U.S. patent application number 17/355081 was filed with the patent office on 2021-10-14 for increased nucleic-acid guided cell editing in yeast.
The applicant listed for this patent is Inscripta, Inc.. Invention is credited to Miles Gander, Paul Hardenbol, Krishna Kannan, Eileen Spindler.
Application Number | 20210317464 17/355081 |
Document ID | / |
Family ID | 1000005671175 |
Filed Date | 2021-10-14 |
United States Patent
Application |
20210317464 |
Kind Code |
A1 |
Kannan; Krishna ; et
al. |
October 14, 2021 |
INCREASED NUCLEIC-ACID GUIDED CELL EDITING IN YEAST
Abstract
The present disclosure provides methods to increase the
percentage of edited yeast cells in a cell population using
nucleic-acid guided editing, and automated multi-module instruments
for performing these methods.
Inventors: |
Kannan; Krishna; (Boulder,
CO) ; Gander; Miles; (Boulder, CO) ; Spindler;
Eileen; (Boulder, CO) ; Hardenbol; Paul;
(Boulder, CO) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Inscripta, Inc. |
Boulder |
CO |
US |
|
|
Family ID: |
1000005671175 |
Appl. No.: |
17/355081 |
Filed: |
June 22, 2021 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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17140056 |
Jan 2, 2021 |
11066675 |
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17355081 |
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16904405 |
Jun 17, 2020 |
10927385 |
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17140056 |
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62866041 |
Jun 25, 2019 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 15/1058 20130101;
C12N 15/80 20130101 |
International
Class: |
C12N 15/80 20060101
C12N015/80; C12N 15/10 20060101 C12N015/10 |
Claims
1. A library of editing vectors for performing nucleic acid-guided
nuclease editing in yeast, where at least one vector in the library
of vectors comprises: a yeast backbone; an origin of replication; a
first non-minimal or non-core constitutive or inducible promoter
driving transcription of an editing cassette followed by a
terminator element 3' to the editing cassette, wherein each editing
cassette comprises a gRNA sequence and donor DNA sequence; a second
non-minimal or non-core constitutive promoter driving transcription
for a degron-survival marker fusion gene followed by a terminator
element 3' to the degron-survival marker fusion gene; a third
non-minimal constitutive or inducible promoter driving
transcription of a nuclease coding sequence with a terminator
element 5' to the nuclease or nuclease fusion coding sequence.
2. The library of editing vectors of claim 1, wherein the library
of editing vectors comprises a collection of vectors where editing
cassettes with different donor DNA sequences are associated with a
different barcode.
3. The library of editing vectors of claim 1, wherein the library
is isothermally assembled.
4. The library of editing vectors of claim 1, wherein the minimal
promoter is located between -35 to +35 of the transcription start
site.
5. The library of editing vectors of claim 1, wherein the degron
survival marker is an antibiotic.
6. The library of editing vectors of claim 5, wherein the
antibiotic is selected from the group consisting of hygromycin,
blasticidin, kanamycin, and nourseothricin.
7. The library of editing vectors of claim 1, wherein the
degron-survival marker fusion gene is an ubiquitin-dependent
degron.
8. The library of editing vectors of claim 7, wherein the
ubiquitin-dependent degron is selected from Ura3-d degron, Ubi-R
degron, Ubi-M degron, Ubi-Q degron, Ubi-E degron, ZF1 degron,
C-terminal phosphodegron; Ts-degron; lt-degron; auxin inducible
degron; DD-degron, LID-degron; PSD degron, B-LID degron; and a TIPI
degron.
9. The library of editing vectors of claim 7, wherein the
ubiquitin-dependent degron is a Ura3-d degron.
10. The library of editing vectors of claim 7, wherein the first,
second, and third non-minimal or non-core constitutive or inducible
promoters are the same.
11. The library of editing vectors of claim 7, wherein the first,
second, and third non-minimal or non-core constitutive or inducible
promoters are different.
12. A library of editing vectors for performing nucleic acid-guided
nuclease editing in yeast, where at least one vector in the library
of vectors comprises: a yeast backbone; an origin of replication; a
first non-minimal or non-core constitutive or inducible promoter
driving transcription of an editing cassette followed by a
terminator element 3' to the editing cassette, wherein each editing
cassette comprises a gRNA sequence and donor DNA sequence; a
minimal promoter or a weak constitutive promoter driving
transcription of a coding sequence for a survival marker gene
followed by a terminator element 3' to the survival marker gene; a
second non-minimal or non-core constitutive or inducible promoter
driving transcription of a nuclease coding sequence with a
terminator element 5' to the nuclease or nuclease fusion coding
sequence.
13. The library of editing vectors of claim 12, wherein the library
of editing vectors comprises a collection of vectors where editing
cassettes with different donor DNA sequences are associated with a
different barcode.
14. The library of editing vectors of claim 122, wherein the
library is isothermally assembled.
15. The library of editing vectors of claim 122, wherein the
minimal promoter is located between -35 to +35 of the transcription
start site.
16. The library of editing vectors of claim 122, wherein the
minimal promoter is selected from the group consisting of any one
of SEQ ID Nos: 1-25.
17. The library of editing vectors of claim 122, wherein the weak
constitutive promoter is selected from the group consisting of any
one of SEQ ID Nos: 26-30.
18. The library of editing vectors of claim 12, wherein the
survival marker gene is an antibiotic.
19. The library of editing vectors of claim 18, wherein the
antibiotic is selected from the group consisting of hygromycin,
blasticidin, kanamycin, and nourseothricin.
20. The library of editing vectors of claim 12, wherein the first
and second non-minimal or non-core constitutive or inducible
promoters are the same.
21. The library of editing vectors of claim 12, wherein the first
and second non-minimal or non-core constitutive or inducible
promoters are different.
Description
RELATED CASES
[0001] This application is a continuation of U.S. Ser. No.
17/140,056, filed 2 Jan. 2021, entitled "Increased Nucleic-Acid
Guided Cell Editing in Yeast", now allowed; which is a continuation
of U.S. Ser. No. 16/904,405, filed 17 Jun. 2020, entitled
"Increased Nucleic-Acid Guided Cell Editing in Yeast", now U.S.
Pat. No. 10,927,385; which claims priority to U.S. Ser. No.
62/866,041 filed 25 Jun. 2019.
INCORPORATION BY REFERENCE
[0002] Submitted with the present application is an electronically
filed sequence listing via EFS-Web as an ASCII formatted sequence
listing, entitled "INSC041US3_SEQ_LIST", created Jun. 8, 2021, and
11 KB in size. The sequence listing is part of the specification
filed Jan. 2, 2021 and is incorporated by reference in its
entirety.
FIELD OF THE INVENTION
[0003] The present disclosure relates to methods and compositions
to increase the percentage of edited yeast cells in a cell
population using nucleic-acid guided editing, and automated
multi-module instruments for performing these methods and using
these compositions.
BACKGROUND OF THE INVENTION
[0004] In the following discussion certain articles and methods
will be described for background and introductory purposes. Nothing
contained herein is to be construed as an "admission" of prior art.
Applicant expressly reserves the right to demonstrate, where
appropriate, that the articles and methods referenced herein do not
constitute prior art under the applicable statutory provisions.
[0005] The ability to make precise, targeted changes to the genome
of living cells has been a long-standing goal in biomedical
research and development. Recently, various nucleases have been
identified that allow for manipulation of gene sequences; hence
gene function. The nucleases include nucleic acid-guided nucleases,
which enable researchers to generate permanent edits in live cells.
Of course, it is desirable to attain the highest editing rates
possible in a cell population; however, in many instances the
percentage of edited cells resulting from nucleic acid-guided
nuclease editing can be in the single digits.
[0006] There is thus a need in the art of nucleic acid-guided
nuclease editing for improved methods, compositions, modules and
instruments for increasing the efficiency of editing. The present
disclosure addresses this need.
SUMMARY OF THE INVENTION
[0007] This Summary is provided to introduce a selection of
concepts in a simplified form that are further described below in
the Detailed Description. This Summary is not intended to identify
key or essential features of the claimed subject matter, nor is it
intended to be used to limit the scope of the claimed subject
matter. Other features, details, utilities, and advantages of the
claimed subject matter will be apparent from the following written
Detailed Description including those aspects illustrated in the
accompanying drawings and defined in the appended claims.
[0008] The present disclosure relates to methods, compositions,
modules and automated multi-module cell processing instruments that
increase the efficiency nucleic-acid guided editing in a yeast cell
population.
[0009] Thus, in some embodiments there is provided an editing
vector for performing nucleic acid-guided nuclease editing in yeast
comprising: a yeast 2-.mu. backbone, a 2.mu. origin of replication;
a standard constitutive or inducible (e.g., non-minimal or
non-core) promoter driving transcription of a gRNA sequence and
donor DNA (HA) sequence followed by a terminator element 3' to the
gRNA and donor DNA sequences; a standard constitutive (e.g.,
non-minimal or non-core) promoter driving transcription of a coding
sequence for a degron-survival marker fusion gene followed by a
terminator element 3' to the degron-survival marker fusion gene; a
standard constitutive or inducible (e.g., non-minimal or non-core)
promoter driving transcription of a nuclease or nuclease fusion
coding sequence with a terminator element 5' to the nuclease coding
sequence; and an origin of replication for propagation of the
editing vector in bacteria.
[0010] In some aspects of this embodiment, the degron is an
ubiquitin-dependent degron and the degron is ubiquitin. In some
aspects, the survival marker is selected from the group of
hygromycin, blasticidin, nourseothricin or kanamycin.
[0011] Additionally there is provided in another embodiment an
editing vector for performing nucleic acid-guided nuclease editing
in yeast comprising: a yeast 2-.mu. backbone, a 2.mu. origin of
replication; a standard constitutive or inducible (e.g.,
non-minimal or non-core) promoter driving transcription of a gRNA
sequence and donor DNA (HA) sequence with followed by a terminator
element 3' to the gRNA and donor DNA sequences; a minimal promoter
driving transcription of a coding sequence for a survival marker
gene followed by a terminator element 3' to the survival marker
gene; a standard constitutive or inducible (e.g., non-minimal or
non-core) promoter driving transcription of a nuclease coding
sequence with a terminator element 5' to the nuclease or nuclease
fusion coding sequence; and an origin of replication for
propagation of the editing vector in bacteria.
[0012] In some aspects, the minimal promoter is the URA3-d
promoter, and in some aspects, the survival marker is selected from
the group of hygromycin, blasticidin, nourseothricin or kanamycin.
In other aspects, the minimal promoter is the pHIS3 promoter, the
pTRP1 promoter, the pLEU2 promoter, the pURA3 promoter, the pTEF1
promoter, or the pHXT7 promoter. In other aspects, the promoter is
a weak constitutive promoter such as the pSSA1 promoter, the pPDA1
promoter, the pCYC1 promoter, the pTPS1 promoter, or the pSSB1
promoter.
[0013] In yet another embodiment there is provided a method for
performing editing in yeast comprising: providing a population of
yeast cells; transforming the population of yeast cells with a
population of editing vectors, wherein each editing vector
comprises: a yeast 2-.mu. backbone, a 2.mu. origin of replication;
a standard constitutive or inducible (e.g., non-minimal or
non-core) promoter driving transcription of a gRNA sequence and
donor DNA (HA) sequence with followed by a terminator element 3' to
the gRNA and donor DNA sequences; a standard constitutive (e.g.,
non-minimal or non-core) promoter driving transcription of a coding
sequence for a degron-survival marker fusion gene followed by a
terminator element 3' to the degron-survival marker fusion gene; a
standard constitutive or inducible (e.g., non-minimal or non-core)
promoter driving transcription of a nuclease or nuclease fusion
coding sequence with a terminator element 5' to the nuclease coding
sequence; and an origin of replication for propagation of the
editing vector in bacteria; growing the transformed yeast cells in
selective medium to select for cells expressing a degron-survival
marker fusion protein; providing conditions to allow the
transformed yeast cells to edit nucleic acid sequences in the yeast
cells; and growing the edited yeast cells.
[0014] In some aspects, the degron portion of the degron-survival
marker fusion gene is selected from a Ura3-d degon, Ubi-R degron,
Ubi-M degron, Ubi-Q degron, Ubi-E degron, ZF1 degron, C-terminal
phosphodegron; Ts-degron; lt-degron; auxin inducible degron;
DD-degron, LID-degron; PSD degron, B-LID degron, and a TIPI
degron.
[0015] Also provided is a method for performing editing in yeast
comprising: providing a population of yeast cells; transforming the
population of yeast cells with a population of editing vectors,
wherein each editing vector comprises: a yeast 2-.mu. backbone, a
2.mu. origin of replication; a standard constitutive or inducible
(e.g., non-minimal or non-core) promoter driving transcription of a
gRNA sequence and donor DNA (HA) sequence with followed by a
terminator element 3' to the gRNA and donor DNA sequences; a
minimal promoter driving transcription of a coding sequence for a
survival marker gene followed by a terminator element 3' to the
survival marker gene; a standard constitutive or inducible (e.g.,
non-minimal or non-core) promoter driving transcription of a
nuclease or nuclease fusion coding sequence with a terminator
element 5' to the nuclease coding sequence; and an origin of
replication for propagation of the editing vector in bacteria;
growing the transformed yeast cells in selective medium to select
for cells expressing a survival marker protein; providing
conditions to allow the transformed yeast cells to edit nucleic
acid sequences in the yeast cells; and growing the edited yeast
cells.
[0016] These aspects and other features and advantages of the
invention are described below in more detail.
BRIEF DESCRIPTION OF THE DRAWINGS
[0017] The foregoing and other features and advantages of the
present invention will be more fully understood from the following
detailed description of illustrative embodiments taken in
conjunction with the accompanying drawings in which:
[0018] FIG. 1A is a representation of (i) a standard constitutive
promoter driving transcription of an antibiotic resistance gene and
(ii) a standard constitutive promoter driving transcription of an
antibiotic resistance gene fused at its N-terminus with a ubiquitin
peptide. FIG. 1B is a representation of (i) a standard constitutive
promoter driving transcription of an antibiotic resistance gene and
(ii) a minimal constitutive promoter driving transcription of an
antibiotic resistance gene. FIG. 1C is an exemplary vector map of a
yeast 2-.mu. plasmid configured for nucleic acid-guided nuclease
editing of a yeast genome, where an antibiotic resistance gene is
fused at its 5' end to a degron coding sequence. FIG. 1D is an
exemplary vector map of a yeast 2-.mu. plasmid configured for
nucleic acid-guided nuclease editing of a yeast genome, where the
transcription of an antibiotic resistance gene is driven by a
minimal constitutive promoter.
[0019] FIGS. 2A-2C depict three different views of an exemplary
automated multi-module cell processing instrument for performing
nucleic acid-guided nuclease editing.
[0020] FIG. 3A depicts one embodiment of a rotating growth vial for
use with the cell growth module described herein and in relation to
FIGS. 3B-3D. FIG. 3B illustrates a perspective view of one
embodiment of a rotating growth vial in a cell growth module
housing. FIG. 3C depicts a cut-away view of the cell growth module
from FIG. 3B. FIG. 3D illustrates the cell growth module of FIG. 3B
coupled to LED, detector, and temperature regulating
components.
[0021] FIG. 4A depicts retentate (top) and permeate (middle)
members for use in a tangential flow filtration module (e.g., cell
growth and/or concentration module), as well as the retentate and
permeate members assembled into a tangential flow assembly
(bottom). FIG. 4B depicts two side perspective views of a reservoir
assembly of a tangential flow filtration module. FIGS. 4C-4E depict
an exemplary top, with fluidic and pneumatic ports and gasket
suitable for the reservoir assemblies shown in FIG. 4B.
[0022] FIGS. 5A and 5B depict the structure and components of an
embodiment of a reagent cartridge. FIG. 5C is a top perspective
view of one embodiment of an exemplary flow-through electroporation
device that may be part of a reagent cartridge. FIG. 5D depicts a
bottom perspective view of one embodiment of an exemplary
flow-through electroporation device that may be part of a reagent
cartridge. FIGS. 5E-5G depict a top perspective view, a top view of
a cross section, and a side perspective view of a cross section of
an FTEP device useful in a multi-module automated cell processing
instrument such as that shown in FIGS. 2A-2C.
[0023] FIG. 6A depicts a simplified graphic of a workflow for
singulating, editing and normalizing cells in a solid wall device.
FIG. 6B is a photograph of a solid wall device with a permeable
bottom on agar, on which yeast cells have been singulated and grown
into clonal colonies. FIG. 6C presents photographs of yeast colony
growth at various time points. FIGS. 6D-6F depict an embodiment of
a solid wall isolation incubation and normalization (SWIIN) module.
FIG. 6G depicts the embodiment of the SWIIN module in FIGS. 6D-6F
further comprising a heater and a heated cover.
[0024] FIG. 7 is a simplified block diagram of an embodiment of an
exemplary automated multi-module cell processing instrument
comprising a solid wall singulation/growth/editing/normalization
module for recursive yeast cell editing.
[0025] FIG. 8 is a simplified process diagram of an alternative
embodiment of an exemplary automated multi-module cell processing
instrument useful for recursive yeast cell editing.
[0026] FIG. 9 is a graph demonstrating real-time monitoring of
growth of S. cerevisiae str. s288c cell culture OD.sub.600
employing the cell growth device as described in relation to FIGS.
3A-3D where a 2-paddle rotating growth vial was used.
[0027] FIG. 10 is a graph plotting filtrate conductivity against
filter processing time for a yeast culture processed in the cell
concentration device/module described in relation to FIGS.
4A-4E.
[0028] FIG. 11 is a bar graph showing the results of
electroporation of S. cerevisiae str. s288c using an FTEP device as
described in relation to FIGS. 5C-5G and a comparator
electroporation method.
[0029] FIGS. 12A-12C comprise three graphs comparing the editing
clonality obtained using a yeast editing vector with an unmodified
hygromycin resistance gene, a degron-fused hygromycin resistance
gene, and a hygromycin resistance gene under the control of a
minimal promoter.
[0030] FIGS. 13A-13C comprise three graphs comparing the editing
clonality obtained using a yeast editing vector with an unmodified
G418 resistance gene, a degron-fused G418 resistance gene, and G418
resistance gene under the control of a minimal promoter.
[0031] FIG. 14 shows plasmid copy number and edit rate of various
plasmid constructs and their edit rates.
[0032] It should be understood that the drawings are not
necessarily to scale, and that like reference numbers refer to like
features.
DETAILED DESCRIPTION
[0033] All of the functionalities described in connection with one
embodiment of the methods, devices or instruments described herein
are intended to be applicable to the additional embodiments of the
methods, devices and instruments described herein except where
expressly stated or where the feature or function is incompatible
with the additional embodiments. For example, where a given feature
or function is expressly described in connection with one
embodiment but not expressly mentioned in connection with an
alternative embodiment, it should be understood that the feature or
function may be deployed, utilized, or implemented in connection
with the alternative embodiment unless the feature or function is
incompatible with the alternative embodiment.
[0034] The practice of the techniques described herein may employ,
unless otherwise indicated, conventional techniques and
descriptions of molecular biology (including recombinant
techniques), cell biology, biochemistry, and genetic engineering
technology, which are within the skill of those who practice in the
art. Such conventional techniques and descriptions can be found in
standard laboratory manuals such as Green and Sambrook, Molecular
Cloning: A Laboratory Manual. 4th, ed., Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y., (2014); Current
Protocols in Molecular Biology, Ausubel, et al. eds., (2017);
Neumann, et al., Electroporation and Electrofusion in Cell Biology,
Plenum Press, New York, 1989; and Chang, et al., Guide to
Electroporation and Electrofusion, Academic Press, California
(1992), all of which are herein incorporated in their entirety by
reference for all purposes. Nucleic acid-guided nuclease techniques
can be found in, e.g., Genome Editing and Engineering from TALENs
and CRISPRs to Molecular Surgery, Appasani and Church (2018); and
CRISPR: Methods and Protocols, Lindgren and Charpentier (2015);
both of which are herein incorporated in their entirety by
reference for all purposes.
[0035] Note that as used herein and in the appended claims, the
singular forms "a," "an," and "the" include plural referents unless
the context clearly dictates otherwise. Thus, for example,
reference to "a cell" refers to one or more cells, and reference to
"the system" includes reference to equivalent steps, methods and
devices known to those skilled in the art, and so forth.
Additionally, it is to be understood that terms such as "left,"
"right," "top," "bottom," "front," "rear," "side," "height,"
"length," "width," "upper," "lower," "interior," "exterior,"
"inner," "outer" that may be used herein merely describe points of
reference and do not necessarily limit embodiments of the present
disclosure to any particular orientation or configuration.
Furthermore, terms such as "first," "second," "third," etc., merely
identify one of a number of portions, components, steps,
operations, functions, and/or points of reference as disclosed
herein, and likewise do not necessarily limit embodiments of the
present disclosure to any particular configuration or
orientation.
[0036] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art to which this invention belongs. All
publications mentioned herein are incorporated by reference for the
purpose of describing and disclosing devices, formulations and
methodologies that may be used in connection with the presently
described invention.
[0037] Where a range of values is provided, it is understood that
each intervening value, between the upper and lower limit of that
range and any other stated or intervening value in that stated
range is encompassed within the invention. The upper and lower
limits of these smaller ranges may independently be included in
smaller ranges, and are also encompassed within the invention,
subject to any specifically excluded limit in the stated range.
Where the stated range includes one or both of the limits, ranges
excluding either or both of those included limits are also included
in the invention.
[0038] In the following description, numerous specific details are
set forth to provide a more thorough understanding of the present
invention. However, it will be apparent to one of skill in the art
that the present invention may be practiced without one or more of
these specific details. In other instances, features and procedures
well known to those skilled in the art have not been described in
order to avoid obscuring the invention. The terms used herein are
intended to have the plain and ordinary meaning as understood by
those of ordinary skill in the art.
[0039] The term "complementary" as used herein refers to
Watson-Crick base pairing between nucleotides and specifically
refers to nucleotides hydrogen-bonded to one another with thymine
or uracil residues linked to adenine residues by two hydrogen bonds
and cytosine and guanine residues linked by three hydrogen bonds.
In general, a nucleic acid includes a nucleotide sequence described
as having a "percent complementarity" or "percent homology" to a
specified second nucleotide sequence. For example, a nucleotide
sequence may have 80%, 90%, or 100% complementarity to a specified
second nucleotide sequence, indicating that 8 of 10, 9 of 10 or 10
of 10 nucleotides of a sequence are complementary to the specified
second nucleotide sequence. For instance, the nucleotide sequence
3'-TCGA-5' is 100% complementary to the nucleotide sequence
5'-AGCT-3'; and the nucleotide sequence 3'-TCGA-5' is 100%
complementary to a region of the nucleotide sequence
5'-TAGCTG-3'.
[0040] The term DNA "control sequences" refers collectively to
promoter sequences, polyadenylation signals, transcription
termination sequences, upstream regulatory domains, origins of
replication, internal ribosome entry sites, nuclear localization
sequences, enhancers, and the like, which collectively provide for
the replication, transcription and translation of a coding sequence
in a recipient cell. Not all of these types of control sequences
need to be present so long as a selected coding sequence is capable
of being replicated, transcribed and--for some
components--translated in an appropriate host cell.
[0041] As used herein the term "donor DNA" or "donor nucleic acid"
refers to nucleic acid that is designed to introduce a DNA sequence
modification (insertion, deletion, substitution) into a locus
(e.g., a target genomic DNA sequence or cellular target sequence)
by homologous recombination using nucleic acid-guided nucleases.
For homology-directed repair, the donor DNA must have sufficient
homology to the regions flanking the "cut site" or site to be
edited in the genomic target sequence. The length of the homology
arm(s) will depend on, e.g., the type and size of the modification
being made. In many instances and preferably, the donor DNA will
have two regions of sequence homology (e.g., two homology arms) to
the genomic target locus. Preferably, an "insert" region or "DNA
sequence modification" region--the nucleic acid modification that
one desires to be introduced into a genome target locus in a
cell--will be located between two regions of homology. The DNA
sequence modification may change one or more bases of the target
genomic DNA sequence at one specific site or multiple specific
sites. A change may include changing 1, 2, 3, 4, 5, 10, 15, 20, 25,
30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 or more base
pairs of the genomic target sequence. A deletion or insertion may
be a deletion or insertion of 1, 2, 3, 4, 5, 10, 15, 20, 25, 30,
40, 50, 75, 100, 150, 200, 300, 400, or 500 or more base pairs of
the genomic target sequence.
[0042] The terms "editing cassette", "CREATE cassette" or "CREATE
editing cassette" refers to a nucleic acid molecule comprising a
coding sequence for transcription of a guide nucleic acid or gRNA
covalently linked to a coding sequence for transcription of a donor
DNA or homology arm.
[0043] As used herein, "enrichment" refers to enriching for edited
cells by singulation, inducing editing, and growth of singulated
cells into terminal-sized colonies (e.g., saturation or
normalization of colony growth).
[0044] The terms "guide nucleic acid" or "guide RNA" or "gRNA"
refer to a polynucleotide comprising 1) a guide sequence capable of
hybridizing to a genomic target locus, and 2) a scaffold sequence
capable of interacting or complexing with a nucleic acid-guided
nuclease.
[0045] "Homology" or "identity" or "similarity" refers to sequence
similarity between two peptides or, more often in the context of
the present disclosure, between two nucleic acid molecules. The
term "homologous region" or "homology arm" refers to a region on
the donor DNA with a certain degree of homology with the target
genomic DNA sequence. Homology can be determined by comparing a
position in each sequence which may be aligned for purposes of
comparison. When a position in the compared sequence is occupied by
the same base or amino acid, then the molecules are homologous at
that position. A degree of homology between sequences is a function
of the number of matching or homologous positions shared by the
sequences.
[0046] "Operably linked" refers to an arrangement of elements where
the components so described are configured so as to perform their
usual function. Thus, control sequences operably linked to a coding
sequence are capable of effecting the transcription, and in some
cases, the translation, of a coding sequence. The control sequences
need not be contiguous with the coding sequence so long as they
function to direct the expression of the coding sequence. Thus, for
example, intervening untranslated yet transcribed sequences can be
present between a promoter sequence and the coding sequence and the
promoter sequence can still be considered "operably linked" to the
coding sequence. In fact, such sequences need not reside on the
same contiguous DNA molecule (i.e. chromosome) and may still have
interactions resulting in altered regulation.
[0047] As used herein, the terms "protein" and "polypeptide" are
used interchangeably. Proteins may or may not be made up entirely
of amino acids.
[0048] A "promoter" or "promoter sequence" is a DNA regulatory
region capable of binding RNA polymerase and initiating
transcription of a polynucleotide or polypeptide coding sequence
such as messenger RNA, ribosomal RNA, small nuclear or nucleolar
RNA, guide RNA, or any kind of RNA transcribed by any class of any
RNA polymerase I, II or III. Promoters may be constitutive or
inducible.
[0049] As used herein the term "selectable marker" refers to a gene
introduced into a cell, which confers a trait suitable for
artificial selection. General use selectable markers are well-known
to those of ordinary skill in the art. Drug selectable markers such
as ampicillin/carbenicillin, kanamycin, nourseothricin N-acetyl
transferase, chloramphenicol, erythromycin, tetracycline,
gentamicin, bleomycin, streptomycin, rifampicin, puromycin,
hygromycin, blasticidin, and G418 may be employed. In other
embodiments, selectable markers include, but are not limited to
sugars such as rhamnose. human nerve growth factor receptor
(detected with a MAb, such as described in U.S. Pat. No.
6,365,373); truncated human growth factor receptor (detected with
MAb); mutant human dihydrofolate reductase (DHFR; fluorescent MTX
substrate available); secreted alkaline phosphatase (SEAP;
fluorescent substrate available); human thymidylate synthase (TS;
confers resistance to anti-cancer agent fluorodeoxyuridine); herpes
simplex virus thymidine kinase (enables negative selection in yeast
by 5-Fluoro-2'-deoxyuridine); human glutathione S-transferase alpha
(GSTA1; conjugates glutathione to the stem cell selective alkylator
busulfan; chemoprotective selectable marker in CD34+ cells); CD24
cell surface antigen in hematopoietic stem cells; human CAD gene to
confer resistance to N-phosphonacetyl-L-aspartate (PALA); human
multi-drug resistance-1 (MDR-1; P-glycoprotein surface protein
selectable by increased drug resistance or enriched by FACS); human
CD25 (IL-2.alpha.; detectable by Mab-FITC); Methylguanine-DNA
methyltransferase (MGMT; selectable by carmustine); and Cytidine
deaminase (CD; selectable by Ara-C). "Selective medium" as used
herein refers to cell growth medium to which has been added a
chemical compound or biological moiety that selects for or against
selectable markers
[0050] As used herein the term "survival marker" refers to a gene
introduced into a cell which confers to that cell the ability to
survive growth in a selective medium.
[0051] The term "specifically binds" as used herein includes an
interaction between two molecules, e.g., an engineered peptide
antigen and a binding target, with a binding affinity represented
by a dissociation constant of about 10.sup.-7 M, about 10.sup.-8 M,
about 10.sup.-9 M, about 10.sup.-10 M, about 10.sup.-11M, about
10.sup.-12M, about 10.sup.-13M, about 10.sup.-14M or about
10.sup.-15 M.
[0052] The terms "target genomic DNA sequence", "cellular target
sequence", "target sequence", or "genomic target locus" refer to
any locus in vitro or in vivo, or in a nucleic acid (e.g., genome
or episome) of a cell or population of cells, in which a change of
at least one nucleotide is desired using a nucleic acid-guided
nuclease editing system. The target sequence can be a genomic locus
or extrachromosomal locus.
[0053] The term "variant" may refer to a polypeptide or
polynucleotide that differs from a reference polypeptide or
polynucleotide but retains essential properties. A typical variant
of a polypeptide differs in amino acid sequence from another
reference polypeptide. Generally, differences are limited so that
the sequences of the reference polypeptide and the variant are
closely similar overall and, in many regions, identical. A variant
and reference polypeptide may differ in amino acid sequence by one
or more modifications (e.g., substitutions, additions, and/or
deletions). A variant of a polypeptide may be a conservatively
modified variant. A substituted or inserted amino acid residue may
or may not be one encoded by the genetic code (e.g., a non-natural
amino acid). A variant of a polypeptide may be naturally occurring,
such as an allelic variant, or it may be a variant that is not
known to occur naturally.
[0054] A "vector" is any of a variety of nucleic acids that
comprise a desired sequence or sequences to be delivered to and/or
expressed in a cell. Vectors are typically composed of DNA,
although RNA vectors are also available. Vectors include, but are
not limited to, plasmids, fosmids, phagemids, virus genomes,
synthetic chromosomes, and the like. The engine/editing vector for
yeast as described herein comprises a coding sequence for a
nuclease or nuclease fusion to be used in the nucleic acid-guided
nuclease systems; a donor nucleic acid, optionally including an
alteration to the cellular target sequence that prevents nuclease
binding at a PAM or spacer in the cellular target sequence after
editing has taken place; a coding sequence for a gRNA where the
gRNA is compatible with the nuclease or nuclease fusion; and a
coding sequence for a survival marker gene either fused to a coding
sequence for a degron or under transcriptional control of an
minimal promoter as described in more detail herein. Further, the
engine/editing vector may also and preferably does comprise a
barcode. In some embodiments, the engine vector and editing vector
may be separate. In this instance, the survival marker fused to a
degron or under transcriptional control of a minimal promoter is on
the editing vector comprising the gRNA and donor DNA. Further, the
engine and editing vectors (whether separate or combined) comprise
control sequences operably linked to, e.g., the nuclease coding
sequence, recombineering system coding sequences (if present),
donor nucleic acid, guide nucleic acid(s), and antibiotic
resistance gene(s).
Nuclease-Directed Genome Editing Generally
[0055] The automated instruments and methods described herein
perform nuclease-directed genome editing, introducing typically
tens, to hundreds, to thousands, to tens of thousands of edits to a
population of yeast cells. In some embodiments, recursive cell
editing is performed where edits are introduced in successive
rounds of editing. A nucleic acid-guided nuclease or nuclease
fusion complexed with an appropriate synthetic guide nucleic acid
in a cell can cut the genome of the cell at a desired location. The
guide nucleic acid helps the nucleic acid-guided nuclease or
nuclease fusion recognize and cut the DNA at a specific target
sequence (either a cellular target sequence or a curing target
sequence). By manipulating the nucleotide sequence of the guide
nucleic acid, the nucleic acid-guided nuclease or nuclease fusion
may be programmed to target any DNA sequence for cleavage as long
as an appropriate protospacer adjacent motif (PAM) is nearby. In
certain aspects, the nucleic acid-guided nuclease editing system
may use two separate guide nucleic acid molecules that combine to
function as a guide nucleic acid, e.g., a CRISPR RNA (crRNA) and
trans-activating CRISPR RNA (tracrRNA). In other aspects, the guide
nucleic acid may be a single guide nucleic acid that includes both
the crRNA and tracrRNA sequences.
[0056] In general, a guide nucleic acid (e.g., gRNA) complexes with
a compatible nucleic acid-guided nuclease or nuclease fusion and
can then hybridize with a target sequence, thereby directing the
nuclease to the target sequence. A guide nucleic acid can be DNA or
RNA; alternatively, a guide nucleic acid may comprise both DNA and
RNA. In some embodiments, a guide nucleic acid may comprise
modified or non-naturally occurring nucleotides. In cases where the
guide nucleic acid comprises RNA, the gRNA may be encoded by a DNA
sequence on a polynucleotide molecule such as a plasmid, linear
construct, or the coding sequence may and preferably does reside
within an editing cassette and is optionally under the control of
an inducible promoter as described below. For additional
information regarding "CREATE" editing cassettes, see U.S. Pat.
Nos. 9,982,278; 10,266,849; 10,240,167; 10,351,877; 10,364,442;
10,435,715; and 10,465,207 and U.S. Ser. Nos. 16/551,517;
16,773,618; and 16,773,712, all of which are incorporated by
reference herein.
[0057] A guide nucleic acid comprises a guide sequence, where the
guide sequence is a polynucleotide sequence having sufficient
complementarity with a target sequence to hybridize with the target
sequence and direct sequence-specific binding of a complexed
nucleic acid-guided nuclease or nuclease fusion to the target
sequence. The degree of complementarity between a guide sequence
and the 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. In some embodiments, a guide sequence is
about or more than about 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 nucleotides in
length. Preferably the guide sequence is 10-30 or 15-20 nucleotides
long, or 15, 16, 17, 18, 19, or 20 nucleotides in length.
[0058] In the present methods and compositions, the guide nucleic
acids are provided as a sequence to be expressed from a plasmid or
vector and comprises both the guide sequence and the scaffold
sequence as a single transcript optionally under the control of an
inducible promoter. The guide nucleic acids are engineered to
target a desired target sequence (either cellular target sequence
or curing target sequence) by altering the guide sequence so that
the guide sequence is complementary to a desired target sequence,
thereby allowing hybridization between the guide sequence and the
target sequence. In general, to generate an edit in the target
sequence, the gRNA/nuclease complex binds to a target sequence as
determined by the guide RNA, and the nuclease or nuclease fusion
recognizes a protospacer adjacent motif (PAM) sequence adjacent to
the target sequence. The target sequence can be any polynucleotide
endogenous or exogenous to a yeast cell, or in vitro. For example,
the target sequence can be a polynucleotide residing in the nucleus
of any eukaryotic cell. A target sequence can be a sequence
encoding a gene product (e.g., a protein) or a non-coding sequence
(e.g., a regulatory polynucleotide, an intron, a PAM, or "junk"
DNA).
[0059] The guide nucleic acid may be and preferably is part of an
editing cassette that encodes the donor nucleic acid that targets a
cellular target sequence. Alternatively, the guide nucleic acid may
not be part of the editing cassette and instead may be encoded on
the editing vector backbone. For example, a sequence coding for a
guide nucleic acid can be assembled or inserted into a vector
backbone first, followed by insertion of the donor nucleic acid in,
e.g., an editing cassette. In other cases, the donor nucleic acid
in, e.g., an editing cassette can be inserted or assembled into a
vector backbone first, followed by insertion of the sequence coding
for the guide nucleic acid. Preferably, the sequence encoding the
guide nucleic acid and the donor nucleic acid are located together
in a rationally-designed editing cassette and are simultaneously
inserted or assembled into a vector backbone to create an editing
vector. In yet other embodiments, the sequence encoding the guide
nucleic acid and the sequence encoding the donor nucleic acid are
both included in the editing cassette.
[0060] The target sequence is associated with a proto-spacer
mutation (PAM), which is a short nucleotide sequence recognized by
the gRNA/nuclease complex. The precise preferred PAM sequence and
length requirements for different nucleic acid-guided nucleases or
nuclease fusions vary; however, PAMs typically are 2-7 base-pair
sequences adjacent or in proximity to the target sequence and,
depending on the nuclease, can be 5' or 3' to the target sequence.
Engineering of the PAM-interacting domain of a nucleic acid-guided
nuclease or nuclease fusion may allow for alteration of PAM
specificity, improve target site recognition fidelity, decrease
target site recognition fidelity, or increase the versatility of a
nucleic acid-guided nuclease or nuclease fusion.
[0061] In certain embodiments, the genome editing of a cellular
target sequence both introduces a desired DNA change to a cellular
target sequence, e.g., the genomic DNA of a cell, and removes,
mutates, or renders inactive a proto-spacer mutation (PAM) region
in the cellular target sequence. Rendering the PAM at the cellular
target sequence inactive precludes additional editing of the cell
genome at that cellular target sequence, e.g., upon subsequent
exposure to a nucleic acid-guided nuclease complexed with a
synthetic guide nucleic acid in later rounds of editing. Thus,
cells having the desired cellular target sequence edit and an
altered PAM can be selected for by using a nucleic acid-guided
nuclease or nuclease fusion complexed with a synthetic guide
nucleic acid complementary to the cellular target sequence. Cells
that did not undergo the first editing event will be cut rendering
a double-stranded DNA break, and thus will not continue to be
viable. The cells containing the desired cellular target sequence
edit and PAM alteration will not be cut, as these edited cells no
longer contain the necessary PAM site and will continue to grow and
propagate.
[0062] The range of target sequences that nucleic acid-guided
nucleases or nuclease fusions can recognize is constrained by the
need for a specific PAM to be located near the desired target
sequence. As a result, it often can be difficult to target edits
with the precision that is necessary for genome editing. It has
been found that nucleases and nuclease fusions can recognize some
PAMs very well (e.g., canonical PAMs), and other PAMs less well or
poorly (e.g., non-canonical PAMs). Because the methods disclosed
herein allow for identification of edited cells in a background of
unedited cells, the methods allow for identification of edited
cells where the PAM is less than optimal; that is, the methods for
identifying edited cells herein allow for identification of edited
cells even if editing efficiency is very low. Additionally, the
present methods expand the scope of target sequences that may be
edited since edits are more readily identified, including cells
where the genome edits are associated with less functional
PAMs.
[0063] As for the nuclease or nuclease fusion component of the
nucleic acid-guided nuclease editing system, a polynucleotide
sequence encoding the nucleic acid-guided nuclease or nuclease
fusion can be codon optimized for expression in particular cell
types, such as yeast cells. The choice of nucleic acid-guided
nuclease or nuclease fusion to be employed depends on many factors,
such as what type of edit is to be made in the target sequence and
whether an appropriate PAM is located close to the desired target
sequence. Nucleases of use in the methods described herein include
but are not limited to Cas 9, Cas 12/CpfI, MAD2, or MAD7 or other
MADzymes. Nuclease fusion enzymes typically comprise a CRISPR
nucleic acid-guided nuclease engineered to cut one DNA strand in
the target DNA rather than making a double-stranded cut, and the
nuclease portion is fused to a reverse transcriptase. For more
information on nickases and nuclease fusion editing see U.S. Ser.
Nos. 16/740,418; 16/740,420 and 16/740,421, all filed 11 Jan. 2020.
As with the guide nucleic acid, the nuclease or nuclease fusion is
encoded by a DNA sequence on a vector and may be under the control
of an inducible promoter. In some embodiments, the promoter may be
separate from but the same as the promoter controlling
transcription of the guide nucleic acid; that is, a separate
promoter drives the transcription of the nuclease or nuclease
fusion and guide nucleic acid sequences but the two promoters may
be the same type of promoter. Alternatively, the promoter
controlling expression of the nuclease or nuclease fusion may be
different from the promoter controlling transcription of the guide
nucleic acid; that is, e.g., the nuclease may be under the control
of, e.g., the pCYC1 promoter, and the guide nucleic acid may be
under the control of the, e.g., SNR52 promoter.
[0064] Another component of the nucleic acid-guided nuclease system
is the donor nucleic acid comprising homology to the cellular
target sequence. The donor nucleic acid is on the same vector and
even in the same editing cassette as the guide nucleic acid and
preferably is (but not necessarily is) under the control of the
same promoter as the editing gRNA (that is, a single promoter
driving the transcription of both the editing gRNA and the donor
nucleic acid). The donor nucleic acid is designed to serve as a
template for homologous recombination with a cellular target
sequence nicked or cleaved by the nucleic acid-guided nuclease as a
part of the gRNA/nuclease complex. A donor nucleic acid
polynucleotide may be of any suitable length, such as about or more
than about 20, 25, 50, 75, 100, 150, 200, 500, or 1000 nucleotides
in length. In certain preferred aspects, the donor nucleic acid can
be provided as an oligonucleotide of between 20-300 nucleotides,
more preferably between 50-250 nucleotides. The donor nucleic acid
comprises a region that is complementary to a portion of the
cellular target sequence (e.g., a homology arm). When optimally
aligned, the donor nucleic acid overlaps with (is complementary to)
the cellular target sequence by, e.g., about 20, 25, 30, 35, 40,
50, 60, 70, 80, 90 or more nucleotides. In many embodiments, the
donor nucleic acid comprises two homology arms (regions
complementary to the cellular target sequence) flanking the
mutation or difference between the donor nucleic acid and the
cellular target sequence. The donor nucleic acid comprises at least
one mutation or alteration compared to the cellular target
sequence, such as an insertion, deletion, modification, or any
combination thereof compared to the cellular target sequence.
[0065] As noted supra, the donor nucleic acid is preferably
provided as part of a rationally-designed editing cassette or
CREATE cassette, which is inserted into an editing vector backbone
where the editing vector backbone may comprise a promoter driving
transcription of the editing gRNA and the donor DNA. Moreover,
there may be more than one, e.g., two, three, four, or more
gRNA/donor nucleic acid pairs inserted into an editing vector
(alternatively, a single rationally-designed editing cassette may
comprise two to several editing gRNA/donor DNA pairs), where each
editing gRNA is under the control of separate different promoters,
separate like promoters, or where all gRNAs/donor nucleic acid
pairs are under the control of a single promoter. In some
embodiments the promoter driving transcription of the editing gRNA
and the donor nucleic acid (or driving more than one editing
gRNA/donor nucleic acid pair) is optionally an inducible promoter
and the promoter driving transcription of the nuclease optionally
is an inducible promoter as well. In some embodiments and
preferably, the nuclease and editing gRNA/donor DNA are under the
control of the same promoter.
[0066] Inducible editing is advantageous in that singulated cells
can be grown for several to many cell doublings before editing is
initiated, which increases the likelihood that cells with edits
will survive, as the double-strand cuts caused by active editing
are largely toxic to the cells. This toxicity results both in cell
death in the edited colonies, as well as possibly a lag in growth
for the edited cells that do survive but must repair and recover
following editing. However, once the edited cells have a chance to
recover, the size of the colonies of the edited cells will
eventually catch up to the size of the colonies of unedited
cells.
[0067] In addition to the donor nucleic acid, an editing cassette
may comprise one or more primer sites. The primer sites can be used
to amplify the editing cassette by using oligonucleotide primers;
for example, if the primer sites flank one or more of the other
components of the editing cassette.
[0068] Also, as described above, the donor nucleic acid may
comprise--in addition to the at least one mutation relative to a
cellular target sequence--one or more PAM sequence alterations that
mutate, delete or render inactive the PAM site in the cellular
target sequence. The PAM sequence alteration in the cellular target
sequence renders the PAM site "immune" to the nucleic acid-guided
nuclease and protects the cellular target sequence from further
editing in subsequent rounds of editing if the same nuclease is
used.
[0069] In addition, the editing cassette may comprise a barcode. A
barcode is a unique DNA sequence that corresponds to the donor DNA
sequence such that the barcode can identify the edit made to the
corresponding cellular target sequence. The barcode typically
comprises four or more nucleotides. In some embodiments, the
editing cassettes comprise a collection or library editing gRNAs
and of donor nucleic acids representing, e.g., gene-wide or
genome-wide libraries of editing gRNAs and donor nucleic acids. The
library of editing cassettes is cloned into vector backbones where,
e.g., each different donor nucleic acid is associated with a
different barcode.
[0070] Additionally, in some embodiments, an editing vector or
plasmid encoding components of the nucleic acid-guided nuclease
system further encodes a nucleic acid-guided nuclease 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 engineered nuclease comprises NLSs at or near
the amino-terminus, NLSs at or near the carboxy-terminus, or a
combination.
[0071] The editing vector comprises (or, if the engine and editing
vector are separate, both the engine and editing vectors comprise)
control sequences operably linked to the component sequences to be
transcribed. As stated above, the promoters driving transcription
of one or more components of the nucleic acid-guided nuclease
editing system optionally are inducible.
Increasing Efficiency of Editing in Yeast
[0072] The present disclosure is drawn to increasing the efficiency
of nucleic acid-guided nuclease editing in yeast. It has been found
that two different approaches increase editing efficiency in yeast
by placing selective pressure on yeast cells to replicate a plasmid
or vector comprising the nuclease, guide nucleic acid (gRNA), and
donor DNA sequences. The first approach involves transforming yeast
cells with an editing plasmid or vector comprising a coding
sequence for a nuclease or nuclease fusion enzyme, a coding
sequence for a guide RNA (gRNA) compatible with the nuclease or
nuclease fusion enzyme, a coding sequence for a donor DNA, an
origin of replication, and a coding sequence for a fusion protein
comprising a coding sequence for a degron fused 5' to a coding
sequence for a survival marker (e.g., an antibiotic resistance
gene). This first approach results in destabilizing the survival
marker protein leading to a decreased half-life for the survival
marker protein. The second approach involves transforming yeast
cells with an editing plasmid or vector comprising a coding
sequence for a nuclease or nuclease fusion or nuclease fusion
enzyme, a coding sequence for a guide RNA (gRNA) compatible with
the nuclease enzyme, a coding sequence for a donor DNA, an origin
of replication, and a minimal promoter driving transcription of a
coding sequence for a survival marker. This second approach
decreases the level of transcription of the survival marker
gene.
[0073] As described above, the term "survival marker" refers to a
coding sequence for a gene product that allows a cell expressing
the gene product to survive in selective medium. That is, cells
expressing the survival marker gene product can grow and
proliferate in a selective medium and cells that do not express the
survival marker gene product cannot grow and proliferate in the
selective medium. Survival markers include the G418 resistance gene
(allowing cells expressing this gene to be able to grow in medium
containing G418), the blasticidin resistance gene (allowing cells
expressing this gene to be able to grow in medium containing
blasticidin), the nourseothricin acetyl transferase gene (allowing
cells expressing this gene to be able to grow in medium containing
nourseothricin) and the hygromycin resistance gene (allowing cells
expressing this gene to be able to grow in medium containing
hygromycin). The key to both approaches is that the yeast cells
transformed with the editing vector express the survival marker
protein allowing the yeast cells to grow in selective medium;
however, in these yeast cells the survival marker protein is
expressed at a low level--due to, in the first instance, a short
protein half-life, and due to, in the second instance, a low level
of transcription/translation of the survival marker protein--such
that selective pressure is placed on these yeast cells to increase
replication of the editing plasmid or vector thereby increasing the
number of copies of the nuclease, gRNA, and donor DNA present.
[0074] In the first approach, graphically depicted in FIG. 1A, a
coding sequence for a degron is fused to the 5' terminus of a
coding region for a survival marker, in this case an antibiotic
resistance gene ("AbxR"). The top-most construct (i) depicts the
antibiotic resistance gene (AbxR) under the control of a eukaryotic
constitutive promoter. A constitutive promoter driving
transcription of AbxR results in high protein expression (high
transcription of the antibiotic resistance gene and thus high
expression of the antibiotic resistance protein) and the antibiotic
resistance protein has a regular half-life. That is, survival
marker proteins typically are stable enough to sustain levels of
the protein required for normal growth under selective conditions.
Below the first construct is a second construct (ii) depicting the
antibiotic resistance gene (AbxR) fused at its 5' terminus to a
degron ("Ubi"), where the transcription of the degron-AbxR fusion
is under the control of a eukaryotic constitutive promoter (e.g.,
the same eukaryotic constitutive promoter as the first construct
(i)). Fusing the survival marker gene (AbxR) to a degron ("Ubi")
under constitutive expression results in high protein expression;
however, the degron promotes destabilization/degradation of the
AbxR protein.
[0075] A degron is a portion of a protein that is important in
regulation of protein degradation rates. Known degrons include
short amino acid sequences, structural motifs, and exposed amino
acids located anywhere in the protein. Degrons are present in a
variety of organisms, from the N-degrons first characterized in
yeast, to the PEST sequence of mouse ornithine decarboxylase.
Although there are many types of different degrons--and a high
degree of variability amongst them--degrons are all similar for
their involvement in regulating the rate of protein degradation.
Mechanisms of degradation are often deemed "ubiquitin dependent" or
"ubiquitin independent." Ubiquitin-dependent degrons are so named
because they are implicated in the polyubiquitination process for
targeting a protein to the proteasome. In contrast, ubiquitin
independent degrons are not necessary for polyubiquitination.
Ubiquitin is a small regulator protein consisting of 76 amino acids
and is found ubiquitously (hence the name) in most tissues of
eukaryotic organisms.
[0076] The addition of ubiquitin to a substrate protein (in this
case, a survival marker protein/antibiotic resistance protein) is
called ubiquitination and thereby marks the substrate protein for
degradation. Ubiquitin degron tags of use in the present methods
and compositions include Ubi-R, a 228 ubiquitin sequence with an
Arginine (R) appended on the 3' end; Ubi-M, a 228 bp ubiquitin
sequence with a Methionine (M) appended on the 3' end; Ubi-Q, a 228
bp ubiquitin sequence with a Glutamine (Q) appended on the 3' end;
and Ubi-E, a 228 bp ubiquitin sequence with a Methionine (M)
appended on the 3' end. In addition to the ubiquitin tags, are
ubiquitin independent degrons such as the ZF1 degron, a 36 amino
acid motif recognized by the SOCS-box protein ZIF-1, which binds to
the elongin C subunit of an ECS ubiquitin ligase complex; the
C-terminal phosphodegrons (CTPD) from the C. elegans OMA-1 protein;
and conditional degrons (e.g., inducible degrons) such as the
Ts-degron and lt-degrons, which are induced by temperature shift
and function when added to the N terminus of a coding protein; the
auxin inducible degron (AID), which is a small protein tag that
interacts with an F-Box ubiquitin ligase complex in the presence of
a small molecule called auxin; DD-based degrons, which are induced
by Shield-1 ligand binding; LID, which is induced by Shield-1
ligand binding and functions only when fused to the C-terminus of a
protein; the PSD and B-LID degrons, which are blue light inducible
degrons; and TIPI, which is a TEV protease expression induced
degron. (See, e.g., Chen, et al., Yeast Research, 12(5):598-607
(2012).)
[0077] In the present degron construct (ii) of FIG. 1A, a coding
sequence for a ubiquitin/N-degron tag ("Ubi") is fused to the
N-terminus of the coding sequence for the survival marker protein
(e.g., the antibiotic resistance gene "AbxR") resulting in a
Ubi-AbxR fusion protein. The ubiquitin/N-degron tag is cleaved off
the fusion protein in vivo (depicted by the "Pac Man"-like
element), generating a protein with an N-terminal amino acid other
than methionine. Certain destabilizing N-terminal amino acid
residues (primarily arginine) decrease the half-life of the protein
carrying the N-degron tag. Here, the ubiquitin tag is cleaved off,
exposing an arginine residue ("R") at the 5' terminus of the
survival marker/antibiotic resistance protein. When arginine ("R")
is exposed at the N-terminus of the survival marker protein, the
survival marker protein is degraded. Degradation of the survival
marker protein places selective pressure on the yeast cell in
selective medium; thus, the yeast cell must replicate the editing
plasmid or vector--that is, increase the plasmid copy number--in
order to survive. The increase in plasmid copy number leads to a
concurrent increase in the copy numbers of the expressed nuclease,
the transcribed gRNA, and the donor DNA.
[0078] FIG. 1B is a representation of (i) a standard constitutive
promoter driving an antibiotic resistance gene and (ii) a minimal
constitutive promoter driving an antibiotic resistance gene. As an
alternative to the approach of destabilizing the survival marker
protein to influence plasmid copy number shown in FIG. 1A, the
approach depicted in FIG. 1B influences plasmid copy number via the
expression level of the survival marker gene. It has been found
that expression levels of a protein can be down-regulated by using
inducible promoters and truncated or minimal (also termed "core")
promoters. Minimal or core promoters typically comprise the minimal
portion of a promoter required to properly initiate transcription,
including one or more of a transcription start site, a binding site
for RNA polymerase, a general transcription factor binding site
such as a TATA box or B recognition element, and a downstream core
promoter element (DPE). Often, the minimal promoter is located
between -35 to +35 of the transcription start site. Use of a
minimal promoter typically guarantees that there is always at least
a low amount of transcription of the target gene (in this case the
survival marker gene). Table 1 lists a number of exemplary minimal
constitutive promoters and Table 2 lists weak constitutive
promoters. (See, e.g., Natsuma and Kanemaki, Ann. Rev. Genetics,
51:83-102 (2017).)
TABLE-US-00001 TABLE 1 Minimal Promoters SEQ Promoter ID Name
Sequence No. Ura3-d TAACCCAACTGCACAGAACAAAAACCTGCAGGAAACGAAGATAAATC
1 pHIS3 ATTGGCATTATCACATAATGAATTATACATTATATAAAGTAATGTGATTTCTTC 2
(100 bp) GAAGAATATACTAAAAAATGAGCAGGCAAGATAAACGAAGGCAAAG pHIS3
CTTCGAAGAATATACTAAAAAATGAGCAGGCAAGATAAACGAAGGCAAAG 3 (50 bp) pHIS3
AATGAGCAGGCAAGATAAACGAAGGCAAAG 4 (30 bp) pHIS3 CAAGATAAACGAAGGCAAAG
5 (20 bp) pTRP1
TTCGGTCGAAAAAAGAAAAGGAGAGGGCCAAGAGGGAGGGCATTGGTGACTA 6 (100 bp)
TTGAGCACGTGAGTATACGTGATTAAGCACACAAAGGCAGCTTGGAGT pTRP1
TATTGAGCACGTGAGTATACGTGATTAAGCACACAAAGGCAGCTTGGAGT 7 (50 bp) pTRP1
GTGATTAAGCACACAAAGGCAGCTTGGAGT 8 (30 bp) pTRP1 ACACAAAGGCAGCTTGGAGT
9 (20 bp) pLEU2
TTTTCCAATAGGTGGTTAGCAATCGTCTTACTTTCTAACTTTTCTTACCTTTTAC 10 (100 bp)
ATTTCAGCAATATATATATATATATTTCAAGGATATACCATTCTA pLEU2
TTTACATTTCAGCAATATATATATATATATTTCAAGGATATACCATTCTA 11 (50 bp) pLEU2
ATATATATATTTCAAGGATATACCATTCTA 12 (30 bp) pLEU2
TTCAAGGATATACCATTCTA 13 (20 bp) pURA3
GGTATATATACGCATATGTGGTGTTGAAGAAACATGAAATTGCCCAGTATTCTT 14 (100 bp)
AACCCAACTGCACAGAACAAAAACCTGCAGGAAACGAAGATAAATC pURA3
TCTTAACCCAACTGCACAGAACAAAAACCTGCAGGAAACGAAGATAAATC 15 (50 bp) pURA3
ACAAAAACCTGCAGGAAACGAAGATAAATC 16 (30 bp) pURA3
GCAGGAAACGAAGATAAATC 17 (20 bp) pTEF1
TCAAGTTTCAGTTTCATTTTTCTTGTTCTATTACAACTTTTTTTACTTCTTGCTCA 18 (100
bp) TTAGAAAGAAAGCATAGCAATCTAATCTAAGTTTTAATTACAAA pTEF1
TGCTCATTAGAAAGAAAGCATAGCAATCTAATCTAAGTTTTAATTACAAA 19 (50 bp) pTEF1
TAGCAATCTAATCTAAGTTTTAATTACAAA 20 (30 bp) pTEF1
ATCTAAGTTTTAATTACAAA 21 (20 bp) pHXT7
TAAAATAATAAAACATCAAGAACAAACAAGCTCAACTTGTCTTTTCTAAGAAC 22 (100 bp)
AAAGAATAAACACAAAAACAAAAAGTTTTTTTAATTTTAATCAAAAA pHXT7
AACAAAGAATAAACACAAAAACAAAAAGTTTTTTTAATTTTAATCAAAAA 23 (50 bp) pHXT7
ACAAAAAGTTTTTTTAATTTTAATCAAAAA 24 (30 bp) pHXT7
TTTTTAATTTTAATCAAAAA 25 (20 bp)
TABLE-US-00002 TABLE 2 Weak Constitutive Promoters Promoter SEQ
Name Sequence ID No. pSSA1
TCGACAAATTGTTACGTTGTGCTTTGATTTCTAAAGCGCTTCTTCACCTGCAGGT 26
TCTGAGCCCTAAGAAAAAAAATTTCCTTGGTTGAAAATGGCGGAAAAAAAAAA
TTCAGAAAAAGAAATAAAGCACGTGTGCGCGGTGTGTGGATGATGGTTTCATC
ATTGTCAACGGCATTTTCGTTCTTGTGGATTGTTGTAAACTTTCCAGAACATTCT
AGAAAGAAAGCACACGGAACGTTTAGAAGCTGTCATTTGCGTTTTTTCTCCAG
ATTTTAGTTGAGAAAGTAATTAAATTATTCTTCTTTTTCCAGAACGTTCCATCGG
CGGCAAAAGGGAGAGAAAGAACCCAAAAAGAAGGGGGGCCATTTAGATTAGC
TGATCGTTTCGAGGACTTCAAGGTTATATAAGGGGTGGATTGATGTATCTTCGA
GAAGGGATTGAGTTGTAGTTTCGTTTCCCAATTCTTACTTAAGTTGTTTTATTTT
CTCTATTTGTAAGATAAGCACATCAAAAGAAAAGTAATCAAGTATTACAAGAA
ACAAAAATTCAAGTAAATAACAGATAAT pPDA1
GAAATTCAAAACTCTCCAGACAAAGCCTGCCATTTGGCCAAGCAAGCTTTTGA 27
CGACGCTATTGCTGAGTTGGACACTCTGTCTGAAGAATCATACAAAGATAGCA
CACTTATCATGCAACTGCTAAGGGACAATTTAACCTTATGGACTTCAGACATGT
CCGAGTCCGGTCAAGCTGAAGACCAACAACAACAACAACAACATCAGCAACA
GCAGCCACCTGCTGCCGCCGAAGGTGAAGCACCAAAGTAAGTATTCTGATAAA
TCTAAAGAGAAATTACTAAAAAAAAGAAAAAAAAAAGAACGGGGGTGTAATA
ATTTGTAGTTCATTATTGCAATTATATATCTATATCTATATATGTATATAACATT
AACATGTGCATGTACACACGTAATCGCGCGTGTACATGTCTATATGTGTTACTT
GAACTATACTGTTTTGACGTGTATGTTTATTTATCTCTCTTCTGATTCCTCCACC
CCTTCCTTACTCAACCGGGTAAATGTCGCATCATGACTCCCGACAATAATCCCC
TCTGGTATAGCGAGAAGCAACTTTAGCTTCTTAACGGCAAGAACTTTTTTATGT
TTGTCGCACCTGTATCTTCACAAAAGTTGGATACAGCAATAAGAAAGGAAACC ACATTTGTGCCA
pCYC1 AGAAAGATGTCAACTGAAAAAAAAAAAGGTGAACACAGGAAAAAAAATAAA 28
AAAAAAAAAAAAAAAAGGAGGACGAAACAAAAAAGTGAAAAAAAATGAAAA
TTTTTTTGGAAAACCAAGAAATGAATTATATTTCCGTGTGAGACGACATCGTCG
AATATGATTCAGGGTAACAGTATTGATGTAATCAATTTCCTACCTGAATCTAAA
ATTCCCGGGAGCAAGATCAAGATGTTTTCACCGATCTTTCCGGTCTCTTTGGCC
GGGGTTTACGGACGATGGCAGAAGACCAAAGCGCCAGTTCATTTGGCGAGCGT
TGGTTGGTGGATCAAGCCCACGCGTAGGCAATCCTCGAGCAGATCCGCCAGGC
GTGTATATATAGCGTGGATGGCCAGGCAACTTTAGTGCTGACACATACAGGCA
TATATATATGTGTGCGACGACACATGATCATATGGCATGCATGTGCTCTGTATG
TATATAAAACTCTTGTTTTCTTCTTTTCTCTAAATATTCTTTCCTTATACATTAGG
ACCTTTGCAGCATAAATTACTATACTTCTATAGACACACAAACACAAATACAC
ACACTAAATTAATA pTPS1
AACCCGGTCTCGAAGAACATCAGCACCACGCCCGCAACGACAAAGAACATTGC 29
AATACACTTGCATATGTGAGCATAGTCGAGCGGTCCGTTCTGTGGTTGATGCTG
TTGTTCTTTCTTCTGTTTGTCAGGGGTGATAGCCATATCTTCGTGCTCTTGTTGC
GATTGTTCTGTTCCATCTGCACCAGAACAAAGAACAAAAGAACAAGGAACAAA
GTCCAAGCACGTCAGCGCTGTTTATAAGGGGATTGACGAGGGATCGGGCCTAG
AGTGCCAGCGCGCCAGGGAGAGGGAGCCCCCTGGGCCCTCATCCGCAGGCTGA
TAGGGGTCACCCCGCTGGGCAGGTCAGGGCAGGGGCTCTCAGGGGGGCGCCAT
GGACAAACTGCACTGAGGTTCTAAGACACATGTATTATTGTGAGTATGTATATA
TAGAGAGAGATTAAGGCGTACAGCCGGGTGGTAGAGATTGATTAACTTGGTAG
TCTTATCTTGTCAATTGAGTTTCTGTCAGTTTCTTCTTGAACAAGCACGCAGCTA
AGTAAGCAACAAAGCAGGCTAACAAACTAGGTACTCACATACAGACTTATTAA GACATAGAACT
pSSB1 CAGAGGAGTACACACGGGACTTGATCGAACAGATCGTGTTACAGTTGCGCTCG 30
CAAAGAATGAAAATGGTTCAGACAAAGGATCAGTTCCTATTTATCTACCATGC
TGCCAAGTATCTTAACAGTCTTTCCGTGAACCAATAGACAGCTATATAAAAGTT
CCTAATTGTGCATTTTTTCAATAACAATACTTATTCATCCTTATAATTATATTCT
AGCTTCGTTGTCATGGGAACATAGCCCATACACCGCAGTTATTTATGATCATTT
CGAACGGGAAGTATGGATGAATCTTTTTTTTTTTTTTTTTATAGCACGCAACTG
AAAAAAAAAAAAAGAAAAATTTTTCATCTTCGCTCGACGTTTCTTTTGTAGTAC
TCATCTCTTTTTATATAAAGATTAATTAGTTATTGTCGCTTTGCTTTTCCTTCTTT
AAAAAATGTTTCTTGCTTTTGGATTTTCAGATGTCCCAAGATCATTACAGTATTT
TAATTGAACAAA
[0079] As noted in FIG. 1B at (i), the survival marker/antibiotic
resistance gene ("AbxR") under the control of a standard
constitutive promoter results in high protein expression, normal
protein half-life, and a low plasmid copy number. Again, because
the survival marker/antibiotic resistance gene is transcribed at a
high rate and thus the survival marker/antibiotic resistance
protein is expressed at a high rate, there is little to no
selective pressure on the yeast cell harboring the editing vector
or plasmid to increase replication of the editing vector or
plasmid, and thus there is no attendant increase in the expression
of the nuclease, transcription of the gRNA, or transcription of the
donor DNA.
[0080] However, in FIG. 1B at (ii), instead of a standard
constitutive promoter, a minimal promoter is used resulting in
reduced transcription of the survival marker/antibiotic resistance
gene ("AbxR"), and thus reduced expression of the survival
marker/antibiotic resistance protein. Here, because the survival
marker/antibiotic resistance gene is transcribed at a low rate and
thus the survival marker/antibiotic resistance protein is expressed
at a low rate, there is increased selective pressure on the yeast
cell harboring the editing vector or plasmid to increase
replication of the editing vector or plasmid. Increasing
replication of the plasmid not only allows the yeast cell to
survive, but additionally increases the expression of the nuclease,
transcription of the gRNA, and copies of the donor DNA.
[0081] FIG. 1C is an exemplary vector map of a yeast 2-.mu. plasmid
configured for nucleic acid-guided nuclease editing of a yeast
genome, where an antibiotic resistance gene is fused at its 5' end
to a degron. As described in relation to FIG. 1A, such an editing
plasmid or vector results in an increase in plasmid copy number in
the host yeast cell. Beginning at 12 o'clock, there is a 2.mu.
origin of replication; an SNR52 promoter driving transcription of a
gRNA and donor DNA (HA) with SNR52 terminator element; a standard
constitutive promoter driving transcription of a coding sequence
for a degron-antibiotic resistance fusion gene with a terminator; a
CYC1 promoter driving transcription of a CRISPR enzyme or nuclease
fusion coding sequence with a CYC1 terminator; an ampicillin
resistance gene to allow for selection in bacteria; and a pUC
origin of replication for propagation of the editing vector in
bacteria. As described above in relation to FIG. 1A, the fusion of
the degron to the survival maker protein results in degradation of
the survival marker protein, which in turn places selective
pressure on the yeast cell in selective medium; thus, the yeast
cell must replicate the editing plasmid or vector--that is,
increase the plasmid copy number--in order to survive. The
increased plasmid copy number leads to an increase in the copy
numbers of the expressed nuclease, the transcribed gRNA, and the
donor DNA.
[0082] FIG. 1D is an exemplary vector map of a yeast 2-.mu. plasmid
configured for nucleic acid-guided nuclease editing of a yeast
genome, where the expression of an antibiotic resistance gene is
driven by a minimal constitutive promoter. As described in relation
to FIG. 1B and like the vector depicted in FIG. 1C, this editing
plasmid or vector results in an increase in plasmid copy number in
the host yeast cell. Beginning at 12 o'clock, there is a 2.mu.
origin of replication; an SNR52 promoter driving transcription of a
gRNA and donor DNA (HA) with SNR52 terminator element; a minimal
promoter driving transcription of a coding sequence for an
antibiotic resistance gene with a terminator; a CYC1 promoter
driving transcription of a CRISPR enzyme or nuclease fusion coding
sequence with a CYC1 terminator; an ampicillin resistance gene to
allow for selection in bacteria; and a pUC origin of replication
for propagation of the editing vector in bacteria. Again, because
the survival marker/antibiotic resistance gene is transcribed at a
low rate and thus the survival marker/antibiotic resistance protein
is expressed at a low rate, there is increased selective pressure
on the yeast cell harboring the editing vector or plasmid to
increase replication of the vector or plasmid. Increasing
replication of the plasmid not only allows the yeast cell to
survive, but increases the expression of the nuclease,
transcription of the gRNA, and copies of the donor DNA.
Automated Cell Editing Instruments and Modules to Perform Nucleic
Acid-Guided Nuclease Editing in Yeast Cells
Automated Cell Editing Instruments
[0083] FIG. 2A depicts an exemplary automated multi-module cell
processing instrument 200 to, e.g., perform one of the exemplary
workflows for targeted gene editing of live yeast cells. The
instrument 200, for example, may be and preferably is designed as a
stand-alone desktop instrument for use within a laboratory
environment. The instrument 200 may incorporate a mixture of
reusable and disposable components for performing the various
integrated processes in conducting automated genome cleavage and/or
editing in cells without human intervention. Illustrated is a
gantry 202, providing an automated mechanical motion system
(actuator) (not shown) that supplies XYZ axis motion control to,
e.g., an automated (i.e., robotic) liquid handling system 258
including, e.g., an air displacement pipettor 232 which allows for
cell processing among multiple modules without human intervention.
In some automated multi-module cell processing instruments, the air
displacement pipettor 232 is moved by gantry 202 and the various
modules and reagent cartridges remain stationary; however, in other
embodiments, the liquid handling system 258 may stay stationary
while the various modules and reagent cartridges are moved. Also
included in the automated multi-module cell processing instrument
200 are reagent cartridges 210 comprising reservoirs 212 and
transformation module 230 (e.g., a flow-through electroporation
device as described in detail in relation to FIGS. 5B-5F), as well
as wash reservoirs 206, cell input reservoir 251 and cell output
reservoir 253. The wash reservoirs 206 may be configured to
accommodate large tubes, for example, wash solutions, or solutions
that are used often throughout an iterative process. Although two
of the reagent cartridges 210 comprise a wash reservoir 206 in FIG.
2A, the wash reservoirs instead could be included in a wash
cartridge where the reagent and wash cartridges are separate
cartridges. In such a case, the reagent cartridge 210 and wash
cartridge 204 may be identical except for the consumables (reagents
or other components contained within the various inserts) inserted
therein.
[0084] In some implementations, the reagent cartridges 210 are
disposable kits comprising reagents and cells for use in the
automated multi-module cell processing/editing instrument 200. For
example, a user may open and position each of the reagent
cartridges 210 comprising various desired inserts and reagents
within the chassis of the automated multi-module cell editing
instrument 200 prior to activating cell processing. Further, each
of the reagent cartridges 210 may be inserted into receptacles in
the chassis having different temperature zones appropriate for the
reagents contained therein.
[0085] Also illustrated in FIG. 2A is the robotic liquid handling
system 258 including the gantry 202 and air displacement pipettor
232. In some examples, the robotic handling system 258 may include
an automated liquid handling system such as those manufactured by
Tecan Group Ltd. of Mannedorf, Switzerland, Hamilton Company of
Reno, Nev. (see, e.g., WO2018015544A1), or Beckman Coulter, Inc. of
Fort Collins, Colo. (see, e.g., US20160018427A1). Pipette tips 215
may be provided in a pipette transfer tip supply 214 for use with
the air displacement pipettor 232.
[0086] Inserts or components of the reagent cartridges 210, in some
implementations, are marked with machine-readable indicia (not
shown), such as bar codes, for recognition by the robotic handling
system 258. For example, the robotic liquid handling system 258 may
scan one or more inserts within each of the reagent cartridges 210
to confirm contents. In other implementations, machine-readable
indicia may be marked upon each reagent cartridge 210, and a
processing system (not shown, but see element 237 of FIG. 2B) of
the automated multi-module cell editing instrument 200 may identify
a stored materials map based upon the machine-readable indicia. In
the embodiment illustrated in FIG. 2A, a cell growth module
comprises a cell growth vial 218 (described in greater detail below
in relation to FIGS. 3A-3D). Additionally seen is the TFF module
222 (described above in detail in relation to FIGS. 4A-4E). Also
illustrated as part of the automated multi-module cell processing
instrument 200 of FIG. 2A is a singulation module 240 (e.g., a
solid wall isolation, incubation and normalization device (SWIIN
device) is shown here) described herein in relation to FIGS. 6D-6G,
served by, e.g., robotic liquid handing system 258 and air
displacement pipettor 232. Additionally seen is a selection module
220. Also note the placement of three heatsinks 255.
[0087] FIG. 2B is a simplified representation of the contents of
the exemplary multi-module cell processing instrument 200 depicted
in FIG. 2A. Cartridge-based source materials (such as in reagent
cartridges 210), for example, may be positioned in designated areas
on a deck of the instrument 200 for access by an air displacement
pipettor 232. The deck of the multi-module cell processing
instrument 200 may include a protection sink such that contaminants
spilling, dripping, or overflowing from any of the modules of the
instrument 200 are contained within a lip of the protection sink.
Also seen are reagent cartridges 210, which are shown disposed with
thermal assemblies 211 which can create temperature zones
appropriate for different regions. Note that one of the reagent
cartridges also comprises a flow-through electroporation device 230
(FTEP), served by FTEP interface (e.g., manifold arm) and actuator
231. Also seen is TFF module 222 with adjacent thermal assembly
225, where the TFF module is served by TFF interface (e.g.,
manifold arm) and actuator 233. Thermal assemblies 225, 235, and
245 encompass thermal electric devices such as Peltier devices, as
well as heatsinks, fans and coolers. The rotating growth vial 218
is within a growth module 234, where the growth module is served by
two thermal assemblies 235. Selection module is seen at 220. Also
seen is the SWIIN module 240, comprising a SWIIN cartridge 241,
where the SWIIN module also comprises a thermal assembly 245,
illumination 243 (in this embodiment, backlighting), SWIIN cover
244, evaporation and condensation control 249, and where the SWIIN
module is served by SWIIN interface (e.g., manifold arm) and
actuator 247. Also seen in this view is touch screen display 201,
display actuator 203, illumination 205 (one on either side of
multi-module cell processing instrument 200), and cameras 239 (one
illumination device on either side of multi-module cell processing
instrument 200). Finally, element 237 comprises electronics, such
as circuit control boards, high-voltage amplifiers, power supplies,
and power entry; as well as pneumatics, such as pumps, valves and
sensors.
[0088] FIG. 2C illustrates a front perspective view of multi-module
cell processing instrument 200 for use in as a desktop version of
the automated multi-module cell editing instrument 200. For
example, a chassis 290 may have a width of about 24-48 inches, a
height of about 24-48 inches and a depth of about 24-48 inches.
Chassis 290 may be and preferably is designed to hold all modules
and disposable supplies used in automated cell processing and to
perform all processes required without human intervention; that is,
chassis 290 is configured to provide an integrated, stand-alone
automated multi-module cell processing instrument. As illustrated
in FIG. 2C, chassis 290 includes touch screen display 201, cooling
grate 264, which allows for air flow via an internal fan (not
shown). The touch screen display provides information to a user
regarding the processing status of the automated multi-module cell
editing instrument 200 and accepts inputs from the user for
conducting the cell processing. In this embodiment, the chassis 290
is lifted by adjustable feet 270a, 270b, 270c and 270d (feet
270a-270c are shown in this FIG. 2C). Adjustable feet 270a-270d,
for example, allow for additional air flow beneath the chassis
290.
[0089] Inside the chassis 290, in some implementations, will be
most or all of the components described in relation to FIGS. 2A and
2B, including the robotic liquid handling system disposed along a
gantry, reagent cartridges 210 including a flow-through
electroporation device, a rotating growth vial 218 in a cell growth
module 234, a tangential flow filtration module 222, a SWIIN module
240 as well as interfaces and actuators for the various modules. In
addition, chassis 290 houses control circuitry, liquid handling
tubes, air pump controls, valves, sensors, thermal assemblies
(e.g., heating and cooling units) and other control mechanisms. For
examples of multi-module cell editing instruments, see U.S. Pat.
Nos. 10,253,316; 10,329,559; 10,323,242; 10,421,959; 10,465,185;
10,519,437; 10,584,333; and 10,584,334 and U.S. Ser. No.
16/750,369, filed 23 Jan. 2020; Ser. No. 16/822,249, filed 18 Mar.
2020; and Ser. No. 16/837,985, filed 1 Apr. 2020, all of which are
herein incorporated by reference in their entirety.
The Rotating Cell Growth Module
[0090] FIG. 3A shows one embodiment of a rotating growth vial 300
for use with the cell growth device and in the automated
multi-module cell processing instruments described herein. The
rotating growth vial 300 is an optically-transparent container
having an open end 304 for receiving liquid media and cells, a
central vial region 306 that defines the primary container for
growing cells, a tapered-to-constricted region 318 defining at
least one light path 310, a closed end 316, and a drive engagement
mechanism 312. The rotating growth vial 300 has a central
longitudinal axis 320 around which the vial rotates, and the light
path 310 is generally perpendicular to the longitudinal axis of the
vial. The first light path 310 is positioned in the lower
constricted portion of the tapered-to-constricted region 318.
Optionally, some embodiments of the rotating growth vial 300 have a
second light path 308 in the tapered region of the
tapered-to-constricted region 318. Both light paths in this
embodiment are positioned in a region of the rotating growth vial
that is constantly filled with the cell culture (cells+growth
media) and are not affected by the rotational speed of the growth
vial. The first light path 310 is shorter than the second light
path 308 allowing for sensitive measurement of OD values when the
OD values of the cell culture in the vial are at a high level
(e.g., later in the cell growth process), whereas the second light
path 308 allows for sensitive measurement of OD values when the OD
values of the cell culture in the vial are at a lower level (e.g.,
earlier in the cell growth process).
[0091] The drive engagement mechanism 312 engages with a motor (not
shown) to rotate the vial. In some embodiments, the motor drives
the drive engagement mechanism 312 such that the rotating growth
vial 300 is rotated in one direction only, and in other
embodiments, the rotating growth vial 300 is rotated in a first
direction for a first amount of time or periodicity, rotated in a
second direction (i.e., the opposite direction) for a second amount
of time or periodicity, and this process may be repeated so that
the rotating growth vial 300 (and the cell culture contents) are
subjected to an oscillating motion. Further, the choice of whether
the culture is subjected to oscillation and the periodicity
therefor may be selected by the user. The first amount of time and
the second amount of time may be the same or may be different. The
amount of time may be 1, 2, 3, 4, 5, or more seconds, or may be 1,
2, 3, 4 or more minutes. In another embodiment, in an early stage
of cell growth the rotating growth vial 400 may be oscillated at a
first periodicity (e.g., every 60 seconds), and then a later stage
of cell growth the rotating growth vial 300 may be oscillated at a
second periodicity (e.g., every one second) different from the
first periodicity.
[0092] The rotating growth vial 300 may be reusable or, preferably,
the rotating growth vial is consumable. In some embodiments, the
rotating growth vial is consumable and is presented to the user
pre-filled with growth medium, where the vial is hermetically
sealed at the open end 304 with a foil seal. A medium-filled
rotating growth vial packaged in such a manner may be part of a kit
for use with a stand-alone cell growth device or with a cell growth
module that is part of an automated multi-module cell processing
system. To introduce cells into the vial, a user need only pipette
up a desired volume of cells and use the pipette tip to punch
through the foil seal of the vial. Open end 304 may optionally
include an extended lip 302 to overlap and engage with the cell
growth device. In automated systems, the rotating growth vial 300
may be tagged with a barcode or other identifying means that can be
read by a scanner or camera (not shown) that is part of the
automated system.
[0093] The volume of the rotating growth vial 300 and the volume of
the cell culture (including growth medium) may vary greatly, but
the volume of the rotating growth vial 300 must be large enough to
generate a specified total number of cells. In practice, the volume
of the rotating growth vial 300 may range from 1-250 mL, 2-100 mL,
from 5-80 mL, 10-50 mL, or from 12-35 mL. Likewise, the volume of
the cell culture (cells+growth media) should be appropriate to
allow proper aeration and mixing in the rotating growth vial 300.
Proper aeration promotes uniform cellular respiration within the
growth media. Thus, the volume of the cell culture should be
approximately 5-85% of the volume of the growth vial or from 20-60%
of the volume of the growth vial. For example, for a 30 mL growth
vial, the volume of the cell culture would be from about 1.5 mL to
about 26 mL, or from 6 mL to about 18 mL.
[0094] The rotating growth vial 300 preferably is fabricated from a
bio-compatible optically transparent material--or at least the
portion of the vial comprising the light path(s) is transparent.
Additionally, material from which the rotating growth vial is
fabricated should be able to be cooled to about 4.degree. C. or
lower and heated to about 55.degree. C. or higher to accommodate
both temperature-based cell assays and long-term storage at low
temperatures. Further, the material that is used to fabricate the
vial must be able to withstand temperatures up to 55.degree. C.
without deformation while spinning. Suitable materials include
cyclic olefin copolymer (COC), glass, polyvinyl chloride,
polyethylene, polyamide, polypropylene, polycarbonate, poly(methyl
methacrylate (PMMA), polysulfone, polyurethane, and co-polymers of
these and other polymers. Preferred materials include
polypropylene, polycarbonate, or polystyrene. In some embodiments,
the rotating growth vial is inexpensively fabricated by, e.g.,
injection molding or extrusion.
[0095] FIG. 3B is a perspective view of one embodiment of a cell
growth device 330. FIG. 3C depicts a cut-away view of the cell
growth device 330 from FIG. 3B. In both figures, the rotating
growth vial 300 is seen positioned inside a main housing 336 with
the extended lip 302 of the rotating growth vial 300 extending
above the main housing 336. Additionally, end housings 352, a lower
housing 332 and flanges 334 are indicated in both figures. Flanges
334 are used to attach the cell growth device 330 to
heating/cooling means or other structure (not shown). FIG. 3C
depicts additional detail. In FIG. 3C, upper bearing 342 and lower
bearing 340 are shown positioned within main housing 336. Upper
bearing 342 and lower bearing 340 support the vertical load of
rotating growth vial 300. Lower housing 332 contains the drive
motor 338. The cell growth device 330 of FIG. 3C comprises two
light paths: a primary light path 344, and a secondary light path
350. Light path 344 corresponds to light path 310 positioned in the
constricted portion of the tapered-to-constricted portion of the
rotating growth vial 300, and light path 350 corresponds to light
path 308 in the tapered portion of the tapered-to-constricted
portion of the rotating growth via 316. Light paths 310 and 308 are
not shown in FIG. 3C but may be seen in FIG. 3A. In addition to
light paths 344 and 340, there is an emission board 348 to
illuminate the light path(s), and detector board 346 to detect the
light after the light travels through the cell culture liquid in
the rotating growth vial 300.
[0096] The motor 338 engages with drive mechanism 312 and is used
to rotate the rotating growth vial 300. In some embodiments, motor
338 is a brushless DC type drive motor with built-in drive controls
that can be set to hold a constant revolution per minute (RPM)
between 0 and about 3000 RPM. Alternatively, other motor types such
as a stepper, servo, brushed DC, and the like can be used.
Optionally, the motor 338 may also have direction control to allow
reversing of the rotational direction, and a tachometer to sense
and report actual RPM. The motor is controlled by a processor (not
shown) according to, e.g., standard protocols programmed into the
processor and/or user input, and the motor may be configured to
vary RPM to cause axial precession of the cell culture thereby
enhancing mixing, e.g., to prevent cell aggregation, increase
aeration, and optimize cellular respiration.
[0097] Main housing 336, end housings 352 and lower housing 332 of
the cell growth device 330 may be fabricated from any suitable,
robust material including aluminum, stainless steel, and other
thermally conductive materials, including plastics. These
structures or portions thereof can be created through various
techniques, e.g., metal fabrication, injection molding, creation of
structural layers that are fused, etc. Whereas the rotating growth
vial 300 is envisioned in some embodiments to be reusable, but
preferably is consumable, the other components of the cell growth
device 330 are preferably reusable and function as a stand-alone
benchtop device or as a module in a multi-module cell processing
system.
[0098] The processor (not shown) of the cell growth device 330 may
be programmed with information to be used as a "blank" or control
for the growing cell culture. A "blank" or control is a vessel
containing cell growth medium only, which yields 100% transmittance
and 0 OD, while the cell sample will deflect light rays and will
have a lower percent transmittance and higher OD. As the cells grow
in the media and become denser, transmittance will decrease and OD
will increase. The processor (not shown) of the cell growth device
330--may be programmed to use wavelength values for blanks
commensurate with the growth media typically used in cell culture
(whether, e.g., mammalian cells, bacterial cells, animal cells,
yeast cells, etc.). Alternatively, a second spectrophotometer and
vessel may be included in the cell growth device 330, where the
second spectrophotometer is used to read a blank at designated
intervals.
[0099] FIG. 3D illustrates a cell growth device 330 as part of an
assembly 360 comprising the cell growth device 330 of FIG. 3B
coupled to light source 390, detector 392, and thermal components
394. The rotating growth vial 300 is inserted into the cell growth
device. Components of the light source 390 and detector 392 (e.g.,
such as a photodiode with gain control to cover 5-log) are coupled
to the main housing of the cell growth device. The lower housing
332 that houses the motor that rotates the rotating growth vial 300
is illustrated, as is one of the flanges 334 that secures the cell
growth device 330 to the assembly. Also, the thermal components 394
illustrated are a Peltier device or thermoelectric cooler. In this
embodiment, thermal control is accomplished by attachment and
electrical integration of the cell growth device 330 to the thermal
components 394 via the flange 334 on the base of the lower housing
332. Thermoelectric coolers are capable of "pumping" heat to either
side of a junction, either cooling a surface or heating a surface
depending on the direction of current flow. In one embodiment, a
thermistor is used to measure the temperature of the main housing
and then, through a standard electronic
proportional-integral-derivative (PID) controller loop, the
rotating growth vial 300 is controlled to approximately
+/-0.5.degree. C.
[0100] In use, cells are inoculated (cells can be pipetted, e.g.,
from an automated liquid handling system or by a user) into
pre-filled growth media of a rotating growth vial 300 by piercing
though the foil seal or film. The programmed software of the cell
growth device 330 sets the control temperature for growth,
typically 30.degree. C., then slowly starts the rotation of the
rotating growth vial 300. The cell/growth media mixture slowly
moves vertically up the wall due to centrifugal force allowing the
rotating growth vial 300 to expose a large surface area of the
mixture to a normal oxygen environment. The growth monitoring
system takes either continuous readings of the OD or OD
measurements at pre-set or pre-programmed time intervals. These
measurements are stored in internal memory and if requested the
software plots the measurements versus time to display a growth
curve. If enhanced mixing is required, e.g., to optimize growth
conditions, the speed of the vial rotation can be varied to cause
an axial precession of the liquid, and/or a complete directional
change can be performed at programmed intervals. The growth
monitoring can be programmed to automatically terminate the growth
stage at a pre-determined OD, and then quickly cool the mixture to
a lower temperature to inhibit further growth.
[0101] One application for the cell growth device 330 is to
constantly measure the optical density of a growing cell culture.
One advantage of the described cell growth device is that optical
density can be measured continuously (kinetic monitoring) or at
specific time intervals; e.g., every 5, 10, 15, 20, 30 45, or 60
seconds, or every 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 minutes. While
the cell growth device 330 has been described in the context of
measuring the optical density (OD) of a growing cell culture, it
should, however, be understood by a skilled artisan given the
teachings of the present specification that other cell growth
parameters can be measured in addition to or instead of cell
culture OD. As with optional measure of cell growth in relation to
the solid wall device or module described supra, spectroscopy using
visible, UV, or near infrared (NIR) light allows monitoring the
concentration of nutrients and/or wastes in the cell culture and
other spectroscopic measurements may be made; that is, other
spectral properties can be measured via, e.g., dielectric impedance
spectroscopy, visible fluorescence, fluorescence polarization, or
luminescence. Additionally, the cell growth device 330 may include
additional sensors for measuring, e.g., dissolved oxygen, carbon
dioxide, pH, conductivity, and the like. For additional details
regarding rotating growth vials and cell growth devices see U.S.
Pat. Nos. 10,435,662; 10,443,031; 10,590,375 and U.S. Ser. No.
16/552,981, filed 7 Aug. 2019; Ser. No. 16/780,640, filed 3 Feb.
2020.
The Cell Concentration Module
[0102] As described above in relation to the rotating growth vial
and cell growth module, in order to obtain an adequate number of
cells for transformation or transfection, cells typically are grown
to a specific optical density in medium appropriate for the growth
of the cells of interest; however, for effective transformation or
transfection, it is desirable to decrease the volume of the cells
as well as render the cells competent via buffer or medium
exchange. Thus, one sub-component or module that is desired in cell
processing systems for the processes listed above is a module or
component that can grow, perform buffer exchange, and/or
concentrate cells and render them competent so that they may be
transformed or transfected with the nucleic acids needed for
engineering or editing the cell's genome.
[0103] FIG. 4A shows a retentate member 422 (top), permeate member
420 (middle) and a tangential flow assembly 410 (bottom) comprising
the retentate member 422, membrane 424 (not seen in FIG. 4A), and
permeate member 420 (also not seen). In FIG. 4A, retentate member
422 comprises a tangential flow channel 402, which has a serpentine
configuration that initiates at one lower corner of retentate
member 422--specifically at retentate port 428--traverses across
and up then down and across retentate member 422, ending in the
other lower corner of retentate member 422 at a second retentate
port 428. Also seen on retentate member 422 are energy directors
491, which circumscribe the region where a membrane or filter (not
seen in this FIG. 4A) is seated, as well as interdigitate between
areas of channel 402. Energy directors 491 in this embodiment mate
with and serve to facilitate ultrasonic welding or bonding of
retentate member 422 with permeate/filtrate member 420 via the
energy director component 491 on permeate/filtrate member 420 (at
right). Additionally, countersinks 423 can be seen, two on the
bottom one at the top middle of retentate member 422. Countersinks
423 are used to couple and tangential flow assembly 410 to a
reservoir assembly (not seen in this FIG. 4A but see FIG. 4B).
[0104] Permeate/filtrate member 420 is seen in the middle of FIG.
4A and comprises, in addition to energy director 491, through-holes
for retentate ports 428 at each bottom corner (which mate with the
through-holes for retentate ports 428 at the bottom corners of
retentate member 422), as well as a tangential flow channel 402 and
two permeate/filtrate ports 426 positioned at the top and center of
permeate member 420. The tangential flow channel 402 structure in
this embodiment has a serpentine configuration and an undulating
geometry, although other geometries may be used. Permeate member
420 also comprises countersinks 423, coincident with the
countersinks 423 on retentate member 420.
[0105] At bottom of FIG. 4A is a tangential flow assembly 410
comprising the retentate member 422 and permeate member 420 seen in
this FIG. 4A. In this view, retentate member 422 is "on top" of the
view, a membrane (not seen in this view of the assembly) would be
adjacent and under retentate member 422 and permeate member 420
(also not seen in this view of the assembly) is adjacent to and
beneath the membrane. Again countersinks 423 are seen, where the
countersinks in the retentate member 422 and the permeate member
420 are coincident and configured to mate with threads or mating
elements for the countersinks disposed on a reservoir assembly (not
seen in FIG. 4A but see FIG. 4B).
[0106] A membrane or filter is disposed between the retentate and
permeate members, where fluids can flow through the membrane but
cells cannot and are thus retained in the flow channel disposed in
the retentate member. Filters or membranes appropriate for use in
the TFF device/module are those that are solvent resistant, are
contamination free during filtration, and are able to retain the
types and sizes of cells of interest. For example, in order to
retain small cell types such as bacterial cells, pore sizes can be
as low as 0.2 .mu.m, however for other cell types, the pore sizes
can be as high as 20 .mu.m. Indeed, the pore sizes useful in the
TFF device/module include filters with sizes from 0.20 .mu.m, 0.21
.mu.m, 0.22 .mu.m, 0.23 .mu.m, 0.24 .mu.m, 0.25 .mu.m, 0.26 .mu.m,
0.27 .mu.m, 0.28 .mu.m, 0.29 .mu.m, 0.30 .mu.m, 0.31 .mu.m, 0.32
.mu.m, 0.33 .mu.m, 0.34 .mu.m, 0.35 .mu.m, 0.36 .mu.m, 0.37 .mu.m,
0.38 .mu.m, 0.39 .mu.m, 0.40 .mu.m, 0.41 .mu.m, 0.42 .mu.m, 0.43
.mu.m, 0.44 .mu.m, 0.45 .mu.m, 0.46 .mu.m, 0.47 .mu.m, 0.48 .mu.m,
0.49 .mu.m, 0.50 .mu.m and larger. The filters may be fabricated
from any suitable non-reactive material including cellulose mixed
ester (cellulose nitrate and acetate) (CME), polycarbonate (PC),
polyvinylidene fluoride (PVDF), polyethersulfone (PES),
polytetrafluoroethylene (PTFE), nylon, glass fiber, or metal
substrates as in the case of laser or electrochemical etching.
[0107] The length of the channel structure 402 may vary depending
on the volume of the cell culture to be grown and the optical
density of the cell culture to be concentrated. The length of the
channel structure typically is from 60 mm to 300 mm, or from 70 mm
to 200 mm, or from 80 mm to 100 mm. The cross-section configuration
of the flow channel 402 may be round, elliptical, oval, square,
rectangular, trapezoidal, or irregular. If square, rectangular, or
another shape with generally straight sides, the cross section may
be from about 10 .mu.m to 1000 .mu.m wide, or from 200 .mu.m to 800
.mu.m wide, or from 300 .mu.m to 700 .mu.m wide, or from 400 .mu.m
to 600 .mu.m wide; and from about 10 .mu.m to 1000 .mu.m high, or
from 200 .mu.m to 800 .mu.m high, or from 300 .mu.m to 700 .mu.m
high, or from 400 .mu.m to 600 .mu.m high. If the cross section of
the flow channel 102 is generally round, oval or elliptical, the
radius of the channel may be from about 50 .mu.m to 1000 .mu.m in
hydraulic radius, or from 5 .mu.m to 800 .mu.m in hydraulic radius,
or from 200 .mu.m to 700 .mu.m in hydraulic radius, or from 300
.mu.m to 600 .mu.m wide in hydraulic radius, or from about 200 to
500 .mu.m in hydraulic radius. Moreover, the volume of the channel
in the retentate 422 and permeate 420 members may be different
depending on the depth of the channel in each member.
[0108] FIG. 4B shows front perspective (top) and rear perspective
(bottom) views of a reservoir assembly 450 configured to be used
with the tangential flow assembly 410 seen in FIG. 4A. Seen in the
front perspective view (e.g., "front" being the side of reservoir
assembly 450 that is coupled to the tangential flow assembly 410
seen in FIG. 4A) are retentate reservoirs 452 on either side of
permeate reservoir 454. Also seen are permeate ports 426, retentate
ports 428, and three threads or mating elements 425 for
countersinks 423 (countersinks 423 not seen in this FIG. 4B).
Threads or mating elements 425 for countersinks 423 are configured
to mate or couple the tangential flow assembly 410 (seen in FIG.
4A) to reservoir assembly 450. Alternatively or in addition,
fasteners, sonic welding or heat stakes may be used to mate or
couple the tangential flow assembly 410 to reservoir assembly 450.
In addition is seen gasket 445 covering the top of reservoir
assembly 450. Gasket 445 is described in detail in relation to FIG.
4E. At left in FIG. 4B is a rear perspective view of reservoir
assembly 450, where "rear" is the side of reservoir assembly 450
that is not coupled to the tangential flow assembly. Seen are
retentate reservoirs 452, permeate reservoir 454, and gasket 445,
where there is a pipette tip 405 inserted in one retentate
reservoir 452.
[0109] The TFF device may be fabricated from any robust material in
which channels (and channel branches) may be milled including
stainless steel, silicon, glass, aluminum, or plastics including
cyclic-olefin copolymer (COC), cyclo-olefin polymer (COP),
polystyrene, polyvinyl chloride, polyethylene, polyamide,
polyethylene, polypropylene, acrylonitrile butadiene,
polycarbonate, polyetheretheketone (PEEK), poly(methyl
methylacrylate) (PMMA), polysulfone, and polyurethane, and
co-polymers of these and other polymers. If the TFF device/module
is disposable, preferably it is made of plastic. In some
embodiments, the material used to fabricate the TFF device/module
is thermally-conductive so that the cell culture may be heated or
cooled to a desired temperature. In certain embodiments, the TFF
device is formed by precision mechanical machining, laser
machining, electro discharge machining (for metal devices); wet or
dry etching (for silicon devices); dry or wet etching, powder or
sandblasting, photostructuring (for glass devices); or
thermoforming, injection molding, hot embossing, or laser machining
(for plastic devices) using the materials mentioned above that are
amenable to this mass production techniques.
[0110] FIG. 4C depicts a top-down view of the reservoir assemblies
450 shown in FIG. 4B. FIG. 4D depicts a cover 444 for reservoir
assembly 450 shown in FIGS. 4B and 4E depicts a gasket 445 that in
operation is disposed on cover 444 of reservoir assemblies 450
shown in FIG. 4B. FIG. 4C is a top-down view of reservoir assembly
450, showing the tops of the two retentate reservoirs 452, one on
either side of permeate reservoir 454. Also seen are grooves 432
that will mate with a pneumatic port (not shown), and fluid
channels 434 that reside at the bottom of retentate reservoirs 452,
which fluidically couple the retentate reservoirs 452 with the
retentate ports 428 (not shown), via the through-holes for the
retentate ports in permeate member 420 and membrane 424 (also not
shown). FIG. 4D depicts a cover 444 that is configured to be
disposed upon the top of reservoir assembly 450. Cover 444 has
round cut-outs at the top of retentate reservoirs 452 and
permeate/filtrate reservoir 454. Again at the bottom of retentate
reservoirs 452 fluid channels 434 can be seen, where fluid channels
434 fluidically couple retentate reservoirs 452 with the retentate
ports 428 (not shown). Also shown are three pneumatic ports 430 for
each retentate reservoir 452 and permeate/filtrate reservoir 454.
FIG. 4E depicts a gasket 445 that is configured to be disposed upon
the cover 444 of reservoir assembly 450. Seen are three fluid
transfer ports 442 for each retentate reservoir 452 and for
permeate/filtrate reservoir 454. Again, three pneumatic ports 430,
for each retentate reservoir 452 and for permeate/filtrate
reservoir 454, are shown.
[0111] The overall work flow for cell growth comprises loading a
cell culture to be grown into a first retentate reservoir,
optionally bubbling air or an appropriate gas through the cell
culture, passing or flowing the cell culture through the first
retentate port then tangentially through the TFF channel structure
while collecting medium or buffer through one or both of the
permeate ports 406, collecting the cell culture through a second
retentate port 404 into a second retentate reservoir, optionally
adding additional or different medium to the cell culture and
optionally bubbling air or gas through the cell culture, then
repeating the process, all while measuring, e.g., the optical
density of the cell culture in the retentate reservoirs
continuously or at desired intervals. Measurements of optical
densities (OD) at programmed time intervals are accomplished using
a 600 nm Light Emitting Diode (LED) that has been columnated
through an optic into the retentate reservoir(s) containing the
growing cells. The light continues through a collection optic to
the detection system which consists of a (digital) gain-controlled
silicone photodiode. Generally, optical density is shown as the
absolute value of the logarithm with base 10 of the power
transmission factors of an optical attenuator: OD=-log 10 (Power
out/Power in). Since OD is the measure of optical attenuation--that
is, the sum of absorption, scattering, and reflection--the TFF
device OD measurement records the overall power transmission, so as
the cells grow and become denser in population, the OD (the loss of
signal) increases. The OD system is pre-calibrated against OD
standards with these values stored in an on-board memory accessible
by the measurement program.
[0112] In the channel structure, the membrane bifurcating the flow
channels retains the cells on one side of the membrane (the
retentate side 422) and allows unwanted medium or buffer to flow
across the membrane into a filtrate or permeate side (e.g.,
permeate member 420) of the device. Bubbling air or other
appropriate gas through the cell culture both aerates and mixes the
culture to enhance cell growth. During the process, medium that is
removed during the flow through the channel structure is removed
through the permeate/filtrate ports 406. Alternatively, cells can
be grown in one reservoir with bubbling or agitation without
passing the cells through the TFF channel from one reservoir to the
other.
[0113] The overall workflow for cell concentration using the TFF
device/module involves flowing a cell culture or cell sample
tangentially through the channel structure. As with the cell growth
process, the membrane bifurcating the flow channels retains the
cells on one side of the membrane and allows unwanted medium or
buffer to flow across the membrane into a permeate/filtrate side
(e.g., permeate member 420) of the device. In this process, a fixed
volume of cells in medium or buffer is driven through the device
until the cell sample is collected into one of the retentate ports
404, and the medium/buffer that has passed through the membrane is
collected through one or both of the permeate/filtrate ports 406.
All types of prokaryotic and eukaryotic cells--both adherent and
non-adherent cells--can be grown in the TFF device. Adherent cells
may be grown on beads or other cell scaffolds suspended in medium
that flow through the TFF device.
[0114] The medium or buffer used to suspend the cells in the cell
concentration device/module may be any suitable medium or buffer
for the type of cells being transformed or transfected, such as LB,
SOC, TPD, YPG, YPAD, MEM, DMEM, IMDM, RPMI, Hanks', PBS and
Ringer's solution, where the media may be provided in a reagent
cartridge as part of a kit.
[0115] In both the cell growth and concentration processes, passing
the cell sample through the TFF device and collecting the cells in
one of the retentate ports 404 while collecting the medium in one
of the permeate/filtrate ports 406 is considered "one pass" of the
cell sample. The transfer between retentate reservoirs "flips" the
culture. The retentate and permeate ports collecting the cells and
medium, respectively, for a given pass reside on the same end of
TFF device/module with fluidic connections arranged so that there
are two distinct flow layers for the retentate and
permeate/filtrate sides, but if the retentate port 404 resides on
the retentate member of device/module (that is, the cells are
driven through the channel above the membrane and the filtrate
(medium) passes to the portion of the channel below the membrane),
the permeate/filtrate port 406 will reside on the permeate member
of device/module and vice versa (that is, if the cell sample is
driven through the channel below the membrane, the filtrate
(medium) passes to the portion of the channel above the membrane).
Due to the high pressures used to transfer the cell culture and
fluids through the flow channel of the TFF device, the effect of
gravity is negligible.
[0116] At the conclusion of a "pass" in either of the growth and
concentration processes, the cell sample is collected by passing
through the retentate port 404 and into the retentate reservoir
(not shown). To initiate another "pass", the cell sample is passed
again through the TFF device, this time in a flow direction that is
reversed from the first pass. The cell sample is collected by
passing through the retentate port 404 and into retentate reservoir
(not shown) on the opposite end of the device/module from the
retentate port 404 that was used to collect cells during the first
pass. Likewise, the medium/buffer that passes through the membrane
on the second pass is collected through the permeate port 406 on
the opposite end of the device/module from the permeate port 406
that was used to collect the filtrate during the first pass, or
through both ports. This alternating process of passing the
retentate (the concentrated cell sample) through the device/module
is repeated until the cells have been grown to a desired optical
density, and/or concentrated to a desired volume, and both permeate
ports (i.e., if there are more than one) can be open during the
passes to reduce operating time. In addition, buffer exchange may
be effected by adding a desired buffer (or fresh medium) to the
cell sample in the retentate reservoir, before initiating another
"pass", and repeating this process until the old medium or buffer
is diluted and filtered out and the cells reside in fresh medium or
buffer. Note that buffer exchange and cell growth may (and
typically do) take place simultaneously, and buffer exchange and
cell concentration may (and typically do) take place
simultaneously. For further information and alternative embodiments
on TFFs see, e.g., U.S. Ser. No. 16/798,302, filed 22 Sep.
2020.
The Cell Transformation Module
[0117] FIGS. 5A and 5B depict the structure and components of an
embodiment of an exemplary reagent cartridge useful in the
automated multi-module instrument described therein. In FIG. 5A,
reagent cartridge 500 comprises a body 502, which has reservoirs
504. One reservoir 504 is shown empty, and two of the reservoirs
have individual tubes (not shown) inserted therein, with individual
tube covers 505. Additionally shown are rows of reservoirs into
which have been inserted co-joined rows of large tubes 503a, and
co-joined rows of small tubes 503b. The co-joined rows of tubes are
presented in a strip, with outer flanges 507 that mate on the
backside of the outer flange (not shown) with an indentation 509 in
the body 502, so as to secure the co-joined rows of tubes (503a and
503b) to the reagent cartridge 500. Shown also is a base 511 of
reagent cartridge body 502. Note that the reservoirs 504 in body
502 are shaped generally like the tubes in the co-joined tubes that
are inserted into these reservoirs 504.
[0118] FIG. 5B depicts the reagent cartridge 500 in FIG. 5A with a
row of co-joined large tubes 503a, a row of co-joined small tubes
503b, and one large tube 560 with a cover 505 removed from (i.e.,
depicted above) the reservoirs 504 of the reagent cartridge 500.
Again, the co-joined rows of tubes are presented in a strip, with
individual large tubes 561 shown, and individual small tubes 555
shown. Again, each strip of co-joined tubes comprises outer flanges
507 that mate on the backside (not shown) of the outer flange with
an indentation 509 in the body 502, to secure the co-joined rows of
tubes (503a and 503b) to the reagent cartridge 500. As in FIG. 5A,
reagent cartridge body 502 comprises a base 511. Reagent cartridge
500 may be made from any suitable material, including stainless
steel, aluminum, or plastics including polyvinyl chloride, cyclic
olefin copolymer (COC), polyethylene, polyamide, polypropylene,
acrylonitrile butadiene, polycarbonate, polyetheretheketone (PEEK),
poly(methyl methylacrylate) (PMMA), polysulfone, and polyurethane,
and co-polymers of these and other polymers. Again, if reagent
cartridge 500 is disposable, it preferably is made of plastic. In
addition, in many embodiments the material used to fabricate the
cartridge is thermally-conductive, as reagent cartridge 500 may
contact a thermal device (not shown) that heats or cools reagents
in the reagent reservoirs 504, including reagents in co-joined
tubes. In some embodiments, the thermal device is a Peltier device
or thermoelectric cooler.
[0119] FIGS. 5C and 5D are top perspective and bottom perspective
views, respectively, of an exemplary FTEP device 550 that may be
part of (e.g., a component in) reagent cartridge 500 in FIGS. 5A
and 5B or may be a stand-alone module; that is, not a part of a
reagent cartridge or other module. FIG. 5C depicts an FTEP device
550. The FTEP device 550 has wells 562, 564 that define cell sample
inlets 552 and cell sample outlets 554. FIG. 5D is a bottom
perspective view of the FTEP device 550 of FIG. 5C. An inlet well
562 and an outlet well 564 can be seen in this view. Also seen in
FIG. 5D are the bottom of an inlet 552 corresponding to well 562,
the bottom of an outlet 554 corresponding to the outlet well 564,
the bottom of a defined flow channel 566 and the bottom of two
electrodes 568 on either side of flow channel 566. The FTEP devices
may comprise push-pull pneumatic means to allow multi-pass
electroporation procedures; that is, cells to electroporated may be
"pulled" from the inlet toward the outlet for one pass of
electroporation, then be "pushed" from the outlet end of the FTEP
device toward the inlet end to pass between the electrodes again
for another pass of electroporation. Further, this process may be
repeated one to many times. For additional information regarding
FTEP devices, see, e.g., U.S. Pat. Nos. 10,435,713; 10,443,074;
10,323,258; and 10,508,288. Further, other embodiments of the
reagent cartridge may provide or accommodate electroporation
devices that are not configured as FTEP devices, such as those
described in U.S. Ser. No. 16/109,156, filed 22 Aug. 2018. For
reagent cartridges useful in the present automated multi-module
cell processing instruments, see, e.g., U.S. Pat. Nos. 10,376,889;
10,406,525; 10,576,474; and U.S. Ser. No. 16/749,757, filed 22 Jan.
2020; and Ser. No. 16/827,222, filed 23 Mar. 2020.
[0120] Additional details of the FTEP devices are illustrated in
FIGS. 5E-5G. Note that in the FTEP devices in FIGS. 5E-5G the
electrodes are placed such that a first electrode is placed between
an inlet and a narrowed region of the flow channel, and the second
electrode is placed between the narrowed region of the flow channel
and an outlet. FIG. 5E shows a top planar view of an FTEP device
550 having an inlet 552 for introducing a fluid containing cells
and exogenous material into FTEP device 550 and an outlet 554 for
removing the transformed cells from the FTEP following
electroporation. The electrodes 568 are introduced through channels
(not shown) in the device. FIG. 5F shows a cutaway view from the
top of the FTEP device 550, with the inlet 552, outlet 554, and
electrodes 568 positioned with respect to a flow channel 566. FIG.
5G shows a side cutaway view of FTEP device 550 with the inlet 552
and inlet channel 572, and outlet 554 and outlet channel 574. The
electrodes 568 are positioned in electrode channels 576 so that
they are in fluid communication with the flow channel 566, but not
directly in the path of the cells traveling through the flow
channel 566. Note that the first electrode is placed between the
inlet and the narrowed region of the flow channel, and the second
electrode is placed between the narrowed region of the flow channel
and the outlet. The electrodes 568 in this aspect of the device are
positioned in the electrode channels 576 which are generally
perpendicular to the flow channel 566 such that the fluid
containing the cells and exogenous material flows from the inlet
channel 572 through the flow channel 566 to the outlet channel 574,
and in the process fluid flows into the electrode channels 576 to
be in contact with the electrodes 568. In this aspect, the inlet
channel, outlet channel and electrode channels all originate from
the same planar side of the device. In certain aspects, however,
the electrodes may be introduced from a different planar side of
the FTEP device than the inlet and outlet channels.
[0121] In the FTEP devices of the disclosure, the toxicity level of
the transformation results in greater than 30% viable cells after
electroporation, preferably greater than 35%, 40%, 45%, 50%, 55%,
60%, 70%, 75%, 80%, 85%, 90%, 95% or even 99% viable cells
following transformation, depending on the cell type and the
nucleic acids being introduced into the cells.
[0122] The housing of the FTEP device can be made from many
materials depending on whether the FTEP device is to be reused,
autoclaved, or is disposable, including stainless steel, silicon,
glass, resin, polyvinyl chloride, polyethylene, polyamide,
polystyrene, polyethylene, polypropylene, acrylonitrile butadiene,
polycarbonate, polyetheretheketone (PEEK), polysulfone and
polyurethane, co-polymers of these and other polymers. Similarly,
the walls of the channels in the device can be made of any suitable
material including silicone, resin, glass, glass fiber, polyvinyl
chloride, polyethylene, polyamide, polyethylene, polypropylene,
acrylonitrile butadiene, polycarbonate, polyetheretheketone (PEEK),
polysulfone and polyurethane, co-polymers of these and other
polymers. Preferred materials include crystal styrene, cyclo-olefin
polymer (COP) and cyclic olephin co-polymers (COC), which allow the
device to be formed entirely by injection molding in one piece with
the exception of the electrodes and, e.g., a bottom sealing film if
present.
[0123] The FTEP devices described herein (or portions of the FTEP
devices) can be created or fabricated via various techniques, e.g.,
as entire devices or by creation of structural layers that are
fused or otherwise coupled. For example, for metal FTEP devices,
fabrication may include precision mechanical machining or laser
machining; for silicon FTEP devices, fabrication may include dry or
wet etching; for glass FTEP devices, fabrication may include dry or
wet etching, powderblasting, sandblasting, or photostructuring; and
for plastic FTEP devices fabrication may include thermoforming,
injection molding, hot embossing, or laser machining. The
components of the FTEP devices may be manufactured separately and
then assembled, or certain components of the FTEP devices (or even
the entire FTEP device except for the electrodes) may be
manufactured (e.g., using 3D printing) or molded (e.g., using
injection molding) as a single entity, with other components added
after molding. For example, housing and channels may be
manufactured or molded as a single entity, with the electrodes
later added to form the FTEP unit. Alternatively, the FTEP device
may also be formed in two or more parallel layers, e.g., a layer
with the horizontal channel and filter, a layer with the vertical
channels, and a layer with the inlet and outlet ports, which are
manufactured and/or molded individually and assembled following
manufacture.
[0124] In specific aspects, the FTEP device can be manufactured
using a circuit board as a base, with the electrodes, filter and/or
the flow channel formed in the desired configuration on the circuit
board, and the remaining housing of the device containing, e.g.,
the one or more inlet and outlet channels and/or the flow channel
formed as a separate layer that is then sealed onto the circuit
board. The sealing of the top of the housing onto the circuit board
provides the desired configuration of the different elements of the
FTEP devices of the disclosure. Also, two to many FTEP devices may
be manufactured on a single substrate, then separated from one
another thereafter or used in parallel. In certain embodiments, the
FTEP devices are reusable and, in some embodiments, the FTEP
devices are disposable. In additional embodiments, the FTEP devices
may be autoclavable.
[0125] The electrodes 508 can be formed from any suitable metal,
such as copper, stainless steel, titanium, aluminum, brass, silver,
rhodium, gold or platinum, or graphite. One preferred electrode
material is alloy 303 (UNS330300) austenitic stainless steel. An
applied electric field can destroy electrodes made from of metals
like aluminum. If a multiple-use (i.e., non-disposable)
flow-through FTEP device is desired-as opposed to a disposable,
one-use flow-through FTEP device--the electrode plates can be
coated with metals resistant to electrochemical corrosion.
Conductive coatings like noble metals, e.g., gold, can be used to
protect the electrode plates.
[0126] As mentioned, the FTEP devices may comprise push-pull
pneumatic means to allow multi-pass electroporation procedures;
that is, cells to be electroporated may be "pulled" from the inlet
toward the outlet for one pass of electroporation, then be "pushed"
from the outlet end of the flow-through FTEP device toward the
inlet end to pass between the electrodes again for another pass of
electroporation. This process may be repeated one to many
times.
[0127] Depending on the type of cells to be electroporated (e.g.,
bacterial, yeast, mammalian) and the configuration of the
electrodes, the distance between the electrodes in the flow channel
can vary widely. For example, where the flow channel decreases in
width, the flow channel may narrow to between 10 .mu.m and 5 mm, or
between 25 .mu.m and 3 mm, or between 50 .mu.m and 2 mm, or between
75 .mu.m and 1 mm. The distance between the electrodes in the flow
channel may be between 1 mm and 10 mm, or between 2 mm and 8 mm, or
between 3 mm and 7 mm, or between 4 mm and 6 mm. The overall size
of the FTEP device may be from 3 cm to 15 cm in length, or 4 cm to
12 cm in length, or 4.5 cm to 10 cm in length. The overall width of
the FTEP device may be from 0.5 cm to 5 cm, or from 0.75 cm to 3
cm, or from 1 cm to 2.5 cm, or from 1 cm to 1.5 cm.
[0128] The region of the flow channel that is narrowed is wide
enough so that at least two cells can fit in the narrowed portion
side-by-side. For example, a typical bacterial cell is 1 .mu.m in
diameter; thus, the narrowed portion of the flow channel of the
FTEP device used to transform such bacterial cells will be at least
2 .mu.m wide. In another example, if a mammalian cell is
approximately 50 .mu.m in diameter, the narrowed portion of the
flow channel of the FTEP device used to transform such mammalian
cells will be at least 100 .mu.m wide. That is, the narrowed
portion of the FTEP device will not physically contort or "squeeze"
the cells being transformed.
[0129] In embodiments of the FTEP device where reservoirs are used
to introduce cells and exogenous material into the FTEP device, the
reservoirs range in volume from 100 .mu.L to 10 mL, or from 500
.mu.L to 75 mL, or from 1 mL to 5 mL. The flow rate in the FTEP
ranges from 0.1 mL to 5 mL per minute, or from 0.5 mL to 3 mL per
minute, or from 1.0 mL to 2.5 mL per minute. The pressure in the
FTEP device ranges from 1-30 psi, or from 2-10 psi, or from 3-5
psi.
[0130] To avoid different field intensities between the electrodes,
the electrodes should be arranged in parallel. Furthermore, the
surface of the electrodes should be as smooth as possible without
pin holes or peaks. Electrodes having a roughness Rz of 1 to 10
.mu.m are preferred. In another embodiment of the invention, the
flow-through electroporation device comprises at least one
additional electrode which applies a ground potential to the FTEP
device. Flow-through electroporation devices (either as a
stand-alone instrument or as a module in an automated multi-module
system) are described in, e.g., U.S. Pat. Nos. 10,435,713;
10,443,074; 10,323,258; and 10,508,288.
Cell Singulation and Enrichment Device
[0131] FIG. 6A depicts a solid wall device 6050 and a workflow for
singulating cells in microwells in the solid wall device. At the
top left of the figure (i), there is depicted solid wall device
6050 with microwells 6052. A section 6054 of substrate 6050 is
shown at (ii), also depicting microwells 6052. At (iii), a side
cross-section of solid wall device 6050 is shown, and microwells
6052 have been loaded, where, in this embodiment, Poisson or
substantial Poisson loading has taken place; that is, each
microwell has one or no cells, and the likelihood that any one
microwell has more than one cell is low. At (iv), workflow 6040 is
illustrated where substrate 6050 having microwells 6052 shows
microwells 6056 with one cell per microwell, microwells 6057 with
no cells in the microwells, and one microwell 6060 with two cells
in the microwell. In step 6051, the cells in the microwells are
allowed to double approximately 2-150 times to form clonal colonies
(v), then editing is allowed to occur 6053.
[0132] After editing 6053, many cells in the colonies of cells that
have been edited die as a result of the double-strand cuts caused
by active editing and there is a lag in growth for the edited cells
that do survive but must repair and recover following editing
(microwells 6058), where cells that do not undergo editing thrive
(microwells 6059) (vi). All cells are allowed to continue grow to
establish colonies and normalize, where the colonies of edited
cells in microwells 6058 catch up in size and/or cell number with
the cells in microwells 6059 that do not undergo editing (vii).
Once the cell colonies are normalized, either pooling 6060 of all
cells in the microwells can take place, in which case the cells are
enriched for edited cells by eliminating the bias from non-editing
cells and fitness effects from editing; alternatively, colony
growth in the microwells is monitored after editing, and slow
growing colonies (e.g., the cells in microwells 6058) are
identified and selected 6061 (e.g., "cherry picked") resulting in
even greater enrichment of edited cells.
[0133] In growing the cells, the medium used will depend, of
course, on the type of cells being edited--e.g., bacterial, yeast
or mammalian. For example, medium for yeast cell growth includes
LB, SOC, TPD, YPG, YPAD, MEM and DMEM.
[0134] FIG. 6B is a photograph of one embodiment of a SWIIN. FIG.
6B is a photograph of a SWIIN device with a permeable bottom on
agar, on which yeast cells have been singulated and grown into
clonal colonies. FIG. 6C presents photographs of yeast colony
growth in a SWIIN at various time points (at 0, 6, 11 and 32
hours).
[0135] A module useful for performing the methods depicted in FIG.
6A is a solid wall isolation, incubation, and normalization (SWIIN)
module. FIG. 6D depicts an embodiment of a SWIIN module 650 from an
exploded top perspective view. In SWIIN module 650 the retentate
member is formed on the bottom of a top of a SWIIN module component
and the permeate member is formed on the top of the bottom of a
SWIIN module component.
[0136] The SWIIN module 650 in FIG. 6D comprises from the top down,
a reservoir gasket or cover 658, a retentate member 604 (where a
retentate flow channel cannot be seen in this FIG. 6D), a
perforated member 601 swaged with a filter (filter not seen in FIG.
6D), a permeate member 608 comprising integrated reservoirs
(permeate reservoirs 652 and retentate reservoirs 654), and two
reservoir seals 662, which seal the bottom of permeate reservoirs
652 and retentate reservoirs 654. A permeate channel 660a can be
seen disposed on the top of permeate member 608, defined by a
raised portion 676 of serpentine channel 660a, and ultrasonic tabs
664 can be seen disposed on the top of permeate member 608 as well.
The perforations that form the wells on perforated member 601 are
not seen in this FIG. 6D; however, through-holes 666 to accommodate
the ultrasonic tabs 664 are seen. In addition, supports 670 are
disposed at either end of SWIIN module 650 to support SWIIN module
650 and to elevate permeate member 608 and retentate member 604
above reservoirs 652 and 654 to minimize bubbles or air entering
the fluid path from the permeate reservoir to serpentine channel
660a or the fluid path from the retentate reservoir to serpentine
channel 660b (neither fluid path is seen in this FIG. 6D).
[0137] In this FIG. 6D, it can be seen that the serpentine channel
660a that is disposed on the top of permeate member 608 traverses
permeate member 608 for most of the length of permeate member 608
except for the portion of permeate member 608 that comprises
permeate reservoirs 652 and retentate reservoirs 654 and for most
of the width of permeate member 608. As used herein with respect to
the distribution channels in the retentate member or permeate
member, "most of the length" means about 95% of the length of the
retentate member or permeate member, or about 90%, 85%, 80%, 75%,
or 70% of the length of the retentate member or permeate member. As
used herein with respect to the distribution channels in the
retentate member or permeate member, "most of the width" means
about 95% of the width of the retentate member or permeate member,
or about 90%, 85%, 80%, 75%, or 70% of the width of the retentate
member or permeate member.
[0138] In this embodiment of a SWIIN module, the perforated member
includes through-holes to accommodate ultrasonic tabs disposed on
the permeate member. Thus, in this embodiment the perforated member
is fabricated from 316 stainless steel, and the perforations form
the walls of microwells while a filter or membrane is used to form
the bottom of the microwells. Typically, the perforations
(microwells) are approximately 150 .mu.m-200 .mu.m in diameter, and
the perforated member is approximately 125 .mu.m deep, resulting in
microwells having a volume of approximately 2.5 nl, with a total of
approximately 200,000 microwells. The distance between the
microwells is approximately 279 .mu.m center-to-center. Though here
the microwells have a volume of approximately 2.5 nl, the volume of
the microwells may be from 1 to 25 nl, or preferably from 2 to 10
nl, and even more preferably from 2 to 4 nl. As for the filter or
membrane, like the filter described previously, filters appropriate
for use are solvent resistant, contamination free during
filtration, and are able to retain the types and sizes of cells of
interest. For example, in order to retain small cell types such as
bacterial cells, pore sizes can be as low as 0.10 .mu.m, however
for other cell types (e.g., such as for mammalian cells), the pore
sizes can be as high as 10.0 .mu.m-20.0 .mu.m or more. Indeed, the
pore sizes useful in the cell concentration device/module include
filters with sizes from 0.10 .mu.m, 0.11 .mu.m, 0.12 .mu.m, 0.13
.mu.m, 0.14 .mu.m, 0.15 .mu.m, 0.16 .mu.m, 0.17 .mu.m, 0.18 .mu.m,
0.19 .mu.m, 0.20 .mu.m, 0.21 .mu.m, 0.22 .mu.m, 0.23 .mu.m, 0.24
.mu.m, 0.25 .mu.m, 0.26 .mu.m, 0.27 .mu.m, 0.28 .mu.m, 0.29 .mu.m,
0.30 .mu.m, 0.31 .mu.m, 0.32 .mu.m, 0.33 .mu.m, 0.34 .mu.m, 0.35
.mu.m, 0.36 .mu.m, 0.37 .mu.m, 0.38 .mu.m, 0.39 .mu.m, 0.40 .mu.m,
0.41 .mu.m, 0.42 .mu.m, 0.43 .mu.m, 0.44 .mu.m, 0.45 .mu.m, 0.46
.mu.m, 0.47 .mu.m, 0.48 .mu.m, 0.49 .mu.m, 0.50 .mu.m and larger.
The filters may be fabricated from any suitable material including
cellulose mixed ester (cellulose nitrate and acetate) (CME),
polycarbonate (PC), polyvinylidene fluoride (PVDF),
polyethersulfone (PES), polytetrafluoroethylene (PTFE), nylon, or
glass fiber.
[0139] The cross-section configuration of the mated serpentine
channel may be round, elliptical, oval, square, rectangular,
trapezoidal, or irregular. If square, rectangular, or another shape
with generally straight sides, the cross section may be from about
2 mm to 15 mm wide, or from 3 mm to 12 mm wide, or from 5 mm to 10
mm wide. If the cross section of the mated serpentine channel is
generally round, oval or elliptical, the radius of the channel may
be from about 3 mm to 20 mm in hydraulic radius, or from 5 mm to 15
mm in hydraulic radius, or from 8 mm to 12 mm in hydraulic
radius.
[0140] Serpentine channels 660a and 660b can have approximately the
same volume or a different volume. For example, each "side" or
portion 660a, 660b of the serpentine channel may have a volume of,
e.g., 2 mL, or serpentine channel 660a of permeate member 608 may
have a volume of 2 mL, and the serpentine channel 660b of retentate
member 604 may have a volume of, e.g., 3 mL. The volume of fluid in
the serpentine channel may range from about 2 mL to about 80 mL, or
about 4 mL to 60 mL, or from 5 mL to 40 mL, or from 6 mL to 20 mL
(note these volumes apply to a SWIIN module comprising a, e.g.,
50-500K perforation member). The volume of the reservoirs may range
from 5 mL to 50 mL, or from 7 mL to 40 mL, or from 8 mL to 30 mL or
from 10 mL to 20 mL, and the volumes of all reservoirs may be the
same or the volumes of the reservoirs may differ (e.g., the volume
of the permeate reservoirs is greater than that of the retentate
reservoirs).
[0141] The serpentine channel portions 660a and 660b of the
permeate member 608 and retentate member 604, respectively, are
approximately 200 mm long, 130 mm wide, and 4 mm thick, though in
other embodiments, the retentate and permeate members can be from
75 mm to 400 mm in length, or from 100 mm to 300 mm in length, or
from 150 mm to 250 mm in length; from 50 mm to 250 mm in width, or
from 75 mm to 200 mm in width, or from 100 mm to 150 mm in width;
and from 2 mm to 15 mm in thickness, or from 4 mm to 10 mm in
thickness, or from 5 mm to 8 mm in thickness. Embodiments the
retentate (and permeate) members may be fabricated from PMMA
(poly(methyl methacrylate) or other materials may be used,
including polycarbonate, cyclic olefin co-polymer (COC), glass,
polyvinyl chloride, polyethylene, polyamide, polypropylene,
polysulfone, polyurethane, and co-polymers of these and other
polymers. Preferably at least the retentate member is fabricated
from a transparent material so that the cells can be visualized
(see, e.g., FIG. 6G and the description thereof). For example, a
video camera may be used to monitor cell growth by, e.g., density
change measurements based on an image of an empty well, with phase
contrast, or if, e.g., a chromogenic marker, such as a chromogenic
protein, is used to add a distinguishable color to the cells.
Chromogenic markers such as blitzen blue, dreidel teal, virginia
violet, vixen purple, prancer purple, tinsel purple, maccabee
purple, donner magenta, cupid pink, seraphina pink, scrooge orange,
and leor orange (the Chromogenic Protein Paintbox, all available
from ATUM (Newark, Calif.)) obviate the need to use fluorescence,
although fluorescent cell markers, fluorescent proteins, and
chemiluminescent cell markers may also be used.
[0142] Because the retentate member preferably is transparent,
colony growth in the SWIIN module can be monitored by automated
devices such as those sold by JoVE (ScanLag.TM. system, Cambridge,
Mass.) (also see Levin-Reisman, et al., Nature Methods, 7:737-39
(2010)). Automated colony pickers may be employed, such as those
sold by, e.g., TECAN (Pickolo.TM. system, Mannedorf, Switzerland);
Hudson Inc. (RapidPick.TM. Springfield, N.J.); Molecular Devices
(QPix 400.TM. system, San Jose, Calif.); and Singer Instruments
(PIXL.TM. system, Somerset, UK).
[0143] Due to the heating and cooling of the SWIIN module,
condensation may accumulate on the retentate member which may
interfere with accurate visualization of the growing cell colonies.
Condensation of the SWIIN module 650 may be controlled by, e.g.,
moving heated air over the top of (e.g., retentate member) of the
SWIIN module 650, or by applying a transparent heated lid over at
least the serpentine channel portion 660b of the retentate member
604. See, e.g., FIG. 6G and the description thereof infra.
[0144] In SWIIN module 650 cells and medium--at a dilution
appropriate for Poisson or substantial Poisson distribution of the
cells in the microwells of the perforated member--are flowed into
serpentine channel 660b from ports in retentate member 604, and the
cells settle in the microwells while the medium passes through the
filter into serpentine channel 660a in permeate member 608. The
cells are retained in the microwells of perforated member 601 as
the cells cannot travel through filter 603. Appropriate medium may
be introduced into permeate member 608 through permeate ports 611.
The medium flows upward through filter 603 to nourish the cells in
the microwells (perforations) of perforated member 601.
Additionally, buffer exchange can be effected by cycling medium
through the retentate and permeate members. In operation, the cells
are deposited into the microwells, are grown for an initial, e.g.,
2-100 doublings, editing may be induced by, e.g., raising the
temperature of the SWIIN to 42.degree. C. to induce a
temperature-inducible promoter or by removing growth medium from
the permeate member and replacing the growth medium with a medium
comprising a chemical component that induces an inducible
promoter.
[0145] Once editing has taken place, the temperature of the SWIIN
may be decreased, or the inducing medium may be removed and
replaced with fresh medium lacking the chemical component thereby
de-activating the inducible promoter. The cells then continue to
grow in the SWIIN module 650 until the growth of the cell colonies
in the microwells is normalized. For the normalization protocol,
once the colonies are normalized, the colonies are flushed from the
microwells by applying fluid or air pressure (or both) to the
permeate member serpentine channel 660a and thus to filter 603 and
pooled. Alternatively, if cherry picking is desired, the growth of
the cell colonies in the microwells is monitored, and slow-growing
colonies are directly selected; or, fast-growing colonies are
eliminated.
[0146] FIG. 6E is a top perspective view of a SWIIN module with the
retentate and perforated members in partial cross section. In this
FIG. 6E, it can be seen that serpentine channel 660a is disposed on
the top of permeate member 608 is defined by raised portions 676
and traverses permeate member 608 for most of the length and width
of permeate member 608 except for the portion of permeate member
608 that comprises the permeate and retentate reservoirs (note only
one retentate reservoir 652 can be seen). Moving from left to
right, reservoir gasket 658 is disposed upon the integrated
reservoir cover 678 (cover not seen in this FIG. 6E) of retentate
member 604. Gasket 658 comprises reservoir access apertures 632a,
632b, 632c, and 632d, as well as pneumatic ports 633a, 633b, 633c
and 633d. Also at the far left end is support 670. Disposed under
permeate reservoir 652 can be seen one of two reservoir seals 662.
In addition to the retentate member being in cross section, the
perforated member 601 and filter 603 (filter 603 is not seen in
this FIG. 6E) are in cross section. Note that there are a number of
ultrasonic tabs 664 disposed at the right end of SWIIN module 650
and on raised portion 676 which defines the channel turns of
serpentine channel 660a, including ultrasonic tabs 664 extending
through through-holes 666 of perforated member 601. There is also a
support 670 at the end distal reservoirs 652, 654 of permeate
member 608.
[0147] FIG. 6F is a side perspective view of an assembled SWIIIN
module 650, including, from right to left, reservoir gasket 658
disposed upon integrated reservoir cover 678 (not seen) of
retentate member 604. Gasket 658 may be fabricated from rubber,
silicone, nitrile rubber, polytetrafluoroethylene, a plastic
polymer such as polychlorotrifluoroethylene, or other flexible,
compressible material. Gasket 658 comprises reservoir access
apertures 632a, 632b, 632c, and 632d, as well as pneumatic ports
633a, 633b, 633c and 633d. Also at the far-left end is support 670
of permeate member 608. In addition, permeate reservoir 652 can be
seen, as well as one reservoir seal 662. At the far-right end is a
second support 670.
[0148] Imaging of cell colonies growing in the wells of the SWIIN
is desired in most implementations for, e.g., monitoring both cell
growth and device performance and imaging is necessary for
cherry-picking implementations. Real-time monitoring of cell growth
in the SWIIN requires backlighting, retentate plate (top plate)
condensation management and a system-level approach to temperature
control, air flow, and thermal management. In some implementations,
imaging employs a camera or CCD device with sufficient resolution
to be able to image individual wells. For example, in some
configurations a camera with a 9-pixel pitch is used (that is,
there are 9 pixels center-to-center for each well). Processing the
images may, in some implementations, utilize reading the images in
grayscale, rating each pixel from low to high, where wells with no
cells will be brightest (due to full or nearly-full light
transmission from the backlight) and wells with cells will be dim
(due to cells blocking light transmission from the backlight).
After processing the images, thresholding is performed to determine
which pixels will be called "bright" or "dim", spot finding is
performed to find bright pixels and arrange them into blocks, and
then the spots are arranged on a hexagonal grid of pixels that
correspond to the spots. Once arranged, the measure of intensity of
each well is extracted, by, e.g., looking at one or more pixels in
the middle of the spot, looking at several to many pixels at random
or pre-set positions, or averaging X number of pixels in the spot.
In addition, background intensity may be subtracted. Thresholding
is again used to call each well positive (e.g., containing cells)
or negative (e.g., no cells in the well). The imaging information
may be used in several ways, including taking images at time points
for monitoring cell growth. Monitoring cell growth can be used to,
e.g., remove the "muffin tops" of fast-growing cells followed by
removal of all cells or removal of cells in "rounds" as described
above, or recover cells from specific wells (e.g., slow-growing
cell colonies); alternatively, wells containing fast-growing cells
can be identified and areas of UV light covering the fast-growing
cell colonies can be projected (or rastered with shutters) onto the
SWIIN to irradiate or inhibit growth of those cells. Imaging may
also be used to assure proper fluid flow in the serpentine channel
660.
[0149] FIG. 6G depicts the embodiment of the SWIIN module in FIGS.
6D-6F further comprising a heat management system including a
heater and a heated cover. The heater cover facilitates the
condensation management that is required for imaging. Assembly 698
comprises a SWIIN module 650 seen lengthwise in cross section,
where one permeate reservoir 652 is seen. Disposed immediately upon
SWIIN module 650 is cover 694 and disposed immediately below SWIIN
module 650 is backlight 680, which allows for imaging. Beneath and
adjacent to the backlight and SWIIN module is insulation 682, which
is disposed over a heatsink 684. In this FIG. 6G, the fins of the
heatsink would be in-out of the page. In addition there is also
axial fan 686 and heat sink 688, as well as two thermoelectric
coolers 692, and a controller 690 to control the pneumatics,
thermoelectric coolers, fan, solenoid valves, etc. The arrows
denote cool air coming into the unit and hot air being removed from
the unit. It should be noted that control of heating allows for
growth of many different types of cells as well as strains of cells
that are, e.g., temperature sensitive, etc., and allows use of
temperature-sensitive promoters. Temperature control allows for
protocols to be adjusted to account for differences in
transformation efficiency, cell growth and viability. For more
details regarding solid wall isolation incubation and normalization
devices see U.S. Pat. Nos. 10,533,152; 10,550,363; 10,532,324;
10,625,212; and U.S. Ser. No. 16/597,826, filed 19 Oct. 2019; Ser.
No. 16/597,831, filed 9 Oct. 2019; Ser. No. 16/693,630, filed 25
Nov. 2019; and Ser. No. 16/686,066, filed 15 Nov. 2019.
Use of the Automated Multi-Module Yeast Cell Processing
Instrument
[0150] FIG. 7 illustrates an embodiment of a multi-module cell
processing instrument. This embodiment depicts an exemplary system
that performs recursive gene editing on a yeast cell population.
The cell processing instrument 700 may include a housing 726, a
reservoir for storing cells to be transformed or transfected 702,
and a cell growth module (comprising, e.g., a rotating growth vial)
704. The cells to be transformed are transferred from a reservoir
to the cell growth module to be cultured until the cells hit a
target OD. Once the cells hit the target OD, the growth module may
cool or freeze the cells for later processing or transfer the cells
to a cell concentration/filtration module 706 where the cells are
subjected to buffer exchange and rendered electrocompetent, and the
volume of the cells may be reduced substantially. Once the cells
have been concentrated to an appropriate volume, the cells are
transferred to electroporation device 708. In addition to the
reservoir for storing cells 702, the multi-module cell processing
instrument includes a reservoir for storing the vector
pre-assembled with editing oligonucleotide cassettes 722. The
pre-assembled nucleic acid vectors are transferred to the
electroporation device 708, which already contains the cell culture
grown to a target OD. In the electroporation device 708, the
nucleic acids are electroporated into the cells. Following
electroporation, the cells are transferred into a recovery and
dilution module 710, where the cells recover briefly
post-transformation.
[0151] After recovery, the cells may be transferred to a storage
module 712, where the cells can be stored at, e.g., 4.degree. C.
for later processing, the cells may be transferred to a reservoir
for cell retrieval 714, or the cells may be diluted and transferred
to a selection/singulation/growth/induction/editing/normalization
(SWIIN) module 720. In the SWIIN 720, the cells are arrayed such
that there is an average of one cell per microwell. The arrayed
cells may be in selection medium to select for cells that have been
transformed or transfected with the editing vector(s). Once
singulated, in one embodiment the cells grow through 2-50 doublings
and establish colonies. Once colonies are established, editing is
induced by providing conditions (e.g., temperature, addition of an
inducing or repressing chemical) to induce editing. Editing is then
initiated and allowed to proceed, the cells are allowed to grow to
terminal size (e.g., normalization of the colonies) in the
microwells and then are treated to conditions that cure the editing
vector from this round. In another embodiment editing is not
induced and the cells are grown, allowed to edit, recover and
normalize, and optionally cure.
[0152] Once cured, the cells can be flushed out of the microwells
and pooled, then transferred to the storage (or recovery) unit 712
or can be transferred back to the growth module 704 for another
round of editing. In between pooling and transfer to a growth
module, there typically is one or more additional steps, such as
cell recovery, medium exchange (rendering the cells
electrocompetent), cell concentration (typically concurrently with
medium exchange by, e.g., filtration. Note that the
selection/singulation/growth/induction/editing/normalization
modules may be the same module, where all processes are performed
in, e.g., a solid wall device, or selection and/or dilution may
take place in a separate vessel before the cells are transferred to
the solid wall
singulation/growth/induction/editing/normalization/editing module
(SWIIN). Similarly, the cells may be pooled after normalization,
transferred to a separate vessel, and cured in the separate vessel.
As an alternative to singulation in, e.g., a solid wall device, the
transformed cells may be grown in--and editing can be induced
in--bulk liquid as described in U.S. Ser. No. 16/399,988, filed 30
Apr. 2019. Once the putatively-edited cells are pooled, they may be
subjected to another round of editing, beginning with growth, cell
concentration and treatment to render electrocompetent, and
transformation by yet another donor nucleic acid in another editing
cassette via the electroporation module 708.
[0153] In electroporation device 708, the yeast cells selected from
the first round of editing are transformed by a second set of
editing oligos (or other type of oligos) and the cycle is repeated
until the cells have been transformed and edited by a desired
number of, e.g., editing cassettes. The multi-module cell
processing instrument exemplified in FIG. 7 is controlled by a
processor 724 configured to operate the instrument based on user
input or is controlled by one or more scripts including at least
one script associated with the reagent cartridge. The processor 724
may control the timing, duration, and temperature of various
processes, the dispensing of reagents, and other operations of the
various modules of the instrument 700. For example, a script or the
processor may control the dispensing of cells, reagents, vectors,
and editing oligonucleotides; which editing oligonucleotides are
used for cell editing and in what order; the time, temperature and
other conditions used in the recovery and expression module, the
wavelength at which OD is read in the cell growth module, the
target OD to which the cells are grown, and the target time at
which the cells will reach the target OD. In addition, the
processor may be programmed to notify a user (e.g., via an
application) as to the progress of the cells in the automated
multi-module cell processing instrument.
[0154] It should be apparent to one of ordinary skill in the art
given the present disclosure that the process described may be
recursive and multiplexed; that is, cells may go through the
workflow described in relation to FIG. 7, then the resulting edited
culture may go through another (or several or many) rounds of
additional editing (e.g., recursive editing) with different editing
vectors. For example, the cells from round 1 of editing may be
diluted and an aliquot of the edited cells edited by editing vector
A may be combined with editing vector B, an aliquot of the edited
cells edited by editing vector A may be combined with editing
vector C, an aliquot of the edited cells edited by editing vector A
may be combined with editing vector D, and so on for a second round
of editing. After round two, an aliquot of each of the
double-edited cells may be subjected to a third round of editing,
where, e.g., aliquots of each of the AB-, AC-, AD-edited cells are
combined with additional editing vectors, such as editing vectors
X, Y, and Z. That is that double-edited cells AB may be combined
with and edited by vectors X, Y, and Z to produce triple-edited
edited cells ABX, ABY, and ABZ; double-edited cells AC may be
combined with and edited by vectors X, Y, and Z to produce
triple-edited cells ACX, ACY, and ACZ; and double-edited cells AD
may be combined with and edited by vectors X, Y, and Z to produce
triple-edited cells ADX, ADY, and ADZ, and so on. In this process,
many permutations and combinations of edits can be executed,
leading to very diverse cell populations and cell libraries. In any
recursive process, it is advantageous to "cure" the previous engine
and editing vectors (or single engine+editing vector in a single
vector system). "Curing" is a process in which one or more vectors
used in the prior round of editing is eliminated from the
transformed cells.
[0155] Curing can be accomplished by, e.g., cleaving the vector(s)
using a curing plasmid thereby rendering the editing and/or engine
vector (or single, combined engine/editing vector) nonfunctional;
diluting the vector(s) in the cell population via cell growth (that
is, the more growth cycles the cells go through, the fewer daughter
cells will retain the editing or engine vector(s)), or by, e.g.,
utilizing a heat-sensitive origin of replication on the editing or
engine vector (or combined engine+editing vector). The conditions
for curing will depend on the mechanism used for curing; that is,
in this example, how the curing plasmid cleaves the editing and/or
engine vector.
[0156] FIG. 8 is a simplified block diagram of an embodiment of an
exemplary automated multi-module cell processing instrument
comprising an isolation, induction, editing, and normalization
module such as a SWIIN, or just by dilute plating on a solid
substrate. The cell processing instrument 800 may include a housing
826, a reservoir of cells to be transformed or transfected 802, and
a growth module (a cell growth device) 804. The cells to be
transformed are transferred from a reservoir to the growth module
to be cultured until the cells hit a target OD. Once the cells hit
the target OD, the growth module may cool or freeze the cells for
later processing, or the cells may be transferred to a cell
concentration/filtration module 830 where the cells are rendered
electrocompetent and concentrated to a volume optimal for cell
transformation. Once concentrated, the cells are then transferred
to an electroporation device 808 (e.g., transformation/transfection
module).
[0157] In addition to the reservoir for storing the cells, the
system 800 may include a reservoir for storing editing cassettes
816 and a reservoir for storing an expression vector backbone 818.
Both the editing oligonucleotide cassettes and the expression
vector backbone are transferred from the reagent cartridge to a
nucleic acid assembly module 828, where the editing oligonucleotide
cassettes are inserted into the expression vector backbone. The
assembled nucleic acids may be transferred into an optional
purification module 822 for desalting and/or other purification
and/or concentration procedures needed to prepare the assembled
nucleic acids for transformation. Alternatively, pre-assembled
nucleic acids, e.g., an editing vector, may be stored within
reservoir 816 or 818. Once the processes carried out by the
purification module 822 are complete, the assembled nucleic acids
are transferred to, e.g., an electroporation device 808, which
already contains the cell culture grown to a target OD and rendered
electrocompetent via concentration module 830. In electroporation
device 808, the assembled nucleic acids are introduced into the
cells. Following electroporation, the cells are transferred into a
combined recovery/selection module 832. For examples of
multi-module cell editing instruments, see U.S. Pat. Nos.
10,253,316; 10,329,559; 10,323,242; 10,421,959; 10,465,185;
10,519,437; 10,584,333; and 10,584,334; and U.S. Ser. No.
16/750,369, filed 23 Jan. 2020; Ser. No. 16/822,249, filed 18 Mar.
2020; and Ser. No. 16/837,985, filed 1 Apr. 2020, all of which are
herein incorporated by reference in their entirety.
[0158] Following recovery, and, optionally, selection, the cells
are transferred to a growth, induction (optional), and editing
module (bulk liquid culture) 840. The cells are allowed to grow
until they go through several to many doublings, then editing
optionally is induced by induction of transcription of one or both
of the nuclease and gRNA. In some embodiments, editing optionally
is induced by transcription of one or both of the nuclease and the
gRNA being under the control of an inducible promoter. In some
embodiments, the inducible promoter is a pL promoter where the
promoter is activated by a rise in temperature of the cell culture
and "deactivated" by lowering the temperature of the cell
culture.
[0159] The recovery, selection, isolation, growth, induction,
editing and storage modules may all be separate, may be arranged
and combined as shown in FIG. 8, or may be arranged or combined in
other configurations. In certain embodiments, recovery and
selection are performed in one module, and isolation, growth,
induction, editing, and re-growth are performed in a separate
module. Alternatively, recovery, selection, isolation, growth,
induction, editing, and re-growth are performed in a single
module.
[0160] Once the cells are edited and re-grown (e.g., recovered from
editing), the cells may be stored, e.g., in a storage module 812,
where the cells can be kept at, e.g., 4.degree. C. until the cells
are used in another round of editing, or the cells may be
transferred to a reservoir for cell retrieval 814. The multi-module
cell processing instrument is controlled by a processor 824
configured to operate the instrument based on user input, as
directed by one or more scripts, or as a combination of user input
or a script. The processor 824 may control the timing, duration,
temperature, and operations of the various modules of the system
800 and the dispensing of reagents. For example, the processor 824
may cool the cells post-transformation until editing is desired,
upon which time the temperature may be raised to a temperature
conducive of genome editing and cell growth. The processor may be
programmed with standard protocol parameters from which a user may
select, a user may specify one or more parameters manually or one
or more scripts associated with the reagent cartridge may specify
one or more operations and/or reaction parameters. In addition, the
processor may notify the user (e.g., via an application to a smart
phone or other device) that the cells have reached the target OD as
well as update the user as to the progress of the cells in the
various modules in the multi-module system.
EXAMPLES
[0161] The following examples are put forth so as to provide those
of ordinary skill in the art with a complete disclosure and
description of how to make and use the present invention, and are
not intended to limit the scope of what the inventors regard as
their invention, nor are they intended to represent or imply that
the experiments below are all of or the only experiments performed.
It will be appreciated by persons skilled in the art that numerous
variations and/or modifications may be made to the invention as
shown in the specific aspects without departing from the spirit or
scope of the invention as broadly described. The present aspects
are, therefore, to be considered in all respects as illustrative
and not restrictive.
Example I: Growth in the Cell Growth Module
[0162] One embodiment of the cell growth device as described herein
was used to grow a yeast cell culture which was monitored in real
time using an embodiment of the cell growth device described
herein. The rotating growth vial/cell growth device was used to
measure OD.sub.600 in real time of yeast S. cerevisiae str. s288c
cells in YPAD medium. The cells were grown at 30.degree. C. using
oscillating rotation and employing a 2-paddle rotating growth vial.
FIG. 9 is a graph showing the results. Note that OD.sub.600 6.0 was
reached in 14 hours.
Example II: Cell Concentration
[0163] The TFF module as described above in relation to FIGS. 4A-4E
has been used successfully to process and perform buffer exchange
on yeast cultures. A yeast culture was initially concentrated to
approximately 5 ml using two passes through the TFF device in
opposite directions. The cells were washed with 50 ml of 1M
sorbitol three times, with three passes through the TFF device
after each wash. After the third pass of the cells following the
last wash with 1M sorbitol, the cells were passed through the TFF
device two times, wherein the yeast cell culture was concentrated
to approximately 525 .mu.l. FIG. 10 presents the filter buffer
exchange performance for yeast cells determined by measuring
filtrate conductivity and filter processing time. Target
conductivity (.about.10 .mu.S/cm) was achieved in approximately 23
minutes utilizing three 50 ml 1M sorbitol washes and three passes
through the TFF device for each wash. The volume of the cells was
reduced from 20 ml to 525 .mu.l. Recovery of approximately 90% of
the cells has been achieved.
Example III: Production and Transformation of Electrocompetent S.
Cerevisiae
[0164] For testing transformation of the FTEP device in yeast,
electrocompetent S. Cerevisiae cells were created using the methods
as generally set forth in Bergkessel and Guthrie, Methods Enzymol.,
529:311-20 (2013). Briefly, YFAP media was inoculated for overnight
growth, with 3 ml inoculate to produce 100 ml of cells. Every 100
ml of culture processed resulted in approximately 1 ml of competent
cells. Cells were incubated at 30.degree. C. in a shaking incubator
until they reached an OD600 of 1.5+/-0.1.
[0165] A conditioning buffer was prepared using 100 mM lithium
acetate, 10 mM dithiothreitol, and 50 mL of buffer for every 100 mL
of cells grown and kept at room temperature. Cells were harvested
in 250 ml bottles at 4300 rpm for 3 minutes, and the supernatant
removed. The cell pellets were suspended in 100 ml of cold 1 M
sorbitol, spun at 4300 rpm for 3 minutes and the supernatant once
again removed. The cells were suspended in conditioning buffer,
then the suspension transferred into an appropriate flask and
shaken at 200 RPM and 30.degree. C. for 30 minutes. The suspensions
were transferred to 50 ml conical vials and spun at 4300 rpm for 3
minutes. The supernatant was removed and the pellet resuspended in
cold 1 M sorbitol. These steps were repeated three times for a
total of three wash-spin-decant steps. The pellet was suspended in
sorbitol to a final OD600 of 150+/-20 per ml.
[0166] A comparative electroporation experiment was performed to
determine the efficiency of transformation of the electrocompetent
S. cerevisiae using the FTEP device. The flow rate was controlled
with a syringe pump (Harvard apparatus PHD ULTRA.TM. 4400). The
suspension of cells with DNA was loaded into a 1 mL glass syringe
(Hamilton 81320 Syringe, PTFE Luer Lock) before mounting on the
pump. The output from the function generator was turned on
immediately after starting the flow. The processed cells flowed
directly into a tube with 1M sorbitol with carbenicillin. Cells
were collected until the same volume electroporated in the
NEPAGENE.TM. had been processed, at which point the flow and the
output from the function generator were stopped. After a 3-hour
recovery in an incubator shaker at 30.degree. C. and 250 rpm, cells
were plated to determine the colony forming units (CFUs) that
survived electroporation and failed to take up a plasmid and the
CFUs that survived electroporation and took up a plasmid. Plates
were incubated at 30.degree. C. Yeast colonies are counted after
48-76 hrs.
[0167] The flow-through electroporation experiments were
benchmarked against 2 mm electroporation cuvettes (Bull dog Bio)
using an in vitro high voltage electroporator (NEPAGENE.TM.
ELEPO21). Stock tubes of cell suspensions with DNA were prepared
and used for side-to-side experiments with the NEPAGENE.TM. and the
flow-through electroporation. The results are shown in FIG. 11. The
device showed better transformation and survival of
electrocompetent S. cerevisiae at 2.5 kV voltages as compared to
the NEPAGENE.TM. method. Input is total number of cells that were
processed.
Example IV: Singulation of Yeast Colonies in a Solid Wall
Device
[0168] Electrocompetent yeast cells were transformed with a cloned
library, an isothermal assembled library, or a process control
sgRNA plasmid (escapee surrogate). Electrocompetent Saccharomyces
cerevisiae cells were prepared as follows: The afternoon before
transformation was to occur, 10 mL of YPAD was inoculated with the
selected Saccharomyces cerevisiae strain. The culture was shaken at
250 RPM and 30.degree. C. overnight. The next day, 100 mL of YPAD
was added to a 250-mL baffled flask and inoculated with the
overnight culture (around 2 mL of overnight culture) until the
OD600 reading reached 0.3+/-0.05. The culture was placed in the
30.degree. C. incubator shaking at 250 RPM and allowed to grow for
4-5 hours, with the OD checked every hour. When the culture reached
an OD600 of approximately 1.5, 50 mL volumes were poured into two
50 mL conical vials, then centrifuged at 4300 RPM for 2 minutes at
room temperature. The supernatant was removed from all 50 mL
conical tubes, while avoiding disturbing the cell pellet. 50 mL of
a Lithium Acetate/Dithiothreitol solution was added to each conical
tube and the pellet was gently resuspended. Both suspensions were
transferred to a 250 mL flask and placed in the shaker; then shaken
at 30.degree. C. and 200 RPM for 30 minutes.
[0169] After incubation was complete, the suspension was
transferred to two 50-mL conical vials. The suspensions then were
centrifuged at 4300 RPM for 3 minutes, then the supernatant was
discarded. Following the lithium acetate/Dithiothreitol treatment
step, cold liquids were used and the cells were kept on ice until
electroporation. 50 mL of 1 M sorbitol was added and the pellet was
resuspended, then centrifuged at 4300 RPM, 3 minutes, 4.degree. C.,
after which the supernatant was discarded. The 1M sorbitol wash was
repeated twice for a total of three washes. 50 .mu.L of 1 M
sorbitol was added to one pellet, cells were resuspended, then
transferred to the other tube to suspend the second pellet. The
volume of the cell suspension was measured and brought to 1 mL with
cold 1 M sorbitol. At this point the cells were electrocompetent
and could be transformed with a cloned library, an isothermal
assembled library, or process control sgRNA plasmids.
[0170] In brief, a required number of 2-mm gap electroporation
cuvettes were prepared by labeling the cuvettes and then chilling
on ice. The appropriate plasmid--or DNA mixture--was added to each
corresponding cuvette and placed back on ice. 100 uL of
electrocompetent cells was transferred to each labelled cuvette,
and each sample was electroporated using appropriate electroporator
conditions. 900 uL of room temperature YPAD Sorbitol media was then
added to each cuvette. The cell suspension was transferred to a 14
ml culture tube and then shaken at 30.degree. C., 250 RPM for 3
hours. After a 3 hr recovery, 9 ml of YPAD containing the
appropriate antibiotic, e.g., G418 or Hygromycin B, was added. At
this point the transformed cells were processed in parallel in the
solid wall device and the standard plating protocol, so as to
compare "normalization" in the sold wall device with the standard
benchtop process. Immediately before cells the cells were
introduced to the permeable-bottom solid wall device, the 0.45
.mu.M filter forming the bottom of the microwells was treated with
a 0.1% TWEEN.TM. solution to effect proper spreading/distribution
of the cells into the microwells of the solid wall device. The
filters were placed into a Swinnex Filter Holder (47 mm,
Millipore.RTM., SX0004700) and 3 ml of a solution with 0.85% NaCl
and 0.1% TWEEN.TM. was pulled through the solid wall device and
filter through using a vacuum. Different TWEEN.TM. concentrations
were evaluated, and it was determined that for a 47 mm diameter
solid wall device with a 0.45 .mu.M filter forming the bottom of
the microwells, a pre-treatment of the solid wall device+filter
with 0.1% TWEEN.TM. was preferred (data not shown).
[0171] At the end of the incubation the perforated disks and
filters (still assembled) were removed from the supporting nutrient
source (in this case an agar plate) and were photographed with a
focused, "transilluminating" light source so that the number and
distribution of loaded microwells on the solid wall device could be
assessed (data not shown). To retrieve cells from the
permeable-bottom solid wall device, the filter was transferred to a
labeled sterile 100 mm petri dish which contained 15 ml of sterile
0.85% NaCl, then the petri dish was placed in a shaking incubator
set to 30.degree. C./80 RPM to gently remove the cells from the
filter and resuspend the cells in the 0.85% NaCl. The cells were
shaken for 15 minutes, then were transferred to a sterile tube,
e.g., a 50 ml conical centrifuge tube. The OD600 of the cell
suspension was measured; at this point the cells can be processed
in different ways depending on the purpose of the study. For
example, if an ADE2 stop codon mutagenesis library is used,
successfully-edited cells should result in colonies with a red
color phenotype when the resuspended cells are spread onto YPD agar
plates and allowed to grow for 4-7 days. This phenotypic difference
allows for a quantification of percentage of edited cells and the
extent of normalization of edited and unedited cells.
Example V: Growth and Editing of S. cerevisae Under Selective
Pressure
[0172] To compare the editing rate of yeast cells transformed with
the vectors depicted in FIGS. 1C and 1D, as well as a "standard"
vector without a degron fusion or minimal promoter, 10 mL of YPAD
medium was inoculated with the IY19 strain of S. cerevisiae. The
culture was incubated at 30.degree. C. while shaking at 250 rpm
overnight. The following day, the overnight culture was diluted to
an OD600=0.3 in 100 ml in fresh YPAD media. The diluted culture was
placed in the 30.degree. C. incubator shaking at 250 rpm and grown
for 4-5 hours. When the culture reached OD600 of .about.1.5, cells
were harvested by centrifuging at 4300 RPM for 3 minutes at room
temperature.
[0173] The harvested cells were resuspended in 50 ml of 100 mM
lithium acetate+10 mM DTT solution and conditioned by shaking at
30.degree. C./200 rpm for 30 minutes. The cells were then harvested
after conditioning by centrifuging at 4300 RPM for 3 minutes at
room temperature. Following centrifugation, the cells were washed
3.times. with 50 mL of ice-cold 1 M sorbitol; at the end of the
final wash, cells were resuspended with lml of ice cold 1M
sorbitol. 100 .mu.l of the cell resuspension was used in every
transformation (standard plasmid backbone, degron plasmid backbone
(see FIG. 1C) and minimal promoter plasmid backbone (see FIG. 1D)).
The editing cassettes were the same for each plasmid backbone. The
competent cells were electroporated in a 2-mm electroporation
cuvette along with the appropriate editing plasmid.
[0174] The plasmid backbone/cassette mix comprised 500 ng of linear
plasmid backbone (standard, degron, and minimal promoter) and 50 ng
of cassette. A Nepagene electroporator used the following
conditions to electroporate each sample: for the poring pulse: a
single pulse at voltage=1800, pulse length=5.0, pulse interval=50.0
msec; for the transfer pulses, three pulses at voltage=100, pulse
length=50.0 msec, pulse interval -50.0. Following electroporation,
900 .mu.L of room temperature YPAD+1M Sorbitol media was added to
each cuvette and the cell suspension was transferred to a pop-cap
15 mL tube. This mix was shaken at 30.degree. C./250 RPM for 3
hours. 1-10 .mu.l of the transformation was then plated on YPD+G418
(200 .mu.g/ml) plates and incubated at 30.degree. C. for 3 days. 96
colonies were picked from transformation plates, and these colonies
were cultured in 1 mL of YPAD+G418 (200 .mu.g/ml) media in a
deep-well plate and grown overnight at 30.degree. C. The 96-well
plate was used for DNA extraction using a SV lysis Promega DNA
extraction kit (Promega, Madison, Wis.) according to manufacturer's
instructions.
[0175] Three different survival marker proteins were tested:
hygromycin (FIGS. 12A, 12B and 12C), kanamycin (FIGS. 13A, 13B, and
13C), and blasticidin (data not shown). The minimal promoter was
the truncated version of the URA3 promoter, URA3-d, comprising only
47 nucleotides located upstream of the start codon. Using
hygromycin as the survival marker, the standard editing plasmid
resulted in clonality of 1.4%, the plasmid coding for the
degron-hygromycin fusion protein resulted in clonality of 10.2%,
and the plasmid with the minimal promoter driving transcription of
the hygromycin gene resulted in 32.6% clonality. Using kanamycin as
the survival marker, the standard editing plasmid resulted in
clonality of 14.7%, the plasmid coding for the degron-kanamycin
fusion protein resulted in clonality of 21.4%, and the plasmid with
the minimal promoter driving transcription of the kanamycin gene
resulted in 39.3% clonality. Preliminary data with the minimal
promoter driving transcription of blasticidin as the survival
marker, the clonality was 6.9% with 19/20 unique edits (data not
shown).
Example VI: Growth and Editing of S. cerevisae Under Selective
Pressure
[0176] FIG. 14 shows the plasmid copy number and edit rate of
various plasmid constructs and their edit rates measured via
shotgun NGS sequencing. The plasmid copy number is calculated by
taking the ratio of median plasmid read depth vs. median genomic
read depth. The histograms show the measured plasmid copy number
from at least 48 isolated colonies. The edit rates were calculated
via next gen sequencing of isolated colonies and are the same
values that appear in FIGS. 12 A-12C and FIGS. 13A-13C. Note the
correlation between plasmid copy number and observed edit rate,
which illustrates the utility of increasing the plasmid copy number
of editing constructs to increase observed editing.
Example VII: Fully-Automated Singleplex RGN-directed Editing
Run
[0177] Singleplex automated genomic editing using MAD7 nuclease was
successfully performed with an automated multi-module instrument of
the disclosure. An ampR plasmid backbone and a lacZ_F172* editing
cassette were assembled via Gibson Assembly.RTM. into an "editing
vector" in an isothermal nucleic acid assembly module included in
the automated instrument. lacZ_F172 functionally knocks out the
lacZ gene. "lacZ_F172*" indicates that the edit happens at the
172nd residue in the lacZ amino acid sequence. Following assembly,
the product was de-salted in the isothermal nucleic acid assembly
module using AMPure beads, washed with 80% ethanol, and eluted in
buffer. The assembled editing vector and recombineering-ready,
electrocompetent E. Coli cells were transferred into a
transformation module for electroporation. The cells and nucleic
acids were combined and allowed to mix for 1 minute, and
electroporation was performed for 30 seconds. The parameters for
the poring pulse were: voltage, 2400 V; length, 5 ms; interval, 50
ms; number of pulses, 1; polarity, +. The parameters for the
transfer pulses were: Voltage, 150 V; length, 50 ms; interval, 50
ms; number of pulses, 20; polarity, +/-. Following electroporation,
the cells were transferred to a recovery module (another growth
module), and allowed to recover in SOC medium containing
chloramphenicol. Carbenicillin was added to the medium after 1
hour, and the cells were allowed to recover for another 2 hours.
After recovery, the cells were held at 4.degree. C. until recovered
by the user.
[0178] After the automated process and recovery, an aliquot of
cells was plated on MacConkey agar base supplemented with lactose
(as the sugar substrate), chloramphenicol and carbenicillin and
grown until colonies appeared. White colonies represented
functionally edited cells, purple colonies represented un-edited
cells. All liquid transfers were performed by the automated liquid
handling device of the automated multi-module cell processing
instrument.
[0179] The result of the automated processing was that
approximately 1.0E.sup.-03 total cells were transformed (comparable
to conventional benchtop results), and the editing efficiency was
83.5%. The lacZ_172 edit in the white colonies was confirmed by
sequencing of the edited region of the genome of the cells.
Further, steps of the automated cell processing were observed
remotely by webcam and text messages were sent to update the status
of the automated processing procedure.
Example VIII: Fully-Automated Recursive Editing Run
[0180] Recursive editing was successfully achieved using the
automated multi-module cell processing system. An ampR plasmid
backbone and a lacZ_V10* editing cassette were assembled via Gibson
Assembly.RTM. into an "editing vector" in an isothermal nucleic
acid assembly module included in the automated system. Similar to
the lacZ_F172 edit, the lacZ_V10 edit functionally knocks out the
lacZ gene. "lacZ_V10" indicates that the edit happens at amino acid
position 10 in the lacZ amino acid sequence. Following assembly,
the product was de-salted in the isothermal nucleic acid assembly
module using AMPure beads, washed with 80% ethanol, and eluted in
buffer. The first assembled editing vector and the
recombineering-ready electrocompetent E. Coli cells were
transferred into a transformation module for electroporation. The
cells and nucleic acids were combined and allowed to mix for 1
minute, and electroporation was performed for 30 seconds. The
parameters for the poring pulse were: voltage, 2400 V; length, 5
ms; interval, 50 ms; number of pulses, 1; polarity, +. The
parameters for the transfer pulses were: Voltage, 150 V; length, 50
ms; interval, 50 ms; number of pulses, 20; polarity, +/-. Following
electroporation, the cells were transferred to a recovery module
(another growth module) allowed to recover in SOC medium containing
chloramphenicol. Carbenicillin was added to the medium after 1
hour, and the cells were grown for another 2 hours. The cells were
then transferred to a centrifuge module and a media exchange was
then performed. Cells were resuspended in TB containing
chloramphenicol and carbenicillin where the cells were grown to
OD600 of 2.7, then concentrated and rendered electrocompetent.
[0181] During cell growth, a second editing vector was prepared in
an isothermal nucleic acid assembly module. The second editing
vector comprised a kanamycin resistance gene, and the editing
cassette comprised a galK Y145* edit. If successful, the galK Y145*
edit confers on the cells the ability to uptake and metabolize
galactose. The edit generated by the galK Y154* cassette introduces
a stop codon at the 154th amino acid reside, changing the tyrosine
amino acid to a stop codon. This edit makes the galK gene product
non-functional and inhibits the cells from being able to metabolize
galactose. Following assembly, the second editing vector product
was de-salted in the isothermal nucleic acid assembly module using
AMPure beads, washed with 80% ethanol, and eluted in buffer. The
assembled second editing vector and the electrocompetent E. Coli
cells (that were transformed with and selected for the first
editing vector) were transferred into a transformation module for
electroporation, using the same parameters as detailed above.
Following electroporation, the cells were transferred to a recovery
module (another growth module), allowed to recover in SOC medium
containing carbenicillin. After recovery, the cells were held at
4.degree. C. until retrieved, after which an aliquot of cells were
plated on LB agar supplemented with chloramphenicol, and kanamycin.
To quantify both lacZ and galK edits, replica patch plates were
generated on two media types: 1) MacConkey agar base supplemented
with lactose (as the sugar substrate), chloramphenicol, and
kanamycin, and 2) MacConkey agar base supplemented with galactose
(as the sugar substrate), chloramphenicol, and kanamycin. All
liquid transfers were performed by the automated liquid handling
device of the automated multi-module cell processing system.
[0182] In this recursive editing experiment, 41% of the colonies
screened had both the lacZ and galK edits, the results of which
were comparable to the double editing efficiencies obtained using a
"benchtop" or manual approach.
[0183] While this invention is satisfied by embodiments in many
different forms, as described in detail in connection with
preferred embodiments of the invention, it is understood that the
present disclosure is to be considered as exemplary of the
principles of the invention and is not intended to limit the
invention to the specific embodiments illustrated and described
herein. Numerous variations may be made by persons skilled in the
art without departure from the spirit of the invention. The scope
of the invention will be measured by the appended claims and their
equivalents. The abstract and the title are not to be construed as
limiting the scope of the present invention, as their purpose is to
enable the appropriate authorities, as well as the general public,
to quickly determine the general nature of the invention. In the
claims that follow, unless the term "means" is used, none of the
features or elements recited therein should be construed as
means-plus-function limitations pursuant to 35 U.S.C. .sctn. 112,
6.
Sequence CWU 1
1
30147DNAArtificial SequenceTruncated promoter 1taacccaact
gcacagaaca aaaacctgca ggaaacgaag ataaatc 472100DNAArtificial
SequenceTRUNCATED PROMOTER SEQUENCE 2attggcatta tcacataatg
aattatacat tatataaagt aatgtgattt cttcgaagaa 60tatactaaaa aatgagcagg
caagataaac gaaggcaaag 100350DNAArtificial SequenceTRUNCATED
PROMOTER SEQUENCE 3cttcgaagaa tatactaaaa aatgagcagg caagataaac
gaaggcaaag 50430DNAArtificial
SequenceAATGAGCAGGCAAGATAAACGAAGGCAAAG 4aatgagcagg caagataaac
gaaggcaaag 30520DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE
5caagataaac gaaggcaaag 206100DNAArtificial SequenceTRUNCATED
PROMOTER SEQUENCE 6ttcggtcgaa aaaagaaaag gagagggcca agagggaggg
cattggtgac tattgagcac 60gtgagtatac gtgattaagc acacaaaggc agcttggagt
100750DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE 7tattgagcac
gtgagtatac gtgattaagc acacaaaggc agcttggagt 50830DNAArtificial
SequenceTRUNCATED PROMOTER SEQUENCE 8gtgattaagc acacaaaggc
agcttggagt 30920DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE
9acacaaaggc agcttggagt 2010100DNAArtificial SequenceTRUNCATED
PROMOTER SEQUENCE 10ttttccaata ggtggttagc aatcgtctta ctttctaact
tttcttacct tttacatttc 60agcaatatat atatatatat ttcaaggata taccattcta
1001150DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE
11tttacatttc agcaatatat atatatatat ttcaaggata taccattcta
501230DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE
12atatatatat ttcaaggata taccattcta 301320DNAArtificial
SequenceTRUNCATED PROMOTER SEQUENCE 13ttcaaggata taccattcta
2014100DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE
14ggtatatata cgcatatgtg gtgttgaaga aacatgaaat tgcccagtat tcttaaccca
60actgcacaga acaaaaacct gcaggaaacg aagataaatc 1001550DNAArtificial
SequenceTRUNCATED PROMOTER SEQUENCE 15tcttaaccca actgcacaga
acaaaaacct gcaggaaacg aagataaatc 501630DNAArtificial
SequenceTRUNCATED PROMOTER SEQUENCE 16acaaaaacct gcaggaaacg
aagataaatc 301720DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE
17gcaggaaacg aagataaatc 2018100DNAArtificial SequenceTRUNCATED
PROMOTER SEQUENCE 18tcaagtttca gtttcatttt tcttgttcta ttacaacttt
ttttacttct tgctcattag 60aaagaaagca tagcaatcta atctaagttt taattacaaa
1001950DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE
19tgctcattag aaagaaagca tagcaatcta atctaagttt taattacaaa
502030DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE
20tagcaatcta atctaagttt taattacaaa 302120DNAArtificial
SequenceTRUNCATED PROMOTER SEQUENCE 21atctaagttt taattacaaa
2022100DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE
22taaaataata aaacatcaag aacaaacaag ctcaacttgt cttttctaag aacaaagaat
60aaacacaaaa acaaaaagtt tttttaattt taatcaaaaa 1002350DNAArtificial
SequenceTRUNCATED PROMOTER SEQUENCE 23aacaaagaat aaacacaaaa
acaaaaagtt tttttaattt taatcaaaaa 502430DNAArtificial
SequenceTRUNCATED PROMOTER SEQUENCE 24acaaaaagtt tttttaattt
taatcaaaaa 302520DNAArtificial SequenceTRUNCATED PROMOTER SEQUENCE
25tttttaattt taatcaaaaa 2026566DNAArtificial SequenceWEAK PROMOTER
SEQUENCE 26tcgacaaatt gttacgttgt gctttgattt ctaaagcgct tcttcacctg
caggttctga 60gccctaagaa aaaaaatttc cttggttgaa aatggcggaa aaaaaaaatt
cagaaaaaga 120aataaagcac gtgtgcgcgg tgtgtggatg atggtttcat
cattgtcaac ggcattttcg 180ttcttgtgga ttgttgtaaa ctttccagaa
cattctagaa agaaagcaca cggaacgttt 240agaagctgtc atttgcgttt
tttctccaga ttttagttga gaaagtaatt aaattattct 300tctttttcca
gaacgttcca tcggcggcaa aagggagaga aagaacccaa aaagaagggg
360ggccatttag attagctgat cgtttcgagg acttcaaggt tatataaggg
gtggattgat 420gtatcttcga gaagggattg agttgtagtt tcgtttccca
attcttactt aagttgtttt 480attttctcta tttgtaagat aagcacatca
aaagaaaagt aatcaagtat tacaagaaac 540aaaaattcaa gtaaataaca gataat
56627654DNAArtificial SequenceWEAK PROMOTER SEQUENCE 27gaaattcaaa
actctccaga caaagcctgc catttggcca agcaagcttt tgacgacgct 60attgctgagt
tggacactct gtctgaagaa tcatacaaag atagcacact tatcatgcaa
120ctgctaaggg acaatttaac cttatggact tcagacatgt ccgagtccgg
tcaagctgaa 180gaccaacaac aacaacaaca acatcagcaa cagcagccac
ctgctgccgc cgaaggtgaa 240gcaccaaagt aagtattctg ataaatctaa
agagaaatta ctaaaaaaaa gaaaaaaaaa 300agaacggggg tgtaataatt
tgtagttcat tattgcaatt atatatctat atctatatat 360gtatataaca
ttaacatgtg catgtacaca cgtaatcgcg cgtgtacatg tctatatgtg
420ttacttgaac tatactgttt tgacgtgtat gtttatttat ctctcttctg
attcctccac 480cccttcctta ctcaaccggg taaatgtcgc atcatgactc
ccgacaataa tcccctctgg 540tatagcgaga agcaacttta gcttcttaac
ggcaagaact tttttatgtt tgtcgcacct 600gtatcttcac aaaagttgga
tacagcaata agaaaggaaa ccacatttgt gcca 65428600DNAArtificial
SequenceWEAK PROMOTER SEQUENCE 28agaaagatgt caactgaaaa aaaaaaaggt
gaacacagga aaaaaaataa aaaaaaaaaa 60aaaaaaagga ggacgaaaca aaaaagtgaa
aaaaaatgaa aatttttttg gaaaaccaag 120aaatgaatta tatttccgtg
tgagacgaca tcgtcgaata tgattcaggg taacagtatt 180gatgtaatca
atttcctacc tgaatctaaa attcccggga gcaagatcaa gatgttttca
240ccgatctttc cggtctcttt ggccggggtt tacggacgat ggcagaagac
caaagcgcca 300gttcatttgg cgagcgttgg ttggtggatc aagcccacgc
gtaggcaatc ctcgagcaga 360tccgccaggc gtgtatatat agcgtggatg
gccaggcaac tttagtgctg acacatacag 420gcatatatat atgtgtgcga
cgacacatga tcatatggca tgcatgtgct ctgtatgtat 480ataaaactct
tgttttcttc ttttctctaa atattctttc cttatacatt aggacctttg
540cagcataaat tactatactt ctatagacac acaaacacaa atacacacac
taaattaata 60029600DNAArtificial SequenceWEAK PROMOTER SEQUENCE
29aacccggtct cgaagaacat cagcaccacg cccgcaacga caaagaacat tgcaatacac
60ttgcatatgt gagcatagtc gagcggtccg ttctgtggtt gatgctgttg ttctttcttc
120tgtttgtcag gggtgatagc catatcttcg tgctcttgtt gcgattgttc
tgttccatct 180gcaccagaac aaagaacaaa agaacaagga acaaagtcca
agcacgtcag cgctgtttat 240aaggggattg acgagggatc gggcctagag
tgccagcgcg ccagggagag ggagccccct 300gggccctcat ccgcaggctg
ataggggtca ccccgctggg caggtcaggg caggggctct 360caggggggcg
ccatggacaa actgcactga ggttctaaga cacatgtatt attgtgagta
420tgtatatata gagagagatt aaggcgtaca gccgggtggt agagattgat
taacttggta 480gtcttatctt gtcaattgag tttctgtcag tttcttcttg
aacaagcacg cagctaagta 540agcaacaaag caggctaaca aactaggtac
tcacatacag acttattaag acatagaact 60030500DNAArtificial SequenceWEAK
PROMOTER SEQUENCE 30cagaggagta cacacgggac ttgatcgaac agatcgtgtt
acagttgcgc tcgcaaagaa 60tgaaaatggt tcagacaaag gatcagttcc tatttatcta
ccatgctgcc aagtatctta 120acagtctttc cgtgaaccaa tagacagcta
tataaaagtt cctaattgtg cattttttca 180ataacaatac ttattcatcc
ttataattat attctagctt cgttgtcatg ggaacatagc 240ccatacaccg
cagttattta tgatcatttc gaacgggaag tatggatgaa tctttttttt
300ttttttttta tagcacgcaa ctgaaaaaaa aaaaaagaaa aatttttcat
cttcgctcga 360cgtttctttt gtagtactca tctcttttta tataaagatt
aattagttat tgtcgctttg 420cttttccttc tttaaaaaat gtttcttgct
tttggatttt cagatgtccc aagatcatta 480cagtatttta attgaacaaa 500
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