U.S. patent application number 09/764587 was filed with the patent office on 2002-08-08 for novel compounds.
Invention is credited to Hayes, Philip David, Michalovich, David.
Application Number | 20020106722 09/764587 |
Document ID | / |
Family ID | 8234643 |
Filed Date | 2002-08-08 |
United States Patent
Application |
20020106722 |
Kind Code |
A1 |
Michalovich, David ; et
al. |
August 8, 2002 |
Novel compounds
Abstract
SBSEMVL polypeptides and polynucleotides and methods for
producing such polypeptides by recombinant techniques are
disclosed. Also disclosed are methods for utilising SBSEMVL
polypeptides and polynucleotides in therapy, and diagnostic assays
for such.
Inventors: |
Michalovich, David; (London,
GB) ; Hayes, Philip David; (Cambridge, GB) |
Correspondence
Address: |
Ratner & Prestia
One Westlakes, Berwyn, Suite 301
P.O. Box 980
Valley Forge
PA
19482-0980
US
|
Family ID: |
8234643 |
Appl. No.: |
09/764587 |
Filed: |
January 18, 2001 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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09764587 |
Jan 18, 2001 |
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09240410 |
Jan 29, 1999 |
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6197544 |
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Current U.S.
Class: |
435/69.1 ;
530/350 |
Current CPC
Class: |
C07K 14/47 20130101 |
Class at
Publication: |
435/69.1 ;
530/350 |
International
Class: |
C12P 021/06; C07K
001/00; C07K 014/00; C07K 017/00 |
Foreign Application Data
Date |
Code |
Application Number |
Jan 30, 1998 |
EP |
98300694.1 |
Claims
What is claimed is:
1. An isolated polypeptide selected from the group consisting of:
(i) an isolated polypeptide comprising a polypeptide sequence
selected from the group having at least 95% identity to the
polypeptide sequence of SEQ ID NO:2; (ii) an isolated polypeptide
comprising the polypeptide sequence of SEQ ID NO:2; or (iii) an
isolated polypeptide which is the polypeptide sequence of SEQ ID
NO:2.
2. An isolated polynucleotide selected from the group consisting
of: (i) an isolated polynucleotide comprising a polynucleotide
sequence encoding a polypeptide sequence that has at least 95%
identity to the polypeptide of SEQ ID NO:2; (ii) an isolated
polynucleotide comprising a polynucleotide sequence which has at
least95% identity to that of SEQ ID NO:1; (iii) an isolated
polynucleotide comprising a polynucleotide sequence encoding the
polypeptide of SEQ ID NO:2; (iv) an isolated polynucleotide
encoding the polypeptide of SEQ ID NO:2; (v) an isolated
polynucleotide which is the polynucleotide of SEQ ID NO:1; (vi) an
isolated polynucleotide obtainable by screening a library under
stringent hybridization conditions with a labeled probe having the
sequence of SEQ ID NO:1 or a fragment thereof; (vii) a
polynucleotide which is the RNA equivalent of a polynucleotide of
(i) to (vi); or or a polynucleotide sequence complementary to said
isolated polynucleotide.
3. An antibody immunospecific for the polypeptide of claim 1.
4. A process for diagnosing a disease or a susceptibility to a
disease in a subject related to expression or activity of the
polypeptide of claim 1 in a subject comprising: (a) determining the
presence or absence of a mutation in the nucleotide sequence
encoding said polypeptide in the genome of said subject; and/or (b)
analyzing for the presence or amount of said polypeptide expression
in a sample derived from said subject.
5. A method for screening compounds to identify those which
stimulate or which inhibit the function of the polypeptide of claim
1 which comprises a method selected from the group consisting of:
(a) measuring the binding of a candidate compound to the
polypeptide (or to the cells or membranes expressing the
polypeptide) or a fusion protein thereof by means of a label
directly or indirectly associated with the candidate compound; (b)
measuring the binding of a candidate compound to the polypeptide
(or to the cells or membranes expressing the polypeptide) or a
fusion protein thereof in the presence of a labeled competitor; (c)
testing whether the candidate compound results in a signal
generated by activation or inhibition of the polypeptide, using
detection systems appropriate to the cells or cell membranes
expressing the polypeptide; (d) mixing a candidate compound with a
solution containing a polypeptide of claim 1, to form a mixture,
measuring activity of the polypeptide in the mixture, and comparing
the activity of the mixture to a standard; or (e) detecting the
effect of a candidate compound on the production of mRNA encoding
said polypeptide and said polypeptide in cells, using for instance,
an ELISA assay.
6. An expression vector comprising a polynucleotide capable of
producing a polypeptide of claim 1 when said expression vector is
present in a compatible host cell.
7. A process for producing a recombinant host cell comprising the
step of introducing the expression vector of claim - into a cell
such that the host cell, under appropriate culture conditions,
produces said polypeptide.
8. A recombinant host cell produced by the process of claim 7.
9. A membrane of a recombinant host cell of claim 8 expressing said
polypeptide.
10. A process for producing a polypeptide comprising culturing a
host cell of claim 8 under conditions sufficient for the production
of said polypeptide and recovering the polypeptide from the
culture.
11. An isolated polynucleotide selected form the group consisting
of (a) an isolated polynucleotide comprising a nucleotide sequence
which has at least 95% identity to SEQ ID NO:3 over the entire
length of SEQ ID NO:3; (b) an isolated polynucleotide comprising
the polynucleotide of SEQ ID NO:3; (c) the polynucleotide of SEQ ID
NO:3; or (d) an isolated polynucleotide comprising a nucleotide
sequence encoding a polypeptide which has at least 95% identity to
the amino acid sequence of SEQ ID NO:4, over the entire length of
SEQ ID NO:4.
12. A polypeptide selected from the group consisting of: (a) a
polypeptide which comprises an amino acid sequence which has at
least 95% identity to that of SEQ ID NO:4 over the entire length of
SEQ ID NO:4; (b) a polypeptide in which the amino acid sequence has
at least 95% identity to the amino acid sequence of SEQ ID NO:4
over the entire length of SEQ ID NO:4; (c) a polypeptide which
comprises the amino acid of SEQ ID NO:4; (d) a polypeptide which is
the polypeptide of SEQ ID NO:4; or (e) a polypeptide which is
encoded by a polynucleotide comprising the sequence contained in
SEQ ID NO:3.
Description
FIELD OF THE INVENTION
[0001] This invention relates to newly identified polypeptides and
polynucleotides encoding such polypeptides, to their use in therapy
and in identifying compounds which may be agonists, antagonists
and/or inhibitors which are potentially useful in therapy, and to
production of such polypeptides and polynucleotides.
BACKGROUND OF THE INVENTION
[0002] The drug discovery process is currently undergoing a
fundamental revolution as it embraces `functional genomics`, that
is, high throughput genome- or gene-based biology. This approach as
a means to identify genes and gene products as therapeutic targets
is rapidly superseding earlier approaches based on `positional
cloning`. A phenotype, that is a biological function or genetic
disease, would be identified and this would then be tracked back to
the responsible gene, based on its genetic map position.
[0003] Functional genomics relies heavily on high-throughput DNA
sequencing technologies and the various tools of bioinformatics to
identify gene sequences of potential interest from the many
molecular biology databases now available. There is a continuing
need to identify and characterise further genes and their related
polypeptides/proteins, as targets for drug discovery.
SUMMARY OF THE INVENTION
[0004] The present invention relates to SBSEMVL, in particular
SBSEMVL polypeptides and SBSEMVL polynucleotides, recombinant
materials and methods for their production. In another aspect, the
invention relates to methods for using such polypeptides and
polynucleotides, including the treatment of neurodegeneration,
spinal injury, neuropathies, neuromuscular disorders, psychiatric
disorders, inflammatory disorders, developmental malformations,
cancer, disorders of the immune system and viral infections,
hereinafter referred to as "the Diseases", amongst others In a
further aspect, the invention relates to methods for identifying
agonists and antagonists/inhibitors using the materials provided by
the invention, and treating conditions associated with SBSEMVL
imbalance with the identified compounds In a still further aspect,
the invention relates to diagnostic assays for detecting diseases
associated with inappropriate SBSEMVL activity or levels.
DESCRIPTION OF THE INVENTION
[0005] In a first aspect, the present invention relates to SBSEMVL
polypeptides. Such peptides include isolated polypeptides
comprising an amino acid sequence which has at least 95% identity,
preferably at least 97-99% identity, to that of SEQ ID NO:2 over
the entire length of SEQ ID NO:2. Such polypeptides include those
comprising the amino acid of SEQ ID NO:2.
[0006] Further peptides of the present invention include isolated
polypeptides in which the amino acid sequence has at least 95%
identity, preferably at least 97-99% identity, to the amino acid
sequence of SEQ ID NO:2 over the entire length of SEQ ID NO:2. Such
polypeptides include the polypeptide of SEQ ID NO:2.
[0007] Further peptides of the present invention include isolated
polypeptides encoded by a polynucleotide comprising the sequence
contained in SEQ ID NO:1.
[0008] Polypeptides of the present invention are believed to be
members of the semaphorin family of polypeptides. They are
therefore of interest because the semaphorin family of proteins
acts as recognition molecules and are known to be involved in
controlling axon outgrowth but are also likely to participate in
other biological processes including immune function and multi-drug
resistance. These properties are hereinafter referred to as
"SBSEMVL activity" or "SBSEMVL polypeptide activity" or "biological
activity of SBSEMVL." Also included amongst these activities are
antigenic and immunogenic activities of said SBSEMVL polypeptides,
in particular the antigenic and immunogenic activities of the
polypeptide of SEQ ID NO:2. Preferably, a polypeptide of the
present invention exhibits at least one biological activity of
SBSEMVL.
[0009] The polypeptides of the present invention may be in the form
of the "mature" protein or may be a part of a larger protein such
as a precursor or a fusion protein. It is often advantageous to
include an additional amino acid sequence which contains secretory
or leader sequences, pro-sequences, sequences which aid in
purification such as multiple histidine residues, or an additional
sequence for stability during recombinant production.
[0010] The present invention also includes variants of the
aforementioned polypeptides, that is polypeptides that vary from
the referents by conservative amino acid substitutions, whereby a
residue is substituted by another with like characteristics.
Typical such substitutions are among Ala, Val, Leu and Ile; among
Ser and Thr; among the acidic residues Asp and Glu; among Asn and
Gln; and among the basic residues Lys and Arg; or aromatic residues
Phe and Tyr. Particularly preferred are variants in which several,
5-10,1-5,1-3, 1-2 or I amino acids are substituted, deleted, or
added in any combination.
[0011] Polypeptides of the present invention can be prepared in any
suitable manner. Such polypeptides include isolated naturally
occurring polypeptides, recombinantly produced polypeptides,
synthetically produced polypeptides, or polypeptides produced by a
combination of these methods. Means for preparing such polypeptides
are well understood in the art.
[0012] In a further aspect, the present invention relates to
SBSEMVL polynucleotides. Such polynucleotides include isolated
polynucleotides comprising a nucleotide sequence encoding a
polypeptide which has at least 95% identity to the amino acid
sequence of SEQ ID NO:2 over the entire length of SEQ ID NO:2. In
this regard, polypeptides which have at least 97% identity are
highly preferred, whilst those with at least 98-99% identity are
more highly preferred, and those with at least 99% identity are
most highly preferred. Such polynucleotides include a
polynucleotide comprising the nucleotide sequence contained in SEQ
ID NO:1 encoding the polypeptide of SEQ ID NO:2.
[0013] Further polynucleotides of the present invention include
isolated polynucleotides comprising a nucleotide sequence that has
at least95% identity to a nucleotide sequence encoding a
polypeptide of SEQ ID NO:2, over the entire coding region. In this
regard, polynucleotides which have at least 97% identity are highly
preferred, whilst those with at least 98-99% identity are more
highly preferred, and those with at least 99% identity are most
highly preferred.
[0014] Further polynucleotides of the present invention include
isolated polynucleotides comprising a nucleotide sequence which has
at least 95% identity to SEQ ID NO:1 over the entire length of SEQ
ID NO:1. In this regard, polynucleotides which have at least 97%
identity are highly preferred, whilst those with at least 98-99%
identity are more highly preferred, and those with at least 99%
identity are most highly preferred. Such polynucleotides include a
polynucleotide comprising the polynucleotide of SEQ ID NO:1 as well
as the polynucleotide of SEQ ID NO:1.
[0015] The invention also provides polynucleotides which are
complementary to all the above described polynucleotides.
[0016] The nucleotide sequence of SEQ ID NO:1 shows homology with
Alcelaphine herpesvirus 1 putative semaphorin (A. Ensser and B.
Fleckenstein, J. Gen. Virol. 76:1063-1067,1995) The nucleotide
sequence of SEQ ID NO:1 is a cDNA sequence and comprises a
polypeptide encoding sequence (nucleotide 1 to 1998) encoding a
polypeptide of 666 amino acids, the polypeptide of SEQ ID NO:2. The
nucleotide sequence encoding the polypeptide of SEQ ID NO:2 may be
identical to the polypeptide encoding sequence contained in SEQ ID
NO:1 or it may be a sequence other than the one contained in SEQ ID
NO:1, which, as a result of the redundancy (degeneracy) of the
genetic code, also encodes the polypeptide of SEQ ID NO:2. The
polypeptide of SEQ ID NO:2 is structurally related to other
proteins of the semaphorin family, having homology and/or
structural similarity with Alcelaphine herpesvirus I putative
semaphorin (A. Ensser and B. Fleckenstein, J. Gen. Virol.
76:1063-1067.1995).
[0017] Preferred polypeptides and polynucleotides of the present
invention are expected to have, inter alia, similar biological
functions/properties to their homologous polypeptides and
polynucleotides. Furthermore, preferred polypeptides and
polynucleotides of the present invention have at least one SBSEMVL
activity.
[0018] The present invention also relates to partial or other
polynucleotide and polypeptide sequences which were first
identified prior to the determination of the corresponding full
length sequences of SEQ ID NO:1 and SEQ ID NO:2.
[0019] Accordingly, in a further aspect, the present invention
provides for an isolated polynucleotide which:
[0020] (a) comprises a nucleotide sequence which has at least 95%
identity, preferably at least 97-99% identity to SEQ ID NO:3 over
the entire length of SEQ ID NO:3;
[0021] (b) has a nucleotide sequence which has at least 95%
identity, preferably at least 97-99% identity, to SEQ ID NO:3 over
the entire length of SEQ ID NO:3;
[0022] (c) the polynucleotide of SEQ ID NO:3; or
[0023] (d) a nucleotide sequence encoding a polypeptide which has
at least95% identity, preferably at least 97-99% identity, to the
amino acid sequence of SEQ ID NO:4 over the entire length of SEQ ID
NO:4;
[0024] as well as the polynucleotide of SEQ ID NO:3.
[0025] The present invention further provides for a polypeptide
which:
[0026] (a) comprises an amino acid sequence which has at least 95%
identity, preferably at least 97-99% identity, to that of SEQ ID
NO:4 over the entire length of SEQ ID NO:4;
[0027] (b) has an amino acid sequence which is at least 95%
identity, preferably at least 97-99% identity, to the amino acid
sequence of SEQ ID NO:4 over the entire length of SEQ ID NO:4;
[0028] (c) comprises the amino acid of SEQ ID NO:4; and
[0029] (d) is the polypeptide of SEQ ID NO:4;
[0030] as well as polypeptides encoded by a polynucleotide
comprising the sequence contained in SEQ ID NO:3.
[0031] The nucleotide sequence of SEQ ID NO:3 and the peptide
sequence encoded thereby are derived from EST (Expressed Sequence
Tag) sequences. It is recognized by those skilled in the art that
there will inevitably be some nucleotide sequence reading errors in
EST sequences (see Adams, M. D. et al, Nature 377 (supp) 3. 1995).
Accordingly, the nucleotide sequence of SEQ ID NO:3 and the peptide
sequence encoded therefrom are therefore subject to the same
inherent limitations in sequence accuracy. Furthermore, the peptide
sequence encoded by SEQ ID NO:3 comprises a region of identity or
close homology and/or close structural similarity (for example a
conservative amino acid difference) with the closest homologous or
structurally similar protein.
[0032] Polynucleotides of the present invention may be obtained,
using standard cloning and screening techniques (for example
Sambrook et al., Molecular Cloning: A Laboratory Manual, 2nd Ed.,
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
(1989)) from a cDNA library derived from mRNA in cells of human
fibroblast cells, placenta, and tonsils. Polynucleotides of the
invention can also be obtained from natural sources such as genomic
DNA libraries or can be synthesized using well known and
commercially available techniques.
[0033] When polynucleotides of the present invention are used for
the recombinant production of polypeptides of the present
invention, the polynucleotide may include the coding sequence for
the mature polypeptide, by itself; or the coding sequence for the
mature polypeptide in reading frame with other coding sequences,
such as those encoding a leader or secretory sequence, a pre-, or
pro- or prepro- protein sequence, or other fusion peptide portions.
For example, a marker sequence which facilitates purification of
the fused polypeptide can be encoded. In certain preferred
embodiments of this aspect of the invention, the marker sequence is
a hexa-histidine peptide, as provided in the pQE vector (Qiagen,
Inc.) and described in Gentz et al., Proc Natl Acad Sci USA (1989)
86:821-824, or is an HA tag. The polynucleotide may also contain
non-coding 5' and 3' sequences, such as transcribed, non-translated
sequences, splicing and polyadenylation signals, ribosome binding
sites and sequences that stabilize mRNA.
[0034] Further embodiments of the present invention include
polynucleotides encoding polypeptide variants which comprise the
amino acid sequence of SEQ ID NO:2 and in which several, for
instance from 5 to 10, 1 to 5, 1 to 3, 1 to 2 or 1, amino acid
residues are substituted, deleted or added, in any combination.
[0035] Polynucleotides which are identical or sufficiently
identical to a nucleotide sequence contained in SEQ ID NO:1, may be
used as hybridization probes for cDNA and genomic DNA or as primers
for a nucleic acid amplification (PCR) reaction, to isolate
full-length cDNAs and genomic clones encoding polypeptides of the
present invention and to isolate cDNA and genomic clones of other
genes (including genes encoding paralogs from human sources and
orthologs and paralogs from species other than human) that have a
high sequence similarity to SEQ ID NO:1. Typically these nucleotide
sequences are 70% identical, preferably 80% identical, more
preferably 90% identical, most preferably 95% identical to that of
the referent. The probes or primers will generally comprise at
least 15 nucleotides, preferably, at least 30 nucleotides and may
have at least 50 nucleotides. Particularly preferred probes will
have between 30 and 50 nucleotides. Particularly preferred primers
will have between 20 and 15 nucleotides.
[0036] A polynucleotide encoding a polypeptide of the present
invention, including homologs from species other than human, may be
obtained by a process which comprises the steps of screening an
appropriate library under stringent hybridization conditions with a
labeled probe having the sequence of SEQ ID NO:1 or a fragment
thereof; and isolating full-length cDNA and genomic clones
containing said polynucleotide sequence. Such hybridization
techniques are well known to the skilled artisan. Preferred
stringent hybridization conditions include overnight incubation at
42.degree. C. in a solution comprising: 50% formamide, 5.times.SSC
(150 mM NaCl, 15 mM trisodium citrate), 50 mM sodium phosphate (pH
7.6), 5.times. Denhardts solution, 10 % dextran sulfate, and 20
microgram/ml denatured, sheared salmon sperm DNA; followed by
washing the filters in 0.1.times. SSC at about 65.degree. C. Thus
the present invention also includes polynucleotides obtainable by
screening an appropriate library under stringent hybridization
conditions with a labeled probe having the sequence of SEQ ID NO:1
or a fragment thereof.
[0037] The skilled artisan will appreciate that, in many cases, an
isolated cDNA sequence will be incomplete, in that the region
coding for the polypeptide is short at the 5' end of the cDNA. This
is a consequence of reverse transcriptase, an enzyme with
inherently low `processivity` (a measure of the ability of the
enzyme to remain attached to the template during the polymerisation
reaction), failing to complete a DNA copy of the mRNA template
during 1st strand cDNA synthesis.
[0038] There are several methods available and well known to those
skilled in the art to obtain full-length cDNAs, or extend short
cDNAs, for example those based on the method of Rapid Amplification
of cDNA ends (RACE) (see, for example, Frohman et al., PNAS USA 85,
8998-9002, 1988). Recent modifications of the technique,
exemplified by the Marathon.TM. technology (Clontech Laboratories
Inc.) for example, have significantly simplified the search for
longer cDNAs. In the Marathon.TM. technology, cDNAs have been
prepared from mRNA extracted from a chosen tissue and an `adaptor`
sequence ligated onto each end. Nucleic acid amplification (PCR) is
then carried out to amplify the `missing` 5' end of the cDNA using
a combination of gene specific and adaptor specific oligonucleotide
primers. The PCR reaction is then repeated using `nested` primers,
that is, primers designed to anneal within the amplified product
(typically an adaptor specific primer that anneals further 3' in
the adaptor sequence and a gene specific primer that anneals
further 5' in the known gene sequence). The products of this
reaction can then be analyzed by DNA sequencing and a full-length
cDNA constructed either by joining the product directly to the
existing cDNA to give a complete sequence, or carrying out a
separate full-length PCR using the new sequence information for the
design of the 5' primer.
[0039] Recombinant polypeptides of the present invention may be
prepared by processes well known in the art from genetically
engineered host cells comprising expression systems. Accordingly,
in a further aspect, the present invention relates to expression
systems which comprise a polynucleotide or polynucleotides of the
present invention, to host cells which are genetically engineered
with such expression systems and to the production of polypeptides
of the invention by recombinant techniques. Cell-free translation
systems can also be employed to produce such proteins using RNAs
derived from the DNA constructs of the present invention.
[0040] For recombinant production, host cells can be genetically
engineered to incorporate expression systems or portions thereof
for polynucleotides of the present invention. Introduction of
polynucleotides into host cells can be effected by methods
described in many standard laboratory manuals, such as Davis et al,
Basic Methods in Molecular Biology (1986) and Sambrook et al.,
(supra). Preferred such methods include, for instance, calcium
phosphate transfection, DEAE-dextran mediated transfection,
transvection, microinjection, cationic lipid-mediated transfection,
electroporation, transduction, scrape loading, ballistic
introduction or infection.
[0041] Representative examples of appropriate hosts include
bacterial cells, such as Streptococci, Staphylococci E. coli,
Streptomyces and Bacillus subtilis cells; fungal cells, such as
yeast cells and Aspergillus cells; insect cells such as Drosophila
S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, HeLa, C
127, 3T3, BHK, HEK 293 and Bowes melanoma cells; and plant
cells.
[0042] A great variety of expression systems can be used, for
instance, chromosomal, episomal and virus-derived systems, e.g.,
vectors derived from bacterial plasmids, from bacteriophage, from
transposons, from yeast episomes, from insertion elements, from
yeast chromosomal elements, from viruses such as baculoviruses,
papova viruses, such as SV40, vaccinia viruses, adenoviruses, fowl
pox viruses, pseudorabies viruses and retroviruses, and vectors
derived from combinations thereof, such as those derived from
plasmid and bacteriophage genetic elements, such as cosmids and
phagemids. The expression systems may contain control regions that
regulate as well as engender expression. Generally, any system or
vector which is able to maintain, propagate or express a
polynucleotide to produce a polypeptide in a host may be used. The
appropriate nucleotide sequence may be inserted into an expression
system by any of a variety of well-known and routine techniques,
such as, for example, those set forth in Sambrook et al., Molecular
Cloning, A Laboratory Manual (supra). Appropriate secretion signals
may be incorporated into the desired polypeptide to allow secretion
of the translated protein into the lumen of the endoplasmic
reticulum, the periplasmic space or the extracellular environment.
These signals may be endogenous to the polypeptide or they may be
heterologous signals.
[0043] If a polypeptide of the present invention is to be expressed
for use in screening assays, it is generally preferred that the
polypeptide be produced at the surface of the cell. In this event,
the cells may be harvested prior to use in the screening assay. If
the polypeptide is secreted into the medium, the medium can be
recovered in order to recover and purify the polypeptide. If
produced intracellularly, the cells must first be lysed before the
polypeptide is recovered.
[0044] Polypeptides of the present invention can be recovered and
purified from recombinant cell cultures by well-known methods
including ammonium sulfate or ethanol precipitation, acid
extraction, anion or cation exchange chromatography,
phosphocellulose chromatography, hydrophobic interaction
chromatography, affinity chromatography, hydroxylapatite
chromatography and lectin chromatography. Most preferably, high
performance liquid chromatography is employed for purification.
Well known techniques for refolding proteins may be employed to
regenerate active conformation when the polypeptide is denatured
during intracellular synthesis, isolation and or purification.
[0045] This invention also relates to the use of polynucleotides of
the present invention as diagnostic reagents. Detection of a
mutated form of the gene characterized by the polynucleotide of SEQ
ID NO:1 which is associated with a dysfunction will provide a
diagnostic tool that can add to, or define, a diagnosis of a
disease, or susceptibility to a disease, which results from
under-expression, over-expression or altered spatial or temporal
expression of the gene. Individuals carrying mutations in the gene
may be detected at the DNA level by a variety of techniques.
[0046] Nucleic acids for diagnosis may be obtained from a subject's
cells, such as from blood, urine, saliva, tissue biopsy or autopsy
material. The genomic DNA may be used directly for detection or may
be amplified enzymatically by using PCR or other amplification
techniques prior to analysis. RNA or cDNA may also be used in
similar fashion. Deletions and insertions can be detected by a
change in size of the amplified product in comparison to the normal
genotype. Point mutations can be identified by hybridizing
amplified DNA to labeled SBSEMVL nucleotide sequences. Perfectly
matched sequences can be distinguished from mismatched duplexes by
RNase digestion or by differences in melting temperatures. DNA
sequence differences may also be detected by alterations in
electrophoretic mobility of DNA fragments in gels, with or without
denaturing agents, or by direct DNA sequencing (see, e.g., Myers et
al., Science (1985) 230:1242). Sequence changes at specific
locations may also be revealed by nuclease protection assays, such
as RNase and S 1 protection or the chemical cleavage method (see
Cotton et al., Proc Natl Acad Sci USA (1985) 85: 4397-4401). In
another embodiment, an array of oligonucleotides probes comprising
SBSEMVL nucleotide sequence or fragments thereof can be constructed
to conduct efficient screening of e.g., genetic mutations. Array
technology methods are well known and have general applicability
and can be used to address a variety of questions in molecular
genetics including gene expression, genetic linkage, and genetic
variability (see for example: M. Chee et al., Science, Vol 274, pp
610-613 (1996)).
[0047] The diagnostic assays offer a process for diagnosing or
determining a susceptibility to the Diseases through detection of
mutation in the SBSEMVL gene by the methods described. In addition,
such diseases may be diagnosed by methods comprising determining
from a sample derived from a subject an abnormally decreased or
increased level of polypeptide or mRNA. Decreased or increased
expression can be measured at the RNA level using any of the
methods well known in the art for the quantitation of
polynucleotides, such as, for example, nucleic acid amplification,
for instance PCR, RT-PCR, RNase protection, Northern blotting and
other hybridization methods. Assay techniques that can be used to
determine levels of a protein, such as a polypeptide of the present
invention, in a sample derived from a host are well-known to those
of skill in the art. Such assay methods include radioimmunoassays,
competitive-binding assays, Western Blot analysis and ELISA
assays.
[0048] Thus in another aspect, the present invention relates to a
diagnostic kit which comprises:
[0049] (a) a polynucleotide of the present invention, preferably
the nucleotide sequence of SEQ ID NO: 1, or a fragment thereof;
[0050] (b) a nucleotide sequence complementary to that of (a);
[0051] (c) a polypeptide of the present invention, preferably the
polypeptide of SEQ ID NO:2 or a fragment thereof; or
[0052] (d) an antibody to a polypeptide of the present invention,
preferably to the polypeptide of SEQ ID NO:2.
[0053] It will be appreciated that in any such kit, (a), (b), (c)
or (d) may comprise a substantial component. Such a kit will be of
use in diagnosing a disease or susceptibility to a disease,
particularly neurodegeneration, spinal injury, neuropathies,
neuromuscular disorders, psychiatric disorders, inflammatory
disorders, developmental malformations, cancer, disorders of the
immune system and viral infections, amongst others.
[0054] The nucleotide sequences of the present invention are also
valuable for chromosomal localization. The sequence is specifically
targeted to, and can hybridize with, a particular location on an
individual human chromosome. The mapping of relevant sequences to
chromosomes according to the present invention is an important
first step in correlating those sequences with gene associated
disease. Once a sequence has been mapped to a precise chromosomal
location, the physical position of the sequence on the chromosome
can be correlated with genetic map data. Such data are found in,
for example, V. McKusick, Mendelian Inheritance in Man (available
on-line through Johns Hopkins University Welch Medical Library).
The relationship between genes and diseases that have been mapped
to the same chromosomal region are then identified through linkage
analysis (coinheritance of physically adjacent genes).
[0055] The differences in the cDNA or genomic sequence between
affected and unaffected individuals can also be determined. If a
mutation is observed in some or all of the affected individuals but
not in any normal individuals, then the mutation is likely to be
the causative agent of the disease.
[0056] The nucleotide sequences of the present invention are also
valuable for tissue localisation. Such techniques allow the
determination of expression patterns of the human SBSEMVL
polypeptides in tissues by detection of the mRNAs that encode them.
These techniques include in situ hybridization techniques and
nucleotide amplification techniques, for example PCR. Such
techniques are well known in the art. Results from these studies
provide an indication of the normal functions of the polypeptides
in the organism. In addition, comparative studies of the normal
expression pattern of human SBSEMVL mRNAs with that of mRNAs
encoded by a human SBSEMVL gene provide valuable insights into the
role of mutant human SBSEMVL polypeptides, or that of inappropriate
expression of normal human SBSEMVL polypeptides, in disease. Such
inappropriate expression may be of a temporal, spatial or simply
quantitative nature.
[0057] The polypeptides of the invention or their fragments or
analogs thereof, or cells expressing them, can also be used as
immunogens to produce antibodies immunospecific for polypeptides of
the present invention. The term "immunospecific" means that the
antibodies have substantially greater affinity for the polypeptides
of the invention than their affinity for other related polypeptides
in the prior art.
[0058] Antibodies generated against polypeptides of the present
invention may be obtained by administering the polypeptides or
epitope-bearing fragments, analogs or cells to an animal,
preferably a non-human animal, using routine protocols. For
preparation of monoclonal antibodies, any technique which provides
antibodies produced by continuous cell line cultures can be used.
Examples include the hybridoma technique (Kohler, G. and Milstein,
C., Nature (1975) 256:495-497), the trioma technique, the human
B-cell hybridoma technique (Kozboret al., Immunology Today (1983)
4:72) and the EBV-hybridoma technique (Cole et al., Monoclonal
Antibodies and Cancer Therapy, 77-96, Alan R. Liss, Inc.,
1985).
[0059] Techniques for the production of single chain antibodies,
such as those described in U.S. Pat. No. 4,946,778, can also be
adapted to produce single chain antibodies to polypeptides of this
invention. Also, transgenic mice, or other organisms, including
other mammals, may be used to express humanized antibodies.
[0060] The above-described antibodies may be employed to isolate or
to identify clones expressing the polypeptide or to purify the
polypeptides by affinity chromatography.
[0061] Antibodies against polypeptides of the present invention may
also be employed to treat the Diseases, amongst others.
[0062] In a further aspect, the present invention relates to
genetically engineered soluble fusion proteins comprising a
polypeptide of the present invention, or a fragment thereof, and
various portions of the constant regions of heavy or light chains
of immunoglobulins of various subclasses (IgG, IgM, IgA, IgE).
Preferred as an immunoglobulin is the constant part of the heavy
chain of human IgG, particularly IgG1, where fusion takes place at
the hinge region. In a particular embodiment, the Fc part can be
removed simply by incorporation of a cleavage sequence which can be
cleaved with blood clotting factor Xa. Furthermore, this invention
relates to processes for the preparation of these fusion proteins
by genetic engineering, and to the use thereof for drug screening,
diagnosis and therapy. A further aspect of the invention also
relates to polynucleotides encoding such fusion proteins. Examples
of fusion protein technology can be found in International Patent
Application Nos. W094/29458 and W094/22914.
[0063] Another aspect of the invention relates to a method for
inducing an immunological response in a mammal which comprises
inoculating the mammal with a polypeptide of the present invention,
adequate to produce antibody and/or T cell immune response to
protect said animal from the Diseases hereinbefore mentioned
amongst others. Yet another aspect of the invention relates to a
method of inducing immunological response in a mammal which
comprises, delivering a polypeptide of the present invention via a
vector directing expression of the polynucleotide and coding for
the polypeptide in vivo in order to induce such an immunological
response to produce antibody to protect said animal from
diseases.
[0064] A further aspect of the invention relates to an
immunological/vaccine formulation (composition) which, when
introduced into a mammalian host, induces an immunological response
in that mammal to a polypeptide of the present invention wherein
the composition comprises a polypeptide or polynucleotide of the
present invention The vaccine formulation may further comprise a
suitable carrier. Since a polypeptide may be broken down in the
stomach, it is preferably administered parenterally (for instance,
subcutaneous, intramuscular, intravenous, or intradermal
injection). Formulations suitable for parenteral administration
include aqueous and non-aqueous sterile injection solutions which
may contain anti-oxidants, buffers, bacteriostats and solutes which
render the formulation isotonic with the blood of the recipient;
and aqueous and non-aqueous sterile suspensions which may include
suspending agents or thickening agents. The formulations may be
presented in unit-dose or multi-dose containers, for example,
sealed ampoules and vials and may be stored in a freeze-dried
condition requiring only the addition of the sterile liquid carrier
immediately prior to use. The vaccine formulation may also include
adjuvant systems for enhancing the immunogenicity of the
formulation, such as oil-in water systems and other systems known
in the art. The dosage will depend on the specific activity of the
vaccine and can be readily determined by routine
experimentation.
[0065] Polypeptides of the present invention are responsible for
one or more biological functions, including one or more disease
states, in particular the Diseases hereinbefore mentioned. It is
therefore desirous to devise screening methods to identify
compounds which stimulate or which inhibit the function of the
polypeptide. Accordingly, in a further aspect, the present
invention provides for a method of screening compounds to identify
those which stimulate or which inhibit the function of the
polypeptide. In general, agonists or antagonists may be employed
for therapeutic and prophylactic purposes for such Diseases as
hereinbefore mentioned. Compounds may be identified from a variety
of sources, for example, cells, cell-free preparations, chemical
libraries, and natural product mixtures. Such agonists, antagonists
or inhibitors so-identified may be natural or modified substrates,
ligands, receptors, enzymes, etc., as the case may be, of the
polypeptide; or may be structural or functional mimetics thereof
(see Coliganet al., Current Protocols in Immunology 1(2):Chapter5
(1991)).
[0066] The screening method may simply measure the binding of a
candidate compound to the polypeptide, or to cells or membranes
bearing the polypeptide, or a fusion protein thereof by means of a
label directly or indirectly associated with the candidate
compound. Alternatively, the screening method may involve
competition with a labeled competitor. Further, these screening
methods may test whether the candidate compound results in a signal
generated by activation or inhibition of the polypeptide, using
detection systems appropriate to the cells bearing the polypeptide.
Inhibitors of activation are generally assayed in the presence of a
known agonist and the effect on activation by the agonist by the
presence of the candidate compound is observed. Constitutively
active polypeptides may be employed in screening methods for
inverse agonists or inhibitors, in the absence of an agonist or
inhibitor, by testing whether the candidate compound results in
inhibition of activation of the polypeptide. Further, the screening
methods may simply comprise the steps of mixing a candidate
compound with a solution containing a polypeptide of the present
invention to form a mixture, measuring SBSEMVL activity in the
mixture, and comparing the SBSEMVL activity of the mixture to a
standard. Fusion proteins, such as those made from Fc portion and
SBSEMVL polypeptide, as hereinbefore described, can also be used
for high-throughput screening assays to identify antagonists for
the polypeptide of the present invention (see D. Bennett et al., J
Mol Recognition, 8:52-58 (1995); and K. Johanson et al., J Biol
Chem, 270(16):9459-9471 (1995)).
[0067] The polynucleotides, polypeptides and antibodies to the
polypeptide of the present invention may also be used to configure
screening methods for detecting the effect of added compounds on
the production of mRNA and polypeptide in cells. For example, an
ELISA assay may be constructed for measuring secreted or cell
associated levels of polypeptide using monoclonal and polyclonal
antibodies by standard methods known in the art. This can be used
to discover agents which may inhibit or enhance the production of
polypeptide(also called antagonist or agonist, respectively) from
suitably manipulated cells or tissues.
[0068] The polypeptide may be used to identify membrane bound or
soluble receptors, if any, through standard receptor binding
techniques known in the art. These include, but are not limited to,
ligand binding and crosslinking assays in which the polypeptide is
labeled with a radioactive isotope (for instance, .sup.125I),
chemically modified (for instance, biotinylated), or fused to a
peptide sequence suitable for detection or purification, and
incubated with a source of the putative receptor (cells, cell
membranes, cell supernatants, tissue extracts, bodily fluids).
Other methods include biophysical techniques such as surface
plasmon resonance and spectroscopy. These screening methods may
also be used to identify agonists and antagonists of the
polypeptide which compete with the binding of the polypeptide to
its receptors, if any. Standard methods for conducting such assays
are well understood in the art.
[0069] Examples of potential polypeptide antagonists include
antibodies or, in some cases, oligonucleotides or proteins which
are closely related to the ligands, substrates, receptors, enzymes,
etc., as the case may be, of the polypeptide, e.g., a fragment of
the ligands, substrates, receptors, enzymes, etc.; or small
molecules which bind to the polypeptide of the present invention
but do not elicit a response, so that the activity of the
polypeptide is prevented.
[0070] Thus, in another aspect, the present invention relates to a
screening kit for identifying agonists, antagonists, ligands,
receptors, substrates, enzymes, etc. for polypeptides of the
present invention; or compounds which decrease or enhance the
production of such polypeptides, which comprises:
[0071] (a) a polypeptide of the present invention;
[0072] (b) a recombinant cell expressing a polypeptide of the
present invention;
[0073] (c) a cell membrane expressing a polypeptide of the present
invention; or
[0074] (d) antibody to a polypeptide of the present invention;
[0075] which polypeptide is preferably that of SEQ ID NO:2.
[0076] It will be appreciated that in any such kit, (a), (b), (c)
or (d) may comprise a substantial component.
[0077] It will be readily appreciated by the skilled artisan that a
polypeptide of the present invention may also be used in a method
for the structure-based design of an agonist, antagonist or
inhibitor of the polypeptide, by:
[0078] (a) determining in the first instance the three-dimensional
structure of the polypeptide;
[0079] (b) deducing the three-dimensional structure for the likely
reactive or binding site(s) of an agonist, antagonist or
inhibitor;
[0080] (c) synthesizing candidate compounds that are predicted to
bind to or react with the deduced binding or reactive site; and
[0081] (d) testing whether the candidate compounds are indeed
agonists, antagonists or inhibitors. It will be further appreciated
that this will normally be an iterative process.
[0082] In a further aspect, the present invention provides methods
of treating abnormal conditions such as, for instance,
neurodegeneration, spinal injury, neuropathies, neuromuscular
disorders, psychiatric disorders, inflammatory disorders,
developmental malformations, cancer, disorders of the immune system
and viral infections, related to either an excess of, or an
under-expression of, SBSEMVL polypeptide activity.
[0083] If the activity of the polypeptide is in excess, several
approaches are available. One approach comprises administering to a
subject in need thereof an inhibitor compound (antagonist) as
hereinabove described, optionally in combination with a
pharmaceutically acceptable carrier, in an amount effective to
inhibit the function of the polypeptide, such as, for example, by
blocking the binding of ligands, substrates, receptors, enzymes,
etc., or by inhibiting a second signal, and thereby alleviating the
abnormal condition. In another approach, soluble forms of the
polypeptides still capable of binding the ligand, substrate,
enzymes, receptors, etc. in competition with endogenous polypeptide
may be administered. Typical examples of such competitors include
fragments of the SBSEMVL polypeptide.
[0084] In still another approach, expression of the gene encoding
endogenous SBSEMVL polypeptide can be inhibited using expression
blocking techniques. Known such techniques involve the use of
antisense sequences, either internally generated or externally
administered (see, for example, O'Connor, J Neurochem (1991) 56:560
in Oligodeoxynucleotides as Antisense Inhibitors of Gene
Expression, CRC Press, Boca Raton, Fla. (1988)). Alternatively,
oligonucleotides which form triple helices ("triplexes") with the
gene can be supplied (see, for example, Lee et al., Nucleic Acids
Res (1979) 6:3073; Cooney et al., Science (1988) 241:456; Dervan et
al., Science (1991) 251:13 60). These oligomers can be administered
per se or the relevant oligomers can be expressed in vivo.
Synthetic antisense or triplex oligonucleotides may comprise
modified bases or modified backbones. Examples of the latter
include methylphosphonate, phosphorothioate or peptide nucleic acid
backbones. Such backbones are incorporated in the antisense or
triplex oligonucleotide in order to provide protection from
degradation by nucleases and are well known in the art. Antisense
and triplex molecules synthesized with these or other modified
backbones also form part of the present invention.
[0085] In addition, expression of the human SBSEMVL polypeptide may
be prevented by using ribozymes specific to the human SBSEMVL mRNA
sequence. Ribozymes are catalytically active RNAs that can be
natural or synthetic (see for example Usman, N, et al., Curr. Opin.
Struct. Biol (1996) 6(4), 527-33.) Synthetic ribozymes can be
designed to specifically cleave human SBSEMVL mRNAs at selected
positions thereby preventing translation of the human SBSEMVL mRNAs
into functional polypeptide. Ribozymes may be synthesized with a
natural ribose phosphate backbone and natural bases, as normally
found in RNA molecules. Alternatively the ribozymes may be
synthesized with non-natural backbones to provide protection from
ribonuclease degradation, for example, 2' -O-methyl RNA, and may
contain modified bases.
[0086] For treating abnormal conditions related to an
under-expression of SBSEMVL and its activity, several approaches
are also available. One approach comprises administering to a
subject a therapeutically effective amount of a compound which
activates a polypeptide of the present invention, i.e., an agonist
as described above, in combination with a pharmaceutically
acceptable carrier, to thereby alleviate the abnormal condition.
Alternatively, gene therapy may be employed to effect the
endogenous production of SBSEMVL by the relevant cells in the
subject. For example, a polynucleotide of the invention may be
engineered for expression in a replication defective retroviral
vector, as discussed above. The retroviral expression construct may
then be isolated and introduced into a packaging cell transduced
with a retroviral plasmid vector containing RNA encoding a
polypeptide of the present invention such that the packaging cell
now produces infectious viral particles containing the gene of
interest. These producer cells may be administered to a subject for
engineering cells in vivo and expression of the polypeptide in
vivo. For an overview of gene therapy, see Chapter 20, Gene Therapy
and other Molecular Genetic-based Therapeutic Approaches, (and
references cited therein) in Human Molecular Genetics, T Strachan
and A P Read, BIOS Scientific Publishers Ltd (1996). Another
approach is to administer a therapeutic amount of a polypeptide of
the present invention in combination with a suitable pharmaceutical
carrier.
[0087] In a further aspect, the present invention provides for
pharmaceutical compositions comprising a therapeutically effective
amount of a polypeptide, such as the soluble form of a polypeptide
of the present invention, agonist/antagonist peptide or small
molecule compound, in combination with a pharmaceutically
acceptable carrier or excipient. Such carriers include, but are not
limited to, saline, buffered saline, dextrose, water, glycerol,
ethanol, and combinations thereof. The invention further relates to
pharmaceutical packs and kits comprising one or more containers
filled with one or more of the ingredients of the aforementioned
compositions of the invention. Polypeptides and other compounds of
the present invention may be employed alone or in conjunction with
other compounds, such as therapeutic compounds.
[0088] The composition will be adapted to the route of
administration, for instance by a systemic or an oral route.
Preferred forms of systemic administration include injection,
typically by intravenous injection. Other injection routes, such as
subcutaneous, intramuscular, or intraperitoneal, can be used.
Alternative means for systemic administration include transmucosal
and transdermal administration using penetrants such as bile salts
or fusidic acids or other detergents. In addition, if a polypeptide
or other compounds of the present invention can be formulated in an
enteric or an encapsulated formulation, oral administration may
also be possible. Administration of these compounds may also be
topical and/or localized, in the form of salves, pastes, gels, and
the like.
[0089] The dosage range required depends on the choice of peptide
or other compounds of the present invention, the route of
administration, the nature of the formulation, the nature of the
subject's condition, and the judgment of the attending
practitioner. Suitable dosages, however, are in the range of
0.1-100 .mu.g/kg of subject. Wide variations in the needed dosage,
however, are to be expected in view of the variety of compounds
available and the differing efficiencies of various routes of
administration. For example, oral administration would be expected
to require higher dosages than administration by intravenous
injection. Variations in these dosage levels can be adjusted using
standard empirical routines for optimization, as is well understood
in the art.
[0090] Polypeptides used in treatment can also be generated
endogenously in the subject, in treatment modalities often referred
to as"gene therapy" as described above. Thus, for example, cells
from a subject may be engineered with a polynucleotide, such as a
DNA or RNA, to encode a polypeptide ex vivo, and for example, by
the use of a retroviral plasmid vector. The cells are then
introduced into the subject.
[0091] Polynucleotide and polypeptide sequences form a valuable
information resource with which to identify further sequences of
similar homology. This is most easily facilitated by storing the
sequence in a computer readable medium and then using the stored
data to search a sequence database using well known searching
tools, such as those in the GCG and Lasergene software packages.
Accordingly, in a further aspect, the present invention provides
for a computer readable medium having stored thereon a
polynucleotide comprising the sequence of SEQ ID NO:1 and/or a
polypeptide sequence encoded thereby.
[0092] The following definitions are provided to facilitate
understanding of certain terms used frequently hereinbefore.
[0093] "Antibodies" as used herein includes polyclonal and
monoclonal antibodies, chimeric, single chain, and humanized
antibodies, as well as Fab fragments, including the products of an
Fab or other immunoglobulin expression library.
[0094] "Isolated" means altered "by the hand of man" from the
natural state. If an "isolated" composition or substance occurs in
nature, it has been changed or removed from its original
environment, or both. For example, a polynucleotide or a
polypeptide naturally present in a living animal is not "isolated,"
but the same polynucleotide or polypeptide separated from the
coexisting materials of its natural state is "isolated", as the
term is employed herein.
[0095] "Polynucleotide" generally refers to any polyribonucleotide
or polydeoxribonucleotide, which may be unmodified RNA or DNA or
modified RNA or DNA. "Polynucleotides" include, without limitation,
single- and double-stranded DNA, DNA that is a mixture of single-
and double-stranded regions, single- and double-stranded RNA, and
RNA that is mixture of single- and double-stranded regions, hybrid
molecules comprising DNA and RNA that may be single-stranded or,
more typically, double-stranded or a mixture of single- and
double-stranded regions. In addition, "polynucleotide" refers to
triple-stranded regions comprising RNA or DNA or both RNA and DNA.
The term "polynucleotide" also includes DNAs or RNAs containing one
or more modified bases and DNAs or RNAs with backbones modified for
stability or for other reasons. "Modified" bases include, for
example, tritylated bases and unusual bases such as inosine. A
variety of modifications may be made to DNA and RNA; thus,
"polynucleotide" embraces chemically, enzymatically or
metabolically modified forms of polynucleotides as typically found
in nature, as well as the chemical forms of DNA and RNA
characteristic of viruses and cells. "Polynucleotide" also embraces
relatively short polynucleotides, often referred to as
oligonucleotides.
[0096] "Polypeptide" refers to any peptide or protein comprising
two or more amino acids joined to each other by peptide bonds or
modified peptide bonds, i.e., peptide isosteres. "Polypeptide"
refers to both short chains, commonly referred to as peptides,
oligopeptides or oligomers, and to longer chains, generally
referred to as proteins. Polypeptides may contain amino acids other
than the 20 gene-encoded amino acids. "Polypeptides" include amino
acid sequences modified either by natural processes, such as
post-translational processing, or by chemical modification
techniques which are well known in the art. Such modifications are
well described in basic texts and in more detailed monographs, as
well as in a voluminous research literature. Modifications may
occur anywhere in a polypeptide, including the peptide backbone,
the amino acid side-chains and the amino or carboxyl termini. It
will be appreciated that the same type of modification may be
present to the same or varying degrees at several sites in a given
polypeptide. Also, a given polypeptide may contain many types of
modifications. Polypeptides may be branched as a result of
ubiquitination, and they may be cyclic, with or without branching.
Cyclic, branched and branched cyclic polypeptides may result from
post-translation natural processes or may be made by synthetic
methods. Modifications include acetylation, acylation,
ADP-ribosylation, amidation, biotinylation, covalent attachment of
flavin, covalent attachment of a heme moiety, covalent attachment
of a nucleotide or nucleotide derivative, covalent attachment of a
lipid or lipid derivative, covalent attachment of
phosphotidylinositol, cross-linking, cyclization, disulfide bond
formation, demethylation, formation of covalent cross-links,
formation of cystine, formation of pyroglutamate, formylation,
gamma-carboxylation, glycosylation, GPI anchor formation,
hydroxylation, iodination, methylation, myristoylation, oxidation,
proteolytic processing, phosphorylation, prenylation, racemization,
selenoylation, sulfation, transfer-RNA mediated addition of amino
acids to proteins such as arginylation, and ubiquitination (see,
for instance, Proteins - Structure and Molecular Properties, 2nd
Ed., T. E. Creighton, W.H. Freeman and Company, New York, 1993;
Wold, F., Post-translational Protein Modifications: Perspectives
and Prospects, pgs. 1-12 in Post-translational Covalent
Modification of Proteins, B. C. Johnson, Ed., Academic Press, New
York, 1983; Seifter et al., "Analysis for protein modifications and
nonprotein cofactors", Meth Enzymol (1990) 182:626-646 and Rattan
et al., "Protein Synthesis: Post-translational Modifications and
Aging", Ann N.Y. Acad Sci (1992) 663:48-62).
[0097] "Variant" refers to a polynucleotide or polypeptide that
differs from a reference polynucleotide or polypeptide, but retains
essential properties. A typical variant of a polynucleotide differs
in nucleotide sequence from another, reference polynucleotide.
Changes in the nucleotide sequence of the variant may or may not
alter the amino acid sequence of a polypeptide encoded by the
reference polynucleotide. Nucleotide changes may result in amino
acid substitutions, additions, deletions, fusions and truncations
in the polypeptide encoded by the reference sequence, as discussed
below. 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 substitutions,
additions, deletions in any combination. A substituted or inserted
amino acid residue may or may not be one encoded by the genetic
code. A variant of a polynucleotide or polypeptide may be a
naturally occurring such as an allelic variant, or it may be a
variant that is not known to occur naturally. Non-naturally
occurring variants of polynucleotides and polypeptides may be made
by mutagenesis techniques or by direct synthesis.
[0098] "Identity," as known in the art, is a relationship between
two or more polypeptide sequences or two or more polynucleotide
sequences, as determined by comparing the sequences. In the art,
"identity" also means the degree of sequence relatedness between
polypeptide or polynucleotide sequences, as the case may be, as
determined by the match between strings of such sequences.
"Identity" and "similarity" can be readily calculated by known
methods, including but not limited to those described in
(Computational Molecular Biology, Lesk, A. M., ed., Oxford
University Press, New York, 1988; Biocomputing: Informatics and
Genome Projects, Smith, D. W., ed., Academic Press, New York, 1993;
Computer Analysis of Sequence Data, Part I, Griffin, A. M., and
Griffin, H. G., eds., Humana Press, New Jersey, 1994; Sequence
Analysis in Molecular Biology, von Heinje, G., Academic Press,
1987; and Sequence Analysis Primer, Gribskov, M. and Devereux, J.,
eds., M Stockton Press, New York, 1991; and Carillo, H., and
Lipman, D., SIAM J. Applied Math., 48: 1073 (1988). Preferred
methods to determine identity are designed to give the largest
match between the sequences tested. Methods to determine identity
and similarity are codified in publicly available computer
programs. Preferred computer program methods to determine identity
and similarity between two sequences include, but are not limited
to, the GCG program package (Devereux, J., et al., Nucleic Acids
Research 12(1): 387 (1984)), BLASTP, BLASTN, and FASTA (Atschul, S.
F. et al., J Molec. Biol. 215: 403-410 (1990). The BLAST X program
is publicly available from NCBI and other sources (BLAST Manual,
Altschul, S., et al, NCBI NLM NIH Bethesda, Md. 20894; Altschul,
S., et al., J Mol. Biol. 215: 403-410 (1990). The well known Smith
Waterman algorithm may also be used to determine identity.
[0099] Preferred parameters for polypeptide sequence comparison
include the following:
[0100] 1) Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453
(1970)
[0101] Comparison matrix: BLOSSUM62 from Hentikoff and Hentikoff,
Proc. Natl. Acad. Sci. USA. 89:10915-10919 (1992)
[0102] Gap Penalty: 12
[0103] Gap Length Penalty: 4
[0104] A program useful with these parameters is publicly available
as the "gap" program from Genetics Computer Group, Madison Wis. The
aforementioned parameters are the default parameters for peptide
comparisons (along with no penalty for end gaps).
[0105] Preferred parameters for polynucleotide comparison include
the following:
[0106] 1) Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453
(1970)
[0107] Comparison matrix: matches=+10, mismatch=0
[0108] Gap Penalty: 50
[0109] Gap Length Penalty: 3
[0110] Available as: The "gap" program from Genetics Computer
Group, Madison Wis. These are the default parameters for nucleic
acid comparisons.
[0111] By way of example, a polynucleotide sequence of the present
invention may be identical to the reference sequence of SEQ ID
NO:1, that is be 100% identical, or it may include up to a certain
integer number of nucleotide alterations as compared to the
reference sequence. Such alterations are selected from the group
consisting of at least one nucleotide deletion, substitution,
including transition and transversion, or insertion, and wherein
said alterations may occur at the 5' or 3' terminal positions of
the reference nucleotide sequence or anywhere between those
terminal positions, interspersed either individually among the
nucleotides in the reference sequence or in one or more contiguous
groups within the reference sequence. The number of nucleotide
alterations is determined by multiplying the total number of
nucleotides in SEQ ID NO:1 by the numerical percent of the
respective percent identity(divided by 100) and subtracting that
product from said total number of nucleotides in SEQ ID NO:1,
or:
n.sub.n.ltoreq.X.sub.n-(X.sub.n.multidot.Y)
[0112] wherein n.sub.n is the number of nucleotide alterations,
X.sub.n is the total number of nucleotides in SEQ ID NO:1, and y
is, for instance, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90
for 90%, 0.95 for 95%, etc., and wherein any non-integer product of
x.sub.n and y is rounded down to the nearest integer prior to
subtracting it from x.sub.n. Alterations of a polynucleotide
sequence encoding the polypeptide of SEQ ID NO:2 may create
nonsense, missense or frameshift mutations in this coding sequence
and thereby alter the polypeptide encoded by the polynucleotide
following such alterations.
[0113] Similarly, a polypeptide sequence of the present invention
may be identical to the reference sequence of SEQ ID NO:2, that is
be 100% identical, or it may include up to a certain integer number
of amino acid alterations as compared to the reference sequence
such that the % identity is less than 100%. Such alterations are
selected from the group consisting of at least one amino acid
deletion, substitution, including conservative and non-conservative
substitution, or insertion, and wherein said alterations may occur
at the amino- or carboxy-terminal positions of the reference
polypeptide sequence or anywhere between those terminal positions,
interspersed either individually among the amino acids in the
reference sequence or in one or more contiguous groups within the
reference sequence. The number of amino acid alterations for a
given % identity is determined by multiplying the total number of
amino acids in SEQ ID NO:2 by the numerical percent of the
respective percent identity(divided by 100) and then subtracting
that product from said total number of amino acids in SEQ ID NO:2,
or:
n.sub.a.ltoreq.x.sub.a-(X.sub.a.multidot.Y)
[0114] wherein n.sub.a is the number of amino acid alterations,
x.sub.a is the total number of amino acids in SEQ ID NO:2, and y
is, for instance 0.70 for 70%, 0.80 for 80%, 0.85 for 85% etc., and
wherein any non-integer product of X.sub.a and y is rounded down to
the nearest integer prior to subtracting it from X.sub.a.
[0115] "Homolog" is a generic term used in the art to indicate a
polynucleotide or polypeptide sequence possessing a high degree of
sequence relatedness to a subject sequence. Such relatedness may be
quantified by determining the degree of identity and/or similarity
between the sequences being compared as hereinbefore described.
Falling within this generic term are the terms "ortholog", meaning
a polynucleotide or polypeptide that is the functional equivalent
of a polynucleotide or polypeptide in another species, and
"paralog" meaning a functionally similar sequence when considered
within the same species.
[0116] "Fusion protein" refers to a protein encoded by two, often
unrelated, fused genes or fragments thereof. In one example, EP-A-0
464 discloses fusion proteins comprising various portions of
constant region of immunoglobulin molecules together with another
human protein or part thereof. In many cases, employing an
immunoglobulin Fc region as a part of a fusion protein is
advantageous for use in therapy and diagnosis resulting in, for
example, improved pharmacokinetic properties [see, e.g., EP-A 0232
262]. On the other hand, for some uses it would be desirable to be
able to delete the Fc part after the fusion protein has been
expressed, detected and purified.
[0117] All publications, including but not limited to patents and
patent applications, cited in this specification are herein
incorporated by reference as if each individual publication were
specifically and individually indicated to be incorporated by
reference herein as though fully set forth.
Sequence CWU 1
1
4 1 2010 DNA HOMO SAPIENS 1 atgacgcctc ctccgcccgg acgtgccgcc
cccagcgcac cgcgcgcccg cgtccctggc 60 ccgccggctc ggttggggct
tccgctgcgg ctgcggctgc tgctgctgct ctgggcggcc 120 gccgcctccg
cccagggcca cctaaggagc ggaccccgca tcttcgccgt ctggaaaggc 180
catgtagggc aggaccgggt ggactttggc cagactgagc cgcacacggt gcttttccac
240 gagccaggca gctcctctgt gtgggtggga ggacgtggca aggtctacct
ctttgacttc 300 cccgagggca agaacgcatc tgtgcgcacg gtgaatatcg
gctccacaaa ggggtcctgt 360 ctggataagc gggactgcga gaactacatc
actctcctgg agaggcggag tgaggggctg 420 ctggcctgtg gcaccaacgc
ccggcacccc agctgctgga acctggtgaa tggcactgtg 480 gtgccacttg
gcgagatgag aggctacgcc cccttcagcc cggacgagaa ctccctggtt 540
ctgtttgaag gggacgaggt gtattccacc atccggaagc aggaatacaa tgggaagatc
600 cctcggttcc gccgcatccg gggcgagagt gagctgtaca ccagtgatac
tgtcatgcag 660 aacccacagt tcatcaaagc caccatcgtg caccaagacc
aggcttacga tgacaagatc 720 tactacttct tccgagagga caatcctgac
aagaatcctg aggctcctct caatgtgtcc 780 cgtgtggccc agttgtgcag
gggggaccag ggtggggaaa gttcactgtc agtctccaag 840 tggaacactt
ttctgaaagc catgctggta tgcagtgatg ctgccaccaa caagaacttc 900
aacaggctgc aagacgtctt cctgctccct gaccccagcg gccagtggag ggacaccagg
960 gtctatggtg ttttctccaa cccctggaac tactcagccg tctgtgtgta
ttccctcggt 1020 gacattgaca aggtcttccg tacctcctca ctcaagggct
accactcaag ccttcccaac 1080 ccgcggcctg gcaagtgcct cccagaccag
cagccgatac ccacagagac cttccaggtg 1140 gctgaccgtc acccagaggt
ggcgcagagg gtggagccca tggggcctct gaagacgcca 1200 ttgttccact
ctaaatacca ctaccagaaa gtggccgtcc accgcatgca agccagccac 1260
ggggagacct ttcatgtgct ttacctaact acagacaggg gcactatcca caaggtggtg
1320 gaaccggggg agcaggagca cagcttcgcc ttcaacatca tggagatcca
gcccttccgc 1380 cgcgcggctg ccatccagac catgtcgctg gatgctgagc
ggaggaagct gtatgtgagc 1440 tcccagtggg aggtgagcca ggtgcccctg
gacctgtgtg aggtctatgg cgggggctgc 1500 cacggttgcc tcatgtcccg
agacccctac tgcggctggg accaaggccg ctgcatctcc 1560 atctacagct
ccgaacggtc agtgctgcaa tccattaatc cagccgagcc acacaaggag 1620
tgtcccaacc ccaaaccaga caaggcccca ctgcagaagg tttccctggc cccaaactct
1680 cgctactacc tgagctgccc catggaatcc cgccacgcca cctactcatg
gcgccacaag 1740 gagaacgtgg agcagagctg cgaacctggt caccagagcc
ccaactgcat cctgttcatc 1800 gagaacctca cggcgcagca gtacggccac
tacttctgcg aggcccagga gggctcctac 1860 ttccgcgagg ctcagcactg
gcagctgctg cccgaggacg gcatcatggc cgagcacctg 1920 ctgggtcatg
cctgtgccct ggccgcctcc ctctggctgg gggtgctgcc cacactcact 1980
cttggcttgc tggtccacta gggcctcccg 2010 2 666 PRT HOMO SAPIENS 2 Met
Thr Pro Pro Pro Pro Gly Arg Ala Ala Pro Ser Ala Pro Arg Ala 1 5 10
15 Arg Val Pro Gly Pro Pro Ala Arg Leu Gly Leu Pro Leu Arg Leu Arg
20 25 30 Leu Leu Leu Leu Leu Trp Ala Ala Ala Ala Ser Ala Gln Gly
His Leu 35 40 45 Arg Ser Gly Pro Arg Ile Phe Ala Val Trp Lys Gly
His Val Gly Gln 50 55 60 Asp Arg Val Asp Phe Gly Gln Thr Glu Pro
His Thr Val Leu Phe His 65 70 75 80 Glu Pro Gly Ser Ser Ser Val Trp
Val Gly Gly Arg Gly Lys Val Tyr 85 90 95 Leu Phe Asp Phe Pro Glu
Gly Lys Asn Ala Ser Val Arg Thr Val Asn 100 105 110 Ile Gly Ser Thr
Lys Gly Ser Cys Leu Asp Lys Arg Asp Cys Glu Asn 115 120 125 Tyr Ile
Thr Leu Leu Glu Arg Arg Ser Glu Gly Leu Leu Ala Cys Gly 130 135 140
Thr Asn Ala Arg His Pro Ser Cys Trp Asn Leu Val Asn Gly Thr Val 145
150 155 160 Val Pro Leu Gly Glu Met Arg Gly Tyr Ala Pro Phe Ser Pro
Asp Glu 165 170 175 Asn Ser Leu Val Leu Phe Glu Gly Asp Glu Val Tyr
Ser Thr Ile Arg 180 185 190 Lys Gln Glu Tyr Asn Gly Lys Ile Pro Arg
Phe Arg Arg Ile Arg Gly 195 200 205 Glu Ser Glu Leu Tyr Thr Ser Asp
Thr Val Met Gln Asn Pro Gln Phe 210 215 220 Ile Lys Ala Thr Ile Val
His Gln Asp Gln Ala Tyr Asp Asp Lys Ile 225 230 235 240 Tyr Tyr Phe
Phe Arg Glu Asp Asn Pro Asp Lys Asn Pro Glu Ala Pro 245 250 255 Leu
Asn Val Ser Arg Val Ala Gln Leu Cys Arg Gly Asp Gln Gly Gly 260 265
270 Glu Ser Ser Leu Ser Val Ser Lys Trp Asn Thr Phe Leu Lys Ala Met
275 280 285 Leu Val Cys Ser Asp Ala Ala Thr Asn Lys Asn Phe Asn Arg
Leu Gln 290 295 300 Asp Val Phe Leu Leu Pro Asp Pro Ser Gly Gln Trp
Arg Asp Thr Arg 305 310 315 320 Val Tyr Gly Val Phe Ser Asn Pro Trp
Asn Tyr Ser Ala Val Cys Val 325 330 335 Tyr Ser Leu Gly Asp Ile Asp
Lys Val Phe Arg Thr Ser Ser Leu Lys 340 345 350 Gly Tyr His Ser Ser
Leu Pro Asn Pro Arg Pro Gly Lys Cys Leu Pro 355 360 365 Asp Gln Gln
Pro Ile Pro Thr Glu Thr Phe Gln Val Ala Asp Arg His 370 375 380 Pro
Glu Val Ala Gln Arg Val Glu Pro Met Gly Pro Leu Lys Thr Pro 385 390
395 400 Leu Phe His Ser Lys Tyr His Tyr Gln Lys Val Ala Val His Arg
Met 405 410 415 Gln Ala Ser His Gly Glu Thr Phe His Val Leu Tyr Leu
Thr Thr Asp 420 425 430 Arg Gly Thr Ile His Lys Val Val Glu Pro Gly
Glu Gln Glu His Ser 435 440 445 Phe Ala Phe Asn Ile Met Glu Ile Gln
Pro Phe Arg Arg Ala Ala Ala 450 455 460 Ile Gln Thr Met Ser Leu Asp
Ala Glu Arg Arg Lys Leu Tyr Val Ser 465 470 475 480 Ser Gln Trp Glu
Val Ser Gln Val Pro Leu Asp Leu Cys Glu Val Tyr 485 490 495 Gly Gly
Gly Cys His Gly Cys Leu Met Ser Arg Asp Pro Tyr Cys Gly 500 505 510
Trp Asp Gln Gly Arg Cys Ile Ser Ile Tyr Ser Ser Glu Arg Ser Val 515
520 525 Leu Gln Ser Ile Asn Pro Ala Glu Pro His Lys Glu Cys Pro Asn
Pro 530 535 540 Lys Pro Asp Lys Ala Pro Leu Gln Lys Val Ser Leu Ala
Pro Asn Ser 545 550 555 560 Arg Tyr Tyr Leu Ser Cys Pro Met Glu Ser
Arg His Ala Thr Tyr Ser 565 570 575 Trp Arg His Lys Glu Asn Val Glu
Gln Ser Cys Glu Pro Gly His Gln 580 585 590 Ser Pro Asn Cys Ile Leu
Phe Ile Glu Asn Leu Thr Ala Gln Gln Tyr 595 600 605 Gly His Tyr Phe
Cys Glu Ala Gln Glu Gly Ser Tyr Phe Arg Glu Ala 610 615 620 Gln His
Trp Gln Leu Leu Pro Glu Asp Gly Ile Met Ala Glu His Leu 625 630 635
640 Leu Gly His Ala Cys Ala Leu Ala Ala Ser Leu Trp Leu Gly Val Leu
645 650 655 Pro Thr Leu Thr Leu Gly Leu Leu Val His 660 665 3 712
DNA HOMO SAPIENS UNSURE (35)(39)(40)(712) OTHER INFORMATION EST
Sequence 3 ccgcctgccg cccagggcca cctaaggagc ggatnctann tcttcgccgt
ctggaaaggc 60 catgtagggc aggaccgggt ggactttggc cagactgagc
cgcacacggt gcttttccac 120 gagccaggca gctcctctgt gtgggtggga
ggacgtggca aggtctacct ctttgacttc 180 cccgagggca agaacgcatc
tgtgcgcacg gtgaatatcg gctccacaaa ggggtcctgt 240 ctggataagc
gggactgcga gaactacatc actctcctgg agaggcggag tgaggggctg 300
ctggcctgtg gcaccaacgc ccggcacccc agctgctgga acctggtgaa tgcactgtgg
360 tgccaccttg gcgagagtgg aggctacgcc cccttcagcc cggacgagaa
cgtcccgtgg 420 ttctgttttg aaggggacga agtgtattcc accatccgga
aagcaaggaa ttacaattgg 480 gaagatcctc ggttccgccg catccggggc
gagagtgagc tgtacaccag tgatactgtc 540 atgcagaacc cacagttcat
caaagccacc atcgtgcacc aagaccaggc ttacgatgac 600 aagatctact
acttcttccg agaggacaat cctgacaaga atcctgaggc tcctctcaat 660
gtgtcccgtg tggcccagtt gtgcaggggg gaccagggtg gggaaagttc an 712 4 215
PRT HOMO SAPIENS 4 Gly Gln Asp Arg Val Asp Phe Gly Gln Thr Glu Pro
His Thr Val Leu 1 5 10 15 Phe His Glu Pro Gly Ser Ser Ser Val Trp
Val Gly Gly Arg Gly Lys 20 25 30 Val Tyr Leu Phe Asp Phe Pro Glu
Gly Lys Asn Ala Ser Val Arg Thr 35 40 45 Val Asn Ile Gly Ser Thr
Lys Gly Ser Cys Leu Asp Lys Arg Asp Cys 50 55 60 Glu Asn Tyr Ile
Thr Leu Leu Glu Arg Arg Ser Glu Gly Leu Leu Ala 65 70 75 80 Cys Gly
Thr Asn Ala Arg His Pro Ser Cys Trp Asn Leu Val Asn Ala 85 90 95
Leu Trp Cys His Leu Gly Glu Ser Gly Gly Tyr Ala Pro Phe Ser Pro 100
105 110 Asp Glu Asn Val Pro Trp Phe Cys Phe Glu Gly Asp Glu Val Tyr
Ser 115 120 125 Thr Ile Arg Lys Ala Arg Asn Tyr Asn Trp Glu Asp Pro
Arg Phe Arg 130 135 140 Arg Ile Arg Gly Glu Ser Glu Leu Tyr Thr Ser
Asp Thr Val Met Gln 145 150 155 160 Asn Pro Gln Phe Ile Lys Ala Thr
Ile Val His Gln Asp Gln Ala Tyr 165 170 175 Asp Asp Lys Ile Tyr Tyr
Phe Phe Arg Glu Asp Asn Pro Asp Lys Asn 180 185 190 Pro Glu Ala Pro
Leu Asn Val Ser Arg Val Ala Gln Leu Cys Arg Gly 195 200 205 Asp Gln
Gly Gly Glu Ser Ser 210 215
* * * * *