 cm dish dishes (advantageously
do not dislodge cells) 2. Add 25 ml RT DPBS (Invitrogen) to each
plate and gently remove cells with a cell scraper. Collect
suspension in 50 ml tubes. 3. Pellet cells at 800.times.g for 10
minutes. 4. Discard supernatant
[0992] Pause Point: Freeze Cell Pellet at -80 C if Desired
5. resuspend pellet in 150 mM NaCl, 20 mM Tris pH 8.0, use 10 ml
per tissue culture plate. 6. Prepare a fresh solution of 10% sodium
deoxycholate in dH2O. Add 1.25 ml of this per tissue culture plate
for a final concentration of 0.5%. Add benzonase nuclease to a
final concentration of 50 units per ml. Mix tube thoroughly. 7.
Incubate at 37.degree. C. for 1 hour (Waterbath). 8. Remove
cellular debris by centrifuging at 3000.times.g for 15 mins.
Transfer to fresh 50 ml tube and ensure all cell debris has been
removed to prevent blocking of heparin columns.
[0993] Heparin Column Purification of AAV1/2:
[0994] 1. Set up HiTrap heparin columns using a peristaltic pump so
that solutions flow through the column at 1 ml per minute. It is
important to ensure no air bubbles are introduced into the heparin
column.
[0995] 2. Equilibrate the column with 10 ml 150 mM NaCl, 20 mM
Tris, pH 8.0 using the peristaltic pump.
[0996] 3. Binding of virus: Apply 50 ml virus solution to column
and allow to flow through.
[0997] 4. Wash step 1: column with 20 ml 100 mM NaCl, 20 mM Tris,
pH 8.0. (using the peristaltic pump)
[0998] 5. Wash step 2: Using a 3 ml or 5 ml syringe continue to
wash the column with 1 ml 200 mM NaCl, 20 mM Tris, pH 8.0, followed
by 1 ml 300 mM NaCl, 20 mM Tris, pH 8.0.
[0999] Discard the flow-through.
[1000] (prepare the syringes with different buffers during the 50
min flow through of virus solution above)
[1001] 6. Elution Using 5 ml syringes and gentle pressure (flow
rate of <1 ml/min) elute the virus from the column by
applying:
[1002] 1.5 ml 400 mM NaCl, 20 mM Tris, pH 8.0
[1003] 3.0 ml 450 mM NaCl, 20 mM Tris, pH 8.0
[1004] 1.5 ml 500 mM NaCl, 20 mM Tris, pH 8.0
[1005] Collect these in a 15 ml centrifuge tube.
[1006] Concentration of AAV1/2:
[1007] 1. Concentration step 1: Concentrate the eluted virus using
Amicon ultra 15 ml centrifugal filter units with a 100,000
molecular weight cutoff. Load column eluate into the concentrator
and centrifuge at 2000.times.g for 2 minutes (at room temperature.
Check concentrated volume--it should be approximately 500 .mu.l. If
necessary, centrifuge in 1 min intervals until correct volume is
reached.
[1008] 2. buffer exchange: Add 1 ml sterile DPBS to filter unit,
centrifuge in 1 min intervals until correct volume (500 ul) is
reached.
[1009] 3. Concentration step 2: Add 500 ul concentrate to an Amicon
Ultra 0.5 ml 100K filter unit. Centrifuge at 6000 g for 2 min.
Check concentrated volume--it should be approximately 100 .mu.l. If
necessary, centrifuge in 1 min intervals until correct volume is
reached.
[1010] 4. Recovery: Invert filter insert and insert into fresh
collection tube. Centrifuge at 1000 g for 2 min.
Aliquot and freeze at -80 C 1 .mu.l is typically required per
injection site, small aliquots (e.g. 5 ul) are therefore
recommended (avoid freeze-thaw of virus). determine
DNaseI-resistant GC particle titer using qPCR (see separate
protocol)
[1011] Materials
Amicon Ultra, 0.5 ml, 100K; MILLIPORE; UFC510024
Amicon Ultra, 15 ml, 100K; MILLIPORE; UFC910024
[1012] Benzonase nuclease; Sigma-Aldrich, E1014 HiTrap Heparin
cartridge; Sigma-Aldrich; 54836 Sodium deoxycholate; Sigma-Aldrich;
D5670
[1013] AAV1 Supernatant Production Protocol
Media: D10+HEPES
[1014] 500 ml bottle DMEM high glucose+Glutamax (Invitrogen) 50 ml
Hyclone FBS (heat-inactivated) (Thermo Fischer) 5.5 ml HEPES
solution (1M, GIBCO) Cells: low passage HEK293FT (passage <10 at
time of virus production) Thaw new cells of passage 2-4 for virus
production, grow up for 2-5 passages Transfection reagent:
Polyethylenimine (PEI) "Max" Dissolve 50 mg PEI "Max" in 50 ml
sterile Ultrapure H20
Adjust pH to 7.1
[1015] Filter with 0.22 um fliptop filter Seal tube and wrap with
parafilm Freeze aliquots at -20.degree. C. (for storage, can also
be used immediately)
Cell Culture
[1016] Culture low passage HEK293FT in D10+HEPES Passage everyday
between 1:2 and 1:2.5 Advantageously do let cells reach more than
85% confluency
For T75
[1017] Warm 10 ml HBSS (--Mg2+, --Ca2+, GIBCO)+1 ml TrypLE Express
(GIBCO) per flask to 37.degree. C. (Waterbath)
[1018] Aspirate media fully
[1019] Add 10 ml warm HBSS gently (to wash out media
completely)
[1020] Add 1 ml TrypLE per Flask
[1021] Place flask in incubator (37.degree. C.) for 1 min
[1022] Rock flask to detach cells
[1023] Add 9 ml D10+HEPES media (37.degree. C.)
[1024] Pipette up and down 5 times to generate single cell
suspension
[1025] Split at 1:2-1:2.5 (12 ml media for T75) ratio (if cells are
growing more slowly, discard and thaw a new batch, they are not in
optimal growth)
[1026] transfer to T225 as soon as enough cells are present (for
ease of handling large amounts of cells)
AAV production (single 15 cm dish scale) Plate 10 million cells in
21.5 ml media into a 15 cm dish Incubate for 18-22 hours at
37.degree. C. Transfection is ideal at 80% confluence per plate
Prewarm 22 ml media (D10+HEPES) Prepare tube with DNA mixture (use
endofree maxiprep DNA): 5.2 ug vector of interest plasmid 8.7 ug
AAV1 serotype plasmid 10.4 ug DF6 plasmid (adenovirus helper
genes)
Vortex to mix
[1027] Add 434 uL DMEM (no serum!) Add 130 ul PEI solution Vortex
5-10 seconds Add DNA/DMEM/PEI mixture to prewarmed media Vortex
briefly to mix Replace media in 15 cm dish with DNA/DMEM/PEI
mixture Return to 37.degree. C. incubator Incubate 48 h before
harvesting (advantageously monitor to ensure medium is not turning
too acidic)
[1028] Virus Harvest:
Remove supernatant from 15 cm dish Filter with 0.45 um filter (low
protein binding) Aliquot and freeze at -80.degree. C. Transduction
(primary neuron cultures in 24-well format, 5DIV) Replace complete
neurobasal media in each well of neurons to be transduced with
fresh neurobasal (usually 400 ul out of 500 ul per well is
replaced) Thaw AAV supernatant in 37.degree. C. waterbath Let
equilibrate in incubator for 30 min Add 250 ul AAV supernatant to
each well
Incubate 24 h at 37.degree. C.
[1029] Remove media/supernatant and replace with fresh complete
neurobasal Expression starts to be visible after 48 h, saturates
around 6-7 Days Post Infection Constructs for pAAV plasmid with GOI
should not exceed 4.8 kb including both ITRS.
[1030] Example of a human codon optimized sequence (i.e. being
optimized for expression in humans) sequence: SaCas9 is provided
below:
TABLE-US-00064 ACCGGTGCCACCATGTACCCATACGATGTTCCAGATTACGC
TTCGCCGAAGAAAAAGCGCAAGGTCGAAGCGTCCATGAAAAGGAACTACA
TTCTGGGGCTGGACATCGGGATTACAAGCGTGGGGTATGGGATTATTGAC
TATGAAACAAGGGACGTGATCGACGCAGGCGTCAGACTGTTCAAGGAGGC
CAACGTGGAAAACAATGAGGGACGGAGAAGCAAGAGGGGAGCCAGGCGCC
TGAAACGACGGAGAAGGCACAGAATCCAGAGGGTGAAGAAACTGCTGTTC
GATTACAACCTGCTGACCGACCATTCTGAGCTGAGTGGAATTAATCCTTA
TGAAGCCAGGGTGAAAGGCCTGAGTCAGAAGCTGTCAGAGGAAGAGTTTT
CCGCAGCTCTGCTGCACCTGGCTAAGCGCCGAGGAGTGCATAACGTCAAT
GAGGTGGAAGAGGACACCGGCAACGAGCTGTCTACAAAGGAACAGATCTC
ACGCAATAGCAAAGCTCTGGAAGAGAAGTATGTCGCAGAGCTGCAGCTGG
AACGGCTGAAGAAAGATGGCGAGGTGAGAGGGTCAATTAATAGGTTCAAG
ACAAGCGACTACGTCAAAGAAGCCAAGCAGCTGCTGAAAGTGCAGAAGGC
TTACCACCAGCTGGATCAGAGCTTCATCGATACTTATATCGACCTGCTGG
AGACTCGGAGAACCTACTATGAGGGACCAGGAGAAGGGAGCCCCTTCGGA
TGGAAAGACATCAAGGAATGGTACGAGATGCTGATGGGACATTGCACCTA
TTTTCCAGAAGAGCTGAGAAGCGTCAAGTACGCTTATAACGCAGATCTGT
ACAACGCCCTGAATGACCTGAACAACCTGGTCATCACCAGGGATGAAAAC
GAGAAACTGGAATACTATGAGAAGTTCCAGATCATCGAAAACGTGTTTAA
GCAGAAGAAAAAGCCTACACTGAAACAGATTGCTAAGGAGATCCTGGTCA
ACGAAGAGGACATCAAGGGCTACCGGGTGACAAGCACTGGAAAACCAGAG
TTCACCAATCTGAAAGTGTATCACGATATTAAGGACATCACAGCACGGAA
AGAAATCATTGAGAACGCCGAACTGCTGGATCAGATTGCTAAGATCCTGA
CTATCTACCAGAGCTCCGAGGACATCCAGGAAGAGCTGACTAACCTGAAC
AGCGAGCTGACCCAGGAAGAGATCGAACAGATTAGTAATCTGAAGGGGTA
CACCGGAACACACAACCTGTCCCTGAAAGCTATCAATCTGATTCTGGATG
AGCTGTGGCATACAAACGACAATCAGATTGCAATCTTTAACCGGCTGAAG
CTGGTCCCAAAAAAGGTGGACCTGAGTCAGCAGAAAGAGATCCCAACCAC
ACTGGTGGACGATTTCATTCTGTCACCCGTGGTCAAGCGGAGCTTCATCC
AGAGCATCAAAGTGATCAACGCCATCATCAAGAAGTACGGCCTGCCCAAT
GATATCATTATCGAGCTGGCTAGGGAGAAGAACAGCAAGGACGCACAGAA
GATGATCAATGAGATGCAGAAACGAAACCGGCAGACCAATGAACGCATTG
AAGAGATTATCCGAACTACCGGGAAAGAGAACGCAAAGTACCTGATTGAA
AAAATCAAGCTGCACGATATGCAGGAGGGAAAGTGTCTGTATTCTCTGGA
GGCCATCCCCCTGGAGGACCTGCTGAACAATCCATTCAACTACGAGGTCG
ATCATATTATCCCCAGAAGCGTGTCCTTCGACAATTCCTTTAACAACAAG
GTGCTGGTCAAGCAGGAAGAGAACTCTAAAAAGGGCAATAGGACTCCTTT
CCAGTACCTGTCTAGTTCAGATTCCAAGATCTCTTACGAAACCTTTAAAA
AGCACATTCTGAATCTGGCCAAAGGAAAGGGCCGCATCAGCAAGACCAAA
AAGGAGTACCTGCTGGAAGAGCGGGACATCAACAGATTCTCCGTCCAGAA
GGATTTTATTAACCGGAATCTGGTGGACACAAGATACGCTACTCGCGGCC
TGATGAATCTGCTGCGATCCTATTTCCGGGTGAACAATCTGGATGTGAAA
GTCAAGTCCATCAACGGCGGGTTCACATCTTTTCTGAGGCGCAAATGGAA
GTTTAAAAAGGAGCGCAACAAAGGGTACAAGCACCATGCCGAAGATGCTC
TGATTATCGCAAATGCCGACTTCATCTTTAAGGAGTGGAAAAAGCTGGAC
AAAGCCAAGAAAGTGATGGAGAACCAGATGTTCGAAGAGAAGCAGGCCGA
ATCTATGCCCGAAATCGAGACAGAACAGGAGTACAAGGAGATTTTCATCA
CTCCTCACCAGATCAAGCATATCAAGGATTTCAAGGACTACAAGTACTCT
CACCGGGTGGATAAAAAGCCCAACAGAGAGCTGATCAATGACACCCTGTA
TAGTACAAGAAAAGACGATAAGGGGAATACCCTGATTGTGAACAATCTGA
ACGGACTGTACGACAAAGATAATGACAAGCTGAAAAAGCTGATCAACAAA
AGTCCCGAGAAGCTGCTGATGTACCACCATGATCCTCAGACATATCAGAA
ACTGAAGCTGATTATGGAGCAGTACGGCGACGAGAAGAACCCACTGTATA
AGTACTATGAAGAGACTGGGAACTACCTGACCAAGTATAGCAAAAAGGAT
AATGGCCCCGTGATCAAGAAGATCAAGTACTATGGGAACAAGCTGAATGC
CCATCTGGACATCACAGACGATTACCCTAACAGTCGCAACAAGGTGGTCA
AGCTGTCACTGAAGCCATACAGATTCGATGTCTATCTGGACAACGGCGTG
TATAAATTTGTGACTGTCAAGAATCTGGATGTCATCAAAAAGGAGAACTA
CTATGAAGTGAATAGCAAGTGCTACGAAGAGGCTAAAAAGCTGAAAAAGA
TTAGCAACCAGGCAGAGTTCATCGCCTCCTTTTACAACAACGACCTGATT
AAGATCAATGGCGAACTGTATAGGGTCATCGGGGTGAACAATGATCTGCT
GAACCGCATTGAAGTGAATATGATTGACATCACTTACCGAGAGTATCTGG
AAAACATGAATGATAAGCGCCCCCCTCGAATTATCAAAACAATTGCCTCT
AAGACTCAGAGTATCAAAAAGTACTCAACCGACATTCTGGGAAACCTGTA
TGAGGTGAAGAGCAAAAAGCACCCTCAGATTATCAAAAAGGGCTAAGAAT TC
Example 35
Minimizing Off Target Cleavage Using Cas9 Nickase and Two Guide
RNAs
[1031] Cas9 is a RNA-guided DNA nuclease that may be targeted to
specific locations in the genome with the help of a 20 bp RNA
guide. However the guide sequence may tolerate some mismatches
between the guide sequence and the DNA-target sequence. The
flexibility is undesirable due to the potential for off-target
cleavage, when the guide RNA targets Cas9 to a an off-target
sequence that has a few bases different from the guide sequence.
For all experimental applications (gene targeting, crop
engineering, therapeutic applications, etc) it is important to be
able to improve the specificity of Cas9 mediated gene targeting and
reduce the likelihood of off-target modification by Cas9.
[1032] Applicants developed a method of using a Cas9 nickase mutant
in combination with two guide RNAs to facilitate targeted double
strand breaks in the genome without off-target modifications. The
Cas9 nickase mutant may be generated from a Cas9 nuclease by
disabling its cleavage activity so that instead of both strands of
the DNA duplex being cleaved only one strand is cleaved. The Cas9
nickase may be generated by inducing mutations in one or more
domains of the Cas9 nuclease, e.g. Ruvc1 or HNH. These mutations
may include but are not limited to mutations in a Cas9 catalytic
domain, e.g in SpCas9 these mutations may be at positions D10 or
H840. These mutations may include but are not limited to D10A,
E762A, H840A. N854A, N863A or D986A in SpCas9 but nickases may be
generated by inducing mutations at corresponding positions in other
CRISPR enzymes or Cas9 orthologs. In a most preferred embodiment of
the invention the Cas9 nickase mutant is a SpCas9 nickase with a
D10A mutation.
[1033] The way this works is that each guide RNA in combination
with Cas9 nickase would induce the targeted single strand break of
a duplex DNA target. Since each guide RNA nicks one strand, the net
result is a double strand break. The reason this method eliminates
off-target mutations is because it is very unlikely to have an
off-target site that has high degrees of similarity for both guide
sequences (20 bp+2 bp(PAM)=22 bp specificity for each guide, and
two guides means any off-target site will have to have close to 44
bp of homologous sequence). Although it is still likely that
individual guides may have off-targets, but those off-targets will
only be nicked, which is unlikely to be repaired by the mutagenic
NHEJ process. Therefore the multiplexing of DNA double strand
nicking provides a powerful way of introducing targeted DNA double
strand breaks without off-target mutagenic effects.
[1034] Applicants carried out experiments involving the
co-transfection of HEK293FT cells with a plasmid encoding
Cas9(D10A) nickase as well as DNA expression cassettes for one or
more guides. Applicants transfected cells using Lipofectamine 2000,
and transfected cells were harvested 48 or 72 hours after
transfections. Double nicking-induced NHEJ were detected using the
SURVEYOR nuclease assay as described previously herein (FIGS. 51,
52 and 53).
[1035] Applicants have further identified parameters that relate to
efficient cleavage by the Cas9 nickase mutant when combined with
two guide RNAs and these parameters include but are not limited to
the length of the 5' overhang. Efficient cleavage is reported for
5' overhang of at least 26 base pairs. In a preferred embodiment of
the invention, the 5' overhang is at least 30 base pairs and more
preferably at least 34 base pairs. Overhangs of up to 200 base
pairs may be acceptable for cleavage, while 5' overhangs less than
100 base pairs are preferred and 5' overhangs less than 50 base
pairs are most preferred (FIGS. 54 and 55).
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Sequence CWU 1
1
434127DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 1gcactgaggg cctatttccc atgattc
27220DNAHomo sapiens 2gagtccgagc agaagaagaa 20320DNAHomo sapiens
3gagtcctagc aggagaagaa 20420DNAHomo sapiens 4gagtctaagc agaagaagaa
20560RNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 5nnnnnnnnnn nnnnnnnnnn
ccnnnnnnnn nnnnnnnnnn nnnnggnnnn nnnnnnnnnn 60660RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 6nnnnnnnnnn nnnnccnnnn nnnnnnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 60760RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 7nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnnnnnnn
nnnggnnnnn nnnnnnnnnn 60860RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 8nnnnnnnnnn nnnnnccnnn nnnnnnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 60960RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 9nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnnnnnnn
nnggnnnnnn nnnnnnnnnn 601060RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 10nnnnnnnnnn nnnnnccnnn nnnnnnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 601160RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 11nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnnnnnnn
nggnnnnnnn nnnnnnnnnn 601260RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 12nnnnnnnnnn nnnnnnnccn nnnnnnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 601360RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 13nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnnnnnnn
ggnnnnnnnn nnnnnnnnnn 601460RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 14nnnnnnnnnn nnnnnnnncc nnnnnnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 601560RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 15nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnnnnnng
gnnnnnnnnn nnnnnnnnnn 601660RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 16nnnnnnnnnn nnnnnnnnnc cnnnnnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 601760RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 17nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 601860RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 18nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 601960RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 19nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnnnnggn
nnnnnnnnnn nnnnnnnnnn 602060RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 20nnnnnnnnnn nnnnnnnnnn nccnnnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 602160RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 21nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnnnggnn
nnnnnnnnnn nnnnnnnnnn 602260RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 22nnnnnnnnnn nnnnnnnnnn nnccnnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 602360RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 23nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnnggnnn
nnnnnnnnnn nnnnnnnnnn 602460RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 24nnnnnnnnnn nnnnnnnnnn nnnccnnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 602560RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 25nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnnggnnnn
nnnnnnnnnn nnnnnnnnnn 602660RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 26nnnnnnnnnn nnnnnnnnnn nnnnccnnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 602760RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 27nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnnggnnnnn
nnnnnnnnnn nnnnnnnnnn 602860RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 28nnnnnnnnnn nnnnnnnnnn nnnnnccnnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 602960RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 29nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nnggnnnnnn
nnnnnnnnnn nnnnnnnnnn 603060RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 30nnnnnnnnnn nnnnnnnnnn nnnnnnccnn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 603160RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 31nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn nggnnnnnnn
nnnnnnnnnn nnnnnnnnnn 603260RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 32nnnnnnnnnn nnnnnnnnnn nnnnnnnccn nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 603360RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 33nnnnnnnnnn nnnnnnnnnn ccnnnnnnnn ggnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 603460RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 34nnnnnnnnnn nnnnnnnnnn nnnnnnnncc nnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 603560RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 35nnnnnnnnnn nnnnnnnnnn ccnnnnnnng gnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 603660RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 36nnnnnnnnnn nnnnnnnnnn nnnnnnnnnc cnnnnnnngg
nnnnnnnnnn nnnnnnnnnn 603760RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 37nnnnnnnnnn nnnnnnnnnn ccnnnnnngg nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 603860RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 38nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn ccnnnnnngg
nnnnnnnnnn nnnnnnnnnn 603960RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 39nnnnnnnnnn nnnnnnnnnn ccnnnnnggn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 604060RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 40nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nccnnnnngg
nnnnnnnnnn nnnnnnnnnn 604160RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 41nnnnnnnnnn nnnnnnnnnn ccnnnnggnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 604260RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 42nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnccnnnngg
nnnnnnnnnn nnnnnnnnnn 604360RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 43nnnnnnnnnn nnnnnnnnnn ccnnnggnnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 604460RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 44nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnccnnngg
nnnnnnnnnn nnnnnnnnnn 604560RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 45nnnnnnnnnn nnnnnnnnnn ccnnggnnnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 604660RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 46nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnccnngg
nnnnnnnnnn nnnnnnnnnn 604760RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 47nnnnnnnnnn nnnnnnnnnn ccnggnnnnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 604860RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 48nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnccngg
nnnnnnnnnn nnnnnnnnnn 604960RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 49nnnnnnnnnn nnnnnnnnnn nccggnnnnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 605060RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 50nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnccggn
nnnnnnnnnn nnnnnnnnnn 605160RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 51nnnnnnnnnn nnnnnnnnnn nnnggnnnnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 605260RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 52nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnggccnnn
nnnnnnnnnn nnnnnnnnnn 605360RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 53nnnnnnnnnn nnnnnnnnnn nncggnnnnn nnnnnnnnnn
nnnnnnnnnn nnnnnnnnnn 605460RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 54nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnggnccnnn
nnnnnnnnnn nnnnnnnnnn 605560RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 55nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nggnnccnnn
nnnnnnnnnn nnnnnnnnnn 605660RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 56nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn ggnnnccnnn
nnnnnnnnnn nnnnnnnnnn 605760RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 57nnnnnnnnnn nnnnnnnnnn nnnnnnnnng gnnnnccnnn
nnnnnnnnnn nnnnnnnnnn 605860RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 58nnnnnnnnnn nnnnnnnnnn nnnnnnnngg nnnnnccnnn
nnnnnnnnnn nnnnnnnnnn 605912RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 59guuuuagagc ua 12607PRTSimian virus 40 60Pro Lys
Lys Lys Arg Lys Val 1 5 6116PRTUnknownsource/note="Description of
Unknown Nucleoplasmin bipartite NLS sequence" 61Lys Arg Pro Ala Ala
Thr Lys Lys Ala Gly Gln Ala Lys Lys Lys Lys 1 5 10 15
629PRTUnknownsource/note="Description of Unknown C-myc NLS
sequence" 62Pro Ala Ala Lys Arg Val Lys Leu Asp 1 5
6311PRTUnknownsource/note="Description of Unknown C-myc NLS
sequence" 63Arg Gln Arg Arg Asn Glu Leu Lys Arg Ser Pro 1 5 10
6438PRTHomo sapiens 64Asn Gln Ser Ser Asn Phe Gly Pro Met Lys Gly
Gly Asn Phe Gly Gly 1 5 10 15 Arg Ser Ser Gly Pro Tyr Gly Gly Gly
Gly Gln Tyr Phe Ala Lys Pro 20 25 30 Arg Asn Gln Gly Gly Tyr 35
6542PRTUnknownsource/note="Description of Unknown IBB domain from
importin-alpha sequence" 65Arg Met Arg Ile Glx Phe Lys Asn Lys Gly
Lys Asp Thr Ala Glu Leu 1 5 10 15 Arg Arg Arg Arg Val Glu Val Ser
Val Glu Leu Arg Lys Ala Lys Lys 20 25 30 Asp Glu Gln Ile Leu Lys
Arg Arg Asn Val 35 40 668PRTUnknownsource/note="Description of
Unknown Myoma T protein sequence" 66Val Ser Arg Lys Arg Pro Arg Pro
1 5 678PRTUnknownsource/note="Description of Unknown Myoma T
protein sequence" 67Pro Pro Lys Lys Ala Arg Glu Asp 1 5 688PRTHomo
sapiens 68Pro Gln Pro Lys Lys Lys Pro Leu 1 5 6912PRTMus musculus
69Ser Ala Leu Ile Lys Lys Lys Lys Lys Met Ala Pro 1 5 10
705PRTInfluenza virus 70Asp Arg Leu Arg Arg 1 5 717PRTInfluenza
virus 71Pro Lys Gln Lys Lys Arg Lys 1 5 7210PRTHepatitus delta
virus 72Arg Lys Leu Lys Lys Lys Ile Lys Lys Leu 1 5 10 7310PRTMus
musculus 73Arg Glu Lys Lys Lys Phe Leu Lys Arg Arg 1 5 10
7420PRTHomo sapiens 74Lys Arg Lys Gly Asp Glu Val Asp Gly Val Asp
Glu Val Ala Lys Lys 1 5 10 15 Lys Ser Lys Lys 20 7517PRTHomo
sapiens 75Arg Lys Cys Leu Gln Ala Gly Met Asn Leu Glu Ala Arg Lys
Thr Lys 1 5 10 15 Lys 7627DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 76nnnnnnnnnn nnnnnnnnnn nnagaaw
277719DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 77nnnnnnnnnn nnnnagaaw
197827DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 78nnnnnnnnnn nnnnnnnnnn nnagaaw
277918DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 79nnnnnnnnnn nnnagaaw
1880137DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic polynucleotide" 80nnnnnnnnnn nnnnnnnnnn
gtttttgtac tctcaagatt tagaaataaa tcttgcagaa 60gctacaaaga taaggcttca
tgccgaaatc aacaccctgt cattttatgg cagggtgttt 120tcgttattta atttttt
13781123DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polynucleotide" 81nnnnnnnnnn
nnnnnnnnnn gtttttgtac tctcagaaat gcagaagcta caaagataag 60gcttcatgcc
gaaatcaaca ccctgtcatt ttatggcagg gtgttttcgt tatttaattt 120ttt
12382110DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polynucleotide" 82nnnnnnnnnn
nnnnnnnnnn gtttttgtac tctcagaaat gcagaagcta caaagataag 60gcttcatgcc
gaaatcaaca ccctgtcatt ttatggcagg gtgttttttt 11083102DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
polynucleotide" 83nnnnnnnnnn nnnnnnnnnn gttttagagc tagaaatagc
aagttaaaat aaggctagtc 60cgttatcaac ttgaaaaagt ggcaccgagt cggtgctttt
tt 1028488DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic oligonucleotide" 84nnnnnnnnnn
nnnnnnnnnn gttttagagc tagaaatagc aagttaaaat aaggctagtc 60cgttatcaac
ttgaaaaagt gttttttt 888576DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 85nnnnnnnnnn nnnnnnnnnn gttttagagc tagaaatagc
aagttaaaat aaggctagtc 60cgttatcatt tttttt 768612DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 86gttttagagc ta 128731DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 87tagcaagtta aaataaggct agtccgtttt t
318827DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 88nnnnnnnnnn nnnnnnnnnn nnagaaw
278933DNAHomo sapiens 89ggacatcgat gtcacctcca atgactaggg tgg
339033DNAHomo sapiens 90cattggaggt gacatcgatg tcctccccat tgg
339133DNAHomo sapiens 91ggaagggcct gagtccgagc agaagaagaa ggg
339233DNAHomo sapiens 92ggtggcgaga ggggccgaga ttgggtgttc agg
339333DNAHomo sapiens 93atgcaggagg gtggcgagag gggccgagat tgg
339432DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 94aaactctaga gagggcctat ttcccatgat tc
3295153DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 95acctctagaa aaaaagcacc gactcggtgc
cactttttca agttgataac ggactagcct 60tattttaact tgctatgctg ttttgtttcc
aaaacagcat agctctaaaa cccctagtca 120ttggaggtga cggtgtttcg
tcctttccac aag 1539652DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 96taatacgact cactatagga agtgcgccac catggcccca aagaagaagc gg
529760DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic primer" 97ggtttttttt tttttttttt tttttttttt
ttttcttact ttttcttttt tgcctggccg 6098984PRTCampylobacter jejuni
98Met Ala Arg Ile Leu Ala Phe Asp Ile Gly Ile Ser Ser Ile Gly Trp 1
5
10 15 Ala Phe Ser Glu Asn Asp Glu Leu Lys Asp Cys Gly Val Arg Ile
Phe 20 25 30 Thr Lys Val Glu Asn Pro Lys Thr Gly Glu Ser Leu Ala
Leu Pro Arg 35 40 45 Arg Leu Ala Arg Ser Ala Arg Lys Arg Leu Ala
Arg Arg Lys Ala Arg 50 55 60 Leu Asn His Leu Lys His Leu Ile Ala
Asn Glu Phe Lys Leu Asn Tyr 65 70 75 80 Glu Asp Tyr Gln Ser Phe Asp
Glu Ser Leu Ala Lys Ala Tyr Lys Gly 85 90 95 Ser Leu Ile Ser Pro
Tyr Glu Leu Arg Phe Arg Ala Leu Asn Glu Leu 100 105 110 Leu Ser Lys
Gln Asp Phe Ala Arg Val Ile Leu His Ile Ala Lys Arg 115 120 125 Arg
Gly Tyr Asp Asp Ile Lys Asn Ser Asp Asp Lys Glu Lys Gly Ala 130 135
140 Ile Leu Lys Ala Ile Lys Gln Asn Glu Glu Lys Leu Ala Asn Tyr Gln
145 150 155 160 Ser Val Gly Glu Tyr Leu Tyr Lys Glu Tyr Phe Gln Lys
Phe Lys Glu 165 170 175 Asn Ser Lys Glu Phe Thr Asn Val Arg Asn Lys
Lys Glu Ser Tyr Glu 180 185 190 Arg Cys Ile Ala Gln Ser Phe Leu Lys
Asp Glu Leu Lys Leu Ile Phe 195 200 205 Lys Lys Gln Arg Glu Phe Gly
Phe Ser Phe Ser Lys Lys Phe Glu Glu 210 215 220 Glu Val Leu Ser Val
Ala Phe Tyr Lys Arg Ala Leu Lys Asp Phe Ser 225 230 235 240 His Leu
Val Gly Asn Cys Ser Phe Phe Thr Asp Glu Lys Arg Ala Pro 245 250 255
Lys Asn Ser Pro Leu Ala Phe Met Phe Val Ala Leu Thr Arg Ile Ile 260
265 270 Asn Leu Leu Asn Asn Leu Lys Asn Thr Glu Gly Ile Leu Tyr Thr
Lys 275 280 285 Asp Asp Leu Asn Ala Leu Leu Asn Glu Val Leu Lys Asn
Gly Thr Leu 290 295 300 Thr Tyr Lys Gln Thr Lys Lys Leu Leu Gly Leu
Ser Asp Asp Tyr Glu 305 310 315 320 Phe Lys Gly Glu Lys Gly Thr Tyr
Phe Ile Glu Phe Lys Lys Tyr Lys 325 330 335 Glu Phe Ile Lys Ala Leu
Gly Glu His Asn Leu Ser Gln Asp Asp Leu 340 345 350 Asn Glu Ile Ala
Lys Asp Ile Thr Leu Ile Lys Asp Glu Ile Lys Leu 355 360 365 Lys Lys
Ala Leu Ala Lys Tyr Asp Leu Asn Gln Asn Gln Ile Asp Ser 370 375 380
Leu Ser Lys Leu Glu Phe Lys Asp His Leu Asn Ile Ser Phe Lys Ala 385
390 395 400 Leu Lys Leu Val Thr Pro Leu Met Leu Glu Gly Lys Lys Tyr
Asp Glu 405 410 415 Ala Cys Asn Glu Leu Asn Leu Lys Val Ala Ile Asn
Glu Asp Lys Lys 420 425 430 Asp Phe Leu Pro Ala Phe Asn Glu Thr Tyr
Tyr Lys Asp Glu Val Thr 435 440 445 Asn Pro Val Val Leu Arg Ala Ile
Lys Glu Tyr Arg Lys Val Leu Asn 450 455 460 Ala Leu Leu Lys Lys Tyr
Gly Lys Val His Lys Ile Asn Ile Glu Leu 465 470 475 480 Ala Arg Glu
Val Gly Lys Asn His Ser Gln Arg Ala Lys Ile Glu Lys 485 490 495 Glu
Gln Asn Glu Asn Tyr Lys Ala Lys Lys Asp Ala Glu Leu Glu Cys 500 505
510 Glu Lys Leu Gly Leu Lys Ile Asn Ser Lys Asn Ile Leu Lys Leu Arg
515 520 525 Leu Phe Lys Glu Gln Lys Glu Phe Cys Ala Tyr Ser Gly Glu
Lys Ile 530 535 540 Lys Ile Ser Asp Leu Gln Asp Glu Lys Met Leu Glu
Ile Asp His Ile 545 550 555 560 Tyr Pro Tyr Ser Arg Ser Phe Asp Asp
Ser Tyr Met Asn Lys Val Leu 565 570 575 Val Phe Thr Lys Gln Asn Gln
Glu Lys Leu Asn Gln Thr Pro Phe Glu 580 585 590 Ala Phe Gly Asn Asp
Ser Ala Lys Trp Gln Lys Ile Glu Val Leu Ala 595 600 605 Lys Asn Leu
Pro Thr Lys Lys Gln Lys Arg Ile Leu Asp Lys Asn Tyr 610 615 620 Lys
Asp Lys Glu Gln Lys Asn Phe Lys Asp Arg Asn Leu Asn Asp Thr 625 630
635 640 Arg Tyr Ile Ala Arg Leu Val Leu Asn Tyr Thr Lys Asp Tyr Leu
Asp 645 650 655 Phe Leu Pro Leu Ser Asp Asp Glu Asn Thr Lys Leu Asn
Asp Thr Gln 660 665 670 Lys Gly Ser Lys Val His Val Glu Ala Lys Ser
Gly Met Leu Thr Ser 675 680 685 Ala Leu Arg His Thr Trp Gly Phe Ser
Ala Lys Asp Arg Asn Asn His 690 695 700 Leu His His Ala Ile Asp Ala
Val Ile Ile Ala Tyr Ala Asn Asn Ser 705 710 715 720 Ile Val Lys Ala
Phe Ser Asp Phe Lys Lys Glu Gln Glu Ser Asn Ser 725 730 735 Ala Glu
Leu Tyr Ala Lys Lys Ile Ser Glu Leu Asp Tyr Lys Asn Lys 740 745 750
Arg Lys Phe Phe Glu Pro Phe Ser Gly Phe Arg Gln Lys Val Leu Asp 755
760 765 Lys Ile Asp Glu Ile Phe Val Ser Lys Pro Glu Arg Lys Lys Pro
Ser 770 775 780 Gly Ala Leu His Glu Glu Thr Phe Arg Lys Glu Glu Glu
Phe Tyr Gln 785 790 795 800 Ser Tyr Gly Gly Lys Glu Gly Val Leu Lys
Ala Leu Glu Leu Gly Lys 805 810 815 Ile Arg Lys Val Asn Gly Lys Ile
Val Lys Asn Gly Asp Met Phe Arg 820 825 830 Val Asp Ile Phe Lys His
Lys Lys Thr Asn Lys Phe Tyr Ala Val Pro 835 840 845 Ile Tyr Thr Met
Asp Phe Ala Leu Lys Val Leu Pro Asn Lys Ala Val 850 855 860 Ala Arg
Ser Lys Lys Gly Glu Ile Lys Asp Trp Ile Leu Met Asp Glu 865 870 875
880 Asn Tyr Glu Phe Cys Phe Ser Leu Tyr Lys Asp Ser Leu Ile Leu Ile
885 890 895 Gln Thr Lys Asp Met Gln Glu Pro Glu Phe Val Tyr Tyr Asn
Ala Phe 900 905 910 Thr Ser Ser Thr Val Ser Leu Ile Val Ser Lys His
Asp Asn Lys Phe 915 920 925 Glu Thr Leu Ser Lys Asn Gln Lys Ile Leu
Phe Lys Asn Ala Asn Glu 930 935 940 Lys Glu Val Ile Ala Lys Ser Ile
Gly Ile Gln Asn Leu Lys Val Phe 945 950 955 960 Glu Lys Tyr Ile Val
Ser Ala Leu Gly Glu Val Thr Lys Ala Glu Phe 965 970 975 Arg Gln Arg
Glu Asp Phe Lys Lys 980 9991DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 99tataatctca taagaaattt aaaaagggac taaaataaag
agtttgcggg actctgcggg 60gttacaatcc cctaaaaccg cttttaaaat t
9110036DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 100attttaccat aaagaaattt
aaaaagggac taaaac 3610195RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 101nnnnnnnnnn nnnnnnnnnn guuuuagucc cgaaagggac
uaaaauaaag aguuugcggg 60acucugcggg guuacaaucc ccuaaaaccg cuuuu
951021115PRTArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polypeptide" 102Met Ser Asp Leu Val
Leu Gly Leu Asp Ile Gly Ile Gly Ser Val Gly 1 5 10 15 Val Gly Ile
Leu Asn Lys Val Thr Gly Glu Ile Ile His Lys Asn Ser 20 25 30 Arg
Ile Phe Pro Ala Ala Gln Ala Glu Asn Asn Leu Val Arg Arg Thr 35 40
45 Asn Arg Gln Gly Arg Arg Leu Ala Arg Arg Lys Lys His Arg Arg Val
50 55 60 Arg Leu Asn Arg Leu Phe Glu Glu Ser Gly Leu Ile Thr Asp
Phe Thr 65 70 75 80 Lys Ile Ser Ile Asn Leu Asn Pro Tyr Gln Leu Arg
Val Lys Gly Leu 85 90 95 Thr Asp Glu Leu Ser Asn Glu Glu Leu Phe
Ile Ala Leu Lys Asn Met 100 105 110 Val Lys His Arg Gly Ile Ser Tyr
Leu Asp Asp Ala Ser Asp Asp Gly 115 120 125 Asn Ser Ser Val Gly Asp
Tyr Ala Gln Ile Val Lys Glu Asn Ser Lys 130 135 140 Gln Leu Glu Thr
Lys Thr Pro Gly Gln Ile Gln Leu Glu Arg Tyr Gln 145 150 155 160 Thr
Tyr Gly Gln Leu Arg Gly Asp Phe Thr Val Glu Lys Asp Gly Lys 165 170
175 Lys His Arg Leu Ile Asn Val Phe Pro Thr Ser Ala Tyr Arg Ser Glu
180 185 190 Ala Leu Arg Ile Leu Gln Thr Gln Gln Glu Phe Asn Pro Gln
Ile Thr 195 200 205 Asp Glu Phe Ile Asn Arg Tyr Leu Glu Ile Leu Thr
Gly Lys Arg Lys 210 215 220 Tyr Tyr His Gly Pro Gly Asn Glu Lys Ser
Arg Thr Asp Tyr Gly Arg 225 230 235 240 Tyr Arg Thr Ser Gly Glu Thr
Leu Asp Asn Ile Phe Gly Ile Leu Ile 245 250 255 Gly Lys Cys Thr Phe
Tyr Pro Asp Glu Phe Arg Ala Ala Lys Ala Ser 260 265 270 Tyr Thr Ala
Gln Glu Phe Asn Leu Leu Asn Asp Leu Asn Asn Leu Thr 275 280 285 Val
Pro Thr Glu Thr Lys Lys Leu Ser Lys Glu Gln Lys Asn Gln Ile 290 295
300 Ile Asn Tyr Val Lys Asn Glu Lys Ala Met Gly Pro Ala Lys Leu Phe
305 310 315 320 Lys Tyr Ile Ala Lys Leu Leu Ser Cys Asp Val Ala Asp
Ile Lys Gly 325 330 335 Tyr Arg Ile Asp Lys Ser Gly Lys Ala Glu Ile
His Thr Phe Glu Ala 340 345 350 Tyr Arg Lys Met Lys Thr Leu Glu Thr
Leu Asp Ile Glu Gln Met Asp 355 360 365 Arg Glu Thr Leu Asp Lys Leu
Ala Tyr Val Leu Thr Leu Asn Thr Glu 370 375 380 Arg Glu Gly Ile Gln
Glu Ala Leu Glu His Glu Phe Ala Asp Gly Ser 385 390 395 400 Phe Ser
Gln Lys Gln Val Asp Glu Leu Val Gln Phe Arg Lys Ala Asn 405 410 415
Ser Ser Ile Phe Gly Lys Gly Trp His Asn Phe Ser Val Lys Leu Met 420
425 430 Met Glu Leu Ile Pro Glu Leu Tyr Glu Thr Ser Glu Glu Gln Met
Thr 435 440 445 Ile Leu Thr Arg Leu Gly Lys Gln Lys Thr Thr Ser Ser
Ser Asn Lys 450 455 460 Thr Lys Tyr Ile Asp Glu Lys Leu Leu Thr Glu
Glu Ile Tyr Asn Pro 465 470 475 480 Val Val Ala Lys Ser Val Arg Gln
Ala Ile Lys Ile Val Asn Ala Ala 485 490 495 Ile Lys Glu Tyr Gly Asp
Phe Asp Asn Ile Val Ile Glu Met Ala Arg 500 505 510 Glu Asn Gln Thr
Thr Gln Lys Gly Gln Lys Asn Ser Arg Glu Arg Met 515 520 525 Lys Arg
Ile Glu Glu Gly Ile Lys Glu Leu Gly Ser Gln Ile Leu Lys 530 535 540
Glu His Pro Val Glu Asn Thr Gln Leu Gln Asn Glu Lys Leu Tyr Leu 545
550 555 560 Tyr Tyr Leu Gln Asn Gly Arg Asp Met Tyr Val Asp Gln Glu
Leu Asp 565 570 575 Ile Asn Arg Leu Ser Asp Tyr Asp Val Asp His Ile
Val Pro Gln Ser 580 585 590 Phe Leu Lys Asp Asp Ser Ile Asp Asn Lys
Val Leu Thr Arg Ser Asp 595 600 605 Lys Asn Arg Gly Lys Ser Asp Asn
Val Pro Ser Glu Glu Val Val Lys 610 615 620 Lys Met Lys Asn Tyr Trp
Arg Gln Leu Leu Asn Ala Lys Leu Ile Thr 625 630 635 640 Gln Arg Lys
Phe Asp Asn Leu Thr Lys Ala Glu Arg Gly Gly Leu Ser 645 650 655 Glu
Leu Asp Lys Ala Gly Phe Ile Lys Arg Gln Leu Val Glu Thr Arg 660 665
670 Gln Ile Thr Lys His Val Ala Gln Ile Leu Asp Ser Arg Met Asn Thr
675 680 685 Lys Tyr Asp Glu Asn Asp Lys Leu Ile Arg Glu Val Lys Val
Ile Thr 690 695 700 Leu Lys Ser Lys Leu Val Ser Asp Phe Arg Lys Asp
Phe Gln Phe Tyr 705 710 715 720 Lys Val Arg Glu Ile Asn Asn Tyr His
His Ala His Asp Ala Tyr Leu 725 730 735 Asn Ala Val Val Gly Thr Ala
Leu Ile Lys Lys Tyr Pro Lys Leu Glu 740 745 750 Ser Glu Phe Val Tyr
Gly Asp Tyr Lys Val Tyr Asp Val Arg Lys Met 755 760 765 Ile Ala Lys
Ser Glu Gln Glu Ile Gly Lys Ala Thr Ala Lys Tyr Phe 770 775 780 Phe
Tyr Ser Asn Ile Met Asn Phe Phe Lys Thr Glu Ile Thr Leu Ala 785 790
795 800 Asn Gly Glu Ile Arg Lys Arg Pro Leu Ile Glu Thr Asn Gly Glu
Thr 805 810 815 Gly Glu Ile Val Trp Asp Lys Gly Arg Asp Phe Ala Thr
Val Arg Lys 820 825 830 Val Leu Ser Met Pro Gln Val Asn Ile Val Lys
Lys Thr Glu Val Gln 835 840 845 Thr Gly Gly Phe Ser Lys Glu Ser Ile
Leu Pro Lys Arg Asn Ser Asp 850 855 860 Lys Leu Ile Ala Arg Lys Lys
Asp Trp Asp Pro Lys Lys Tyr Gly Gly 865 870 875 880 Phe Asp Ser Pro
Thr Val Ala Tyr Ser Val Leu Val Val Ala Lys Val 885 890 895 Glu Lys
Gly Lys Ser Lys Lys Leu Lys Ser Val Lys Glu Leu Leu Gly 900 905 910
Ile Thr Ile Met Glu Arg Ser Ser Phe Glu Lys Asn Pro Ile Asp Phe 915
920 925 Leu Glu Ala Lys Gly Tyr Lys Glu Val Lys Lys Asp Leu Ile Ile
Lys 930 935 940 Leu Pro Lys Tyr Ser Leu Phe Glu Leu Glu Asn Gly Arg
Lys Arg Met 945 950 955 960 Leu Ala Ser Ala Gly Glu Leu Gln Lys Gly
Asn Glu Leu Ala Leu Pro 965 970 975 Ser Lys Tyr Val Asn Phe Leu Tyr
Leu Ala Ser His Tyr Glu Lys Leu 980 985 990 Lys Gly Ser Pro Glu Asp
Asn Glu Gln Lys Gln Leu Phe Val Glu Gln 995 1000 1005 His Lys His
Tyr Leu Asp Glu Ile Ile Glu Gln Ile Ser Glu Phe 1010 1015 1020 Ser
Lys Arg Val Ile Leu Ala Asp Ala Asn Leu Asp Lys Val Leu 1025 1030
1035 Ser Ala Tyr Asn Lys His Arg Asp Lys Pro Ile Arg Glu Gln Ala
1040 1045 1050 Glu Asn Ile Ile His Leu Phe Thr Leu Thr Asn Leu Gly
Ala Pro 1055 1060 1065 Ala Ala Phe Lys Tyr Phe Asp Thr Thr Ile Asp
Arg Lys Arg Tyr 1070 1075 1080 Thr Ser Thr Lys Glu Val Leu Asp Ala
Thr Leu Ile His Gln Ser 1085 1090 1095 Ile Thr Gly Leu Tyr Glu Thr
Arg Ile Asp Leu Ser Gln Leu Gly 1100 1105 1110 Gly Asp 1115
1031374PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic polypeptide" 103Met Asp Lys Lys Tyr Ser Ile Gly
Leu Asp Ile Gly Thr Asn Ser Val 1 5 10 15 Gly Trp Ala Val Ile Thr
Asp Glu Tyr Lys Val Pro Ser Lys Lys Phe 20 25 30 Lys Val Leu Gly
Asn Thr Asp Arg His Ser Ile Lys Lys Asn Leu Ile 35 40 45 Gly Ala
Leu Leu Phe Asp Ser Gly Glu Thr Ala Glu Ala Thr Arg Leu 50 55 60
Lys Arg Thr Ala Arg Arg Arg Tyr Thr Arg Arg Lys Asn Arg Ile Cys 65
70 75 80 Tyr Leu Gln Glu Ile Phe Ser Asn Glu Met Ala Lys Val Asp
Asp Ser 85 90
95 Phe Phe His Arg Leu Glu Glu Ser Phe Leu Val Glu Glu Asp Lys Lys
100 105 110 His Glu Arg His Pro Ile Phe Gly Asn Ile Val Asp Glu Val
Ala Tyr 115 120 125 His Glu Lys Tyr Pro Thr Ile Tyr His Leu Arg Lys
Lys Leu Val Asp 130 135 140 Ser Thr Asp Lys Ala Asp Leu Arg Leu Ile
Tyr Leu Ala Leu Ala His 145 150 155 160 Met Ile Lys Phe Arg Gly His
Phe Leu Ile Glu Gly Asp Leu Asn Pro 165 170 175 Asp Asn Ser Asp Val
Asp Lys Leu Phe Ile Gln Leu Val Gln Thr Tyr 180 185 190 Asn Gln Leu
Phe Glu Glu Asn Pro Ile Asn Ala Ser Gly Val Asp Ala 195 200 205 Lys
Ala Ile Leu Ser Ala Arg Leu Ser Lys Ser Arg Arg Leu Glu Asn 210 215
220 Leu Ile Ala Gln Leu Pro Gly Glu Lys Lys Asn Gly Leu Phe Gly Asn
225 230 235 240 Leu Ile Ala Leu Ser Leu Gly Leu Thr Pro Asn Phe Lys
Ser Asn Phe 245 250 255 Asp Leu Ala Glu Asp Ala Lys Leu Gln Leu Ser
Lys Asp Thr Tyr Asp 260 265 270 Asp Asp Leu Asp Asn Leu Leu Ala Gln
Ile Gly Asp Gln Tyr Ala Asp 275 280 285 Leu Phe Leu Ala Ala Lys Asn
Leu Ser Asp Ala Ile Leu Leu Ser Asp 290 295 300 Ile Leu Arg Val Asn
Thr Glu Ile Thr Lys Ala Pro Leu Ser Ala Ser 305 310 315 320 Met Ile
Lys Arg Tyr Asp Glu His His Gln Asp Leu Thr Leu Leu Lys 325 330 335
Ala Leu Val Arg Gln Gln Leu Pro Glu Lys Tyr Lys Glu Ile Phe Phe 340
345 350 Asp Gln Ser Lys Asn Gly Tyr Ala Gly Tyr Ile Asp Gly Gly Ala
Ser 355 360 365 Gln Glu Glu Phe Tyr Lys Phe Ile Lys Pro Ile Leu Glu
Lys Met Asp 370 375 380 Gly Thr Glu Glu Leu Leu Val Lys Leu Asn Arg
Glu Asp Leu Leu Arg 385 390 395 400 Lys Gln Arg Thr Phe Asp Asn Gly
Ser Ile Pro His Gln Ile His Leu 405 410 415 Gly Glu Leu His Ala Ile
Leu Arg Arg Gln Glu Asp Phe Tyr Pro Phe 420 425 430 Leu Lys Asp Asn
Arg Glu Lys Ile Glu Lys Ile Leu Thr Phe Arg Ile 435 440 445 Pro Tyr
Tyr Val Gly Pro Leu Ala Arg Gly Asn Ser Arg Phe Ala Trp 450 455 460
Met Thr Arg Lys Ser Glu Glu Thr Ile Thr Pro Trp Asn Phe Glu Glu 465
470 475 480 Val Val Asp Lys Gly Ala Ser Ala Gln Ser Phe Ile Glu Arg
Met Thr 485 490 495 Asn Phe Asp Lys Asn Leu Pro Asn Glu Lys Val Leu
Pro Lys His Ser 500 505 510 Leu Leu Tyr Glu Tyr Phe Thr Val Tyr Asn
Glu Leu Thr Lys Val Lys 515 520 525 Tyr Val Thr Glu Gly Met Arg Lys
Pro Ala Phe Leu Ser Gly Glu Gln 530 535 540 Lys Lys Ala Ile Val Asp
Leu Leu Phe Lys Thr Asn Arg Lys Val Thr 545 550 555 560 Val Lys Gln
Leu Lys Glu Asp Tyr Phe Lys Lys Ile Glu Cys Phe Asp 565 570 575 Ser
Val Glu Ile Ser Gly Val Glu Asp Arg Phe Asn Ala Ser Leu Gly 580 585
590 Thr Tyr His Asp Leu Leu Lys Ile Ile Lys Asp Lys Asp Phe Leu Asp
595 600 605 Asn Glu Glu Asn Glu Asp Ile Leu Glu Asp Ile Val Leu Thr
Leu Thr 610 615 620 Leu Phe Glu Asp Arg Glu Met Ile Glu Glu Arg Leu
Lys Thr Tyr Ala 625 630 635 640 His Leu Phe Asp Asp Lys Val Met Lys
Gln Leu Lys Arg Arg Arg Tyr 645 650 655 Thr Gly Trp Gly Arg Leu Ser
Arg Lys Leu Ile Asn Gly Ile Arg Asp 660 665 670 Lys Gln Ser Gly Lys
Thr Ile Leu Asp Phe Leu Lys Ser Asp Gly Phe 675 680 685 Ala Asn Arg
Asn Phe Met Gln Leu Ile His Asp Asp Ser Leu Thr Phe 690 695 700 Lys
Glu Asp Ile Gln Lys Ala Gln Val Ser Gly Gln Gly Asp Ser Leu 705 710
715 720 His Glu His Ile Ala Asn Leu Ala Gly Ser Pro Ala Ile Lys Lys
Gly 725 730 735 Ile Leu Gln Thr Val Lys Val Val Asp Glu Leu Val Lys
Val Met Gly 740 745 750 Arg His Lys Pro Glu Asn Ile Val Ile Glu Met
Ala Arg Glu Thr Asn 755 760 765 Glu Asp Asp Glu Lys Lys Ala Ile Gln
Lys Ile Gln Lys Ala Asn Lys 770 775 780 Asp Glu Lys Asp Ala Ala Met
Leu Lys Ala Ala Asn Gln Tyr Asn Gly 785 790 795 800 Lys Ala Glu Leu
Pro His Ser Val Phe His Gly His Lys Gln Leu Ala 805 810 815 Thr Lys
Ile Arg Leu Trp His Gln Gln Gly Glu Arg Cys Leu Tyr Thr 820 825 830
Gly Lys Thr Ile Ser Ile His Asp Leu Ile Asn Asn Ser Asn Gln Phe 835
840 845 Glu Val Asp His Ile Leu Pro Leu Ser Ile Thr Phe Asp Asp Ser
Leu 850 855 860 Ala Asn Lys Val Leu Val Tyr Ala Thr Ala Asn Gln Glu
Lys Gly Gln 865 870 875 880 Arg Thr Pro Tyr Gln Ala Leu Asp Ser Met
Asp Asp Ala Trp Ser Phe 885 890 895 Arg Glu Leu Lys Ala Phe Val Arg
Glu Ser Lys Thr Leu Ser Asn Lys 900 905 910 Lys Lys Glu Tyr Leu Leu
Thr Glu Glu Asp Ile Ser Lys Phe Asp Val 915 920 925 Arg Lys Lys Phe
Ile Glu Arg Asn Leu Val Asp Thr Arg Tyr Ala Ser 930 935 940 Arg Val
Val Leu Asn Ala Leu Gln Glu His Phe Arg Ala His Lys Ile 945 950 955
960 Asp Thr Lys Val Ser Val Val Arg Gly Gln Phe Thr Ser Gln Leu Arg
965 970 975 Arg His Trp Gly Ile Glu Lys Thr Arg Asp Thr Tyr His His
His Ala 980 985 990 Val Asp Ala Leu Ile Ile Ala Ala Ser Ser Gln Leu
Asn Leu Trp Lys 995 1000 1005 Lys Gln Lys Asn Thr Leu Val Ser Tyr
Ser Glu Asp Gln Leu Leu 1010 1015 1020 Asp Ile Glu Thr Gly Glu Leu
Ile Ser Asp Asp Glu Tyr Lys Glu 1025 1030 1035 Ser Val Phe Lys Ala
Pro Tyr Gln His Phe Val Asp Thr Leu Lys 1040 1045 1050 Ser Lys Glu
Phe Glu Asp Ser Ile Leu Phe Ser Tyr Gln Val Asp 1055 1060 1065 Ser
Lys Phe Asn Arg Lys Ile Ser Asp Ala Thr Ile Tyr Ala Thr 1070 1075
1080 Arg Gln Ala Lys Val Gly Lys Asp Lys Ala Asp Glu Thr Tyr Val
1085 1090 1095 Leu Gly Lys Ile Lys Asp Ile Tyr Thr Gln Asp Gly Tyr
Asp Ala 1100 1105 1110 Phe Met Lys Ile Tyr Lys Lys Asp Lys Ser Lys
Phe Leu Met Tyr 1115 1120 1125 Arg His Asp Pro Gln Thr Phe Glu Lys
Val Ile Glu Pro Ile Leu 1130 1135 1140 Glu Asn Tyr Pro Asn Lys Gln
Ile Asn Glu Lys Gly Lys Glu Val 1145 1150 1155 Pro Cys Asn Pro Phe
Leu Lys Tyr Lys Glu Glu His Gly Tyr Ile 1160 1165 1170 Arg Lys Tyr
Ser Lys Lys Gly Asn Gly Pro Glu Ile Lys Ser Leu 1175 1180 1185 Lys
Tyr Tyr Asp Ser Lys Leu Gly Asn His Ile Asp Ile Thr Pro 1190 1195
1200 Lys Asp Ser Asn Asn Lys Val Val Leu Gln Ser Val Ser Pro Trp
1205 1210 1215 Arg Ala Asp Val Tyr Phe Asn Lys Thr Thr Gly Lys Tyr
Glu Ile 1220 1225 1230 Leu Gly Leu Lys Tyr Ala Asp Leu Gln Phe Glu
Lys Gly Thr Gly 1235 1240 1245 Thr Tyr Lys Ile Ser Gln Glu Lys Tyr
Asn Asp Ile Lys Lys Lys 1250 1255 1260 Glu Gly Val Asp Ser Asp Ser
Glu Phe Lys Phe Thr Leu Tyr Lys 1265 1270 1275 Asn Asp Leu Leu Leu
Val Lys Asp Thr Glu Thr Lys Glu Gln Gln 1280 1285 1290 Leu Phe Arg
Phe Leu Ser Arg Thr Met Pro Lys Gln Lys His Tyr 1295 1300 1305 Val
Glu Leu Lys Pro Tyr Asp Lys Gln Lys Phe Glu Gly Gly Glu 1310 1315
1320 Ala Leu Ile Lys Val Leu Gly Asn Val Ala Asn Ser Gly Gln Cys
1325 1330 1335 Lys Lys Gly Leu Gly Lys Ser Asn Ile Ser Ile Tyr Lys
Val Arg 1340 1345 1350 Thr Asp Val Leu Gly Asn Gln His Ile Ile Lys
Asn Glu Gly Asp 1355 1360 1365 Lys Pro Lys Leu Asp Phe 1370
1046PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic 6xHis tag" 104His His His His His His 1 5
10515PRTArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic peptide" 105Gly Gly Gly Gly Ser Gly Gly Gly Gly
Ser Gly Gly Gly Gly Ser 1 5 10 15 10615PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 106Glu Ala Ala Ala Lys Glu Ala Ala Ala Lys Glu Ala Ala Ala
Lys 1 5 10 15 10718PRTArtificial Sequencesource/note="Description
of Artificial Sequence Synthetic peptide" 107Gly Gly Gly Gly Gly
Ser Gly Gly Gly Gly Gly Ser Gly Gly Gly Gly1 5 10 15 Gly Ser
10823DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 108gccaaattgg acgaccctcg cgg
2310923DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 109cgaggagacc cccgtttcgg tgg
2311023DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 110cccgccgccg ccgtggctcg agg
2311123DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 111tgagctctac gagatccaca agg
2311223DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 112ctcaaaattc ataccggttg tgg
2311323DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 113cgttaaacaa caaccggact tgg
2311423DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 114ttcaccccgc ggcgctgaat ggg
2311523DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 115accactacca gtccgtccac agg
2311623DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 116agcctttctg aacacatgca cgg
2311739DNAHomo sapiens 117cctgccatca atgtggccat gcatgtgttc
agaaaggct 3911839DNAHomo sapiens 118cctgccatca atgtggccgt
gcatgtgttc agaaaggct 3911923DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 119cactgcttaa gcctcgctcg agg 2312023DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 120tcaccagcaa tattcgctcg agg 2312123DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 121caccagcaat attccgctcg agg 2312223DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 122tagcaacaga catacgctcg agg 2312323DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 123gggcagtagt aatacgctcg agg 2312423DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 124ccaattccca tacattattg tac
231254677DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polynucleotide" 125tctttcttgc
gctatgacac ttccagcaaa aggtagggcg ggctgcgaga cggcttcccg 60gcgctgcatg
caacaccgat gatgcttcga ccccccgaag ctccttcggg gctgcatggg
120cgctccgatg ccgctccagg gcgagcgctg tttaaatagc caggcccccg
attgcaaaga 180cattatagcg agctaccaaa gccatattca aacacctaga
tcactaccac ttctacacag 240gccactcgag cttgtgatcg cactccgcta
agggggcgcc tcttcctctt cgtttcagtc 300acaacccgca aacatgtacc
catacgatgt tccagattac gcttcgccga agaaaaagcg 360caaggtcgaa
gcgtccgaca agaagtacag catcggcctg gacatcggca ccaactctgt
420gggctgggcc gtgatcaccg acgagtacaa ggtgcccagc aagaaattca
aggtgctggg 480caacaccgac cggcacagca tcaagaagaa cctgatcgga
gccctgctgt tcgacagcgg 540cgaaacagcc gaggccaccc ggctgaagag
aaccgccaga agaagataca ccagacggaa 600gaaccggatc tgctatctgc
aagagatctt cagcaacgag atggccaagg tggacgacag 660cttcttccac
agactggaag agtccttcct ggtggaagag gataagaagc acgagcggca
720ccccatcttc ggcaacatcg tggacgaggt ggcctaccac gagaagtacc
ccaccatcta 780ccacctgaga aagaaactgg tggacagcac cgacaaggcc
gacctgcggc tgatctatct 840ggccctggcc cacatgatca agttccgggg
ccacttcctg atcgagggcg acctgaaccc 900cgacaacagc gacgtggaca
agctgttcat ccagctggtg cagacctaca accagctgtt 960cgaggaaaac
cccatcaacg ccagcggcgt ggacgccaag gccatcctgt ctgccagact
1020gagcaagagc agacggctgg aaaatctgat cgcccagctg cccggcgaga
agaagaatgg 1080cctgttcggc aacctgattg ccctgagcct gggcctgacc
cccaacttca agagcaactt 1140cgacctggcc gaggatgcca aactgcagct
gagcaaggac acctacgacg acgacctgga 1200caacctgctg gcccagatcg
gcgaccagta cgccgacctg tttctggccg ccaagaacct 1260gtccgacgcc
atcctgctga gcgacatcct gagagtgaac accgagatca ccaaggcccc
1320cctgagcgcc tctatgatca agagatacga cgagcaccac caggacctga
ccctgctgaa 1380agctctcgtg cggcagcagc tgcctgagaa gtacaaagag
attttcttcg accagagcaa 1440gaacggctac gccggctaca ttgacggcgg
agccagccag gaagagttct acaagttcat 1500caagcccatc ctggaaaaga
tggacggcac cgaggaactg ctcgtgaagc tgaacagaga 1560ggacctgctg
cggaagcagc ggaccttcga caacggcagc atcccccacc agatccacct
1620gggagagctg cacgccattc tgcggcggca ggaagatttt tacccattcc
tgaaggacaa 1680ccgggaaaag atcgagaaga tcctgacctt ccgcatcccc
tactacgtgg gccctctggc 1740caggggaaac agcagattcg cctggatgac
cagaaagagc gaggaaacca tcaccccctg 1800gaacttcgag gaagtggtgg
acaagggcgc ttccgcccag agcttcatcg agcggatgac 1860caacttcgat
aagaacctgc ccaacgagaa ggtgctgccc aagcacagcc tgctgtacga
1920gtacttcacc gtgtataacg agctgaccaa agtgaaatac gtgaccgagg
gaatgagaaa 1980gcccgccttc ctgagcggcg agcagaaaaa ggccatcgtg
gacctgctgt tcaagaccaa 2040ccggaaagtg accgtgaagc agctgaaaga
ggactacttc aagaaaatcg agtgcttcga 2100ctccgtggaa atctccggcg
tggaagatcg gttcaacgcc tccctgggca cataccacga 2160tctgctgaaa
attatcaagg acaaggactt cctggacaat gaggaaaacg aggacattct
2220ggaagatatc gtgctgaccc tgacactgtt tgaggacaga gagatgatcg
aggaacggct 2280gaaaacctat gcccacctgt tcgacgacaa agtgatgaag
cagctgaagc ggcggagata 2340caccggctgg ggcaggctga gccggaagct
gatcaacggc atccgggaca agcagtccgg 2400caagacaatc ctggatttcc
tgaagtccga cggcttcgcc aacagaaact tcatgcagct 2460gatccacgac
gacagcctga cctttaaaga ggacatccag aaagcccagg tgtccggcca
2520gggcgatagc ctgcacgagc acattgccaa tctggccggc agccccgcca
ttaagaaggg 2580catcctgcag acagtgaagg tggtggacga gctcgtgaaa
gtgatgggcc ggcacaagcc 2640cgagaacatc gtgatcgaaa tggccagaga
gaaccagacc acccagaagg gacagaagaa 2700cagccgcgag agaatgaagc
ggatcgaaga gggcatcaaa gagctgggca gccagatcct 2760gaaagaacac
cccgtggaaa acacccagct gcagaacgag aagctgtacc tgtactacct
2820gcagaatggg cgggatatgt acgtggacca ggaactggac atcaaccggc
tgtccgacta 2880cgatgtggac catatcgtgc ctcagagctt tctgaaggac
gactccatcg acaacaaggt 2940gctgaccaga agcgacaaga accggggcaa
gagcgacaac gtgccctccg aagaggtcgt 3000gaagaagatg aagaactact
ggcggcagct gctgaacgcc aagctgatta cccagagaaa 3060gttcgacaat
ctgaccaagg ccgagagagg cggcctgagc gaactggata aggccggctt
3120catcaagaga cagctggtgg aaacccggca gatcacaaag cacgtggcac
agatcctgga 3180ctcccggatg aacactaagt acgacgagaa tgacaagctg
atccgggaag tgaaagtgat 3240caccctgaag tccaagctgg tgtccgattt
ccggaaggat ttccagtttt acaaagtgcg 3300cgagatcaac aactaccacc
acgcccacga cgcctacctg aacgccgtcg tgggaaccgc 3360cctgatcaaa
aagtacccta agctggaaag cgagttcgtg tacggcgact acaaggtgta
3420cgacgtgcgg aagatgatcg ccaagagcga gcaggaaatc ggcaaggcta
ccgccaagta 3480cttcttctac agcaacatca tgaacttttt caagaccgag
attaccctgg ccaacggcga 3540gatccggaag cggcctctga tcgagacaaa
cggcgaaacc ggggagatcg tgtgggataa 3600gggccgggat tttgccaccg
tgcggaaagt gctgagcatg ccccaagtga atatcgtgaa 3660aaagaccgag
gtgcagacag gcggcttcag caaagagtct atcctgccca agaggaacag
3720cgataagctg atcgccagaa agaaggactg ggaccctaag aagtacggcg
gcttcgacag 3780ccccaccgtg gcctattctg tgctggtggt ggccaaagtg
gaaaagggca agtccaagaa 3840actgaagagt gtgaaagagc tgctggggat
caccatcatg gaaagaagca gcttcgagaa 3900gaatcccatc gactttctgg
aagccaaggg ctacaaagaa gtgaaaaagg acctgatcat 3960caagctgcct
aagtactccc tgttcgagct ggaaaacggc cggaagagaa tgctggcctc
4020tgccggcgaa ctgcagaagg gaaacgaact ggccctgccc tccaaatatg
tgaacttcct 4080gtacctggcc agccactatg agaagctgaa gggctccccc
gaggataatg agcagaaaca 4140gctgtttgtg gaacagcaca agcactacct
ggacgagatc atcgagcaga tcagcgagtt 4200ctccaagaga gtgatcctgg
ccgacgctaa tctggacaaa gtgctgtccg cctacaacaa 4260gcaccgggat
aagcccatca gagagcaggc cgagaatatc atccacctgt ttaccctgac
4320caatctggga gcccctgccg ccttcaagta ctttgacacc accatcgacc
ggaagaggta 4380caccagcacc aaagaggtgc tggacgccac cctgatccac
cagagcatca ccggcctgta 4440cgagacacgg atcgacctgt ctcagctggg
aggcgacagc cccaagaaga agagaaaggt 4500ggaggccagc taaggatccg
gcaagactgg ccccgcttgg caacgcaaca gtgagcccct 4560ccctagtgtg
tttggggatg tgactatgta ttcgtgtgtt ggccaacggg tcaacccgaa
4620cagattgata cccgccttgg catttcctgt cagaatgtaa cgtcagttga tggtact
46771263150DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polynucleotide" 126tctttcttgc
gctatgacac ttccagcaaa aggtagggcg ggctgcgaga cggcttcccg 60gcgctgcatg
caacaccgat gatgcttcga ccccccgaag ctccttcggg gctgcatggg
120cgctccgatg ccgctccagg gcgagcgctg tttaaatagc caggcccccg
attgcaaaga 180cattatagcg agctaccaaa gccatattca aacacctaga
tcactaccac ttctacacag 240gccactcgag cttgtgatcg cactccgcta
agggggcgcc tcttcctctt cgtttcagtc 300acaacccgca aacatgccta
agaagaagag gaaggttaac acgattaaca tcgctaagaa 360cgacttctct
gacatcgaac tggctgctat cccgttcaac actctggctg accattacgg
420tgagcgttta gctcgcgaac agttggccct tgagcatgag tcttacgaga
tgggtgaagc 480acgcttccgc aagatgtttg agcgtcaact taaagctggt
gaggttgcgg ataacgctgc 540cgccaagcct ctcatcacta ccctactccc
taagatgatt gcacgcatca acgactggtt 600tgaggaagtg aaagctaagc
gcggcaagcg cccgacagcc ttccagttcc tgcaagaaat 660caagccggaa
gccgtagcgt acatcaccat taagaccact ctggcttgcc taaccagtgc
720tgacaataca accgttcagg ctgtagcaag cgcaatcggt cgggccattg
aggacgaggc 780tcgcttcggt cgtatccgtg accttgaagc taagcacttc
aagaaaaacg ttgaggaaca 840actcaacaag cgcgtagggc acgtctacaa
gaaagcattt atgcaagttg tcgaggctga 900catgctctct aagggtctac
tcggtggcga ggcgtggtct tcgtggcata aggaagactc 960tattcatgta
ggagtacgct gcatcgagat gctcattgag tcaaccggaa tggttagctt
1020acaccgccaa aatgctggcg tagtaggtca agactctgag actatcgaac
tcgcacctga 1080atacgctgag gctatcgcaa cccgtgcagg tgcgctggct
ggcatctctc cgatgttcca 1140accttgcgta gttcctccta agccgtggac
tggcattact ggtggtggct attgggctaa 1200cggtcgtcgt cctctggcgc
tggtgcgtac tcacagtaag aaagcactga tgcgctacga 1260agacgtttac
atgcctgagg tgtacaaagc gattaacatt gcgcaaaaca ccgcatggaa
1320aatcaacaag aaagtcctag cggtcgccaa cgtaatcacc aagtggaagc
attgtccggt 1380cgaggacatc cctgcgattg agcgtgaaga actcccgatg
aaaccggaag acatcgacat 1440gaatcctgag gctctcaccg cgtggaaacg
tgctgccgct gctgtgtacc gcaaggacaa 1500ggctcgcaag tctcgccgta
tcagccttga gttcatgctt gagcaagcca ataagtttgc 1560taaccataag
gccatctggt tcccttacaa catggactgg cgcggtcgtg tttacgctgt
1620gtcaatgttc aacccgcaag gtaacgatat gaccaaagga ctgcttacgc
tggcgaaagg 1680taaaccaatc ggtaaggaag gttactactg gctgaaaatc
cacggtgcaa actgtgcggg 1740tgtcgacaag gttccgttcc ctgagcgcat
caagttcatt gaggaaaacc acgagaacat 1800catggcttgc gctaagtctc
cactggagaa cacttggtgg gctgagcaag attctccgtt 1860ctgcttcctt
gcgttctgct ttgagtacgc tggggtacag caccacggcc tgagctataa
1920ctgctccctt ccgctggcgt ttgacgggtc ttgctctggc atccagcact
tctccgcgat 1980gctccgagat gaggtaggtg gtcgcgcggt taacttgctt
cctagtgaaa ccgttcagga 2040catctacggg attgttgcta agaaagtcaa
cgagattcta caagcagacg caatcaatgg 2100gaccgataac gaagtagtta
ccgtgaccga tgagaacact ggtgaaatct ctgagaaagt 2160caagctgggc
actaaggcac tggctggtca atggctggct tacggtgtta ctcgcagtgt
2220gactaagcgt tcagtcatga cgctggctta cgggtccaaa gagttcggct
tccgtcaaca 2280agtgctggaa gataccattc agccagctat tgattccggc
aagggtctga tgttcactca 2340gccgaatcag gctgctggat acatggctaa
gctgatttgg gaatctgtga gcgtgacggt 2400ggtagctgcg gttgaagcaa
tgaactggct taagtctgct gctaagctgc tggctgctga 2460ggtcaaagat
aagaagactg gagagattct tcgcaagcgt tgcgctgtgc attgggtaac
2520tcctgatggt ttccctgtgt ggcaggaata caagaagcct attcagacgc
gcttgaacct 2580gatgttcctc ggtcagttcc gcttacagcc taccattaac
accaacaaag atagcgagat 2640tgatgcacac aaacaggagt ctggtatcgc
tcctaacttt gtacacagcc aagacggtag 2700ccaccttcgt aagactgtag
tgtgggcaca cgagaagtac ggaatcgaat cttttgcact 2760gattcacgac
tccttcggta cgattccggc tgacgctgcg aacctgttca aagcagtgcg
2820cgaaactatg gttgacacat atgagtcttg tgatgtactg gctgatttct
acgaccagtt 2880cgctgaccag ttgcacgagt ctcaattgga caaaatgcca
gcacttccgg ctaaaggtaa 2940cttgaacctc cgtgacatct tagagtcgga
cttcgcgttc gcgtaaggat ccggcaagac 3000tggccccgct tggcaacgca
acagtgagcc cctccctagt gtgtttgggg atgtgactat 3060gtattcgtgt
gttggccaac gggtcaaccc gaacagattg atacccgcct tggcatttcc
3120tgtcagaatg taacgtcagt tgatggtact 3150127125DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
polynucleotide" 127gaaattaata cgactcacta tannnnnnnn nnnnnnnnnn
nngttttaga gctagaaata 60gcaagttaaa ataaggctag tccgttatca acttgaaaaa
gtggcaccga gtcggtgctt 120ttttt 1251288452DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
polynucleotide" 128tgcggtattt cacaccgcat caggtggcac ttttcgggga
aatgtgcgcg gaacccctat 60ttgtttattt ttctaaatac attcaaatat gtatccgctc
atgagattat caaaaaggat 120cttcacctag atccttttaa attaaaaatg
aagttttaaa tcaatctaaa gtatatatga 180gtaaacttgg tctgacagtt
accaatgctt aatcagtgag gcacctatct cagcgatctg 240tctatttcgt
tcatccatag ttgcctgact ccccgtcgtg tagataacta cgatacggga
300gggcttacca tctggcccca gtgctgcaat gataccgcga gacccacgct
caccggctcc 360agatttatca gcaataaacc agccagccgg aagggccgag
cgcagaagtg gtcctgcaac 420tttatccgcc tccatccagt ctattaattg
ttgccgggaa gctagagtaa gtagttcgcc 480agttaatagt ttgcgcaacg
ttgttgccat tgctacaggc atcgtggtgt cacgctcgtc 540gtttggtatg
gcttcattca gctccggttc ccaacgatca aggcgagtta catgatcccc
600catgttgtgc aaaaaagcgg ttagctcctt cggtcctccg atcgttgtca
gaagtaagtt 660ggccgcagtg ttatcactca tggttatggc agcactgcat
aattctctta ctgtcatgcc 720atccgtaaga tgcttttctg tgactggtga
gtactcaacc aagtcattct gagaatagtg 780tatgcggcga ccgagttgct
cttgcccggc gtcaatacgg gataataccg cgccacatag 840cagaacttta
aaagtgctca tcattggaaa acgttcttcg gggcgaaaac tctcaaggat
900cttaccgctg ttgagatcca gttcgatgta acccactcgt gcacccaact
gatcttcagc 960atcttttact ttcaccagcg tttctgggtg agcaaaaaca
ggaaggcaaa atgccgcaaa 1020aaagggaata agggcgacac ggaaatgttg
aatactcata ctcttccttt ttcaatatta 1080ttgaagcatt tatcagggtt
attgtctcat gaccaaaatc ccttaacgtg agttttcgtt 1140ccactgagcg
tcagaccccg tagaaaagat caaaggatct tcttgagatc ctttttttct
1200gcgcgtaatc tgctgcttgc aaacaaaaaa accaccgcta ccagcggtgg
tttgtttgcc 1260ggatcaagag ctaccaactc tttttccgaa ggtaactggc
ttcagcagag cgcagatacc 1320aaatactgtt cttctagtgt agccgtagtt
aggccaccac ttcaagaact ctgtagcacc 1380gcctacatac ctcgctctgc
taatcctgtt accagtggct gttgccagtg gcgataagtc 1440gtgtcttacc
gggttggact caagacgata gttaccggat aaggcgcagc ggtcgggctg
1500aacggggggt tcgtgcacac agcccagctt ggagcgaacg acctacaccg
aactgagata 1560cctacagcgt gagctatgag aaagcgccac gcttcccgaa
gggagaaagg cggacaggta 1620tccggtaagc ggcagggtcg gaacaggaga
gcgcacgagg gagcttccag ggggaaacgc 1680ctggtatctt tatagtcctg
tcgggtttcg ccacctctga cttgagcgtc gatttttgtg 1740atgctcgtca
ggggggcgga gcctatggaa aaacgccagc aacgcggcct ttttacggtt
1800cctggccttt tgctggcctt ttgctcacat gttctttcct gcgttatccc
ctgattctgt 1860ggataaccgt attaccgcct ttgagtgagc tgataccgct
cgccgcagcc gaacgaccga 1920gcgcagcgag tcagtgagcg aggaagcggt
cgctgaggct tgacatgatt ggtgcgtatg 1980tttgtatgaa gctacaggac
tgatttggcg ggctatgagg gcgggggaag ctctggaagg 2040gccgcgatgg
ggcgcgcggc gtccagaagg cgccatacgg cccgctggcg gcacccatcc
2100ggtataaaag cccgcgaccc cgaacggtga cctccacttt cagcgacaaa
cgagcactta 2160tacatacgcg actattctgc cgctatacat aaccactcag
ctagcttaag atcccatcaa 2220gcttgcatgc cgggcgcgcc agaaggagcg
cagccaaacc aggatgatgt ttgatggggt 2280atttgagcac ttgcaaccct
tatccggaag ccccctggcc cacaaaggct aggcgccaat 2340gcaagcagtt
cgcatgcagc ccctggagcg gtgccctcct gataaaccgg ccagggggcc
2400tatgttcttt acttttttac aagagaagtc actcaacatc ttaaaatggc
caggtgagtc 2460gacgagcaag cccggcggat caggcagcgt gcttgcagat
ttgacttgca acgcccgcat 2520tgtgtcgacg aaggcttttg gctcctctgt
cgctgtctca agcagcatct aaccctgcgt 2580cgccgtttcc atttgcagga
gattcgaggt accatgtacc catacgatgt tccagattac 2640gcttcgccga
agaaaaagcg caaggtcgaa gcgtccgaca agaagtacag catcggcctg
2700gacatcggca ccaactctgt gggctgggcc gtgatcaccg acgagtacaa
ggtgcccagc 2760aagaaattca aggtgctggg caacaccgac cggcacagca
tcaagaagaa cctgatcgga 2820gccctgctgt tcgacagcgg cgaaacagcc
gaggccaccc ggctgaagag aaccgccaga 2880agaagataca ccagacggaa
gaaccggatc tgctatctgc aagagatctt cagcaacgag 2940atggccaagg
tggacgacag cttcttccac agactggaag agtccttcct ggtggaagag
3000gataagaagc acgagcggca ccccatcttc ggcaacatcg tggacgaggt
ggcctaccac 3060gagaagtacc ccaccatcta ccacctgaga aagaaactgg
tggacagcac cgacaaggcc 3120gacctgcggc tgatctatct ggccctggcc
cacatgatca agttccgggg ccacttcctg 3180atcgagggcg acctgaaccc
cgacaacagc gacgtggaca agctgttcat ccagctggtg 3240cagacctaca
accagctgtt cgaggaaaac cccatcaacg ccagcggcgt ggacgccaag
3300gccatcctgt ctgccagact gagcaagagc agacggctgg aaaatctgat
cgcccagctg 3360cccggcgaga agaagaatgg cctgttcggc aacctgattg
ccctgagcct gggcctgacc 3420cccaacttca agagcaactt cgacctggcc
gaggatgcca aactgcagct gagcaaggac 3480acctacgacg acgacctgga
caacctgctg gcccagatcg gcgaccagta cgccgacctg 3540tttctggccg
ccaagaacct gtccgacgcc atcctgctga gcgacatcct gagagtgaac
3600accgagatca ccaaggcccc cctgagcgcc tctatgatca agagatacga
cgagcaccac 3660caggacctga ccctgctgaa agctctcgtg cggcagcagc
tgcctgagaa gtacaaagag 3720attttcttcg accagagcaa gaacggctac
gccggctaca ttgacggcgg agccagccag 3780gaagagttct acaagttcat
caagcccatc ctggaaaaga tggacggcac cgaggaactg 3840ctcgtgaagc
tgaacagaga ggacctgctg cggaagcagc ggaccttcga caacggcagc
3900atcccccacc agatccacct gggagagctg cacgccattc tgcggcggca
ggaagatttt 3960tacccattcc tgaaggacaa ccgggaaaag atcgagaaga
tcctgacctt ccgcatcccc 4020tactacgtgg gccctctggc caggggaaac
agcagattcg cctggatgac cagaaagagc 4080gaggaaacca tcaccccctg
gaacttcgag gaagtggtgg acaagggcgc ttccgcccag 4140agcttcatcg
agcggatgac caacttcgat aagaacctgc ccaacgagaa ggtgctgccc
4200aagcacagcc tgctgtacga gtacttcacc gtgtataacg agctgaccaa
agtgaaatac 4260gtgaccgagg gaatgagaaa gcccgccttc ctgagcggcg
agcagaaaaa ggccatcgtg 4320gacctgctgt tcaagaccaa ccggaaagtg
accgtgaagc agctgaaaga ggactacttc 4380aagaaaatcg agtgcttcga
ctccgtggaa atctccggcg tggaagatcg gttcaacgcc 4440tccctgggca
cataccacga tctgctgaaa attatcaagg acaaggactt cctggacaat
4500gaggaaaacg aggacattct ggaagatatc gtgctgaccc tgacactgtt
tgaggacaga 4560gagatgatcg aggaacggct gaaaacctat gcccacctgt
tcgacgacaa agtgatgaag 4620cagctgaagc ggcggagata caccggctgg
ggcaggctga gccggaagct gatcaacggc 4680atccgggaca agcagtccgg
caagacaatc ctggatttcc tgaagtccga cggcttcgcc 4740aacagaaact
tcatgcagct gatccacgac gacagcctga cctttaaaga ggacatccag
4800aaagcccagg tgtccggcca gggcgatagc ctgcacgagc acattgccaa
tctggccggc 4860agccccgcca ttaagaaggg catcctgcag acagtgaagg
tggtggacga gctcgtgaaa 4920gtgatgggcc ggcacaagcc cgagaacatc
gtgatcgaaa tggccagaga gaaccagacc 4980acccagaagg gacagaagaa
cagccgcgag agaatgaagc ggatcgaaga gggcatcaaa 5040gagctgggca
gccagatcct gaaagaacac cccgtggaaa acacccagct gcagaacgag
5100aagctgtacc tgtactacct gcagaatggg cgggatatgt acgtggacca
ggaactggac 5160atcaaccggc tgtccgacta cgatgtggac catatcgtgc
ctcagagctt tctgaaggac 5220gactccatcg acaacaaggt gctgaccaga
agcgacaaga accggggcaa gagcgacaac 5280gtgccctccg aagaggtcgt
gaagaagatg aagaactact ggcggcagct gctgaacgcc 5340aagctgatta
cccagagaaa gttcgacaat ctgaccaagg ccgagagagg cggcctgagc
5400gaactggata aggccggctt catcaagaga cagctggtgg aaacccggca
gatcacaaag 5460cacgtggcac agatcctgga ctcccggatg aacactaagt
acgacgagaa tgacaagctg 5520atccgggaag tgaaagtgat caccctgaag
tccaagctgg tgtccgattt ccggaaggat 5580ttccagtttt acaaagtgcg
cgagatcaac aactaccacc acgcccacga cgcctacctg 5640aacgccgtcg
tgggaaccgc cctgatcaaa aagtacccta agctggaaag cgagttcgtg
5700tacggcgact acaaggtgta cgacgtgcgg aagatgatcg ccaagagcga
gcaggaaatc 5760ggcaaggcta ccgccaagta cttcttctac agcaacatca
tgaacttttt caagaccgag 5820attaccctgg ccaacggcga gatccggaag
cggcctctga tcgagacaaa cggcgaaacc 5880ggggagatcg tgtgggataa
gggccgggat tttgccaccg tgcggaaagt gctgagcatg 5940ccccaagtga
atatcgtgaa aaagaccgag gtgcagacag gcggcttcag caaagagtct
6000atcctgccca agaggaacag cgataagctg atcgccagaa agaaggactg
ggaccctaag 6060aagtacggcg gcttcgacag ccccaccgtg gcctattctg
tgctggtggt ggccaaagtg 6120gaaaagggca agtccaagaa actgaagagt
gtgaaagagc tgctggggat caccatcatg 6180gaaagaagca gcttcgagaa
gaatcccatc gactttctgg aagccaaggg ctacaaagaa 6240gtgaaaaagg
acctgatcat caagctgcct aagtactccc tgttcgagct ggaaaacggc
6300cggaagagaa tgctggcctc tgccggcgaa ctgcagaagg gaaacgaact
ggccctgccc 6360tccaaatatg tgaacttcct gtacctggcc agccactatg
agaagctgaa gggctccccc 6420gaggataatg agcagaaaca gctgtttgtg
gaacagcaca agcactacct ggacgagatc 6480atcgagcaga tcagcgagtt
ctccaagaga gtgatcctgg ccgacgctaa tctggacaaa 6540gtgctgtccg
cctacaacaa gcaccgggat aagcccatca gagagcaggc cgagaatatc
6600atccacctgt ttaccctgac caatctggga gcccctgccg ccttcaagta
ctttgacacc 6660accatcgacc ggaagaggta caccagcacc aaagaggtgc
tggacgccac cctgatccac 6720cagagcatca ccggcctgta cgagacacgg
atcgacctgt ctcagctggg aggcgacagc 6780cccaagaaga agagaaaggt
ggaggccagc taacatatga ttcgaatgtc tttcttgcgc 6840tatgacactt
ccagcaaaag gtagggcggg ctgcgagacg gcttcccggc gctgcatgca
6900acaccgatga tgcttcgacc ccccgaagct ccttcggggc tgcatgggcg
ctccgatgcc 6960gctccagggc gagcgctgtt taaatagcca ggcccccgat
tgcaaagaca ttatagcgag 7020ctaccaaagc catattcaaa cacctagatc
actaccactt ctacacaggc cactcgagct 7080tgtgatcgca ctccgctaag
ggggcgcctc ttcctcttcg tttcagtcac aacccgcaaa 7140catgacacaa
gaatccctgt tacttctcga ccgtattgat tcggatgatt cctacgcgag
7200cctgcggaac gaccaggaat tctgggaggt gagtcgacga gcaagcccgg
cggatcaggc 7260agcgtgcttg cagatttgac ttgcaacgcc cgcattgtgt
cgacgaaggc ttttggctcc 7320tctgtcgctg tctcaagcag catctaaccc
tgcgtcgccg tttccatttg cagccgctgg 7380cccgccgagc cctggaggag
ctcgggctgc cggtgccgcc ggtgctgcgg gtgcccggcg 7440agagcaccaa
ccccgtactg gtcggcgagc ccggcccggt gatcaagctg ttcggcgagc
7500actggtgcgg tccggagagc ctcgcgtcgg agtcggaggc gtacgcggtc
ctggcggacg 7560ccccggtgcc ggtgccccgc ctcctcggcc gcggcgagct
gcggcccggc accggagcct 7620ggccgtggcc ctacctggtg atgagccgga
tgaccggcac cacctggcgg tccgcgatgg 7680acggcacgac cgaccggaac
gcgctgctcg ccctggcccg cgaactcggc cgggtgctcg 7740gccggctgca
cagggtgccg ctgaccggga acaccgtgct caccccccat tccgaggtct
7800tcccggaact gctgcgggaa cgccgcgcgg cgaccgtcga ggaccaccgc
gggtggggct 7860acctctcgcc ccggctgctg gaccgcctgg aggactggct
gccggacgtg gacacgctgc 7920tggccggccg cgaaccccgg ttcgtccacg
gcgacctgca cgggaccaac atcttcgtgg 7980acctggccgc gaccgaggtc
accgggatcg tcgacttcac cgacgtctat gcgggagact 8040cccgctacag
cctggtgcaa ctgcatctca acgccttccg gggcgaccgc gagatcctgg
8100ccgcgctgct cgacggggcg cagtggaagc ggaccgagga cttcgcccgc
gaactgctcg 8160ccttcacctt cctgcacgac ttcgaggtgt tcgaggagac
cccgctggat ctctccggct 8220tcaccgatcc ggaggaactg gcgcagttcc
tctgggggcc gccggacacc gcccccggcg 8280cctgataagg atccggcaag
actggccccg cttggcaacg caacagtgag cccctcccta 8340gtgtgtttgg
ggatgtgact atgtattcgt gtgttggcca acgggtcaac ccgaacagat
8400tgatacccgc cttggcattt cctgtcagaa tgtaacgtca gttgatggta ct
845212927DNAHomo sapiens 129ccgtgccggg cggggagacc gccatgg
2713022DNAHomo sapiens 130ggcccggctg tggctgagga gc 2213120DNAHomo
sapiens 131cggtctcccg cccggcacgg 2013226DNAHomo sapiens
132gctcctcagc cacagccggg ccgggt 2613312DNAHomo sapiens
133cgaccctgga aa 1213414DNAHomo sapiens 134ccccgccgcc accc
1413518DNAHomo sapiens 135tttccagggt cgccatgg 1813610DNAHomo
sapiens 136ggcggcgggg 1013720DNAHomo sapiens 137acccttgtta
gccacctccc 2013820DNAHomo sapiens 138gaacgcagtg ctcttcgaag
2013920DNAHomo sapiens 139ctcacgccct gctccgtgta 2014020DNAHomo
sapiens 140ggcgacaact acttcctggt 2014120DNAHomo sapiens
141ctcacgccct gctccgtgta 2014220DNAHomo sapiens 142gggcgacaac
tacttcctgg 2014320DNAHomo sapiens 143cctcttcagg gccggggtgg
2014420DNAHomo sapiens 144gaggacccag gtggaactgc 2014520DNAHomo
sapiens 145tcagctccag gcggtcctgg 2014620DNAHomo sapiens
146agcagcagca gcagtggcag
2014720DNAHomo sapiens 147tgggcaccgt cagctccagg 2014820DNAHomo
sapiens 148cagcagtggc agcggccacc 2014920DNAHomo sapiens
149acctctcccc tggccctcat 2015020DNAHomo sapiens 150ccaggaccgc
ctggagctga 2015120DNAHomo sapiens 151ccgtcagctc caggcggtcc
2015220DNAHomo sapiens 152agcagcagca gcagtggcag 2015320DNAHomo
sapiens 153atgtgccaag caaagcctca 2015420DNAHomo sapiens
154ttcggtcatg cccgtggatg 2015520DNAHomo sapiens 155gtcgttgaaa
ttcatcgtac 2015620DNAHomo sapiens 156accacctgtg aagagtttcc
2015720DNAHomo sapiens 157cgtcgttgaa attcatcgta 2015820DNAHomo
sapiens 158accacctgtg aagagtttcc 2015920DNAMus musculus
159gaacgcagtg cttttcgagg 2016020DNAMus musculus 160acccttgttg
gccacctccc 2016120DNAMus musculus 161ggtgacaact actatctggt
2016220DNAMus musculus 162ctcacaccct gctccgtgta 2016320DNAMus
musculus 163gggtgacaac tactatctgg 2016420DNAMus musculus
164ctcacaccct gctccgtgta 2016520DNAMus musculus 165cgagaacgca
gtgcttttcg 2016620DNAMus musculus 166acccttgttg gccacctccc
2016720DNAMus musculus 167atgagccaag caaatcctca 2016820DNAMus
musculus 168ttccgtcatg cccgtggaca 2016920DNAMus musculus
169cttcgttgaa aaccattgta 2017020DNAMus musculus 170ccacctctga
agagtttcct 2017120DNAMus musculus 171cttcgttgaa aaccattgta
2017220DNAMus musculus 172accacctctg aagagtttcc 2017320DNAMus
musculus 173cttccactca ctctgcgatt 2017420DNAMus musculus
174accatgtctc agtgtcaagc 2017520DNAMus musculus 175ggcggcaaca
gcggcaacag 2017620DNAMus musculus 176actgctctgc gtggctgcgg
2017720DNAMus musculus 177ccgcagccac gcagagcagt 2017820DNAMus
musculus 178gcacctctcc tcgccccgat 2017923DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 179gagggcctat ttcccatgat tcc 23180126DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 180aaaaaaagca ccgactcggt gccacttttt caagttgata acggactagc
cttattttaa 60cttgctattt ctagctctaa aacnnnnnnn nnnnnnnnnn nnccggtgtt
tcgtcctttc 120cacaag 12618124DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 181caccgnnnnn nnnnnnnnnn nnnn 2418224DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 182aaacnnnnnn nnnnnnnnnn nnnc 24183126DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 183aaaaaaagca ccgactcggt gccacttttt caagttgata acggactagc
cttattttaa 60cttgctattt ctagctctaa aacccctagt cattggaggt gaccggtgtt
tcgtcctttc 120cacaag 12618424DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 184caccgtcacc tccaatgact aggg 2418524DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 185aaacccctag tcattggagg tgac 24186192DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 186cagaagaaga agggctccca tcacatcaac cggtggcgca ttgccacgaa
gcaggccaat 60ggggaggaca tcgatgtcac ctccaatgac aagcttgcta gcggtgggca
accacaaacc 120cacgagggca gagtgctgct tgctgctggc caggcccctg
cgtgggccca agctggactc 180tggccactcc ct 192187192DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 187agggagtggc cagagtccag cttgggccca cgcaggggcc tggccagcag
caagcagcac 60tctgccctcg tgggtttgtg gttgcccacc gctagcaagc ttgtcattgg
aggtgacatc 120gatgtcctcc ccattggcct gcttcgtggc aatgcgccac
cggttgatgt gatgggagcc 180cttcttcttc tg 19218820DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 188ccatcccctt ctgtgaatgt 2018920DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 189ggagattgga gacacggaga 2019020DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 190ggctccctgg gttcaaagta 2019121DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 191agaggggtct ggatgtcgta a 2119224DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 192cgccagggtt ttcccagtca cgac 2419351DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 193gagggtctcg tccttgcggc cgcgctagcg agggcctatt tcccatgatt c
51194133DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 194ctcggtctcg gtaaaaaagc
accgactcgg tgccactttt tcaagttgat aacggactag 60ccttatttta acttgctatt
tctagctcta aaacnnnnnn nnnnnnnnnn nnnnggtgtt 120tcgtcctttc cac
13319541DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 195gagggtctct ttaccggtga
gggcctattt cccatgattc c 41196133DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 196ctcggtctcc tcaaaaaagc accgactcgg tgccactttt tcaagttgat
aacggactag 60ccttatttta acttgctatt tctagctcta aaacnnnnnn nnnnnnnnnn
nnnnggtgtt 120tcgtcctttc cac 13319740DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 197gagggtctct ttgagctcga gggcctattt cccatgattc
40198133DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 198ctcggtctcg cgtaaaaaag
caccgactcg gtgccacttt ttcaagttga taacggacta 60gccttatttt aacttgctat
ttctagctct aaaacnnnnn nnnnnnnnnn nnnnnggtgt 120ttcgtccttt cca
13319927DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 199gagggtctct tacgcgtgtg
tctagac 2720098DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 200ctcggtctca aggacaggga
agggagcagt ggttcacgcc tgtaatccca gcaatttggg 60aggccaaggt gggtagatca
cctgagatta ggagttgc 9820130DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 201cctgtccttg cggccgcgct agcgagggcc 3020231DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 202cacgcggccg caaggacagg gaagggagca g 31203327PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
polypeptide" 203Met Val Ser Lys Gly Glu Glu Leu Phe Thr Gly Val Val
Pro Ile Leu 1 5 10 15 Val Glu Leu Asp Gly Asp Val Asn Gly His Lys
Phe Ser Val Ser Gly 20 25 30 Glu Gly Glu Gly Asp Ala Thr Tyr Gly
Lys Leu Thr Leu Lys Phe Ile 35 40 45 Cys Thr Thr Gly Lys Leu Pro
Val Pro Trp Pro Thr Leu Val Thr Thr 50 55 60 Leu Thr Tyr Gly Val
Gln Cys Phe Ser Arg Tyr Pro Asp His Met Lys 65 70 75 80 Gln His Asp
Phe Phe Lys Ser Ala Met Pro Glu Gly Tyr Val Gln Glu 85 90 95 Arg
Thr Ile Phe Phe Lys Asp Asp Gly Asn Tyr Lys Thr Arg Ala Glu 100 105
110 Val Lys Phe Glu Gly Asp Thr Leu Val Asn Arg Ile Glu Leu Lys Gly
115 120 125 Ile Asp Phe Lys Glu Asp Gly Asn Ile Leu Gly His Lys Leu
Glu Tyr 130 135 140 Asn Tyr Asn Ser His Asn Val Tyr Ile Met Ala Asp
Lys Gln Lys Asn 145 150 155 160 Gly Ile Lys Val Asn Phe Lys Ile Arg
His Asn Ile Glu Asp Gly Ser 165 170 175 Val Gln Leu Ala Asp His Tyr
Gln Gln Asn Thr Pro Ile Gly Asp Gly 180 185 190 Pro Val Leu Leu Pro
Asp Asn His Tyr Leu Ser Thr Gln Ser Ala Leu 195 200 205 Ser Lys Asp
Pro Asn Glu Lys Arg Asp His Met Val Leu Leu Glu Phe 210 215 220 Val
Thr Ala Ala Gly Ile Thr Leu Gly Met Asp Glu Leu Tyr Lys Ser 225 230
235 240 Gly Leu Arg Ser Arg Glu Glu Glu Glu Glu Thr Asp Ser Arg Met
Pro 245 250 255 His Leu Asp Ser Pro Gly Ser Ser Gln Pro Arg Arg Ser
Phe Leu Ser 260 265 270 Arg Val Ile Arg Ala Ala Leu Pro Leu Gln Leu
Leu Leu Leu Leu Leu 275 280 285 Leu Leu Leu Ala Cys Leu Leu Pro Ala
Ser Glu Asp Asp Tyr Ser Cys 290 295 300 Thr Gln Ala Asn Asn Phe Ala
Arg Ser Phe Tyr Pro Met Leu Arg Tyr 305 310 315 320 Thr Asn Gly Pro
Pro Pro Thr 325 2043243DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
polynucleotide" 204accggtgcca ccatgtaccc atacgatgtt ccagattacg
cttcgccgaa gaaaaagcgc 60aaggtcgaag cgtccatgaa aaggaactac attctggggc
tggacatcgg gattacaagc 120gtggggtatg ggattattga ctatgaaaca
agggacgtga tcgacgcagg cgtcagactg 180ttcaaggagg ccaacgtgga
aaacaatgag ggacggagaa gcaagagggg agccaggcgc 240ctgaaacgac
ggagaaggca cagaatccag agggtgaaga aactgctgtt cgattacaac
300ctgctgaccg accattctga gctgagtgga attaatcctt atgaagccag
ggtgaaaggc 360ctgagtcaga agctgtcaga ggaagagttt tccgcagctc
tgctgcacct ggctaagcgc 420cgaggagtgc ataacgtcaa tgaggtggaa
gaggacaccg gcaacgagct gtctacaaag 480gaacagatct cacgcaatag
caaagctctg gaagagaagt atgtcgcaga gctgcagctg 540gaacggctga
agaaagatgg cgaggtgaga gggtcaatta ataggttcaa gacaagcgac
600tacgtcaaag aagccaagca gctgctgaaa gtgcagaagg cttaccacca
gctggatcag 660agcttcatcg atacttatat cgacctgctg gagactcgga
gaacctacta tgagggacca 720ggagaaggga gccccttcgg atggaaagac
atcaaggaat ggtacgagat gctgatggga 780cattgcacct attttccaga
agagctgaga agcgtcaagt acgcttataa cgcagatctg 840tacaacgccc
tgaatgacct gaacaacctg gtcatcacca gggatgaaaa cgagaaactg
900gaatactatg agaagttcca gatcatcgaa aacgtgttta agcagaagaa
aaagcctaca 960ctgaaacaga ttgctaagga gatcctggtc aacgaagagg
acatcaaggg ctaccgggtg 1020acaagcactg gaaaaccaga gttcaccaat
ctgaaagtgt atcacgatat taaggacatc 1080acagcacgga aagaaatcat
tgagaacgcc gaactgctgg atcagattgc taagatcctg 1140actatctacc
agagctccga ggacatccag gaagagctga ctaacctgaa cagcgagctg
1200acccaggaag agatcgaaca gattagtaat ctgaaggggt acaccggaac
acacaacctg 1260tccctgaaag ctatcaatct gattctggat gagctgtggc
atacaaacga caatcagatt 1320gcaatcttta accggctgaa gctggtccca
aaaaaggtgg acctgagtca gcagaaagag 1380atcccaacca cactggtgga
cgatttcatt ctgtcacccg tggtcaagcg gagcttcatc 1440cagagcatca
aagtgatcaa cgccatcatc aagaagtacg gcctgcccaa tgatatcatt
1500atcgagctgg ctagggagaa gaacagcaag gacgcacaga agatgatcaa
tgagatgcag 1560aaacgaaacc ggcagaccaa tgaacgcatt gaagagatta
tccgaactac cgggaaagag 1620aacgcaaagt acctgattga aaaaatcaag
ctgcacgata tgcaggaggg aaagtgtctg 1680tattctctgg aggccatccc
cctggaggac ctgctgaaca atccattcaa ctacgaggtc 1740gatcatatta
tccccagaag cgtgtccttc gacaattcct ttaacaacaa ggtgctggtc
1800aagcaggaag agaactctaa aaagggcaat aggactcctt tccagtacct
gtctagttca 1860gattccaaga tctcttacga aacctttaaa aagcacattc
tgaatctggc caaaggaaag 1920ggccgcatca gcaagaccaa aaaggagtac
ctgctggaag agcgggacat caacagattc 1980tccgtccaga aggattttat
taaccggaat ctggtggaca caagatacgc tactcgcggc 2040ctgatgaatc
tgctgcgatc ctatttccgg gtgaacaatc tggatgtgaa agtcaagtcc
2100atcaacggcg ggttcacatc ttttctgagg cgcaaatgga agtttaaaaa
ggagcgcaac 2160aaagggtaca agcaccatgc cgaagatgct ctgattatcg
caaatgccga cttcatcttt 2220aaggagtgga aaaagctgga caaagccaag
aaagtgatgg agaaccagat gttcgaagag 2280aagcaggccg aatctatgcc
cgaaatcgag acagaacagg agtacaagga gattttcatc 2340actcctcacc
agatcaagca tatcaaggat ttcaaggact acaagtactc tcaccgggtg
2400gataaaaagc ccaacagaga gctgatcaat gacaccctgt atagtacaag
aaaagacgat 2460aaggggaata ccctgattgt gaacaatctg aacggactgt
acgacaaaga taatgacaag 2520ctgaaaaagc tgatcaacaa aagtcccgag
aagctgctga tgtaccacca tgatcctcag 2580acatatcaga aactgaagct
gattatggag cagtacggcg acgagaagaa cccactgtat 2640aagtactatg
aagagactgg gaactacctg accaagtata gcaaaaagga taatggcccc
2700gtgatcaaga agatcaagta ctatgggaac aagctgaatg cccatctgga
catcacagac 2760gattacccta acagtcgcaa caaggtggtc aagctgtcac
tgaagccata cagattcgat 2820gtctatctgg acaacggcgt gtataaattt
gtgactgtca agaatctgga tgtcatcaaa 2880aaggagaact actatgaagt
gaatagcaag tgctacgaag aggctaaaaa gctgaaaaag 2940attagcaacc
aggcagagtt catcgcctcc ttttacaaca acgacctgat taagatcaat
3000ggcgaactgt atagggtcat cggggtgaac aatgatctgc tgaaccgcat
tgaagtgaat 3060atgattgaca tcacttaccg agagtatctg gaaaacatga
atgataagcg cccccctcga 3120attatcaaaa caattgcctc taagactcag
agtatcaaaa agtactcaac cgacattctg 3180ggaaacctgt atgaggtgaa
gagcaaaaag caccctcaga ttatcaaaaa gggctaagaa 3240ttc
3243205102DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic polynucleotide" 205gttttagagc
tatgctgttt tgaatggtcc caaaacggaa gggcctgagt ccgagcagaa 60gaagaagttt
tagagctatg ctgttttgaa tggtcccaaa ac 102206100DNAHomo sapiens
206cggaggacaa agtacaaacg gcagaagctg gaggaggaag ggcctgagtc
cgagcagaag 60aagaagggct cccatcacat caaccggtgg cgcattgcca
10020750DNAHomo sapiens 207agctggagga ggaagggcct gagtccgagc
agaagaagaa gggctcccac 5020830RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 208gaguccgagc agaagaagaa guuuuagagc
3020949DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 209agctggagga ggaagggcct
gagtccgagc agaagagaag ggctcccac 4921053DNAHomo sapiens
210ctggaggagg aagggcctga gtccgagcag aagaagaagg gctcccatca cat
5321152DNAHomo sapiens 211ctggaggagg aagggcctga gtccgagcag
aagagaaggg ctcccatcac at 5221254DNAHomo sapiens 212ctggaggagg
aagggcctga gtccgagcag aagaaagaag ggctcccatc acat 5421350DNAHomo
sapiens 213ctggaggagg aagggcctga gtccgagcag aagaagggct cccatcacat
5021447DNAHomo sapiens 214ctggaggagg aagggcctga gcccgagcag
aagggctccc atcacat 4721548DNAHomo sapiens 215ctggaggagg aagggcctga
gtccgagcag aagaagaagg gctcccat 4821620RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 216gaguccgagc agaagaagau 2021720RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 217gaguccgagc agaagaagua 2021820RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 218gaguccgagc agaagaacaa 2021920RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 219gaguccgagc agaagaugaa 2022020RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 220gaguccgagc agaaguagaa 2022120RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 221gaguccgagc agaugaagaa 2022220RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 222gaguccgagc acaagaagaa 2022320RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 223gaguccgagg agaagaagaa 2022420RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 224gaguccgugc agaagaagaa 2022520RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 225gagucggagc agaagaagaa 2022620RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 226gagaccgagc agaagaagaa 2022724DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 227aatgacaagc ttgctagcgg tggg 2422839DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 228aaaacggaag ggcctgagtc cgagcagaag aagaagttt
3922939DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 229aaacaggggc cgagattggg
tgttcagggc agaggtttt 3923038DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 230aaaacggaag ggcctgagtc cgagcagaag aagaagtt
3823140DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 231aacggaggga ggggcacaga
tgagaaactc agggttttag 4023238DNAHomo sapiens 232agcccttctt
cttctgctcg gactcaggcc cttcctcc 3823340DNAHomo sapiens 233cagggaggga
ggggcacaga tgagaaactc aggaggcccc 4023480DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 234ggcaatgcgc caccggttga tgtgatggga gcccttctag
gaggccccca gagcagccac 60tggggcctca acactcaggc 8023533DNAHomo
sapiens 235catcgatgtc ctccccattg gcctgcttcg tgg 3323633DNAHomo
sapiens 236ttcgtggcaa tgcgccaccg gttgatgtga tgg 3323733DNAHomo
sapiens 237tcgtggcaat gcgccaccgg ttgatgtgat ggg 3323833DNAHomo
sapiens 238tccagcttct gccgtttgta ctttgtcctc cgg 3323933DNAHomo
sapiens 239ggagggaggg gcacagatga gaaactcagg agg 3324033DNAHomo
sapiens 240aggggccgag attgggtgtt cagggcagag agg 3324133DNAMus
musculus 241caagcactga gtgccattag ctaaatgcat agg 3324233DNAMus
musculus 242aatgcatagg gtaccaccca caggtgccag ggg 3324333DNAMus
musculus 243acacacatgg gaaagcctct gggccaggaa agg 3324437DNAHomo
sapiens 244ggaggaggta gtatacagaa acacagagaa gtagaat 3724537DNAHomo
sapiens 245agaatgtaga ggagtcacag aaactcagca ctagaaa
3724698DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 246ggacgaaaca ccggaaccat
tcaaaacagc atagcaagtt aaaataaggc tagtccgtta 60tcaacttgaa aaagtggcac
cgagtcggtg cttttttt 98247186DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
polynucleotide" 247ggacgaaaca ccggtagtat taagtattgt tttatggctg
ataaatttct ttgaatttct 60ccttgattat ttgttataaa agttataaaa taatcttgtt
ggaaccattc aaaacagcat 120agcaagttaa aataaggcta gtccgttatc
aacttgaaaa agtggcaccg agtcggtgct 180tttttt 18624895DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 248gggttttaga gctatgctgt tttgaatggt cccaaaacgg
gtcttcgaga agacgtttta 60gagctatgct gttttgaatg gtcccaaaac ttttt
9524936DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 249aaacnnnnnn nnnnnnnnnn
nnnnnnnnnn nnnngt 3625036DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 250taaaacnnnn nnnnnnnnnn nnnnnnnnnn nnnnnn
3625184DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 251gtggaaagga cgaaacaccg
ggtcttcgag aagacctgtt ttagagctag aaatagcaag 60ttaaaataag gctagtccgt
tttt 8425246RNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic oligonucleotide" 252nnnnnnnnnn
nnnnnnnnng uuauuguacu cucaagauuu auuuuu 4625391RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 253guuacuuaaa ucuugcagaa gcuacaaaga uaaggcuuca
ugccgaaauc aacacccugu 60cauuuuaugg caggguguuu ucguuauuua a
9125470DNAHomo sapiens 254ttttctagtg ctgagtttct gtgactcctc
tacattctac ttctctgtgt ttctgtatac 60tacctcctcc 70255122DNAHomo
sapiens 255ggaggaaggg cctgagtccg agcagaagaa gaagggctcc catcacatca
accggtggcg 60cattgccacg aagcaggcca atggggagga catcgatgtc acctccaatg
actagggtgg 120gc 12225648RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 256acnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnguuuuaga
gcuaugcu 4825767DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic oligonucleotide" 257agcauagcaa
guuaaaauaa ggctaguccg uuaucaacuu gaaaaagugg caccgagucg 60gugcuuu
6725862RNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 258nnnnnnnnnn nnnnnnnnnn
guuuuagagc uagaaauagc aaguuaaaau aaggcuaguc 60cg
6225973DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 259tgaatggtcc caaaacggaa
gggcctgagt ccgagcagaa gaagaagttt tagagctatg 60ctgttttgaa tgg
7326069DNAHomo sapiens 260ctggtcttcc acctctctgc cctgaacacc
caatctcggc ccctctcgcc accctcctgc 60atttctgtt 69261138DNAMus
musculus 261acccaagcac tgagtgccat tagctaaatg catagggtac cacccacagg
tgccaggggc 60ctttcccaaa gttcccagcc ccttctccaa cctttcctgg cccagaggct
ttcccatgtg 120tgtggctgga ccctttga 13826221DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 262aaaaccaccc ttctctctgg c 2126321DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 263ggagattgga gacacggaga g 2126420DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 264ctggaaagcc aatgcctgac 2026520DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 265ggcagcaaac tccttgtcct 2026620DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 266gtgctttgca gaggcctacc 2026720DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 267cctggagcgc atgcagtagt 2026822DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 268accttctgtg tttccaccat tc 2226920DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 269ttggggagtg cacagacttc 2027030DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
probe" 270tagctctaaa acttcttctt ctgctcggac 3027130DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
probe" 271ctagccttat tttaacttgc tatgctgttt 3027299RNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 272nnnnnnnnnn nnnnnnnnnn guuuuagagc uagaaauagc
aaguuaaaau aaggcuaguc 60cguuaucaac uugaaaaagu ggcaccgagu cggugcuuu
9927312DNAHomo sapiens 273tagcgggtaa gc 1227412DNAHomo sapiens
274tcggtgacat gt 1227512DNAHomo sapiens 275actccccgta gg
1227612DNAHomo sapiens 276actgcgtgtt aa 1227712DNAHomo sapiens
277acgtcgcctg at 1227812DNAHomo sapiens 278taggtcgacc ag
1227912DNAHomo sapiens 279ggcgttaatg at 1228012DNAHomo sapiens
280tgtcgcatgt ta 1228112DNAHomo sapiens 281atggaaacgc at
1228212DNAHomo sapiens 282gccgaattcc tc 1228312DNAHomo sapiens
283gcatggtacg ga 1228412DNAHomo sapiens 284cggtactctt ac
1228512DNAHomo sapiens 285gcctgtgccg ta 1228612DNAHomo sapiens
286tacggtaagt cg 1228712DNAHomo sapiens 287cacgaaatta cc
1228812DNAHomo sapiens 288aaccaagata cg 1228912DNAHomo sapiens
289gagtcgatac gc 1229012DNAHomo sapiens 290gtctcacgat cg
1229112DNAHomo sapiens 291tcgtcgggtg ca 1229212DNAHomo sapiens
292actccgtagt ga 1229312DNAHomo sapiens 293caggacgtcc gt
1229412DNAHomo sapiens 294tcgtatccct ac 1229512DNAHomo sapiens
295tttcaaggcc gg 1229612DNAHomo sapiens 296cgccggtgga at
1229712DNAHomo sapiens 297gaacccgtcc ta 1229812DNAHomo sapiens
298gattcatcag cg 1229912DNAHomo sapiens 299acaccggtct tc
1230012DNAHomo sapiens 300atcgtgccct aa 1230112DNAHomo sapiens
301gcgtcaatgt tc 1230212DNAHomo sapiens 302ctccgtatct cg
1230312DNAHomo sapiens 303ccgattcctt cg 1230412DNAHomo sapiens
304tgcgcctcca gt 1230512DNAHomo sapiens 305taacgtcgga gc
1230612DNAHomo sapiens 306aaggtcgccc at 1230712DNAHomo sapiens
307gtcggggact at 1230812DNAHomo sapiens 308ttcgagcgat tt
1230912DNAHomo sapiens 309tgagtcgtcg ag 1231012DNAHomo sapiens
310tttacgcaga gg 1231112DNAHomo sapiens 311aggaagtatc gc
1231212DNAHomo sapiens 312actcgatacc at 1231312DNAHomo sapiens
313cgctacatag ca 1231412DNAHomo sapiens 314ttcataaccg gc
1231512DNAHomo sapiens 315ccaaacggtt aa 1231612DNAHomo sapiens
316cgattccttc gt 1231712DNAHomo sapiens 317cgtcatgaat aa
1231812DNAHomo sapiens 318agtggcgatg ac 1231912DNAHomo sapiens
319cccctacggc ac 1232012DNAHomo sapiens 320gccaacccgc ac
1232112DNAHomo sapiens 321tgggacaccg gt 1232212DNAHomo sapiens
322ttgactgcgg cg 1232312DNAHomo sapiens 323actatgcgta gg
1232412DNAHomo sapiens 324tcacccaaag cg 1232512DNAHomo sapiens
325gcaggacgtc cg 1232612DNAHomo sapiens 326acaccgaaaa cg
1232712DNAHomo sapiens 327cggtgtattg ag 1232812DNAHomo sapiens
328cacgaggtat gc 1232912DNAHomo sapiens 329taaagcgacc cg
1233012DNAHomo sapiens 330cttagtcggc ca 1233112DNAHomo sapiens
331cgaaaacgtg gc 1233212DNAHomo sapiens 332cgtgccctga ac
1233312DNAHomo sapiens 333tttaccatcg aa 1233412DNAHomo sapiens
334cgtagccatg tt 1233512DNAHomo sapiens 335cccaaacggt ta
1233612DNAHomo sapiens 336gcgttatcag aa 1233712DNAHomo sapiens
337tcgatggtaa ac 1233812DNAHomo sapiens 338cgactttttg ca
1233912DNAHomo sapiens 339tcgacgactc ac 1234012DNAHomo sapiens
340acgcgtcaga ta 1234112DNAHomo sapiens 341cgtacggcac ag
1234212DNAHomo sapiens 342ctatgccgtg ca 1234312DNAHomo sapiens
343cgcgtcagat at 1234412DNAHomo sapiens 344aagatcggta gc
1234512DNAHomo sapiens 345cttcgcaagg ag 1234612DNAHomo sapiens
346gtcgtggact ac 1234712DNAHomo sapiens 347ggtcgtcatc aa
1234812DNAHomo sapiens 348gttaacagcg tg 1234912DNAHomo sapiens
349tagctaaccg tt 1235012DNAHomo sapiens 350agtaaaggcg ct
1235112DNAHomo sapiens 351ggtaatttcg tg 1235215DNAHomo sapiens
352cagaagaaga agggc 1535351DNAHomo sapiens 353ccaatgggga ggacatcgat
gtcacctcca atgactaggg tggtgggcaa c 5135415DNAHomo sapiens
354ctctggccac tccct 1535552DNAHomo sapiens 355acatcgatgt cacctccaat
gacaagcttg ctagcggtgg gcaaccacaa ac 5235625DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 356caccgnnnnn nnnnnnnnnn nnnnn
2535725DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 357aaacnnnnnn nnnnnnnnnn nnnnc
2535854DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 358aacaccgggt cttcgagaag
acctgtttta gagctagaaa tagcaagtta aaat 5435954DNAArtificial
Sequencesource/note="Description of Artificial Sequence
Synthetic
oligonucleotide" 359caaaacgggt cttcgagaag acgttttaga gctatgctgt
tttgaatggt ccca 543604104DNAHomo sapiensCDS(1)..(4104) 360atg gac
aag aag tac agc atc ggc ctg gac atc ggc acc aac tct gtg 48Met Asp
Lys Lys Tyr Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val 1 5 10 15
ggc tgg gcc gtg atc acc gac gag tac aag gtg ccc agc aag aaa ttc
96Gly Trp Ala Val Ile Thr Asp Glu Tyr Lys Val Pro Ser Lys Lys Phe
20 25 30 aag gtg ctg ggc aac acc gac cgg cac agc atc aag aag aac
ctg atc 144Lys Val Leu Gly Asn Thr Asp Arg His Ser Ile Lys Lys Asn
Leu Ile 35 40 45 gga gcc ctg ctg ttc gac agc ggc gaa aca gcc gag
gcc acc cgg ctg 192Gly Ala Leu Leu Phe Asp Ser Gly Glu Thr Ala Glu
Ala Thr Arg Leu 50 55 60 aag aga acc gcc aga aga aga tac acc aga
cgg aag aac cgg atc tgc 240Lys Arg Thr Ala Arg Arg Arg Tyr Thr Arg
Arg Lys Asn Arg Ile Cys 65 70 75 80 tat ctg caa gag atc ttc agc aac
gag atg gcc aag gtg gac gac agc 288Tyr Leu Gln Glu Ile Phe Ser Asn
Glu Met Ala Lys Val Asp Asp Ser 85 90 95 ttc ttc cac aga ctg gaa
gag tcc ttc ctg gtg gaa gag gat aag aag 336Phe Phe His Arg Leu Glu
Glu Ser Phe Leu Val Glu Glu Asp Lys Lys 100 105 110 cac gag cgg cac
ccc atc ttc ggc aac atc gtg gac gag gtg gcc tac 384His Glu Arg His
Pro Ile Phe Gly Asn Ile Val Asp Glu Val Ala Tyr 115 120 125 cac gag
aag tac ccc acc atc tac cac ctg aga aag aaa ctg gtg gac 432His Glu
Lys Tyr Pro Thr Ile Tyr His Leu Arg Lys Lys Leu Val Asp 130 135 140
agc acc gac aag gcc gac ctg cgg ctg atc tat ctg gcc ctg gcc cac
480Ser Thr Asp Lys Ala Asp Leu Arg Leu Ile Tyr Leu Ala Leu Ala His
145 150 155 160 atg atc aag ttc cgg ggc cac ttc ctg atc gag ggc gac
ctg aac ccc 528Met Ile Lys Phe Arg Gly His Phe Leu Ile Glu Gly Asp
Leu Asn Pro 165 170 175 gac aac agc gac gtg gac aag ctg ttc atc cag
ctg gtg cag acc tac 576Asp Asn Ser Asp Val Asp Lys Leu Phe Ile Gln
Leu Val Gln Thr Tyr 180 185 190 aac cag ctg ttc gag gaa aac ccc atc
aac gcc agc ggc gtg gac gcc 624Asn Gln Leu Phe Glu Glu Asn Pro Ile
Asn Ala Ser Gly Val Asp Ala 195 200 205 aag gcc atc ctg tct gcc aga
ctg agc aag agc aga cgg ctg gaa aat 672Lys Ala Ile Leu Ser Ala Arg
Leu Ser Lys Ser Arg Arg Leu Glu Asn 210 215 220 ctg atc gcc cag ctg
ccc ggc gag aag aag aat ggc ctg ttc ggc aac 720Leu Ile Ala Gln Leu
Pro Gly Glu Lys Lys Asn Gly Leu Phe Gly Asn 225 230 235 240 ctg att
gcc ctg agc ctg ggc ctg acc ccc aac ttc aag agc aac ttc 768Leu Ile
Ala Leu Ser Leu Gly Leu Thr Pro Asn Phe Lys Ser Asn Phe 245 250 255
gac ctg gcc gag gat gcc aaa ctg cag ctg agc aag gac acc tac gac
816Asp Leu Ala Glu Asp Ala Lys Leu Gln Leu Ser Lys Asp Thr Tyr Asp
260 265 270 gac gac ctg gac aac ctg ctg gcc cag atc ggc gac cag tac
gcc gac 864Asp Asp Leu Asp Asn Leu Leu Ala Gln Ile Gly Asp Gln Tyr
Ala Asp 275 280 285 ctg ttt ctg gcc gcc aag aac ctg tcc gac gcc atc
ctg ctg agc gac 912Leu Phe Leu Ala Ala Lys Asn Leu Ser Asp Ala Ile
Leu Leu Ser Asp 290 295 300 atc ctg aga gtg aac acc gag atc acc aag
gcc ccc ctg agc gcc tct 960Ile Leu Arg Val Asn Thr Glu Ile Thr Lys
Ala Pro Leu Ser Ala Ser 305 310 315 320 atg atc aag aga tac gac gag
cac cac cag gac ctg acc ctg ctg aaa 1008Met Ile Lys Arg Tyr Asp Glu
His His Gln Asp Leu Thr Leu Leu Lys 325 330 335 gct ctc gtg cgg cag
cag ctg cct gag aag tac aaa gag att ttc ttc 1056Ala Leu Val Arg Gln
Gln Leu Pro Glu Lys Tyr Lys Glu Ile Phe Phe 340 345 350 gac cag agc
aag aac ggc tac gcc ggc tac att gac ggc gga gcc agc 1104Asp Gln Ser
Lys Asn Gly Tyr Ala Gly Tyr Ile Asp Gly Gly Ala Ser 355 360 365 cag
gaa gag ttc tac aag ttc atc aag ccc atc ctg gaa aag atg gac 1152Gln
Glu Glu Phe Tyr Lys Phe Ile Lys Pro Ile Leu Glu Lys Met Asp 370 375
380 ggc acc gag gaa ctg ctc gtg aag ctg aac aga gag gac ctg ctg cgg
1200Gly Thr Glu Glu Leu Leu Val Lys Leu Asn Arg Glu Asp Leu Leu Arg
385 390 395 400 aag cag cgg acc ttc gac aac ggc agc atc ccc cac cag
atc cac ctg 1248Lys Gln Arg Thr Phe Asp Asn Gly Ser Ile Pro His Gln
Ile His Leu 405 410 415 gga gag ctg cac gcc att ctg cgg cgg cag gaa
gat ttt tac cca ttc 1296Gly Glu Leu His Ala Ile Leu Arg Arg Gln Glu
Asp Phe Tyr Pro Phe 420 425 430 ctg aag gac aac cgg gaa aag atc gag
aag atc ctg acc ttc cgc atc 1344Leu Lys Asp Asn Arg Glu Lys Ile Glu
Lys Ile Leu Thr Phe Arg Ile 435 440 445 ccc tac tac gtg ggc cct ctg
gcc agg gga aac agc aga ttc gcc tgg 1392Pro Tyr Tyr Val Gly Pro Leu
Ala Arg Gly Asn Ser Arg Phe Ala Trp 450 455 460 atg acc aga aag agc
gag gaa acc atc acc ccc tgg aac ttc gag gaa 1440Met Thr Arg Lys Ser
Glu Glu Thr Ile Thr Pro Trp Asn Phe Glu Glu 465 470 475 480 gtg gtg
gac aag ggc gct tcc gcc cag agc ttc atc gag cgg atg acc 1488Val Val
Asp Lys Gly Ala Ser Ala Gln Ser Phe Ile Glu Arg Met Thr 485 490 495
aac ttc gat aag aac ctg ccc aac gag aag gtg ctg ccc aag cac agc
1536Asn Phe Asp Lys Asn Leu Pro Asn Glu Lys Val Leu Pro Lys His Ser
500 505 510 ctg ctg tac gag tac ttc acc gtg tat aac gag ctg acc aaa
gtg aaa 1584Leu Leu Tyr Glu Tyr Phe Thr Val Tyr Asn Glu Leu Thr Lys
Val Lys 515 520 525 tac gtg acc gag gga atg aga aag ccc gcc ttc ctg
agc ggc gag cag 1632Tyr Val Thr Glu Gly Met Arg Lys Pro Ala Phe Leu
Ser Gly Glu Gln 530 535 540 aaa aag gcc atc gtg gac ctg ctg ttc aag
acc aac cgg aaa gtg acc 1680Lys Lys Ala Ile Val Asp Leu Leu Phe Lys
Thr Asn Arg Lys Val Thr 545 550 555 560 gtg aag cag ctg aaa gag gac
tac ttc aag aaa atc gag tgc ttc gac 1728Val Lys Gln Leu Lys Glu Asp
Tyr Phe Lys Lys Ile Glu Cys Phe Asp 565 570 575 tcc gtg gaa atc tcc
ggc gtg gaa gat cgg ttc aac gcc tcc ctg ggc 1776Ser Val Glu Ile Ser
Gly Val Glu Asp Arg Phe Asn Ala Ser Leu Gly 580 585 590 aca tac cac
gat ctg ctg aaa att atc aag gac aag gac ttc ctg gac 1824Thr Tyr His
Asp Leu Leu Lys Ile Ile Lys Asp Lys Asp Phe Leu Asp 595 600 605 aat
gag gaa aac gag gac att ctg gaa gat atc gtg ctg acc ctg aca 1872Asn
Glu Glu Asn Glu Asp Ile Leu Glu Asp Ile Val Leu Thr Leu Thr 610 615
620 ctg ttt gag gac aga gag atg atc gag gaa cgg ctg aaa acc tat gcc
1920Leu Phe Glu Asp Arg Glu Met Ile Glu Glu Arg Leu Lys Thr Tyr Ala
625 630 635 640 cac ctg ttc gac gac aaa gtg atg aag cag ctg aag cgg
cgg aga tac 1968His Leu Phe Asp Asp Lys Val Met Lys Gln Leu Lys Arg
Arg Arg Tyr 645 650 655 acc ggc tgg ggc agg ctg agc cgg aag ctg atc
aac ggc atc cgg gac 2016Thr Gly Trp Gly Arg Leu Ser Arg Lys Leu Ile
Asn Gly Ile Arg Asp 660 665 670 aag cag tcc ggc aag aca atc ctg gat
ttc ctg aag tcc gac ggc ttc 2064Lys Gln Ser Gly Lys Thr Ile Leu Asp
Phe Leu Lys Ser Asp Gly Phe 675 680 685 gcc aac aga aac ttc atg cag
ctg atc cac gac gac agc ctg acc ttt 2112Ala Asn Arg Asn Phe Met Gln
Leu Ile His Asp Asp Ser Leu Thr Phe 690 695 700 aaa gag gac atc cag
aaa gcc cag gtg tcc ggc cag ggc gat agc ctg 2160Lys Glu Asp Ile Gln
Lys Ala Gln Val Ser Gly Gln Gly Asp Ser Leu 705 710 715 720 cac gag
cac att gcc aat ctg gcc ggc agc ccc gcc att aag aag ggc 2208His Glu
His Ile Ala Asn Leu Ala Gly Ser Pro Ala Ile Lys Lys Gly 725 730 735
atc ctg cag aca gtg aag gtg gtg gac gag ctc gtg aaa gtg atg ggc
2256Ile Leu Gln Thr Val Lys Val Val Asp Glu Leu Val Lys Val Met Gly
740 745 750 cgg cac aag ccc gag aac atc gtg atc gcc atg gcc aga gag
aac cag 2304Arg His Lys Pro Glu Asn Ile Val Ile Ala Met Ala Arg Glu
Asn Gln 755 760 765 acc acc cag aag gga cag aag aac agc cgc gag aga
atg aag cgg atc 2352Thr Thr Gln Lys Gly Gln Lys Asn Ser Arg Glu Arg
Met Lys Arg Ile 770 775 780 gaa gag ggc atc aaa gag ctg ggc agc cag
atc ctg aaa gaa cac ccc 2400Glu Glu Gly Ile Lys Glu Leu Gly Ser Gln
Ile Leu Lys Glu His Pro 785 790 795 800 gtg gaa aac acc cag ctg cag
aac gag aag ctg tac ctg tac tac ctg 2448Val Glu Asn Thr Gln Leu Gln
Asn Glu Lys Leu Tyr Leu Tyr Tyr Leu 805 810 815 cag aat ggg cgg gat
atg tac gtg gac cag gaa ctg gac atc aac cgg 2496Gln Asn Gly Arg Asp
Met Tyr Val Asp Gln Glu Leu Asp Ile Asn Arg 820 825 830 ctg tcc gac
tac gat gtg gac gcc atc gtg cct cag agc ttt ctg aag 2544Leu Ser Asp
Tyr Asp Val Asp Ala Ile Val Pro Gln Ser Phe Leu Lys 835 840 845 gac
gac tcc atc gac gcc aag gtg ctg acc aga agc gac aag gcc cgg 2592Asp
Asp Ser Ile Asp Ala Lys Val Leu Thr Arg Ser Asp Lys Ala Arg 850 855
860 ggc aag agc gac aac gtg ccc tcc gaa gag gtc gtg aag aag atg aag
2640Gly Lys Ser Asp Asn Val Pro Ser Glu Glu Val Val Lys Lys Met Lys
865 870 875 880 aac tac tgg cgg cag ctg ctg aac gcc aag ctg att acc
cag aga aag 2688Asn Tyr Trp Arg Gln Leu Leu Asn Ala Lys Leu Ile Thr
Gln Arg Lys 885 890 895 ttc gac aat ctg acc aag gcc gag aga ggc ggc
ctg agc gaa ctg gat 2736Phe Asp Asn Leu Thr Lys Ala Glu Arg Gly Gly
Leu Ser Glu Leu Asp 900 905 910 aag gcc ggc ttc atc aag aga cag ctg
gtg gaa acc cgg cag atc aca 2784Lys Ala Gly Phe Ile Lys Arg Gln Leu
Val Glu Thr Arg Gln Ile Thr 915 920 925 aag cac gtg gca cag atc ctg
gac tcc cgg atg aac act aag tac gac 2832Lys His Val Ala Gln Ile Leu
Asp Ser Arg Met Asn Thr Lys Tyr Asp 930 935 940 gag aat gac aag ctg
atc cgg gaa gtg aaa gtg atc acc ctg aag tcc 2880Glu Asn Asp Lys Leu
Ile Arg Glu Val Lys Val Ile Thr Leu Lys Ser 945 950 955 960 aag ctg
gtg tcc gat ttc cgg aag gat ttc cag ttt tac aaa gtg cgc 2928Lys Leu
Val Ser Asp Phe Arg Lys Asp Phe Gln Phe Tyr Lys Val Arg 965 970 975
gag atc aac aac tac cac cac gcc cac gcc gcc tac ctg aac gcc gtc
2976Glu Ile Asn Asn Tyr His His Ala His Ala Ala Tyr Leu Asn Ala Val
980 985 990 gtg gga acc gcc ctg atc aaa aag tac cct aag ctg gaa agc
gag ttc 3024Val Gly Thr Ala Leu Ile Lys Lys Tyr Pro Lys Leu Glu Ser
Glu Phe 995 1000 1005 gtg tac ggc gac tac aag gtg tac gac gtg cgg
aag atg atc gcc 3069Val Tyr Gly Asp Tyr Lys Val Tyr Asp Val Arg Lys
Met Ile Ala 1010 1015 1020 aag agc gag cag gaa atc ggc aag gct acc
gcc aag tac ttc ttc 3114Lys Ser Glu Gln Glu Ile Gly Lys Ala Thr Ala
Lys Tyr Phe Phe 1025 1030 1035 tac agc aac atc atg aac ttt ttc aag
acc gag att acc ctg gcc 3159Tyr Ser Asn Ile Met Asn Phe Phe Lys Thr
Glu Ile Thr Leu Ala 1040 1045 1050 aac ggc gag atc cgg aag cgg cct
ctg atc gag aca aac ggc gaa 3204Asn Gly Glu Ile Arg Lys Arg Pro Leu
Ile Glu Thr Asn Gly Glu 1055 1060 1065 acc ggg gag atc gtg tgg gat
aag ggc cgg gat ttt gcc acc gtg 3249Thr Gly Glu Ile Val Trp Asp Lys
Gly Arg Asp Phe Ala Thr Val 1070 1075 1080 cgg aaa gtg ctg agc atg
ccc caa gtg aat atc gtg aaa aag acc 3294Arg Lys Val Leu Ser Met Pro
Gln Val Asn Ile Val Lys Lys Thr 1085 1090 1095 gag gtg cag aca ggc
ggc ttc agc aaa gag tct atc ctg ccc aag 3339Glu Val Gln Thr Gly Gly
Phe Ser Lys Glu Ser Ile Leu Pro Lys 1100 1105 1110 agg aac agc gat
aag ctg atc gcc aga aag aag gac tgg gac cct 3384Arg Asn Ser Asp Lys
Leu Ile Ala Arg Lys Lys Asp Trp Asp Pro 1115 1120 1125 aag aag tac
ggc ggc ttc gac agc ccc acc gtg gcc tat tct gtg 3429Lys Lys Tyr Gly
Gly Phe Asp Ser Pro Thr Val Ala Tyr Ser Val 1130 1135 1140 ctg gtg
gtg gcc aaa gtg gaa aag ggc aag tcc aag aaa ctg aag 3474Leu Val Val
Ala Lys Val Glu Lys Gly Lys Ser Lys Lys Leu Lys 1145 1150 1155 agt
gtg aaa gag ctg ctg ggg atc acc atc atg gaa aga agc agc 3519Ser Val
Lys Glu Leu Leu Gly Ile Thr Ile Met Glu Arg Ser Ser 1160 1165 1170
ttc gag aag aat ccc atc gac ttt ctg gaa gcc aag ggc tac aaa 3564Phe
Glu Lys Asn Pro Ile Asp Phe Leu Glu Ala Lys Gly Tyr Lys 1175 1180
1185 gaa gtg aaa aag gac ctg atc atc aag ctg cct aag tac tcc ctg
3609Glu Val Lys Lys Asp Leu Ile Ile Lys Leu Pro Lys Tyr Ser Leu
1190 1195 1200 ttc gag ctg gaa aac ggc cgg aag aga atg ctg gcc tct
gcc ggc 3654Phe Glu Leu Glu Asn Gly Arg Lys Arg Met Leu Ala Ser Ala
Gly 1205 1210 1215 gaa ctg cag aag gga aac gaa ctg gcc ctg ccc tcc
aaa tat gtg 3699Glu Leu Gln Lys Gly Asn Glu Leu Ala Leu Pro Ser Lys
Tyr Val 1220 1225 1230 aac ttc ctg tac ctg gcc agc cac tat gag aag
ctg aag ggc tcc 3744Asn Phe Leu Tyr Leu Ala Ser His Tyr Glu Lys Leu
Lys Gly Ser 1235 1240 1245 ccc gag gat aat gag cag aaa cag ctg ttt
gtg gaa cag cac aag 3789Pro Glu Asp Asn Glu Gln Lys Gln Leu Phe Val
Glu Gln His Lys 1250 1255 1260 cac tac ctg gac gag atc atc gag cag
atc agc gag ttc tcc aag 3834His Tyr Leu Asp Glu Ile Ile Glu Gln Ile
Ser Glu Phe Ser Lys 1265 1270 1275 aga gtg atc ctg gcc gac gct aat
ctg gac aaa gtg ctg tcc gcc 3879Arg Val Ile Leu Ala Asp Ala Asn Leu
Asp Lys Val Leu Ser Ala 1280 1285 1290 tac aac aag cac cgg gat aag
ccc atc aga gag cag gcc gag aat 3924Tyr Asn Lys His Arg Asp Lys Pro
Ile Arg Glu Gln Ala Glu Asn 1295 1300 1305 atc
atc cac ctg ttt acc ctg acc aat ctg gga gcc cct gcc gcc 3969Ile Ile
His Leu Phe Thr Leu Thr Asn Leu Gly Ala Pro Ala Ala 1310 1315 1320
ttc aag tac ttt gac acc acc atc gac cgg aag agg tac acc agc 4014Phe
Lys Tyr Phe Asp Thr Thr Ile Asp Arg Lys Arg Tyr Thr Ser 1325 1330
1335 acc aaa gag gtg ctg gac gcc acc ctg atc cac cag agc atc acc
4059Thr Lys Glu Val Leu Asp Ala Thr Leu Ile His Gln Ser Ile Thr
1340 1345 1350 ggc ctg tac gag aca cgg atc gac ctg tct cag ctg gga
ggc gac 4104Gly Leu Tyr Glu Thr Arg Ile Asp Leu Ser Gln Leu Gly Gly
Asp 1355 1360 1365 3611368PRTHomo sapiens 361Met Asp Lys Lys Tyr
Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val 1 5 10 15 Gly Trp Ala
Val Ile Thr Asp Glu Tyr Lys Val Pro Ser Lys Lys Phe 20 25 30 Lys
Val Leu Gly Asn Thr Asp Arg His Ser Ile Lys Lys Asn Leu Ile 35 40
45 Gly Ala Leu Leu Phe Asp Ser Gly Glu Thr Ala Glu Ala Thr Arg Leu
50 55 60 Lys Arg Thr Ala Arg Arg Arg Tyr Thr Arg Arg Lys Asn Arg
Ile Cys 65 70 75 80 Tyr Leu Gln Glu Ile Phe Ser Asn Glu Met Ala Lys
Val Asp Asp Ser 85 90 95 Phe Phe His Arg Leu Glu Glu Ser Phe Leu
Val Glu Glu Asp Lys Lys 100 105 110 His Glu Arg His Pro Ile Phe Gly
Asn Ile Val Asp Glu Val Ala Tyr 115 120 125 His Glu Lys Tyr Pro Thr
Ile Tyr His Leu Arg Lys Lys Leu Val Asp 130 135 140 Ser Thr Asp Lys
Ala Asp Leu Arg Leu Ile Tyr Leu Ala Leu Ala His 145 150 155 160 Met
Ile Lys Phe Arg Gly His Phe Leu Ile Glu Gly Asp Leu Asn Pro 165 170
175 Asp Asn Ser Asp Val Asp Lys Leu Phe Ile Gln Leu Val Gln Thr Tyr
180 185 190 Asn Gln Leu Phe Glu Glu Asn Pro Ile Asn Ala Ser Gly Val
Asp Ala 195 200 205 Lys Ala Ile Leu Ser Ala Arg Leu Ser Lys Ser Arg
Arg Leu Glu Asn 210 215 220 Leu Ile Ala Gln Leu Pro Gly Glu Lys Lys
Asn Gly Leu Phe Gly Asn 225 230 235 240 Leu Ile Ala Leu Ser Leu Gly
Leu Thr Pro Asn Phe Lys Ser Asn Phe 245 250 255 Asp Leu Ala Glu Asp
Ala Lys Leu Gln Leu Ser Lys Asp Thr Tyr Asp 260 265 270 Asp Asp Leu
Asp Asn Leu Leu Ala Gln Ile Gly Asp Gln Tyr Ala Asp 275 280 285 Leu
Phe Leu Ala Ala Lys Asn Leu Ser Asp Ala Ile Leu Leu Ser Asp 290 295
300 Ile Leu Arg Val Asn Thr Glu Ile Thr Lys Ala Pro Leu Ser Ala Ser
305 310 315 320 Met Ile Lys Arg Tyr Asp Glu His His Gln Asp Leu Thr
Leu Leu Lys 325 330 335 Ala Leu Val Arg Gln Gln Leu Pro Glu Lys Tyr
Lys Glu Ile Phe Phe 340 345 350 Asp Gln Ser Lys Asn Gly Tyr Ala Gly
Tyr Ile Asp Gly Gly Ala Ser 355 360 365 Gln Glu Glu Phe Tyr Lys Phe
Ile Lys Pro Ile Leu Glu Lys Met Asp 370 375 380 Gly Thr Glu Glu Leu
Leu Val Lys Leu Asn Arg Glu Asp Leu Leu Arg 385 390 395 400 Lys Gln
Arg Thr Phe Asp Asn Gly Ser Ile Pro His Gln Ile His Leu 405 410 415
Gly Glu Leu His Ala Ile Leu Arg Arg Gln Glu Asp Phe Tyr Pro Phe 420
425 430 Leu Lys Asp Asn Arg Glu Lys Ile Glu Lys Ile Leu Thr Phe Arg
Ile 435 440 445 Pro Tyr Tyr Val Gly Pro Leu Ala Arg Gly Asn Ser Arg
Phe Ala Trp 450 455 460 Met Thr Arg Lys Ser Glu Glu Thr Ile Thr Pro
Trp Asn Phe Glu Glu 465 470 475 480 Val Val Asp Lys Gly Ala Ser Ala
Gln Ser Phe Ile Glu Arg Met Thr 485 490 495 Asn Phe Asp Lys Asn Leu
Pro Asn Glu Lys Val Leu Pro Lys His Ser 500 505 510 Leu Leu Tyr Glu
Tyr Phe Thr Val Tyr Asn Glu Leu Thr Lys Val Lys 515 520 525 Tyr Val
Thr Glu Gly Met Arg Lys Pro Ala Phe Leu Ser Gly Glu Gln 530 535 540
Lys Lys Ala Ile Val Asp Leu Leu Phe Lys Thr Asn Arg Lys Val Thr 545
550 555 560 Val Lys Gln Leu Lys Glu Asp Tyr Phe Lys Lys Ile Glu Cys
Phe Asp 565 570 575 Ser Val Glu Ile Ser Gly Val Glu Asp Arg Phe Asn
Ala Ser Leu Gly 580 585 590 Thr Tyr His Asp Leu Leu Lys Ile Ile Lys
Asp Lys Asp Phe Leu Asp 595 600 605 Asn Glu Glu Asn Glu Asp Ile Leu
Glu Asp Ile Val Leu Thr Leu Thr 610 615 620 Leu Phe Glu Asp Arg Glu
Met Ile Glu Glu Arg Leu Lys Thr Tyr Ala 625 630 635 640 His Leu Phe
Asp Asp Lys Val Met Lys Gln Leu Lys Arg Arg Arg Tyr 645 650 655 Thr
Gly Trp Gly Arg Leu Ser Arg Lys Leu Ile Asn Gly Ile Arg Asp 660 665
670 Lys Gln Ser Gly Lys Thr Ile Leu Asp Phe Leu Lys Ser Asp Gly Phe
675 680 685 Ala Asn Arg Asn Phe Met Gln Leu Ile His Asp Asp Ser Leu
Thr Phe 690 695 700 Lys Glu Asp Ile Gln Lys Ala Gln Val Ser Gly Gln
Gly Asp Ser Leu 705 710 715 720 His Glu His Ile Ala Asn Leu Ala Gly
Ser Pro Ala Ile Lys Lys Gly 725 730 735 Ile Leu Gln Thr Val Lys Val
Val Asp Glu Leu Val Lys Val Met Gly 740 745 750 Arg His Lys Pro Glu
Asn Ile Val Ile Ala Met Ala Arg Glu Asn Gln 755 760 765 Thr Thr Gln
Lys Gly Gln Lys Asn Ser Arg Glu Arg Met Lys Arg Ile 770 775 780 Glu
Glu Gly Ile Lys Glu Leu Gly Ser Gln Ile Leu Lys Glu His Pro 785 790
795 800 Val Glu Asn Thr Gln Leu Gln Asn Glu Lys Leu Tyr Leu Tyr Tyr
Leu 805 810 815 Gln Asn Gly Arg Asp Met Tyr Val Asp Gln Glu Leu Asp
Ile Asn Arg 820 825 830 Leu Ser Asp Tyr Asp Val Asp Ala Ile Val Pro
Gln Ser Phe Leu Lys 835 840 845 Asp Asp Ser Ile Asp Ala Lys Val Leu
Thr Arg Ser Asp Lys Ala Arg 850 855 860 Gly Lys Ser Asp Asn Val Pro
Ser Glu Glu Val Val Lys Lys Met Lys 865 870 875 880 Asn Tyr Trp Arg
Gln Leu Leu Asn Ala Lys Leu Ile Thr Gln Arg Lys 885 890 895 Phe Asp
Asn Leu Thr Lys Ala Glu Arg Gly Gly Leu Ser Glu Leu Asp 900 905 910
Lys Ala Gly Phe Ile Lys Arg Gln Leu Val Glu Thr Arg Gln Ile Thr 915
920 925 Lys His Val Ala Gln Ile Leu Asp Ser Arg Met Asn Thr Lys Tyr
Asp 930 935 940 Glu Asn Asp Lys Leu Ile Arg Glu Val Lys Val Ile Thr
Leu Lys Ser 945 950 955 960 Lys Leu Val Ser Asp Phe Arg Lys Asp Phe
Gln Phe Tyr Lys Val Arg 965 970 975 Glu Ile Asn Asn Tyr His His Ala
His Ala Ala Tyr Leu Asn Ala Val 980 985 990 Val Gly Thr Ala Leu Ile
Lys Lys Tyr Pro Lys Leu Glu Ser Glu Phe 995 1000 1005 Val Tyr Gly
Asp Tyr Lys Val Tyr Asp Val Arg Lys Met Ile Ala 1010 1015 1020 Lys
Ser Glu Gln Glu Ile Gly Lys Ala Thr Ala Lys Tyr Phe Phe 1025 1030
1035 Tyr Ser Asn Ile Met Asn Phe Phe Lys Thr Glu Ile Thr Leu Ala
1040 1045 1050 Asn Gly Glu Ile Arg Lys Arg Pro Leu Ile Glu Thr Asn
Gly Glu 1055 1060 1065 Thr Gly Glu Ile Val Trp Asp Lys Gly Arg Asp
Phe Ala Thr Val 1070 1075 1080 Arg Lys Val Leu Ser Met Pro Gln Val
Asn Ile Val Lys Lys Thr 1085 1090 1095 Glu Val Gln Thr Gly Gly Phe
Ser Lys Glu Ser Ile Leu Pro Lys 1100 1105 1110 Arg Asn Ser Asp Lys
Leu Ile Ala Arg Lys Lys Asp Trp Asp Pro 1115 1120 1125 Lys Lys Tyr
Gly Gly Phe Asp Ser Pro Thr Val Ala Tyr Ser Val 1130 1135 1140 Leu
Val Val Ala Lys Val Glu Lys Gly Lys Ser Lys Lys Leu Lys 1145 1150
1155 Ser Val Lys Glu Leu Leu Gly Ile Thr Ile Met Glu Arg Ser Ser
1160 1165 1170 Phe Glu Lys Asn Pro Ile Asp Phe Leu Glu Ala Lys Gly
Tyr Lys 1175 1180 1185 Glu Val Lys Lys Asp Leu Ile Ile Lys Leu Pro
Lys Tyr Ser Leu 1190 1195 1200 Phe Glu Leu Glu Asn Gly Arg Lys Arg
Met Leu Ala Ser Ala Gly 1205 1210 1215 Glu Leu Gln Lys Gly Asn Glu
Leu Ala Leu Pro Ser Lys Tyr Val 1220 1225 1230 Asn Phe Leu Tyr Leu
Ala Ser His Tyr Glu Lys Leu Lys Gly Ser 1235 1240 1245 Pro Glu Asp
Asn Glu Gln Lys Gln Leu Phe Val Glu Gln His Lys 1250 1255 1260 His
Tyr Leu Asp Glu Ile Ile Glu Gln Ile Ser Glu Phe Ser Lys 1265 1270
1275 Arg Val Ile Leu Ala Asp Ala Asn Leu Asp Lys Val Leu Ser Ala
1280 1285 1290 Tyr Asn Lys His Arg Asp Lys Pro Ile Arg Glu Gln Ala
Glu Asn 1295 1300 1305 Ile Ile His Leu Phe Thr Leu Thr Asn Leu Gly
Ala Pro Ala Ala 1310 1315 1320 Phe Lys Tyr Phe Asp Thr Thr Ile Asp
Arg Lys Arg Tyr Thr Ser 1325 1330 1335 Thr Lys Glu Val Leu Asp Ala
Thr Leu Ile His Gln Ser Ile Thr 1340 1345 1350 Gly Leu Tyr Glu Thr
Arg Ile Asp Leu Ser Gln Leu Gly Gly Asp 1355 1360 1365 36257DNAHomo
sapiensCDS(1)..(57) 362ggc acc att aaa gaa aat atc att ggt gtt tcc
tat gat gaa tat aga 48Gly Thr Ile Lys Glu Asn Ile Ile Gly Val Ser
Tyr Asp Glu Tyr Arg 1 5 10 15 tac aga agc 57Tyr Arg Ser
36319PRTHomo sapiens 363Gly Thr Ile Lys Glu Asn Ile Ile Gly Val Ser
Tyr Asp Glu Tyr Arg 1 5 10 15 Tyr Arg Ser 36448DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 364att aaa gaa aat atc att ggc ttt gtt tcc tat gat
gaa tat aga tac 48Ile Lys Glu Asn Ile Ile Gly Phe Val Ser Tyr Asp
Glu Tyr Arg Tyr1 5 10 15 36516PRTArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
peptide" 365Ile Lys Glu Asn Ile Ile Gly Phe Val Ser Tyr Asp Glu Tyr
Arg Tyr 1 5 10 15 36650DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 366ccnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn
nnnnnnnngg 5036746DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic oligonucleotide" 367ccnnnnnnnn
nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnngg 4636842DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 368ccnnnnnnnn nnnnnnnnnn nnnnnnnnnn nnnnnnnnnn gg
4236938DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 369ccnnnnnnnn nnnnnnnnnn
nnnnnnnnnn nnnnnngg 3837034DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 370ccnnnnnnnn nnnnnnnnnn nnnnnnnnnn nngg
3437130DNAArtificial Sequencesource/note="Description of Artificial
Sequence Synthetic oligonucleotide" 371ccnnnnnnnn nnnnnnnnnn
nnnnnnnngg 3037226DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic oligonucleotide" 372ccnnnnnnnn
nnnnnnnnnn nnnngg 2637322DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 373ccnnnnnnnn nnnnnnnnnn gg 2237418DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 374ccnnnnnnnn nnnnnngg 1837516DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 375ccnnnnnnnn nnnngg 1637615DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 376ccnnnnnnnn nnngg 1537714DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 377ccnnnnnnnn nngg 1437813DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 378ccnnnnnnnn ngg 1337912DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 379ccnnnnnnnn gg 1238011DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 380ccnnnnnnng g 1138110DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 381ccnnnnnngg 1038212DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
oligonucleotide" 382ggnnnnnnnn cc 12383125DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 383aaaaaaagca ccgactcggt gccacttttt caagttgata acggactagc
cttattttaa 60cttgctattt ctagctctaa aactcacatc aaccggtggc gcaggtgttt
cgtcctttcc 120acaag 125384125DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 384aaaaaaagca ccgactcggt gccacttttt caagttgata acggactagc
cttattttaa 60cttgctattt ctagctctaa aactcacatc aaccggtggc gcaggtgttt
cgtcctttcc 120acaag 125385125DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 385aaaaaaagca ccgactcggt gccacttttt caagttgata acggactagc
cttattttaa 60cttgctattt ctagctctaa aacgaggaca aagtacaaac ggcggtgttt
cgtcctttcc 120acaag 125386125DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 386aaaaaaagca ccgactcggt gccacttttt caagttgata acggactagc
cttattttaa 60cttgctattt ctagctctaa aacgaggaca aagtacaaac ggcggtgttt
cgtcctttcc 120acaag 125387125DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 387aaaaaaagca ccgactcggt gccacttttt caagttgata acggactagc
cttattttaa 60cttgctattt ctagctctaa aacgtggcgc attgccacga agcggtgttt
cgtcctttcc 120acaag 125388125DNAArtificial
Sequencesource/note="Description of Artificial Sequence Synthetic
primer" 388aaaaaaagca ccgactcggt gccacttttt caagttgata acggactagc
cttattttaa 60cttgctattt ctagctctaa aaccgagggc agagtgctgc ttgggtgttt
cgtcctttcc 120acaag 125389125DNAArtificial
Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 389aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgagtccg agcagaagaa gaaggtgttt cgtcctttcc 120acaag
125390125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 390aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgaggaca aagtacaaac ggcggtgttt cgtcctttcc 120acaag
125391125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 391aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacagcagaa gaagaagggc tccggtgttt cgtcctttcc 120acaag
125392125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 392aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aactcacatc aaccggtggc gcaggtgttt cgtcctttcc 120acaag
125393125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 393aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacccctggc ccaggtgaag gtgggtgttt cgtcctttcc 120acaag
125394125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 394aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aactccctcc ctggcccagg tgaggtgttt cgtcctttcc 120acaag
125395125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 395aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgaaccgg aggacaaagt acaggtgttt cgtcctttcc 120acaag
125396125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 396aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacaggtgaa ggtgtggttc cagggtgttt cgtcctttcc 120acaag
125397125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 397aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacggtgaag gtgtggttcc agaggtgttt cgtcctttcc 120acaag
125398125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 398aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgaaccgg aggacaaagt acaggtgttt cgtcctttcc 120acaag
125399125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 399aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacccctggc ccaggtgaag gtgggtgttt cgtcctttcc 120acaag
125400125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 400aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacaggtgaa ggtgtggttc cagggtgttt cgtcctttcc 120acaag
125401125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 401aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgaggaca aagtacaaac ggcggtgttt cgtcctttcc 120acaag
125402125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 402aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgggaggg aggggcacag atgggtgttt cgtcctttcc 120acaag
125403125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 403aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aaccaccttc acctgggcca gggggtgttt cgtcctttcc 120acaag
125404125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 404aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacaccctag tcattggagg tgaggtgttt cgtcctttcc 120acaag
125405125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 405aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aaccagagca gccactgggg cctggtgttt cgtcctttcc 120acaag
125406125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 406aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aaccaccttc acctgggcca gggggtgttt cgtcctttcc 120acaag
125407125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 407aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacccccatt ggcctgcttc gtgggtgttt cgtcctttcc 120acaag
125408125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 408aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacattggcc tgcttcgtgg caaggtgttt cgtcctttcc 120acaag
125409125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 409aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aactcctcct ccagcttctg ccgggtgttt cgtcctttcc 120acaag
125410125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 410aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aaccctccag cttctgccgt ttgggtgttt cgtcctttcc 120acaag
125411125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 411aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacattggcc tgcttcgtgg caaggtgttt cgtcctttcc 120acaag
125412125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 412aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgcagcaa gcagcactct gccggtgttt cgtcctttcc 120acaag
125413125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 413aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacttcttct tctgctcgga ctcggtgttt cgtcctttcc 120acaag
125414125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 414aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacaccggag gacaaagtac aaaggtgttt cgtcctttcc 120acaag
125415125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 415aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aactcttctt ctgctcggac tcaggtgttt cgtcctttcc 120acaag
125416125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 416aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgttgatg tgatgggagc cctggtgttt cgtcctttcc 120acaag
125417125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 417aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgggccag ggagggaggg gcaggtgttt cgtcctttcc 120acaag
125418125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 418aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgggaggg aggggcacag atgggtgttt cgtcctttcc 120acaag
125419125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 419aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacccggttc tggaaccaca cctggtgttt cgtcctttcc 120acaag
125420125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 420aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aactcacctg ggccagggag ggaggtgttt cgtcctttcc 120acaag
125421125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 421aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aactcacctg ggccagggag ggaggtgttt cgtcctttcc 120acaag
125422125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 422aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgttctgg aaccacacct tcaggtgttt cgtcctttcc 120acaag
125423125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 423aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgggaggg aggggcacag atgggtgttt cgtcctttcc 120acaag
125424125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 424aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgggccag ggagggaggg gcaggtgttt cgtcctttcc 120acaag
125425125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 425aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgttctgg aaccacacct tcaggtgttt cgtcctttcc 120acaag
125426125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 426aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacaggtgaa ggtgtggttc cagggtgttt cgtcctttcc 120acaag
125427125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 427aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgaaccgg aggacaaagt acaggtgttt cgtcctttcc 120acaag
125428125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 428aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aaccaaaccc acgagggcag agtggtgttt cgtcctttcc 120acaag
125429125DNAArtificial Sequencesource/note="Description of
Artificial Sequence Synthetic primer" 429aaaaaaagca ccgactcggt
gccacttttt caagttgata acggactagc cttattttaa 60cttgctattt ctagctctaa
aacgagtttc tcatctgtgc cccggtgttt cgtcctttcc 120acaag
125430684DNAHomo
sapiensCDS(1)..(123)CDS(127)..(159)CDS(163)..(399)CDS(403)..(684)
430aaa acc acc ctt ctc tct ggc cca ctg tgt cct ctt cct gcc ctg cca
48Lys Thr Thr Leu Leu Ser Gly Pro Leu Cys Pro Leu Pro Ala Leu Pro 1
5 10 15 tcc cct tct gtg aat gtt aga ccc atg gga gca gct ggt cag agg
gga 96Ser Pro Ser Val Asn Val Arg Pro Met Gly Ala Ala Gly Gln Arg
Gly 20 25 30 ccc cgg cct ggg gcc cct aac cct atg tag cct cag tct
tcc cat cag 144Pro Arg Pro Gly Ala Pro Asn Pro Met Pro Gln Ser Ser
His Gln 35 40 45 gct ctc agc tca gcc tga gtg ttg agg ccc cag tgg
ctg ctc tgg ggg 192Ala Leu Ser Ser Ala Val Leu Arg Pro Gln Trp Leu
Leu Trp Gly 50 55 60 cct cct gag ttt ctc atc tgt gcc cct ccc tcc
ctg gcc cag gtg aag 240Pro Pro Glu Phe Leu Ile Cys Ala Pro Pro Ser
Leu Ala Gln Val Lys 65 70 75 gtg tgg ttc cag aac cgg agg aca aag
tac aaa cgg cag aag ctg gag 288Val Trp Phe Gln Asn Arg Arg Thr Lys
Tyr Lys Arg Gln Lys Leu Glu 80 85 90 gag gaa ggg cct gag tcc gag
cag aag aag aag ggc tcc cat cac atc 336Glu Glu Gly Pro Glu Ser Glu
Gln Lys Lys Lys Gly Ser His His Ile 95 100 105 110 aac cgg tgg cgc
att gcc acg aag cag gcc aat ggg gag gac atc gat 384Asn Arg Trp Arg
Ile Ala Thr Lys Gln Ala Asn Gly Glu Asp Ile Asp 115 120 125 gtc acc
tcc aat gac tag ggt ggg caa cca caa acc cac gag ggc aga 432Val Thr
Ser Asn Asp Gly Gly Gln Pro Gln Thr His Glu Gly Arg 130 135 140 gtg
ctg ctt gct gct ggc cag gcc cct gcg tgg gcc caa gct gga ctc 480Val
Leu Leu Ala Ala Gly Gln Ala Pro Ala Trp Ala Gln Ala Gly Leu 145 150
155 tgg cca ctc cct ggc cag gct ttg ggg agg cct gga gtc atg gcc cca
528Trp Pro Leu Pro Gly Gln Ala Leu Gly Arg Pro Gly Val Met Ala Pro
160 165 170 cag ggc ttg aag ccc ggg gcc gcc att gac aga ggg aca agc
aat ggg 576Gln Gly Leu Lys Pro Gly Ala Ala Ile Asp Arg Gly Thr Ser
Asn Gly 175 180 185 ctg gct gag gcc tgg gac cac ttg gcc ttc tcc tcg
gag agc ctg cct 624Leu Ala Glu Ala Trp Asp His Leu Ala Phe Ser Ser
Glu Ser Leu Pro 190 195 200 205 gcc tgg gcg ggc ccg ccc gcc acc gca
gcc tcc cag ctg ctc tcc gtg 672Ala Trp Ala Gly Pro Pro Ala Thr Ala
Ala Ser Gln Leu Leu Ser Val 210 215 220 tct cca atc tcc 684Ser Pro
Ile Ser 225 43141PRTHomo sapiens 431Lys Thr Thr Leu Leu Ser Gly Pro
Leu Cys Pro Leu Pro Ala Leu Pro 1 5 10 15 Ser Pro Ser Val Asn Val
Arg Pro Met Gly Ala Ala Gly Gln Arg Gly 20 25 30 Pro Arg Pro Gly
Ala Pro Asn Pro Met 35 40 43211PRTHomo sapiens 432Pro Gln Ser Ser
His Gln Ala Leu Ser Ser Ala 1 5 10 43379PRTHomo sapiens 433Val Leu
Arg Pro Gln Trp Leu Leu Trp Gly Pro Pro Glu Phe Leu Ile 1 5 10 15
Cys Ala Pro Pro Ser Leu Ala Gln Val Lys Val Trp Phe Gln Asn Arg 20
25 30 Arg Thr Lys Tyr Lys Arg Gln Lys Leu Glu Glu Glu Gly Pro Glu
Ser 35 40 45 Glu Gln Lys Lys Lys Gly Ser His His Ile Asn Arg Trp
Arg Ile Ala 50 55 60 Thr Lys Gln Ala Asn Gly Glu Asp Ile Asp Val
Thr Ser Asn Asp 65 70 75 43494PRTHomo sapiens 434Gly Gly Gln Pro
Gln Thr His Glu Gly Arg Val Leu Leu Ala Ala Gly 1 5 10 15 Gln Ala
Pro Ala Trp Ala Gln Ala Gly Leu Trp Pro Leu Pro Gly Gln 20 25 30
Ala Leu Gly Arg Pro Gly Val Met Ala Pro Gln Gly Leu Lys Pro Gly 35
40 45 Ala
Ala Ile Asp Arg Gly Thr Ser Asn Gly Leu Ala Glu Ala Trp Asp 50 55
60 His Leu Ala Phe Ser Ser Glu Ser Leu Pro Ala Trp Ala Gly Pro Pro
65 70 75 80 Ala Thr Ala Ala Ser Gln Leu Leu Ser Val Ser Pro Ile Ser
85 90
* * * * *
References