U.S. patent application number 09/840787 was filed with the patent office on 2002-05-16 for human regulatory molecules.
This patent application is currently assigned to Incyte Pharmaceuticals, Inc. Invention is credited to Au-Young, Janice, Bandman, Olga, Corley, Neil C., Guegler, Karl J., Hillman, Jennifer L., Lal, Preeti, Shah, Purvi, Yue, Henry.
Application Number | 20020058264 09/840787 |
Document ID | / |
Family ID | 25464445 |
Filed Date | 2002-05-16 |
United States Patent
Application |
20020058264 |
Kind Code |
A1 |
Lal, Preeti ; et
al. |
May 16, 2002 |
Human regulatory molecules
Abstract
The invention provides human regulatory molecules and the
polynucleotides which identify and encode them. The invention also
provides expression vectors, host cells, agonists, antibodies and
antagonists. The invention further provides methods for diagnosing
and treating disorders associated with expression of human
regulatory molecules.
Inventors: |
Lal, Preeti; (Santa Clara,
CA) ; Hillman, Jennifer L.; (Mountain View, CA)
; Bandman, Olga; (Mountain View, CA) ; Shah,
Purvi; (Sunnyvale, CA) ; Au-Young, Janice;
(Berkeley, CA) ; Yue, Henry; (Sunnyvale, CA)
; Guegler, Karl J.; (Menlo Park, CA) ; Corley,
Neil C.; (Mountain View, CA) |
Correspondence
Address: |
INCYTE GENOMICS, INC.
PATENT DEPARTMENT
3160 Porter Drive
Palo Alto
CA
94304
US
|
Assignee: |
Incyte Pharmaceuticals, Inc
|
Family ID: |
25464445 |
Appl. No.: |
09/840787 |
Filed: |
September 26, 2001 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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09840787 |
Sep 26, 2001 |
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09518865 |
Mar 3, 2000 |
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09518865 |
Mar 3, 2000 |
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09234613 |
Jan 20, 1999 |
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6132973 |
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09234613 |
Jan 20, 1999 |
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08933750 |
Sep 23, 1997 |
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5932442 |
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Current U.S.
Class: |
435/6.16 ;
435/183; 435/320.1; 435/325; 435/69.1; 536/23.2 |
Current CPC
Class: |
A61P 31/00 20180101;
Y10T 436/143333 20150115; C07K 14/4702 20130101; A61P 35/00
20180101; A61K 38/00 20130101; C12N 9/93 20130101 |
Class at
Publication: |
435/6 ; 435/69.1;
435/320.1; 435/325; 435/183; 536/23.2 |
International
Class: |
C12Q 001/68; C07H
021/04; C12N 009/00; C12N 005/06; C12P 021/02 |
Claims
What is claimed is:
1. A purified protein comprising an amino acid sequence selected
from SEQ ID NOs: 1-49.
2. An isolated polynucleotide comprising a nucleic acid sequence
encoding the protein of claim 1 or the complement of the
polynucleotide.
3. A composition comprising a polynucleotide of claim 2 and a
reporter molecule.
4. An isolated polynucleotide comprising a nucleic acid sequence
selected from SEQ ID NOs:50-98 and the complement of the
polynucleotide.
5. A vector containing the polynucleotide of claim 2.
6. A host cell containing the vector of claim 5.
7. A method for using a polynucleotide to produce a protein
comprising: a) culturing the host cell of claim 6 under conditions
for the expression of the protein, and b) recovering the protein
from the host cell culture.
8. A method for using a polynucleotide to detect expression of a
nucleic acid in a sample, the method comprising: a) hybridizing the
polynucleotide of claim 2 to nucleic acids of the sample, thereby
forming a hybridization complex, and b) detecting hybridization
complex formation, wherein complex formation indicates the
expression of the polynucleotide in the sample.
9. The method of claim 8 wherein the polynucleotide is attached to
a substrate or bonded to the surface of a microarray.
10. The method of claim 8 wherein the nucleic acids of the sample
are amplified prior to hybridization.
11. A method of using a polynucleotide to screen a plurality of
molecules to identify a ligand, the method comprising: a) combining
the polynucleotide of claim 2 with a plurality of molecules under
conditions to allow specific binding, and b) detecting specific
binding, thereby identifying a ligand which specifically binds the
polynucleotide.
12. The method of claim 11 wherein the molecules are selected from
DNA molecules, RNA molecules, peptide nucleic acids, artificial
chromosome constructions, peptides, and transcription factors.
13. A method for diagnosing a disease associated with gene
expression in a sample containing nucleic acids, the method
comprising: a) hybridizing a polynucleotide of claim 2 to nucleic
acids of the sample under conditions to form a hybridization
complex, b) comparing hybridization complex formation with
standards, thereby diagnosing the disease.
14. The method of claim 13 wherein expression is diagnostic of
cancer or immune response.
15. A composition comprising the protein of claim 1 and a
pharmaceutical carrier or a labeling moiety.
16. A method for using a protein to screen a plurality of molecules
to identify a ligand, the method comprising: a) combining the
protein of claim 1 with the molecules under conditions to allow
specific binding, and b) detecting specific binding, thereby
identifying a ligand which specifically binds the protein.
17. The method of claim 16 wherein the molecules are selected from
DNA molecules, RNA molecules, peptide nucleic acids, peptides,
pharmaceutical agents, proteins, mimetics, agonists, antagonists,
Ned antibodies, immunoglobulins, inhibitors, and drugs.
18. A method of using a protein to prepare and purify antibodies
comprising: a) immunizing a animal with the protein of claim 1
under conditions to elicit an antibody response, b) isolating
animal antibodies, c) attaching the protein to a substrate, d)
contacting the substrate with isolated antibodies under conditions
to allow specific binding to the protein, e) dissociating the
antibodies from the protein, thereby obtaining purified
antibodies.
19. An antibody which specifically binds a protein of claim 1.
20. A method for using an antibody to detect protein expression in
a sample, the method comprising: a) combining the antibody of claim
19 with a sample under conditions to form antibody:protein
complexes, and b) detecting complex formation with standards,
wherein detection indicates expression of the protein in the
sample.
Description
[0001] This application is a divisional of U.S. Pat. No. 09/518,865
filed 3 Mar. 2000, which was a divisional of U.S. Pat. No
6,132,973, issued 17 Oct. 2000, which was a divisional of U.S. Pat.
No. 5,932,442, issued 3 Aug. 1999.
FIELD OF THE INVENTION
[0002] This invention relates to nucleic acid and amino acid
sequences of human regulatory molecules which are implicated in
disease and to the use of these sequences in the diagnosis and
treatment of diseases associated with cell proliferation.
BACKGROUND OF THE INVENTION
[0003] Cells grow and differentiate, carry out their structural or
metabolic roles, participate in organismal development, and respond
to their environment by altering their gene expression. Cellular
functions are controlled by the timing and amount of expression
attributable to thousands of individual genes. The regulation of
expression is metabolically vital in that it conserves energy and
prevents the synthesis and accumulation of intermediates such as
RNA and incomplete or inactive proteins when the gene product is
not needed.
[0004] Regulatory protein molecules function to control gene
expression. These molecules turn individual or groups of genes on
and off in response to various inductive mechanisms of the cell or
organism; act as transcription factors by determining whether or
not transcription is initiated, enhanced, or repressed; and splice
transcripts as dictated in a particular cell or tissue. Although
regulatory molecules interact with short stretches of DNA scattered
throughout the entire genome, most gene expression is regulated
near the site at which transcription starts or within the open
reading frame of the gene being expressed. The regulated stretches
of the DNA can be simple and interact with only a single protein,
or they can require several proteins acting as part of a complex in
order to regulate gene expression.
[0005] The double helix structure and repeated sequences of DNA
create external features which can be recognized by the regulatory
molecules. These external features are hydrogen bond donor and
acceptor groups, hydrophobic patches, major and minor grooves, and
regular, repeated stretches of sequence which cause distinct bends
in the helix. Such features provide recognition sites for the
binding of regulatory proteins. Typically, these recognition sites
are less than 20 nucleotides in length although multiple sites may
be adjacent to each other, and each may exert control over a single
gene. Hundreds of these DNA sequences have been identified, and
each is recognized by a different protein or complex of proteins
which carry out gene regulation.
[0006] The regulatory protein molecules or complexes recognize and
bind to specific nucleotide sequences of upstream (5')
nontranslated regions, which precede the first translated exon of
the open reading frame (ORF); of intron junctions, which occur
between the many exons of the OR; and of downstream (3')
untranslated regions, which follow the ORF. The regulatory molecule
surface features are extensively complementary to the surface
features of the double helix. Even though each individual contact
between the protein(s) and helix may be relatively weak (hydrogen
bonds, ionic bonds, and/or hydrophobic interactions) and the 20 or
more contacts occurring between the protein and DNA result in a
highly specific and very strong interaction.
Families of regulatory molecules
[0007] Many of the regulatory molecules incorporate one of a set of
DNA-binding structural motifs, each of which contains either
.alpha. helices or .beta. sheets and binds to the major groove of
DNA. Seven of the structural motifs common to regulatory molecules
are helix-turn-helix, homeodomains, zinc finger, steroid receptor,
.beta. sheets, leucine zipper, and helix-loop-helix.
[0008] The helix-turn-helix motif is constructed from two .alpha.
helices connected by a short chain of amino acids, which
constitutes the "turn". The two helices interact with each other to
form a fixed angle. The more carboxy-terminal helix is called the
recognition helix because it fits into the major groove of the DNA.
The amino acid side chains of the helix recognize the specific DNA
sequence to which the protein binds. The H remaining structure
varies a great deal among the regulatory proteins incorporating
this motif. The helix-turn-helix configuration is not stable
without the rest of the protein and will not bind to DNA without
other peptide regions providing stability. Other peptide regions
also interact with the DNA, increasing the number of unique
sequences a helix-turn-helix can recognize.
[0009] Many sequence-specific DNA binding proteins actually bind as
symmetric dimers to DNA sequences that are composed of two very
similar half-sites, also arranged symmetrically. This configuration
allows each protein monomer to interact in the same way with the
DNA recognition site and doubles the number of contacts with the
DNA. This doubling of contacts greatly increases the binding
affinity while only doubling the free energy of the interaction.
Helix-turn-helix motifs always bind to DNA that is in the B-DNA
form.
[0010] The homeodomain motif is found in a special group of
helix-turn-helix proteins that are encoded by homeotic selector
genes, so called because the proteins encoded by these genes
control developmental switches. For example, mutations in these
genes cause one body part to be converted into another in the fruit
fly, Drosophila. These genes have been found in every eukaryotic
organism studied. The helix-turn-helix region of different
homeodomains is always surrounded by the same structure, but not
necessarily the same sequence, and the motif is always presented to
DNA the same way. This helix-turn-helix configuration is stable by
itself and, when isolated, can still bind to DNA. It may be
significant that the helices in homeodomains are generally longer
than the helices in most HLH regulatory proteins. Portions of the
motif which interact most directly with DNA differ among these two
families. Detailed examples of DNA-protein binding are described in
Pabo and Sauer (1992; Ann Rev Biochem 61:1053-95).
[0011] A third motif incorporates zinc molecules into the crucial
portion of the protein. These proteins are most often referred to
as having zinc fingers, although their structure can be one of
several types. Proteins in this family often contain tandem repeats
of the 30-residue zinc finger motif, including the sequence
patterns Cys-X.sub.2 or 4-Cys-X.sub.12-His-X.sub.3--His. Each of
these regulatory proteins has an a helix and an antiparallel .beta.
sheet. Two histidines in the .alpha. helix and 2 cysteines near the
turn in the .beta. sheet interact with the zinc ion which holds the
.alpha. helix and the .beta. sheet together. Contact with the DNA
is made by the arginine preceding the .alpha. helix, and by the
second, third, and sixth residues of the .alpha. helix. When this
arrangement is repeated as a cluster of several fingers, .alpha. of
each finger can contact and interact with the major groove of the
DNA. By changing the number of zinc fingers, the specificity and
strength of the binding interaction can be altered.
[0012] The steroid receptors are a family of intracellular proteins
that include receptors for steroids, retinoids, vitamin D, thyroid
hormones, and other important compounds. The DNA binding domain of
these proteins contains about 70 residues, eight of which are
conserved cysteines. The steroid receptor motif forms a structure
in which two a helices are packed perpendicularly to each other,
forming more of a globular shape than a finger. Each helix has a
zinc ion which holds a peptide loop against the N-terminal end of
the helix. The first helix fits into the major groove of DNA, and
side chains make contacts with edges of the DNA base pairs. The
steroid receptor proteins, like the helix-turn-helix proteins, form
dimers that bind the DNA. The second helix of each monomer contacts
the phosphate groups of the DNA backbone and also provides the
dimerization interface. In some cases, multiple choices can exist
for heterodimerization which produces another mechanism for
fine-tuning the regulation of numerous genes.
[0013] Another family of regulatory protein molecules uses a motif
consisting of a two-stranded antiparallel .beta.sheet to recognize
the major groove of DNA. The exact DNA sequence recognized by the
motif depends on the amino acid sequence in the .beta. sheet from
which the amino acid side chains extend and contact the DNA. In two
prokaryotic examples of the .beta. sheet, the regulatory proteins
form tetramers when binding DNA.
[0014] The leucine zipper motif commonly forms dimers and has a
30-40 residue motif in which two .alpha. helices (one from each
monomer) are joined to form a short coiled-coil. The helices are
held together by interactions among hydrophobic amino acid side
chains (often on heptad-repeated leucines) that extend from one
side of each helix. Beyond this, the helices separate, and each
basic region contacts the major groove of DNA. Proteins with the
leucine zipper motif can also form either homodimers or
heterodimers, thus extending the specific combinations available to
activate or repress expression.
[0015] Yet another motif is the helix-loop-helix, which consists of
a short .alpha. helix connected by a loop to a longer .alpha.
helix. The loop is flexible and allows the two helices to fold back
against each other. The .alpha. helices bind both to DNA and to the
HLH structure of another protein. The second protein can be the
same (producing homodimers) or different (producing heterodimers).
Some HLH monomers lack sufficient .alpha. helix to bind DNA, but
they can still form heterodimers which can serve to inactivate
specific regulatory proteins.
[0016] Hundreds of regulatory proteins have been identified to
date, and more are being characterized in a wide variety of
organisms. Most regulatory proteins have at least one of the common
structural motifs for making contact with DNA, but several
regulatory proteins, such as the p53 tumor suppressor gene, do not
share their structure with other known regulatory proteins.
Variations on the known motifs and new motifs have been and are
currently being characterized (Faisst and Meyer (1992) Nucl Acids
Res 20:3-26).
[0017] Although binding of DNA to a regulatory protein is very
specific, there is no way to predict the exact DNA sequence to
which a particular regulatory protein will bind or the primary
structure of a regulatory protein for a specific DNA sequence.
Thus, interactions of DNA and regulatory proteins are not limited
to the motifs described above. Other domains of the proteins often
form crucial contacts with the DNA, and accessory proteins can
provide interactions which may convert a particular protein complex
to an activator or a represser or may prevent binding (Alberts et
al. (1994)Molecular Biology of the Cell, Garland Publishing, New
York NY, pp.40.sup.1-74).
Diseases and disorders related to gene regulation
[0018] Many neoplastic growths in humans can be traced to problems
of gene regulation. Malignant growth of cells may be the result of
excess transcriptional activator or loss of an inhibitor or
suppressor (Cleary (1992) Cancer Surv 15:89-104). Alternatively,
gene fusion may produce chimeric loci with switched domains, such
that the level of activation is no longer correct for the gene
specificity of that factor.
[0019] The cellular response to infection or trauma is beneficial
when genes are appropriately expressed. However, when
hyper-responsivity or another imbalance occurs for any reason,
disregulation of gene expression may cause considerable tissue or
organ damage. This damage is well documented in immunological
responses to allergens, heart attack, stroke, and infections
(Harrison's Principles of Internal Medicine, 13/e.COPYRGT., (1994)
McGraw Hill and Teton Data Systems, Jackson Wyo.). In addition, the
accumulation of somatic mutations and the increasing inability to
regulate cellular responses is seen in the prevalence of
osteoarthritis and onset of other aging disorders.
[0020] The discovery of new human regulatory protein molecules
which are expressed during disease development and the
polynucleotides which encode them satisfies a need in the art by
providing compositions which are useful in the diagnosis and
treatment of diseases associated with cell proliferation,
particularly immune responses and cancers.
SUMMARY OF THE INVENTION
[0021] The invention features purified proteins, human regulatory
molecules, collectively referred to as HRM and individually
referred to as HRM-1 through HRM-49. In one embodiment, the
purified protein comprises an amino acid sequence selected from SEQ
ID NO:1 through SEQ ID NO:49 and portions thereof..
[0022] The invention provides isolated polynucleotides encoding HRM
and complements of the encoding polynucleotides. In one embodiment,
the polynucleotide comprises a nucleic acid sequence selected from
SEQ ID NOs:50-98 and complements thereof.
[0023] The invention also provides a polynucleotide, or a
complement or a fragment thereof, which is used as a probe to
hybridize to any one of the polynucleotides of SEQ ID NOs:50-98.
The invention further provides a composition comprising the
isolated and purified polynucleotides of SEQ ID NOs:50-98. In
addition, the invention provides a composition comprising a
polynucleotide selected from SEQ ID NOs:50-98 and complements and
fragments thereof and a reporter molecule or stabilizing moiety.
The invention still further provides a method for detecting
expression of a polynucleotide which encodes a human regulatory
molecule in a sample, the method comprising hybridizing the
complement of a polynucleotide encoding HRM to nucleic acids of the
sample under conditions to form a hybridization complex; and
detecting hybridization complex formation, wherein complex
formation indicates the expression of the polynucleotide encoding
the human regulatory molecule in the sample. In one aspect, the
complement of the polynucleotide encoding HRM is immobilized on a
substrate. In another aspect, the substrate is a microarray.
[0024] The invention provides a vector containing at least a
fragment of any one of the polynucleotides selected from SEQ ID
NOs:50-98. In one embodiment, the vector is contained within a host
cell. The invention also provides a method for producing a protein
or a portion thereof, the method comprising culturing a host cell
containing a vector containing at least a fragment of a
polynucleotide encoding an HRM under conditions for the expression
of the protein; and recovering the protein from the host cell
culture.
[0025] The invention further provides a composition comprising a
purified HRM and a labeling moiety or a pharmaceutical carrier. The
invention still further provides a method for using an HRM to
screen a plurality of molecules in order to obtain a ligand which
specifically binds the HRM, the method comprising combining the
protein with the molecules under conditions which allow specific
binding, recovering the bound protein, separating the protein,
thereby obtaining the ligand. In one aspect, the molecules are
selected from libraries of agonists, antibodies, antagonists,
drugs, inhibitors, peptides, proteins, and pharmaceutical
agents.
[0026] The invention still further provides a method for using a
protein to produce and purify an antibody, the method comprising
immunizing a animal with an HRM under conditions to elicit an
antibody response; isolating animal antibodies; attaching the
protein to a substrate; contacting the substrate with sera
containing antibodies under conditions to allow specific binding to
the HRM; dissociating the antibodies from the HRM, thereby
obtaining purified antibodies.
[0027] The invention provides a purified antibody which
specifically binds an HRM. The invention also provides a method for
using an antibody to detect protein expression in a sample, the
method comprising combining the antibody specifically binding HRM
with a sample under conditions to form antibody:protein complexes
and detecting complex formation, wherein detection indicates
expression of the protein in the sample. In one aspect, expression
of the HRM is diagnostic of cancer. In another aspect, expression
is diagnostic of immune response.
[0028] The invention also provides a method for diagnosing a
disease associated with gene expression in a sample containing
nucleic acids, the method comprising hybridizing a polynucleotide
to nucleic acids of the sample under conditions to form a
hybridization complex, comparing hybridization complex formation to
standards, thereby diagnosing the disease. In one aspect, the
disease is selected from a disorder characterized by cell
proliferation such as a cancer, an developmental disorder, or an
immune response.
[0029] The invention provides a method for treating a cancer
comprising administering to a subject in need of such treatment a
composition containing purified HRM. The invention also provides a
method for treating a cancer comprising administering to a subject
in need of such treatment an antagonist which specifically binds
HRM. The invention further provides a method for treating an immune
response associated with the increased expression or activity of
HRM comprising administering to a subject in need of such treatment
an antagonist which specifically binds HRM. The invention still
further provides a method for stimulating cell proliferation
comprising administering purified HRM to a cell.
DESCRIPTION OF THE INVENTION
[0030] Before the present proteins, polynucleotide, and methods are
described, it is to be understood that this invention is not
limited to any particular methodology, protocol, cell line, vector,
or reagent, as these may vary. It must also be noted that in the
appended claims, the singular forms "a", "an", and "the" include
plural reference unless the context clearly dictates otherwise. For
example, reference to "a host cell" includes a plurality of such
host cells; reference to an "antibody" includes one or more
antibodies and equivalents thereof known to those skilled in the
art.
[0031] Unless defined herein, all technical and scientific terms
have the same meanings commonly understood by one of ordinary skill
in the art to which this invention belongs. The terminology is used
for the purpose of describing particular embodiments and is not
intended to limit the scope of the present invention which will be
limited only by the appended claims. Although any methods and
materials similar or equivalent to those described can be used in
the practice or testing of the invention, the preferred methods,
devices, and materials are now described. All publications are
incorporated herein by reference for the purpose of describing and
disclosing the cell lines, vectors, arrays and methodologies which
are reported in the publications and which might be used in
connection with the invention. Nothing herein is to be construed as
an admission that the invention is not entitled to antedate such
disclosure by virtue of prior invention.
[0032] DEFINITIONS
[0033] "Agonist" refers to a molecule which specifically binds to
and modulates the activity of HRM.
[0034] An "allele" is an alternative form of the polynucleotide or
gene encoding HRM. Alleles result from at least one mutation in the
nucleic acid sequence and may result in the expression of altered
mRNAs or proteins whose structure or function may or may not be
altered. Any given gene may have none, one, or many allelic forms.
Common mutational changes which give rise to alleles are generally
ascribed to additions, deletions, or substitutions of nucleotides.
Each of these types of changes may occur alone, or in combination
with the others, one or more times in a given sequence. Similarly a
polynucleotide may be altered to produce deliberate amino acid
substitutions. Theses substitutions may be made on the basis of
similarity in polarity, charge, solubility, hydrophobicity,
hydrophilicity, and/or the amphipathic nature of the residues as
long as the biological or immunological activity of HRM is
retained. For example, negatively charged residues include aspartic
acid and glutamic acid; positively charged residues include lysine
and arginine; and residues with uncharged polar head groups having
similar hydrophilicity values include leucine, isoleucine, and
valine, glycine and alanine, asparagine and glutamine, serine and
threonine, and phenylalanine and tyrosine.
[0035] "Antagonist" refers to a molecule which, when bound to HRM,
decreases the amount or the duration of the biological or
immunological activity of HRM. Antagonists may include proteins,
nucleic acids, carbohydrates, fats or any other molecules which
decrease the effect of HRM.
[0036] "Antibody" refers to intact molecules, or fragments thereof
such as Fa, F(ab').sub.2, and Fv, which are capable of binding the
antigenic determinant of an HRM.
[0037] "Biologically active" refers to a protein having structural,
regulatory, or biochemical functions of a naturally occurring
molecule. Likewise, "immunologically active" refers to the
capability of the natural, recombinant, or synthetic protein or
peptide to induce a specific immune response in animals or cells
and to bind with specific antibodies.
[0038] "Complementary" refers to the natural binding of
polynucleotides under permissive salt and temperature conditions by
base-pairing. For example, the sequence "A-G-T" binds to the
complementary sequence "T-C-A". The degree of complementarity
between nucleic acids has significant effects on the efficiency and
strength of hybridization. This is important in amplification
reactions and in the design and use of peptide nucleic acid
molecules.
[0039] A "composition" refers to a combination comprising a
plurality of polynucleotides or a specific polynucleotide or
protein and at least one other molecule. Such other molecules may
include reporter molecules, labeling moieties, pharmaceutical
carriers, carbohydrates, and the like.
[0040] "Consensus" refers to a nucleic acid sequence which has been
resequenced to resolve uncalled bases, has been extended using
XL-PCR kit (Applied Biosystems (ABI), Foster City Calif.) in the 5'
and/or the 3' direction and resequenced, or has been assembled to
full length from overlapping shorter fragments using a computer
program for fragment assembly such as that described in U.S. Ser.
No. 09/276,534, filed 25 Mar. 1999.
[0041] "Derivative" refers to the chemical modification of a
polynucleotide or protein. Such modifications may include
replacement of hydrogen by an alkyl, acyl, or amino group. A
nucleic acid derivative may encode a protein which retains the
biological or immunological function of the natural molecule. A
derivative protein is one which is modified by glycosylation,
pegylation, or any similar process but still retains the biological
or immunological function of the native protein.
[0042] "Differential expression" refers to an increased,
upregulated or present, or decreased, downregulated or absent, gene
expression as detected by presence, absence or at least about
two-fold changes in the amount of transcribed messenger RNA or
translated protein in a sample.
[0043] "Disorder" refers to a condition, disease or syndrome in
which a polynucleotide or a protein of the invention is
differentially expressed. Such a disorder includes cancers or
immune responses as they are set forth below.
[0044] "HRM" refers to any one or all of the human proteins, HRMs
1-49, as it was obtained from any species including bovine, ovine,
porcine, murine, equine, and preferably human, or from any source
whether natural, synthetic, semi-synthetic, or recombinant.
[0045] "Hybridization complex" refers to a complex formed between
two nucleic acids by the formation of hydrogen bonds between
complementary base pairs; these hydrogen bonds form in an
antiparallel configuration and may be further stabilized by base
stacking interactions. A hybridization complex may be formed in
solution or between one nucleic acid present in solution and
another nucleic acid immobilized on a substrate.
[0046] "Isolated" refers to a polynucleotide that is removed from
its natural environment or separated from other components with
which it is naturally associated.
[0047] "Ligand" refers to any agent, molecule, or compound which
will bind specifically to a polynucleotide or to a protein. Such
ligands stabilize or modulate the activity of polynucleotides or
proteins and may be composed of inorganic and/or organic substances
including minerals, cofactors, nucleic acids, proteins,
carbohydrates, fats, and lipids.
[0048] "Microarray" refers to an arrangement of distinct
polynucleotides on a substrate "Oligonucleotide" refers to a
nucleic acid sequence about 6 nucleotides to about 60 nucleotides
in length which may be used in amplification or hybridization
assays. Equivalent terms include "amplimers","primers",
"oligomers", and "probes", as these are commonly defined in the
art. "Peptide nucleic acid" refers to an anti-gene agent which
comprises an oligonucleotide of at least five nucleotides in length
linked to a peptide backbone of amino acid residues which ends in a
terminal lysine which confers solubility to the molecule.
[0049] "Polynucleotide" refers to nucleic acid molecule having a
nucleic acid sequence and to DNA or RNA of genomic or synthetic
origin which may be single- or double-stranded and represent the
sense or antisense strand. "Fragment" refers to a nucleic acid
sequence which is more than about 60 nucleotides in length.
[0050] "Portion" refers to a fragment of an HRM which ranges in
size from five amino acid residues to the entire amino acid
sequence minus one amino acid.
[0051] "Protein" refers to an oligopeptide, peptide, or polypeptide
having an amino acid sequence whether naturally occurring or
synthetic molecules. Portions of HRM are preferably about 5 to
about 15 amino acids in length and retain the biological or the
immunological activity of the HRM.
[0052] "Purified" refers to a peptide or protein that is removed
from its natural environment, isolated or separated from other
components with which it is naturally associated.
[0053] "Reporter molecules" or "labeling moieties" include
radionuclides, enzymes, fluorescent, chemiluminescent, or
chromogenic agents as well as substrates, cofactors, inhibitors,
magnetic particles, and the like.
[0054] "Sample" is used in its broadest sense and may comprise a
bodily fluid, extract from a cell, chromosome, organelle, or
membrane isolated from a cell, a cell, genomic DNA, RNA, or cDNA
(in solution or bound to a solid support), a tissue, a tissue
print, and the like.
[0055] "Specific binding" refers to that interaction between a
polynucleotide or protein of the invention and any ligand which
specifically binds to it and which is selected from a DNA or an RNA
molecule, a peptide nucleic acid, a peptide, a protein, an agonist,
an antibody, an antagonist, an inhibitor, a mimetic, a
pharmaceutical agent, a drug, a transcription factor, or an
artificial chromosome construction. The interaction is dependent
upon the presence of a particular sequence or three dimensional
structure recognized by the binding molecule.
[0056] "Substrate" refers to any rigid or semi-rigid support to
which polynucleotides or proteins are bound and includes membranes,
filters, chips, slides, wafers, fibers, magnetic or nomnmagnetic
beads, gels, capillaries or other tubing, plates, polymers, and
microparticles with a variety of surface forms including wells,
trenches, pins, channels and pores.
[0057] "Variant" refers to molecules that are recognized variations
of a polynucleotide or a protein encoded by the polynucleotide.
Splice variants may be determined by BLAST score, wherein the score
is at least 100, and most preferably at least 400. Allelic variants
have a high percent identity to the polynucleotides and may differ
by about three bases per hundred bases. "Single nucleotide
polymorphism" (SNP) refers to a change in a single base as a result
of a substitution, insertion or deletion. The change may be
conservative (purine for purine) or non-conservative (purine to
pyrimidine) and may or may not result in a change in an encoded
amino acid or its secondary, tertiary, or quaternary structure.
[0058] THE INVENTION
[0059] The invention is based on the discovery of human regulatory
molecules (HRM) and the polynucleotides encoding HRM, and on the
use of these compositions for the diagnosis and treatment of
diseases associated with cell proliferation. Table 1 shows the
protein and polynucleotide identification numbers, protein
abbreviation, Incyte Clone number, cDNA library, and the closest
NCBI homolog and NCBI sequence identifier for each of the human
regulatory molecules.
1TABLE 1 Protein Nucleotide Abbreviation Clone ID Library NCBI
Homolog SEQ ID NO:1 SEQ ID NO:50 HRM-1 133 U937NOT01 g285947
KIAA0105 SEQ ID NO:2 SEQ ID NO:51 HRM-2 1762 U937NOT01 g1518121
Ascaris suum SEQ ID NO:3 SEQ ID NO:52 HRM-3 1847 U937NOT01 g1302211
Saccharomyces cerevisiae SEQ ID NO:4 SEQ ID NO:53 HRM-4 9337
HMC1NOT01 g1613852 Human zinc finger protein (zf2) SEQ ID NO:5 SEQ
ID NO:54 HRM-5 9476 HMC1NOT01 g755784 S. cerevisiae SEQ ID NO:6 SEQ
ID NO:55 HRM-6 10370 THP1PLB01 g895845 Human putative p64 CLCP
protein SEQ ID NO:7 SEQ ID NO:56 HRM-7 30137 THP1NOB01 g1710241
Human clone 23733 mRNA SEQ ID NO:8 SEQ ID NO:57 HRM-8 77180
SYNORAB01 g5372 S. cerevisiae SEQ ID NO:9 SEQ ID NO:58 HRM-9 98974
PITUNOR01 g1627704 Caenorhabditis elegans SEQ ID NO:10 SEQ ID NO:59
HRM-10 118160 MUSCNOT01 g220594 Mus musculus SEQ ID NO:11 SEQ ID
NO:60 HRM-11 140516 TLYMNOR01 g1086723 C. elegans SEQ ID NO:12 SEQ
ID NO:61 HRM-12 207452 SPLNNOT02 g1314086 S. cerevisiae SEQ ID
NO:13 SEQ ID NO:62 HRM-13 208836 SPLNNOT02 g662126 S. cerevisiae
SEQ ID NO:14 SEQ ID NO:63 HRM-14 569710 MMLR3DT01 g1698719 Human
zinc finger protein SEQ ID NO:15 SEQ ID NO:64 HRM-15 606742
BRSTTUT01 g1710201 Human clone 23679 mRNA SEQ ID NO:16 SEQ ID NO:65
HRM-16 611135 COLNNOT01 g506882 C elegans SEQ ID NO:17 SEQ ID NO:66
HRM-17 641127 BRSTNOT03 g1310668 Human Hok-2 gene product SEQ ID
NO:18 SEQ ID NO:67 HRM-18 691768 LUNGTUT02 g309183 Mus musculus SEQ
ID NO:19 SEQ ID NO:68 HRM-19 724157 SYNOOAT01 g577542 C. elegans
C16C10 SEQ ID NO:20 SEQ ID NO:69 HRM-20 864683 BRAITUT03 g1418563
C. elegans SEQ ID NO:21 SEQ ID NO:70 HRM-21 933353 CERVNOT01
g1657672 C. elegans SEQ ID NO:22 SEQ ID NO:71 HRM-22 1404643
LATRTUT02 g459002 C. elegans SEQ ID NO:23 SEQ ID NO:72 HRM-23
1561587 SPLNNOT04 g868266 C. elegans SEQ ID NO:24 SEQ ID NO:73
HRM-24 1568361 UTRSNOT05 g1834503 Human mucin SEQ ID NO:25 SEQ ID
NO:74 HRM-25 1572888 LNODNOT03 g603396 S. cerevisiae YER156c SEQ ID
NO:26 SEQ ID NO:75 HRM-26 1573677 LNODNOT03 g849195 S. cerevisiae
D9481.16 SEQ ID NO:27 SEQ ID NO:76 HRM-27 1574624 LNODNOT03
g1067025 C. elegans R07E5.14 SEQ ID NO:28 SEQ ID NO:77 HRM-28
1577239 LNODNOT03 g728657 S. cerevisiae SEQ ID NO:29 SEQ ID NO:78
HRM-29 1598203 BLADNOT03 g1200033 C. elegans F35G2 SEQ ID NO:30 SEQ
ID NO:79 HRM-30 1600438 BLADNOT03 g286001 KIAA0005 SEQ ID NO:31 SEQ
ID NO:80 HRM-31 1600518 BLADNOT03 g790405 C. elegans SEQ ID NO:32
SEQ ID NO:81 HRM-32 1602473 BLADNOT03 g1574570 Haemophilus
influenzae SEQ ID NO:33 SEQ ID NO:82 HRM-33 1605720 LUNGNOT15
g1055080 C. elegans SEQ ID NO:34 SEQ ID NO:83 HRM-34 1610501
COLNTUT06 g313741 S. cerevisiae YBL0514 SEQ ID NO:35 SEQ ID NO:84
HRM-35 1720770 BLADNOT06 g1006641 C. elegans F46C5 SEQ ID NO:36 SEQ
ID NO:85 HRM-36 1832295 BRAINON01 g561637 Human enigma protein SEQ
ID NO:37 SEQ ID NO:86 HRM-37 1990522 CORPNOT02 g558396 S.
cerevisiae SEQ ID NO:38 SEQ ID NO:87 HRM-38 2098087 BRAITUT02
g1066284 Mus musculus uterine mRNA SEQ ID NO:39 SEQ ID NO:88 HRM-39
2112230 BRAITUT03 g861306 C. elegans SEQ ID NO:40 SEQ ID NO:89
HRM-40 2117050 BRSTTUT02 g687821 C. elegans SEQ ID NO:41 SEQ ID
NO:90 HRM-41 2184712 SININOT01 g868241 C. elegans C56C10 SEQ ID
NO:42 SEQ ID NO:91 HRM-42 2290475 BRAINON01 g733605 C. elegans SEQ
ID NO:43 SEQ ID NO:92 HRM-43 2353452 LUNGNOT20 g1507666
Schizosaccharomyces pombe SEQ ID NO:44 SEQ ID NO:93 HRM-44 2469611
THP1NOT03 g1495332 C. elegans SEQ ID NO:45 SEQ ID NO:94 HRM-45
2515476 LIVRTUT04 g1665790 KIAA0262 SEQ ID NO:46 SEQ ID NO:95
HRM-46 2754573 THP1AZS08 g478990 Human RNA binding protein SEQ ID
NO:47 SEQ ID NO:96 HRM-47 2926777 TLYMNOT04 g687823 C. elegans SEQ
ID NO:48 SEQ ID NO:97 HRM-48 3217567 TESTNOT07 g1841547 Human HLA
class III region SEQ ID NO:49 SEQ ID NO:98 HRM-49 3339274 SPLNNOT10
g1177434 Human mRNA
[0060] HRM-1 (SEQ ID NO:1) was identified in Incyte Clone 133 from
the U937NOT01 CDNA library using a computer search for amino acid
sequence alignments. A consensus sequence, SEQ ID NO:50, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 133 (U937NOT01), 013508 (THP1PLB01), 210174
(SPLNNOT02), 1655863 (PROSTUT08), 1725724 (PROSNOT14), 1858205
(PROSNOT18), and 2646014 (OVARTUT05).
[0061] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO: 1. HRM-1 is 151
amino acids in length and has four potential phosphorylation sites
at T2, S14, S69, and T111. HRM-1 has sequence homology with human
KIAA0105 (g285947) and is found in cDNA libraries which have
proliferating cells and are associated with cancer or immune
response.
[0062] HRM-2 (SEQ ID NO:2) was identified in Incyte Clone 1762 from
the U937NOT01 cDNA library using a computer search for amino acid
sequence alignments. A consensus sequence, SEQ ID NO:51, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 1762 (U937NOT01), 1254927 (LUNGFET03), and 2070865
(ISLTNOT01).
[0063] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:2. HRM-2 is 185
amino acids in length and has a potential N glycosylation site at
N108; eight potential phosphorylation sites at T22, S26, T27, S31,
T51, T70, and T135; a leucine zipper motif at
L.sub.136KDVVWGLNSLFTDLLNFDDPL; and a ubiquitin conjugation motif
at W.sub.105HPNITETGEICLSL. HRM-2 has sequence homology with a gene
from Ascaris suum (g1518121) and is found in cDNA libraries which
have secretory or proliferating cells and are associated with
development.
[0064] HRM-3 (SEQ ID NO:3) was identified in Incyte Clone 1847 from
the U937NOT01 cDNA library using a computer search for amino acid
sequence alignments. A consensus sequence, SEQ ID NO:52, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 274 (U937NOT01), 1847 (U937NOT01), 262233
(HNT2AGTO1), 972977 (MUSCNOT02), and 1859611(PROSNOT18).
[0065] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:3. HRM-3 is 59
amino acids in length and has four potential N glycosylation sites
at N147, N352, N410, and N421, and 17 potential phosphorylation
sites at S13, T21, S43, S89, S131, S207, T243, S278, T286, S335,
S337, S350, S354, S369, S380, S412, and S542. HRM-3 has sequence
homology with a saccharomyces cerevisiae protein (g130221 1) and is
found in cDNA libraries which have proliferating or immortalized
cells.
[0066] HRM-4 (SEQ ID NO:4) was identified in Incyte Clone 9337 from
the HMC1NOT01 cDNA library using a computer search for amino acid
sequence alignments. A consensus sequence, SEQ ID NO:53, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 9337 (HMC1NOT01), 670279 (CRBLNOT01), 717305
(PROSTUT01), 968249 (BRSTNOT05), and 1546506 (PROSTUT04).
[0067] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:4. HRM-4 is 338
amino acids in length and has a potential N glycosylation site at
N327, 11 potential phosphorylation sites at T15, S36, S42, S50,
T51, S73, S144, S176, T256, S140, and T329; and five zinc finger
motifs at C.sub.192RC.sub.194SECGKI FRNPRYFSVHKKIH,
C.sub.222QDCGKGFVQSSSLTQHQRVH, C.sub.250OQECGRTFNDRSAISQH- LRTH,
C.sub.278QDCGKAFRQSSHLIRHQRTH, and C.sub.306NKCGKAFTQSSHLIGHQRTH.
HRM-4 has sequence homology with a human zinc finger protein
(g1613852) and is found in cDNA libraries which have proliferating,
cancerous, or secretory cells.
[0068] HRM-5 (SEQ ID NO:5) was identified in Incyte Clone 9476 from
the HMCINOT01 cDNA library using a computer search for amino acid
sequence alignments. A consensus sequence, SEQ ID NO:54, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 9476 (HMC1NOT01), 010403 (THP1PLB01), 495099
(HNT2NOT01), 1670783 (BMARNOT03), 1997203 (BRSTTUT03), and 2190637
(THYRTUT03).
[0069] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:5. HRM-5 is 456
amino acids in length and has a potential N glycosylation site at
N385; 14 potential phosphorylation sites at T9, T12, S58, T74,
T163, T139, S175, T211, T239, T272, S331, T367, T420, and S443, and
an ATP/GTP binding motif at G.sub.70PPGTGKT77. HRM-5 has sequence
homology with a S. cerevisiae protein (g755784) and is found in
cDNA libraries which have dividing, cancerous or immortalized cells
and are associated with immune response.
[0070] HRM-6 (SEQ ID NO:6) was identified in Incyte Clone 10370
from the THP1PLB01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:55, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 010370 (THP1PLB01), 109018 (AMLBNOT01), 259388
(HNT2RAT01), and 1518624 (BLADTUT04).
[0071] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:6. HRM-6 is 210
amino acids in length and has one potential N-glycosylation site at
N11 and nine potential phosphorylation sites at T13, T21, T46,
T124, S125, S132, T143, T167, and T191. HRM-6 has sequence homology
with a putative p64 CLCP human protein (g895845) and is found in
cDNA libraries which have dividing, cancerous or immortalized cells
and are associated with immune response.
[0072] HRM-7 (SEQ ID NO:7) was identified in Incyte Clone 30137
from the THP1PLB01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:56, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 30137 (THP1NOB01), 531638 (BRAINOT03), 1653122
(PROSTUT08), and 1682227 (PROSNOT15).
[0073] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:7. HRM-7 is 255
amino acids in length and has one potential N glycosylation site at
N86 and 12 potential phosphorylation sites at T9, T28, S32, S61,
S94, S142, S156, S160, T169, S118, S220, and S236. HRM-7 has
sequence homology with human clone 23733 (g1710241) and is found in
cDNA libraries which have dividing, cancerous or immortalized cells
and are associated with immune response.
[0074] HRM-8 (SEQ ID NO:8) was identified in Incyte Clone 77180
from the SYNORAB01cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:57, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 077180 (SYNORAB01), 604706 (BRSTTUT01), 977901
(BRSTNOT02), 1870373 (SKINBIT01), and 2169441 (ENDCNOT03).
[0075] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:8. HRM-8 is 188
amino acids in length and has one potential amidation site,
Q170GKR; two potential N glycosylation sites at N60 and N68; and
four potential phosphorylation sites at S70, T164, T166, and S183.
HRM-8 has sequence homology with a S. cerevisiae protein (g5372)
and is found in cDNA libraries which have dividing, cancerous or
immortalized cells and are associated with immune response.
[0076] HRM-9 (SEQ ID NO:9) was identified in Incyte Clone 98974
from the PITUNOR01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:58, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 98974 (PITUNOR01), 443924 (MPHGNOT03), 1401540
(BRAITUT08), 1507305 (BRAITUT07), 1700814 (BLADTUT05), and 1809947
(PROSTUT12).
[0077] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:9. HRM-9 is 531
amino acids in length and has one potential N glycosylation site at
N480; 37 potential phosphorylation sites at S19, T22, S38, T64,
T76, T91, Si117, Si118, S158, T164, T177, T182, T200, T267, Y281,
Y311, Y322, S333, S394, S402, S404, S409, S414, S416, S418, S429
S434, S439, S440, S456, S460, S466, S478, S505, S510, S524, S528,
and one potential glycosaminoglycan motif at S434GSG. HRM-9
sequence homology with a Caenorhabditis elegans protein (g1627704)
and is found in cDNA libraries which have secretory, proliferating
or immune cells.
[0078] HRM-10 (SEQ ID NO: 10) was identified in Incyte Clone 118160
from the MUSCNOT01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:59, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 118160 (MUSCNOT01), 323015 (EOSIHET02), and 1856519
(PROSNOT18).
[0079] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:10. HRM-10 is 348
amino acids in length and has two potential N glycosylation sites
at N150 and N317; 17 potential phosphorylation sites at T23, T45,
S60, T126, S130, S140, S145, S151, S154, S158, S186, Y208, Y234,
S217, T271, T303, and S327, and a transcription factor signature at
C.sub.310SKCKKKNCTYNQVQTRSA DEPMTTFVLCNEC. HRM-10 has sequence
homology with a Mus musculus protein (g220594) and is found in cDNA
libraries which have secretory or immune associations.
[0080] HRM-11 (SEQ ID NO:11) was identified in Incyte Clone 140516
from the TLYMNOR01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:60, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 140516 (TLYMNOR01), 143729 (TLYMNOR01), 1346014
(PROSNOT11), and 2074866 (ISLTNOT01).
[0081] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:11. HRM-11 is 393
amino acids in length and has 14 potential phosphorylation sites at
S22, T33, S41, S69, T156, Y157, S166, S199, T242, T308, T324, S350,
T359, S378. HRM-11 has sequence homology with a C. elegans protein
(g1086723) and is found in cDNA libraries which have proliferating,
secretory or immune cells.
[0082] HRM-12 (SEQ ID NO: 12) was identified in Incyte Clone 207452
from the SPLNNOT02 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:61, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 207452 (SPLNNOT02), 238306 (SINTNOT02), 1559492
(SPLNNOT04), and 1852567 (LUNGFET03).
[0083] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:12. HRM-12 is 320
amino acids in length and one potential amidation site at
E.sub.210GKK; two potential N glycosylation sites atN12 and N314;
seven potential phosphorylation sites at S34, S51, S56, Slll, T157,
S198, and S318; one potential glycosaminoglycan motif, S224GAG; one
immunoglobulin major histocompatibility motif, F.sub.305FCNVFH; and
two mitochondrial carrier protein signatures, P.sub.35FDVIKIRF and
P.sub.138VDVLRTRF. HRM-12 has sequence homology with a S.
cerevisiae protein (gl31.sup.4086) and is found in cDNA libraries
which have secretory and proliferating cells.
[0084] HRM-13 (SEQ ID NO: 13) was identified in Incyte Clone 208836
from the SPLNNOT02 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:62, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 26879 (SPLNFET01), 208836 (SPLNNOT02), and 1916142
(PROSTUT04).
[0085] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:13. HRM-13 is 343
amino acids in length and has one potential N glycosylation site at
N172; 17 potential phosphorylation sites at S45, S46, T62, S73,
S84, S85, S102, S105, T124, S137, Y153, T192, S216, Y226, Y241,
S253 and T293; and a zinc finger motif at C.sub.277RHYFCESCA.
HRM-13 has sequence homology with a S. cerevisiae protein (g662126)
and is found in cDNA libraries which have proliferating cells and
are associated with immune response.
[0086] HRM-14 (SEQ ID NO:14) was identified in Incyte Clone 569710
from the MMLR3DT01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:63, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 145344 (TLYMNOR01) and 569710 (MMLR3DT01).
[0087] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:14. HRM-14 is 368
amino acids in length and has 10 potential phosphorylation sites at
S5, T16, T125, S132, S142, S157, S167, S185, S208, and S246; and
four zinc finger motifs at C.sub.253DECGKHFSQGSALILHQRIH,
C.sub.281,VECGKAFSRSSILVQH QRVH, C.sub.309LECGKAFSQNSGLINHQRIH, and
C.sub.337VQCGKSYSQSSNLFRHQRRH. HRM-14 has sequence homology with a
human zinc finger protein (gl698719) and is found in cDNA libraries
which are associated with immune response.
[0088] HRM-15 (SEQ ID NO:15) was identified in Incyte Clone 606742
from the BRSTTUT01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:64, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 606742 (BRSTIUT01) and 1559478 (SPLNNOT04).
[0089] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:15. HRM-15 is 158
amino acids in length and has two potential myristylation sites,
G92GFHGQ and G96QMHSR, and one potential PKC phosphosphorylation
site, S40. HRM-15 has sequence homology with human clone 23679
(g1710201) and is found in cDNA libraries with proliferating,
secretory and/or cancerous cells.
[0090] HRM-16 (SEQ ID NO: 16) was identified in Incyte Clone 611135
from the COLNNOT01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:65, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 611135 (COLNNOT01), 659029 (BRAINOT03), and 1861691
(PROSNOT19).
[0091] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:16. HRM-16 is 334
amino acids in length and has 11 potential phosphorylation sites at
S17, T29, T128, S133, S162, S176, S263, T257, S263, S277, and S294.
HRM-16 has sequence homology with a C. elegans protein (g506882)
and is found in cDNA libraries with secretory cells.
[0092] HRM-17 (SEQ ID NO: 17) was identified in Incyte Clone 641127
from the BRSTNOT03 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:66, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 641127 (BRSTNOT03) and 673153 (CRBLNOT01).
[0093] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO: 17. HRM-17 is 488
amino acids in length and has one N glycosylation site at N215; 11
potential phosphorylation sites at S70, S78, S92, T102, S111, T190,
Y235, S303, S329, S415, and T471; and eight zinc finger motifs at
C.sub.237EQCGKGFTRSSSLLIHQAVH, C.sub.265DKCGKGFTRSSSLLIHHAVH,
C.sub.293DKCGKGFSQSSKLHIHQRVH, C.sub.321,EECGMSFS QRSNLHIHQRVH,
C.sub.349GECGKGFSQSSNLHIHRCIH, C.sub.377YECGKGFSQSSDLRIHLRVH,
C.sub.405GKCGKGFSQSSKLLIHQRVH, and C.sub.433SKCGKGFSQSSNLHIHQRVH.
HRM-17 has sequence homology with a human HOK-2 gene product
(g1310668) and is found in cDNA libraries associated with sensory
and secretory functions.
[0094] HRM-18 (SEQ ID NO:18) was identified in Incyte Clone 691768
from the LUNGTUT02 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:67, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 691768 (LUNGTUT02), 1417161 (BRAINOT12) and 1931861
(COLNNOT16).
[0095] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:18. HRM-18 is 255
amino acids in length and has one potential N glycosylation site at
N102 and 13 potential phosphorylation sites at S21, T90, T109,
S111, T124, S134, S139, T141, S158, S172, S181, S187, and T206.
HRM-18 has sequence homology with a M. musculus protein (g309183)
and is found in cDNA libraries with proliferating or cancerous
cells.
[0096] HRM-19 (SEQ ID NO:19) was identified in Incyte Clone 724157
from the SYNOOAT01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:68, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 724157 (SYNOOAT01), 1516153 (PANCTUT01), and 1610152
(COLNTUT06).
[0097] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO: 19. HRM-19 is 351
amino acids in length and has eight potential phosphorylation sites
at T30, S41, S53, T135, S172, S187, T273, and S331; one potential
glycosaminoglycan site, S.sub.18GTG; and one potenti mitochondrial
carrier motif, P.sub.13,LDVVKVRL. HRM-19 has sequence homology with
C. elegans C16C10 (g577542) and is found in cDNA libraries
associated with cell proliferation, cancer and immune response.
[0098] HRM-20 (SEQ ID NO:20) was identified in Incyte Clone 864683
from the BRAITUT03 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:69, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 486297 (HNT2RATO1), 864683 (BRAITUT03), 1314465
(BLADTUT02), 1610776 (COLNTUT06), 1856771 (PROSNOT18), 1866081
(PROSNOT19), 1932221 (COLNNOT16), and 2125225 (BRSTNOT07).
[0099] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:20. HRM-20 is 535
amino acids in length and has three potential N glycosylation sites
at N202, N252, and N523; and 17 potential phosphorylation sites at
S2, S12, S42, S49, S102, S157, T165, T171, T232, T255, T317, S332,
S428, T441, S453, S500, and S509. HRM-20 has sequence homology with
a C. elegans protein (g1418563) and is found in cDNA libraries
associated with cell proliferation, cancer and immune response.
2 HRM-21 (SEQ ID NO:21)
[0100] Was identified in Incyte Clone 933353 from the CERVNOT01
cDNA library using a computer search for amino acid sequence
alignments. A consensus sequence, SEQ ID NO:70, was derived from
the extended and overlapping nucleic acid sequences: Incyte Clones
928904 (BRAINOT04), 933353 (CERVNOT01), and 2452674
(ENDANOT01).
[0101] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:21. HRM-21 is 201
amino acids in length and has one potential N glycosylation site at
N82; five potential phosphorylation sites at T70, S83, S98, S154,
and Ti 87; and one tyrosine phosphatase motif at
V.sub.130HCKAGRSRSATM. HRM-21 has sequence homology with a C.
elegans protein (g1657672) and is found in cDNA libraries
associated with immune response.
3 HRM-22 (SEQ ID NO:22)
[0102] Was identified in Incyte Clone 1404643 from the LATRTUT02
cDNA library using a computer search for amino acid sequence
alignments. A consensus sequence, SEQ ID NO:71, was derived from
the extended and overlapping nucleic acid sequences: Incyte Clones
878243 (LUNGAST01), 1404643 (LATRTUT02), 1508343 (LUNGNOT14) and
2585156 (BRAITUT22).
[0103] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:22. HRM-22 is 239
amino acids in length and has four potential phosphorylation sites
at S5, S89, S133, and T211. HRM-22 has sequence homology with a C.
elegans protein (g459002) and is found in cDNA libraries associated
with cell proliferation, cancer and immune response.
4 HRM-23 (SEQ ID NO:23)
[0104] Was identified in Incyte Clone 1561587 from the SPLNNOT04
cDNA library using a computer search for amino acid sequence
alignments. A consensus sequence, SEQ ID NO:72, was derived from
the extended and overlapping nucleic acid sequences: Incyte Clones
522573 (MMLR2DTO1), 773822 (COLNNOT05), 1304839 (PLACNOT02),
1381253 (BRAITUT08), 1452511 (PENITUT01), 1539060 (SINTIUT01),
1561587 (SPLNNOT04), and 2416572 (HNT3AZTO1).
[0105] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:23. HRM-23 is 244
amino acids in length and has five potential phosphorylation sites
at T40, S75, T84, T89, and S194. HRM-23 has sequence homology with
a C. elegans protein (g868266) and is found in cDNA libraries
associated with cell proliferation, cancer and immune response.
5TABLE 1 Protein Nucleotide Abbreviation Clone ID Library NCBI
Homolog SEQ ID NO:1 SEQ ID NO:50 HRM-1 133 U937NOT01 g285947
KIAA0105 SEQ ID NO:2 SEQ ID NO:51 HRM-2 1762 U937NOT01 g1518121
Ascaris suum SEQ ID NO:3 SEQ ID NO:52 HRM-3 1847 U937NOT01 g1302211
Saccharomyces cerevisiae SEQ ID NO:4 SEQ ID NO:53 HRM-4 9337
HMC1NOT01 g1613852 Human zinc finger protein (zf2) SEQ ID NO:5 SEQ
ID NO:54 HRM-5 9476 HMC1NOT01 g755784 S. cerevisiae SEQ ID NO:6 SEQ
ID NO:55 HRM-6 10370 THP1PLB01 g895845 Human putative p64 CLCP
protein SEQ ID NO:7 SEQ ID NO:56 HRM-7 30137 THP1NOB01 g1710241
Human clone 23733 mRNA SEQ ID NO:8 SEQ ID NO:57 HRM-8 77180
SYNORAB01 g5372 S. cerevisiae SEQ ID NO:9 SEQ ID NO:58 HRM-9 98974
PITUNOR01 g1627704 Caenorhabditis elegans SEQ ID NO:10 SEQ ID NO:59
HRM-10 118160 MUSCNOT01 g220594 Mus musculus SEQ ID NO:11 SEQ ID
NO:60 HRM-11 140516 TLYMNOR01 g1086723 C. elegans SEQ ID NO:12 SEQ
ID NO:61 HRM-12 207452 SPLNNOT02 g1314086 S. cerevisiae SEQ ID
NO:13 SEQ ID NO:62 HRM-13 208836 SPLNNOT02 g662126 S. cerevisiae
SEQ ID NO:14 SEQ ID NO:63 HRM-14 569710 MMLR3DT01 g1698719 Human
zinc finger protein SEQ ID NO:15 SEQ ID NO:64 HRM-15 606742
BRSTTUT01 g1710201 Human clone 23679 mRNA SEQ ID NO:16 SEQ ID NO:65
HRM-16 611135 COLNNOT01 g506882 C elegans SEQ ID NO:17 SEQ ID NO:66
HRM-17 641127 BRSTNOT03 g1310668 Human Hok-2 gene product SEQ ID
NO:18 SEQ ID NO:67 HRM-18 691768 LUNGTUT02 g309183 Mus musculus SEQ
ID NO:19 SEQ ID NO:68 HRM-19 724157 SYNOOAT01 g577542 C. elegans
C16C10 SEQ ID NO:20 SEQ ID NO:69 HRM-20 864683 BRAITUT03 g1418563
C. elegans SEQ ID NO:21 SEQ ID NO:70 HRM-21 933353 CERVNOT01
g1657672 C. elegans SEQ ID NO:22 SEQ ID NO:71 HRM-22 1404643
LATRTUT02 g459002 C. elegans SEQ ID NO:23 SEQ ID NO:72 HRM-23
1561587 SPLNNOT04 g868266 C. elegans SEQ ID NO:24 SEQ ID NO:73
HRM-24 1568361 UTRSNOT05 g1834503 Human mucin SEQ ID NO:25 SEQ ID
NO:74 HRM-25 1572888 LNODNOT03 g603396 S. cerevisiae YER156c SEQ ID
NO:26 SEQ ID NO:75 HRM-26 1573677 LNODNOT03 g849195 S. cerevisiae
D9481.16 SEQ ID NO:27 SEQ ID NO:76 HRM-27 1574624 LNODNOT03
g1067025 C. elegans R07E5.14 SEQ ID NO:28 SEQ ID NO:77 HRM-28
1577239 LNODNOT03 g728657 S. cerevisiae SEQ ID NO:29 SEQ ID NO:78
HRM-29 1598203 BLADNOT03 g1200033 C. elegans F35G2 SEQ ID NO:30 SEQ
ID NO:79 HRM-30 1600438 BLADNOT03 g286001 KIAA0005 SEQ ID NO:31 SEQ
ID NO:80 HRM-31 1600518 BLADNOT03 g790405 C. elegans SEQ ID NO:32
SEQ ID NO:81 HRM-32 1602473 BLADNOT03 g1574570 Haemophilus
influenzae SEQ ID NO:33 SEQ ID NO:82 HRM-33 1605720 LUNGNOT15
g1055080 C. elegans SEQ ID NO:34 SEQ ID NO:83 HRM-34 1610501
COLNTUT06 g313741 S. cerevisiae YBL0514 SEQ ID NO:35 SEQ ID NO:84
HRM-35 1720770 BLADNOT06 g1006641 C. elegans F46C5 SEQ ID NO:36 SEQ
ID NO:85 HRM-36 1832295 BRAINON01 g561637 Human enigma protein SEQ
ID NO:37 SEQ ID NO:86 HRM-37 1990522 CORPNOT02 g558396 S.
cerevisiae SEQ ID NO:38 SEQ ID NO:87 HRM-38 2098087 BRAITUT02
g1066284 Mus musculus uterine mRNA SEQ ID NO:39 SEQ ID NO:88 HRM-39
2112230 BRAITUT03 g861306 C. elegans SEQ ID NO:40 SEQ ID NO:89
HRM-40 2117050 BRSTTUT02 g687821 C. elegans SEQ ID NO:41 SEQ ID
NO:90 HRM-41 2184712 SININOT01 g868241 C.elegans C56C10 SEQ ID
NO:42 SEQ ID NO:91 HRM-42 2290475 BRAINON01 g733605 C. elegans SEQ
ID NO:43 SEQ ID NO:92 HRM-43 2353452 LUNGNOT20 g1507666
Schizosaccharomyces pombe SEQ ID NO:44 SEQ ID NO:93 HRM-44 2469611
THP1NOT03 g1495332 C. elegans SEQ ID NO:45 SEQ ID NO:94 HRM-45
2515476 LIVRTUT04 g1665790 KIAA0262 SEQ ID NO:46 SEQ ID NO:95
HRM-46 2754573 THP1AZS08 g478990 Human RNA binding protein SEQ ID
NO:47 SEQ ID NO:96 HRM-47 2926777 TLYMNOT04 g687823 C. elegans SEQ
ID NO:48 SEQ ID NO:97 HRM-48 3217567 TESTNOT07 g1841547 Human HLA
class III region SEQ ID NO:49 SEQ ID NO:98 HRM-49 3339274 SPLNNOT10
g1177434 Human mRNA
[0106] HRM-24 (SEQ ID NO:24) was identified in Incete Clone 1568361
from the UTRSNOT05 cDNA library using a computer search for amino
acid sequence. A consensus sequence, SEQ ID NO;73, was derived from
the extended and overlapping nucleic acid sequences: Incyte Clones
927874 (BRAINOT04), 1255220 (MENITUT03), 1242340 (LUNGNOT03), 13495
(LATRTU02), 1381263 (BRAITUT08), 1500028 (SINTBST01), 1568361
(UTRSNOT05), 1653237 (PROSTUT08), 1975340 (PANCTUT02), and 3274608
(PROSBPT06).
[0107] In one embodiment, the invention encompasses a protein
compraising the amino acid sequence of SEQ ID NO:24, HRM-24 is 431
amino acids in length and has five potential N glycosylation sites
at N75, N95 N171, N202, and N298; eight potential phosphorylation
sites at S2, S3, T11, T13, S17, Y316, T375, and T415, and a leucine
zipper motif, L.sub.96SAFNNILSNLGYILLGLLFLL. HRM-24 has sequence
homology with human mucin (g1834503) and is found cDNA libraries
proliferating, cancerus or inflamed cells.
[0108] HRM-25 (SEQ ID NO;25) was identified in Incyte Clone 1572888
from the LNODNOT03 cDNA library using a computer search for amino
acid sequence aligments. A consensus sequence SEQ ID NO:74 was
derived from the extended and overlapping nucleic acid sequence:
Incyte Clones 1438142 (PANCNT08), 1572888 (LNODNOT03), and 1665075
(BRSTNOT09).
[0109] In one embodiment, the invention encompases a protein
compraising the amino acid sequence of SEQ ID NO:25. HRM-25 is 376
amino acids in length and has one N glycosylation site five
potential phosphorylation sites at S111, T150, S151, T159, and,
S196. HRM-25 has sequence homology with S. cerevisiae YER156c
(g603396) and is found in cDNA libraries with secretory cells.
[0110] HRM-26 (SEQ ID NO:26) was identifie in Incyte Clone 1573677
from the LONDNOT03 cDNA library using a computer search for amino
acid sequence aligments. A concensus sequence, SEQ ID NO:75, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 040360 (TBLYNOT01), 065573 (PLACNOB01), 228382
(PANCNOT01), 1457788 (COLNFET02), 1573677 (LNODNOT03), and 1854560
(HNT3AZT01)
[0111] In one embodiment, the invention encompasses a protein
compraising the amino acid sequence of SEQ ID NO:26 is 340 amino
acids in length and has one potential N glycosylation site at N213
and 13 potential phosphorylation site at T10, S22, T53, T56, S160,
S168, S170, S177, S201, S226 S297, S303, and T329. HRM-26 has
sequence homology with S. cerevisiae D9481.16 (g849195) and its
found in cNDA libraries associated with secretion, immune response,
and cancer.
[0112] HRM-27 (SEQ ID NO:27) was identified in Icyte Clone 1574624
from the LNODNOT03 cDNA library using a coomputer search for amino
acid sequence aligments. A concesnsus sequence, SEQ ID NO:76 was
derived from the extended and overlapping nucleic acid sequence:
Incyte Clones 90012 (HYPONOB01), 888491 (STOMTUT01), and 1574624
(LNODNOT03).
[0113] In one embodimen, the invention encompasses a protein
comprising the amino acids sequence of SEQ ID NO:27. HRM-27 is 174
amino acids in length and has one N glycosylation site at N51 and
five potential phosphorylation sites at S111, T150, S151, T159, and
T196. HRM-27 has sequence homology with a C. elegants protein
(g1067025) and is found in cDNA libraries associated with
secretion, immune responce and ancer.
[0114] HRM-28 (SEQ ID NO:28) was identified in Incyte Clones
1577239 from the LNODNOT03 cDNA library using a computer search for
amino acid sequence aligments. A concensus sequence, SEQ ID NO:77,
was derived from the extended and overlapping nucleic acid
sequences: Incyte Clones 100565 (ADRENOT01), 1336693 (COLNNOT13 ),
and 1577239 (LNODNOT03).
[0115] In one embodiment, the invention encompasses a protein
comprising the amino acids sequence of SEQ ID NO:28, HRM-28 is 179
amino acids in length and has one potential N glycosylation site at
N60 and five potential phosphorylation site at Y61, S62, Y104,
T136, and Y142. HRM-28 has sequence homology with a S. cerevisiae
protein (g728657) and is found in cDNA libraries associated with
sevretion and immune response.
[0116] HRM-29 (SEQ ID NO:29) was identified in Incyte Clone 1598203
from the BLADNOT-03 cDNA library using a computer search for amino
acid sequence aligments. A consensus sequence, SEQ ID NO:78, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clone 1598203 (BLADNOT03), 1697035 (COLNNOT23), and 1932332
(COLNNOT16).
[0117] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO;29. HRM-29 is 205
amino acids in length and has one potential N glycocylation site at
N117 and five potential phosphorylation sites at T68, T118, S137,
S140, and S159. HRM-29 has sequence homology with a C. elegants
protein (g1200033) and is found in cDNA libraries associated with
secretion.
[0118] HRM-30 (SEQ ID NO:30) was identified in Incyte Clone 1600438
fron the BLADNOT03 cDNA library using a computer search for amino
acid sequence aligments. A consensus sequence, SEQ ID NO:79, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 835283 (PROSNOT07), 1600044 (BLADNOT03), 1600438
(BLANDOT03), and 1922072 (BRSTTUT01).
[0119] In one embodiment, the invention encompasses a protein
comprising the acid sequenceof SEQ ID NO:30. HRM-30 is 419 amino
acids in length and has one potential N glycosylation site at N161;
twelve potential phosphorylation sites at T16, S57, T67, T83, S100,
T107, S144, S206, T254, Y351, S412, and S414; a leucine zipper
motif, l.sub.38NEAGDDLEAVAKFLDSGSRL; and an ATP/GTP binding motif,
A.sub.385HVAKGKS. HRM-30 has sequence homology with human KIAA0005
(g286001) and is found in cDna libraries associated with secretion
and cancer.
[0120] HRM-31 (SEQ ID NO:31) was identified in Incyte Clone 1600518
from the BLADNOT03 cNDA library using a computer search for amino
acid sequence aligment. A consensus sequence, SEQ ID NO;80, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 389679 (THYMNOT02), 1600518 (BLADNOT03), 2055734
(BEPINOT02), and 2509270 CONUTUT01).
[0121] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:31. HRM-31 is 376
amino acid in length and has one potential N glycosylation site at
N161 and 14 potential phosphorylation sites at T30, S65, S75, S95,
S106, T134, S159, S224, T228, T250, T292, S299, T303, and S323 and
a glycosaminoglycan motif, S14 GPG. HRM-31 has sequence homology
with a C. elegants protein (g790405) and is found in cNDA libraries
associated with immune response, secretion and cancer.
[0122] HRM-32 (SEQ ID NO:32) was identified in Incyte Clone 1602473
from the BLADNOT03 cDNA library using a computer search for amino
acid sequence aligments. A consensus sequence, SEQ ID NO:81, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 1351857 (LATRTUT02), 1602473 (BLADNOT03), and 2478778
(SMCANOT01).
[0123] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:32. HRM-32 is 237
amino acids in length and has seven potential phosphorylation site
at T51, T68, S92, S143, T171, S193, and S203. HRM-32 has sequence
homology with a Haemophilus influenzae protein (g1574570) and is
found in cDNA libraries associated with immune response, and
cancer.
[0124] HRM-33 (SEQ ID NO:33) was identified in Incyte Clone
16057220 from the LUNGNOT15 cDNA library using a computer search
for amino acid sequence aligment. A consensus sequence, SEQ ID
NO:82, was derived from the extended and overlapping nucleic acid
sequences: Incyte Clones 660915 (BRAINOT03), 1347135 (PROSNOT11),
and 1605720 (LUNGNOT15).
[0125] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:33. HRM-33 is 152
amino acids in length and has four potential phosphorylation sites
at S10, S23, T34, and S66; and a leucine zipper motif,
L.sub.77AVGNYRLKEYEKALKYVRGLL. HRM-33 has sequence homology with C.
elegans (g155080) and is found in cDNA libraries associated with
secretion and immune response.
[0126] HRM-34 (SEQ ID NO:34) was identified in Incyte Clone 1610501
from the COLNTUT06 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:83, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 1610501 (COLNTUT06) and 2477716 (SMCANOT01).
[0127] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:34. HRM-34 is 179
amino acids in length and has five potential phosphorylation sites
at S32, S48, T45, T50, and T52. HRM-34 has sequence homology with a
S. cerevisiae protein (g313741) and is found in cDNA libraries
associated with cancer and immune response.
[0128] HRM-35 (SEQ ID NO:35) was identified in Incyte Clone 1720770
from the BLADNOT06 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:84, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 681455 (UTRSNOT02), 813292 (LUNGNOT04), 1223029
(COLNTUT02), 1444186 (THYRNOT03), 1522592 (BLADTUT04), 1720770
(BLADNOT06), and 1798409 (COLNNOT27).
[0129] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:35. HRM-35 is 196
amino acids in length and has an amidation motif, H.sub.179GKR, and
seven potential phosphorylation sites at S2, S6, S31,S84, S90,
T136, and T161. HRM-35 has sequence homology with a C.elegans
protein (g1006641) and is found in cDNA libraries associated with
secretion, immune response, and cancer.
[0130] HRM-36 (SEQ ID NO:36) was identified in Incyte Clone 1832295
from the BRAINON01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:85, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 060275 (LUNGNOT01), 1823989 (GBLATUT01), and 1832295
(BRAINON01).
[0131] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:36. HRM-36 is 612
amino acids in length and has 12 potential N glycosylation sites at
N36, N95, N139, N146, N151, N176, N188, N226, N243, N353, N371, and
N482; and 16 potent at S58, S92, S112, T153, T198, T248, S308,
S373, T400, T420, T428, Y438, T458, T472, S527, and S556. HRM-36
has sequence homology with human enigma protein (g561.sup.637) and
is found in cDNA libraries associated with secretion and immune
response.
[0132] HRM-37 (SEQ ID NO:37) was identified in Incyte Clone 1990522
from the CORPNOT02 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:86, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 264363 (HNT2AGTO0), 1990522 (CORPNOT02), and 2451448
(ENDANOT01).
[0133] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:37. HRM-37 is 101
amino acids in length and has a PKC phosphorylation site at S62.
HRM-37 has sequence homology with a S. cerevisiae protein (g558396)
and is found in cDNA libraries associated with immune response.
[0134] HRM-38 (SEQ ID NO:38) was identified in Incyte Clone 2098087
from the BRAITUT02 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:87, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 690359 (LUNGTUT02), 1429907 (SINTBST01), and 2098087
(BRAITUT02).
[0135] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:38. HRM-38 is 132
amino acids in length and has a potential ATP/GTP binding motif at
G.sub.74ARNLLKS. HRM-38 has sequence homology with M. musculus
uterine protein (g166284) and is found in cDNA libraries associated
with immune response.
[0136] HRM-39 (SEQ ID NO:39) was identified in Incyte Clone 2112230
from the BRAITUT03 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:88, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 1383278 (BRAITUT08), 1646103 (PROSTUT09), 2112230
(BRAITUT03), and 2510591 (CONUTUT01).
[0137] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:39. HRM-39 is 188
amino acids in length and has a potential N glycosylation site at
N87 and eight potential phosphorylation sites at T10, T28, S74,
S93, T121, T128, Y168, and T169. HRM-39 homology with a C. elegans
protein (g861306) and is found in cDNA libraries from cancerous
tissues.
[0138] HRM-40 (SEQ ID NO:40) was identified in Incyte Clone 2117050
from the BRAITUT02 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:89, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 941515 (ADRENOT03), 1549443 (PROSNOT06), 2113261
(BRAITUT03), 2117050 (BRSTTUT02), and 2530536 (GBLANOT02).
[0139] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:40. HRM-40 is 86
amino acids in length and has a potential N glycosylation site at
N58 and four potential phosphorylation sites at T2, S9, T26, and
T27. HRM-40 has sequence homology with a C. elegans protein
(g687821) and is found in cDNA libraries involved in cell
proliferation, secretion, cancer, and immune response.
[0140] HRM-41 (SEQ ID NO:41) was identified in Incyte Clone 2184712
from the SININOT01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:90, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 922736 (RATRNOT02), 1976003 (PANCTUT02), and 2184712
(SININOT01).
[0141] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:41. HRM-41 is 222
amino acids in length and has a potential amidation site,
K.sub.10GKK; a potential glycosaminoglycan site, S.sub.2GLG; a
potential N glycosylation site, N95; and seven potential
phosphorylation sites at T18, T29, T50, S84, T98, S112, and S188.
HRM-41 has sequence homology with a C. elegant protein (g868241)
and is found in cDNA libraries involved in cell proliferation,
secretion, cancer, and immune response.
[0142] HRM-42 (SEQ ID NO:42) was identified in Incyte Clone 2290475
from the BRAINON01 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:91, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 238339 (SINTNOT02), 1657945 (URETTUT01), 1848691
(LUNGFET03), 2044604 (THPlT7T01), 2290475 (BRAINON01), and 2514944
(LIVRTUT04).
[0143] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:42. HRM-42 is 300
amino acids in length and has a potential N glycosylation site, N5;
seven potential phosphorylation sites at S23, S71, S132, S142,
T176, T192, and S293; and a Mutt signature,
G.sub.165MVDPGEKISATLKREFGEE. HRM-42 has sequence homology with a
C. elegans protein (g733605) and is found in cDNA libraries
involved in cell proliferation, secretion, cancer, and immune
response.
[0144] HRM-43 (SEQ ID NO:43) was identified in Incyte Clone 2353452
from the LUNGNOT20 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:92, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 1000164 (BRSTNOT03), 1308080 (COLNFET02), 1900151
(BLADTUT06), and 2353452 (LUNGNOT20).
[0145] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:43. HRM-43 is 112
amino acids in length and has six potential phosphorylation sites
at T23, T43, S44, T79, T84, and T98. HRM-43 has sequence homology
with a Schizosaccharomvces pombe protein (gl507666) and is found in
cDNA libraries involved in cell proliferation, secretion, cancer,
and immune response.
[0146] HRM-44 (SEQ ID NO:44) was identified in Incyte Clone 2469611
from the THPlNOT03 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:93, was
derived from the extended and overlapping nucleic acid sequences:
Incyte clones 003088 (HMClNOT01), 1448981 (PLACNOT02), 1453563
(PENITUT01), 1824146 (GBLATUT01), 2369282 (ADRENOT07), 2469611
(THPlNOT03), and 2622587 (KERANOT02).
[0147] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:44. HRM-44 is 251
amino acids in length and has a potential glycosaminoglycan site,
S218GFG, and four potential phosphorylation sites at T8, S83, S212,
and S226. HRM-44 has sequence homology with a C. elegans protein
(gl495332) and is found in cDNA libraries involved in cell
proliferation, secretion, cancer, and immune response.
[0148] HRM-45 (SEQ ID NO:45) was identified in Incyte Clone 2515476
from the LIVRTUT04 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:94, was
derived from the extended and overlapping nucleic acid sequences:
Incyte clones 18414 (HUVELPB01), 78341 (SYNORAB01), 143277
(TLYMNOR01), 181574 (PLACNOB01), 832996 (PROSTUT04), 962753
(BRSTTUT03), 1413604 (BRAINOT12), and 2515476 (LIVRTUT04).
[0149] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:45. HRM-45 is 811
amino acids in length and has three potential amidation sites at
G.sub.113GRR, W.sub.165GKR, and G.sub.790GKK; four potential N
glycosylation sites at N22, N56, N79, and N145; 24 potential
phosphorylation sites at T11, S13, S30, S60, Y71, S81, S85, S86,
S103, S254, S256, T377, S388, S425, S456, S487, T544, S552, S574,
T659, S678, S702, S746, and S753; a potential glycosaminoglycan
site, S.sub.160GHG; and a potential zinc finger motif at
C.sub.240GHIFCWACI. HRM-45 has sequence homology with human
KIAA0262 (g1665790) and is found in cDNA libraries involved in cell
proliferation, secretion, cancer, and immune response.
[0150] HRM-46 (SEQ ID NO:46) was identified in Incyte Clone 2754573
from the THPlAZSO8 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:95, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 263630 (HNT2AGTO1), 412307 (BRSTNOT01), 491644
(HNT2AGTO1), 1253094 (LUNGFET03), 2270603 (PROSNON01), 2280508
(PROSNON01), 2375670 (ISLTNOT01), 2754573 (THPlAZS08), and 3151587
(ADRENON04).
[0151] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:46. HRM-46 is 352
amino acids in length and has two potential N glycosylation sites
at N141 and N294, and thirteen potential phosphorylation sites at
S8, T67, T106, T110, T121, S122, S169, S206, T210, S215, S256,
S260, and T296. HRM-46 has sequence homology with human RNA binding
protein (g478990) and is found in cDNA libraries involved in cell
proliferation, secretion, and immune response.
[0152] HRM-47 (SEQ ID NO:47) was identified in Incyte Clone 2926777
from the TLYMNOT04 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:96, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 040208 (TBLYNOT01), 900242 (BRSTTUT03), 963500
(BRSTTUT03), 1996474 (BRSTTUT03), and 2926777 (TLYMNOT04).
[0153] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:47. HRM-47 is 432
amino acids in length and has a potential N glycosylation site at
N417 and 24 potential phosphorylation sites at T51, S73, T122,
T133, S177, S206, T226, T238, S293, S300, S304, S309, T325, S333,
S339, S353, S360, Y361, S384, S390, T403, T412, T419, and S425
homology with a C. elegans protein (g687823) and is found in cDNA
libraries involved in cell proliferation, secretion, cancer, and
immune response.
[0154] HRM-48 (SEQ ID NO:48) was identified in Incyte Clone 3217567
from the TESTNOT07 cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:97, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 905037 (COLNNOT07), 1287503 (BRAINOT11), and 3217567
(TESTNOT07).
[0155] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:48. HRM-48 is 180
amino acids in length and has a potential zinc finger motif,
C42GHLYCWPCL, and five potential phosphorylation sites at T33, T57,
S84, T148, and S160. HRM-48 has sequence homology with human HLA
class III region (g1841547) and is found in cDNA libraries involved
in secretion and immune response.
[0156] HRM-49 (SEQ ID NO:49) was identified in Incyte Clone 3339274
from the SPLNNOT10cDNA library using a computer search for amino
acid sequence alignments. A consensus sequence, SEQ ID NO:98, was
derived from the extended and overlapping nucleic acid sequences:
Incyte Clones 532254 (BRAINOT03), 941336 (ADRENOT03), 2447649
(THPlNOT03), and 3339274 (SPLNNOT10).
[0157] In one embodiment, the invention encompasses a protein
comprising the amino acid sequence of SEQ ID NO:49. HRM-49 is 137
amino acids in length and has three potential phosphorylation sites
at Ti 11, T91, and S119. HRM-49 has sequence homology with a
deduced human translational inhibitor (g1177434) and is found in
cDNA libraries involved in secretion and immune response.
[0158] The invention also encompasses HRM variants which retain the
biological or functional activity of HRM. A preferred HRM variant
is one having at least 60% amino acid sequence identity to an amino
acid sequence selected from SEQ ID NOs: 1-49.
[0159] The invention also encompasses polynucleotides which encode
HRM. Accordingly, any nucleic acid sequence which encodes the amino
acid sequence of HRM can be used to produce recombinant molecules
which express HRM. In a particular embodiment, the invention
encompasses a polynucleotide comprising a nucleic acid sequence
selected from SEQ ID NOs:50-98 and fragment and complements
thereof.
[0160] It will be appreciated by those skilled in the art that as a
result of the degeneracy of the genetic code, a multitude of
polynucleotides encoding HRM, some bearing minimal homology to the
polynucleotides of any known and naturally occurring gene, may be
produced. Thus, the invention contemplates each and every possible
variation of polynucleotide that could be made by selecting
combinations based on possible codon choices. These combinations
are made in accordance with the standard triplet genetic code as
applied to the polynucleotide of naturally occurring HRM, and all
such variations are to be considered as being specifically
disclosed.
[0161] Although polynucleotides which encode HRM and its variants
are preferably capable of hybridizing to the polynucleotide of the
naturally occurring HRM under selected conditions of stringency, it
may be advantageous to produce polynucleotides encoding HRM or its
derivatives possessing a different codon usage. Codons may be
selected to increase the rate at which expression of the peptide
occurs in a particular prokaryotic or eukaryotic host in accordance
with the frequency with which particular codons are utilized by the
host. Other reasons for altering the polynucleotide encoding HRM
and its derivatives without altering the encoded amino acid
sequences include the production of RNA transcripts having more
desirable properties, such as a greater half-life, than transcripts
produced from the naturally occurring sequence.
[0162] The invention also encompasses production of
polynucleotides, or fragments thereof, which encode HRM and its
derivatives, entirely by synthetic chemistry. After production, the
synthetic sequence may be inserted into any of the many available
expression vectors and cell systems using reagents that are well
known in the art. Moreover, synthetic chemistry may be used to
introduce mutations into a sequence encoding HRM or any fragment
thereof.
[0163] Also encompassed by the invention are polynucleotides that
are capable of hybridizing to the nucleic acids of a sample, and in
particular, the polynucleotides or the complements thereof shown in
SEQ ID NOs:50-98, under various conditions of stringency as taught
in Wahl and Berger (1987; Methods Enzymol 152:399-407) and Kimmel
(1987; Methods Enzymol 152:507-511).
[0164] Methods for DNA sequencing which are well known and
generally available in the art and may be used to practice any of
the embodiments of the invention. The methods may employ such
enzymes as the Klenow fragment of DNA polymerase I, SEQUENASE, Taq
DNA polymerase and thermostable T7 DNA polymerase (Amersham
Pharmacia Biotech (APB), Piscataway NJ), or combinations of
polymerases and proofreading exonucleases such as those found in
the ELONGASE amplification system (Life Technologies, Gaithersburg
MD). Preferably, the process is automated with machines such as the
MICROLAB system (Hamilton, Reno NV), DNA ENGINE thermal cycler (MJ
Research, Watertown MA), and the Catalyst preparation and 373 and
377 PRISM DNA sequencing systems (ABI).
[0165] The nucleic acid sequences encoding HRM may be extended
utilizing a partial nucleotide sequence and employing various
methods known in the art to detect upstream sequences such as
promoters and regulatory elements. For example, one method which
may be employed, "restriction-site" PCR, uses universal primers to
retrieve unknown sequence adjacent to a known locus (Sarkar (1993)
PCR Methods Applic 2:318-322). In particular, genomic DNA is first
amplified in the presence of primer to a linker sequence and a
primer specific to the known region. The amplified sequences are
then subjected to a second round of PCR with the same linker primer
and another specific primer internal to the first one. Products of
each round of PCR are transcribed with an RNA polymerase and
sequenced using reverse transcriptase.
[0166] Inverse PCR may also be used to amplify or extend sequences
using divergent primers based on a known region (Triglia et al.
(1988) Nucleic Acids Res 16:8186). The primers may be designed
using commercially available software such as OLIGO software
(Molecular Insights, Cascade CO), or another program, to be 22-30
nucleotides in length, to have a GC content of 50% or more, and to
anneal to the target sequence at temperatures about 68-72 C. The
method uses several restriction enzymes to generate a fragment in
the known region of a gene. The fragment is then circularized by
intramolecular ligation and used as a PCR template.
[0167] Another method which may be used is capture PCR which
involves PCR amplification of DNA fragments adjacent to a known
sequence in human and yeast artificial chromosome DNA (Lagerstrom
et al. (1991) PCR Methods Applic 1:111-119). In this method,
multiple restriction enzyme digestions and ligations may also be
used to place an engineered double-stranded sequence into an
unknown fragment of the DNA molecule before performing PCR.
[0168] Another method which may be used to retrieve unknown
sequences is that of Parker et al. (1991; Nucleic Acids Res
19:3055-3060). One may also use PCR, nested primers, and
PROMOTERFINDER libraries (Clontech, Palo Alto CA) to walk genomic
DNA. This process avoids the need to screen libraries of cDNAs for
longer sequences and is very useful in finding intron/exon
junctions.
[0169] When screening for full-length cDNAs, it is preferable to
use libraries that have been size-selected to include larger cDNAs.
Also, random-primed libraries are preferable, in that they will
contain more sequences which contain the 5' regions of genes. Use
of a randomly primed library may be especially preferable for
situations in which an oligo d(T) library does not yield a
full-length cDNA. Genomic libraries may be useful for extension of
sequence into 5' non-transcribed regulatory regions.
[0170] Capillary electrophoresis systems which are commercially
available may be used to analyze the size or confirm the sequence
of sequencing or PCR products. In particular, capillary sequencing
may employ flowable polymers for electrophoretic separation, four
different fluorescent dyes (one for each nucleotide) which are
laser activated, and detection of the emitted wavelengths by a
charge coupled device camera. Output/light intensity may be
converted to electrical signal using software integral to the
system, and the entire process from loading of samples to computer
analysis and electronic data display may be computer controlled.
Capillary electrophoresis is especially preferable for the
sequencing of small pieces of DNA which might be present in limited
amounts in a particular sample.
[0171] In another embodiment of the invention, polynucleotides or
fragments thereof which encode HRM may be used in recombinant DNA
molecules to direct expression of HRM, portions or functional
equivalents thereof, in host cells. Due to the inherent degeneracy
of the genetic code, other DNA sequences which encode the same or a
functionally equivalent amino acid sequence may be produced, and
these sequences may be used to clone and express HRM.
[0172] As will be understood by those of skill in the art, it may
be advantageous to produce HRM-encoding polynucleotides possessing
non-naturally occurring codons. For example, codons preferred by a
particular prokaryotic or eukaryotic host can be selected to
increase the rate of protein expression or to produce an RNA
transcript having desirable properties, such as a half-life which
is longer than that of a transcript generated from the naturally
occurring sequence.
[0173] The polynucleotides of the present invention can be
engineered using methods generally known in the art in order to
alter HRM encoding sequences for a variety of reasons, including
but not limited to, alterations which modify the cloning,
processing, and/or expression of the gene product. DNA shuffling by
random fragmentation and PCR reassembly of gene fragments and
synthetic oligonucleotides may be used to engineer the
polynucleotides. For example, site-directed mutagenesis may be used
to insert new restriction sites, alter glycosylation patterns,
change codon preference, produce splice variants, introduce
mutations, and so forth.
[0174] In another embodiment of the invention, natural, modified,
or recombinant nucleic acid sequences encoding HRM may be ligated
to a heterologous sequence to encode a fusion protein. For example,
to screen peptide libraries for inhibitors of HRM activity, it may
be useful to encode a chimeric HRM protein that can be recognized
by a commercially available antibody. A fusion protein may also be
engineered to contain a a cleavage site located between the HRM
encoding sequence and the heterologous protein sequence, so that
HRM may be cleaved and purified away from the heterologous
moiety.
[0175] In another embodiment, sequences encoding HRM may be
synthesized, in whole or in part, using chemical methods well known
in the art (Caruthers et al. (1980) Nucleic Acids Symp Ser. (7)
215-223, Horn et al. (1980) Nucleic Acids Symp. Ser. (7) 225-232).
Alternatively, the protein itself may be produced using chemical
methods to synthesize the amino acid sequence of HRM, or a portion
thereof. For example, peptide synthesis can be performed using
various solid-phase techniques (Roberge et al. (1995) Science
269:202-204) and automated synthesis may be achieved, for example,
using the 43 1A Peptide synthesizer (ABI).
[0176] The newly synthesized peptide may be purified by preparative
high performance liquid chromatography (see Creighton (1983)
Proteins Structures and Molecular Principles, WH Freeman, New York
N.Y.). The composition of the synthetic peptides may be confirmed
by amino acid analysis or sequencing (e.g., the Edman degradation
procedure; Creighton, supra). Additionally, the amino acid sequence
of HRM, or any part thereof, may be altered during direct synthesis
and/or combined using chemical methods with sequences from other
proteins, or any part thereof, to produce a variant protein.
[0177] In order to express a biologically active HRM, the
polynucleotides encoding HRM or functional equivalents, may be
inserted into expression vector, i.e., a vector which contains the
necessary elements for the transcription and translation of the
inserted coding sequence.
[0178] Methods which are well known to those skilled in the art may
be used to construct expression vectors containing sequences
encoding HRM and transcriptional and translational control
elements. These methods include in vitro recombinant DNA
techniques, synthetic techniques, and in vivo genetic
recombination. Such techniques are described in Sambrook et al.
(1989; Molecular Cloning, A Laboratory Manual, Cold Spring Harbor
Press, Plainview N.Y.) and Ausubel et al. (1989; Current Protocols
in Molecular Biology, John Wiley & Sons, New York N.Y.).
[0179] A variety of expression vector/host systems may be utilized
to contain and express sequences encoding HRM. These include, but
are not limited to, microorganisms such as bacteria transformed
with recombinant bacteriophage, plasmid, or cosmid DNA expression
vectors; yeast transformed with yeast expression vectors; insect
cell systems infected with baculovirus expression vectors; plant
cell systems transformed with virus expression vectors (e.g.,
cauliflower mosaic virus or tobacco mosaic virus) or with bacterial
expression vectors (Ti or pBR322 plasmids); or animal cell systems.
The invention is not limited by the host cell employed.
[0180] The "control elements" or "regulatory sequences" are those
non-translated regions of the vector enhancers, promoters, 5' and
3' untranslated regions--which interact with host cellular proteins
to carry out transcription and translation. Such elements may vary
in their strength and specificity. Depending on the vector system
and host utilized, any number of transcription and translation
elements, including constitutive and inducible promoters, may be
used. For example, when cloning in bacterial systems, inducible
promoters such as the hybrid lacZ promoter of the BLUESCRIPT
phagemid (Stratagene, LaJolla CA) or the pSport1 plasmid (Life
Technologies) may be used. The baculovirus polyhedrin promoter may
be used in insect cells. Promoters or enhancers derived from the
genomes of plant cells (e.g., heat shock, RUBISCO; and storage
protein genes) or from plant viruses (e.g., viral promoters or
leader sequences) may be cloned into the vector if the protein is
to be produced in plant cells. In mammalian cell systems, promoters
from mammalian genes or from mammalian viruses are preferable. If
it is necessary to generate a cell line that contains multiple
copies of the sequence encoding HRM, vectors based on SV40 or EBV
may be used with an selectable marker.
[0181] In bacterial systems, a number of expression vectors may be
selected depending upon the use intended for HRM. For example, when
large quantities of HRM are needed for the induction of antibodies,
vectors which direct high level expression of fusion proteins that
are readily purified may be used. Such vectors include, but are not
limited to, the multifunctional E. coli cloning and expression
vectors such as BLUESCRIPT phagemid (Stratagene), in which the
sequence encoding HRM may be ligated into the vector in frame with
sequences for the amino-terminal Met and the subsequent 7 residues
of .beta.-galactosidase so that a hybrid protein is produced; pIN
vectors (Van Heeke and Schuster (1989) J Biol Chem 264:5503-5509);
and the like. pGEX vectors (APB) may also be used to express
foreign proteins as fusion proteins with glutathione S-transferase
(GST). In general, such fusion proteins are soluble and can easily
be purified from lysed cells by adsorption to glutathione-agarose
beads followed by elution in the presence of free glutathione.
Proteins made in such systems may be designed to include heparin,
thrombin, or factor XA protease cleavage sites so that the cloned
protein of interest can be released from the GST moiety at
will.
[0182] In the yeast, Saccharomyces cerevisiae, a number of vectors
containing constitutive or inducible promoters such as alpha
factor, alcohol oxidase, and PGH may be used. For reviews, see
Ausubel (supra) and Grant et al. (1987; Methods Enzymol
153:516-544).
[0183] In cases where plant cell expression is desired, the
expression of sequences encoding HRM may be driven by any of a
number of promoters. For example, viral promoters such as the 35S
and 19S promoters of CaMV may be used alone or in combination with
the omega leader sequence from TMV (Takamatsu (1987) EMBO J
6:307-311). Alternatively, plant promoters such as the small
subunit of RUBISCO or heat shock promoters may be used (Coruzzi et
al. (1984) EMBO J 3:1671-1680; Broglie et al. (1984) Science
224:838-843; and Winter et al. (1991) Results Probl Cell Differ
17:85-105). These constructs can be introduced into plant cells by
direct DNA transformation or pathogen-mediated transfection. Such
techniques are described in a number of generally available reviews
(see, for example, Hobbs or Murry, hi: McGraw Hill Yearbook of
Science and Technolog (1992) McGraw Hill, New York N.Y.; pp.
191-196).
[0184] An insect system may also be used to express HRM. For
example, in one such system, Autographa californica nuclear
polyhedrosis virus (AcNPV) is used as a vector to express foreign
genes in Spodoptera frugiperda cells or in Trichoplusia larvae. The
sequences encoding HRM may be cloned into a non-essential region of
the virus, such as the polyhedrin gene, and placed under control of
the polyhedrin promoter. Successful insertion of HRM will render
the polyhedrin gene inactive and produce recombinant virus lacking
coat protein. The recombinant viruses may then be used to infect,
for example, S. frugiperda cells or Trichoplusia larvae in which
HRM may be expressed (Engelhard et al. (1994) Proc Nat Acad Sci
91:3224-3227).
[0185] In mammalian host cells, a number of viral-based expression
systems may be utilized. In cases where an adenovirus is used as an
expression vector, sequences encoding HRM may be ligated into an
adenovirus transcription/translation complex consisting of the late
promoter and tripartite leader sequence. Insertion in a
non-essential El or E3 region of the viral genome may be used to
obtain a viable virus which is capable of expressing HRM in
infected host cells (Logan and Shenk (1984) Proc Natl Acad Sci
81:3655-3659). In addition, transcription enhancers, such as the
Rous sarcoma virus (RSV) enhancer, may be used to increase
expression in mammalian host cells.
[0186] Human artificial chromosomes (HACs) may also be employed to
deliver larger fragments of DNA than can be contained and expressed
in a plasmid. HACs of 6 to 10 M are constructed and delivered via
conventional delivery methods (liposomes, polycationic amino
polymers, or vesicles) for therapeutic purposes.
[0187] Specific initiation signals may also be used to achieve more
efficient translation of sequences encoding HRM. Such signals
include the ATG initiation codon and adjacent sequences. In cases
where sequences encoding HRM, its initiation codon, and upstream
sequences are inserted into the expression vector, no additional
transcriptional or translational control signals may be needed.
However, in cases where only coding sequence, or a fragment
thereof, is inserted, exogenous translational control signals
including the ATG initiation codon should be provided. Furthermore,
the initiation codon should be in the correct reading frame to
ensure translation of the entire insert. Exogenous translational
elements and initiation codons may be of various origins, both
natural and synthetic. The efficiency of expression may be enhanced
by the inclusion of enhancers which are for the particular cell
system which is used, such as those described in the literature
(Scharf et al. (1994) Results Probl Cell Differ 20:125-162).
[0188] In addition, a host cell strain may be chosen for its
ability to modulate the expression of the inserted sequences or to
process the expressed protein in the desired fashion. Such
modifications of the protein include, but are not limited to,
acetylation, carboxylation, glycosylation, phosphorylation,
lipidation, and acylation. Post-translational processing which
cleaves a "prepro" form of the protein may also be used to
facilitate correct insertion, folding and/or function. Different
host cells which have specific cellular machinery and
characteristic mechanisms for post-translational activities (e.g.,
CHO, HeLa, MDCK, HEK293, and WI38), are available from the ATCC
(Manassas VA) and may be chosen to ensure the correct modification
and processing of the foreign protein.
[0189] For long-term, high-yield production of recombinant
proteins, stable expression is preferred. For example, cell lines
which stably express HRM may be transformed using expression
vectors which may contain viral origins of replication and/or
endogenous expression elements and a selectable marker gene on the
same or on a separate vector. Following the introduction of the
vector, cells may be allowed to grow for 1-2 days in an enriched
media before they are switched to selective media. The purpose of
the selectable marker is to confer resistance to selection, and its
presence allows growth and recovery of cells which successfully
express the introduced sequences. Resistant clones of stably
transformed cells may be proliferated using tissue culture
techniques to the cell type.
[0190] Any number of selection systems may be used to recover
transformed cell lines. These include, but are not limited to, the
herpes simplex virus thymidine kinase (Wigler et al. (1977) Cell
11:223-32) and adenine phosphoribosyltransferase (Lowy et al.
(1980) Cell 22:817-23) genes which can be employed in tk- or
aprt-cells, respectively. Also, antimetabolite, antibiotic or
herbicide resistance can be used as the basis for selection; for
example, dhfr which confers resistance to methotrexate (Wigler et
al. (1980) Proc Natl Acad Sci 77:3567-70); npt, which confers
resistance to the aminoglycosides, neomycin and G-418
(Colbere-Garapin et al (1981) J Mol Biol 150:1-14); and als or pat,
which confer resistance to chlorsulfuron and phosphinotricin
acetyltransferase, respectively (Murry, supra). Additional
selectable genes have been described, for example, trpB, which
allows cells to utilize indole in place of tryptophan, or hisD,
which allows cells to utilize histinol in place of histidine
(Hartman and Mulligan (1988) Proc Natl Acad Sci 85:8047-51).
Recently, the use of visible markers has gained popularity with
such markers as anthocyanins, .beta. glucuronidase and its
substrate GUS, and luciferase and its substrate luciferin, being
widely used not only to identify transformants, but also to
quantify the amount of transient or stable protein expression
attributable to a specific vector system (Rhodes et al. (1995)
Methods Mol Biol 55:121-131).
[0191] Although the presence/absence of marker gene expression
suggests that the gene of interest is also present, its presence
and expression may need to be confirmed. For example, if the
sequence encoding HRM is inserted within a marker gene sequence,
transformed cells containing sequences encoding HRM can be
identified by the absence of marker gene function. Alternatively, a
marker gene can be placed in tandem with a sequence encoding HRM
under the control of a single promoter. Expression of the marker
gene in response to induction or selection usually indicates
expression of the tandem gene as well.
[0192] Alternatively, host cells which contain the nucleic acid
sequence encoding HRM and express HRM may be identified by a
variety of procedures known to those of skill in the art. These
procedures include, but are not limited to, DNA-DNA or DNA-RNA
hybridizations and protein bioassay or immunoassay techniques which
include membrane, solution, or chip based technologies for the
detection and/or quantification of nucleic acid or protein.
[0193] The presence of polynucleotides encoding HRM can be detected
by DNA-DNA or DNA-RNA hybridization or PCR amplification. Nucleic
acid amplification based assays involve the use of oligonucleotides
based on the polynucleotides encoding HRM to detect transformants
containing DNA or RNA encoding HRM.
[0194] A variety of protocols for detecting and measuring the
expression of HRM, using either polyclonal or monoclonal antibodies
specific for the protein are known in the art. Examples include
enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA),
and fluorescence activated cell sorting (FACS). A two-site,
monoclonal-based immunoassay utilizing monoclonal antibodies
reactive to two non-interfering epitopes on HRM is preferred, but a
competitive binding assay may be employed. These and other assays
are described, among other places, in Hampton et al. (1990;
Serological Methods, a Laboratory Manual, APS Press, St Paul Minn.)
and Maddox et al. (1983; J Exp Med 158:1211-1216).
[0195] A wide variety of labels and conjugation techniques are
known by those skilled in the art and may be used in various
nucleic acid and amino acid assays. Means for producing labeled
hybridization or PCR probes for detecting sequences related to
polynucleotides encoding HRM include oligolabeling, nick
translation, end-labeling or PCR amplification using a labeled
nucleotide. Alternatively, the sequences encoding HRM, or any
fragments thereof may be cloned into a vector for the production of
an mRNA probe. Such vectors are known in the art, are commercially
available, and may be used to synthesize RNA probes in vitro by
addition of an RNA polymerase such as T7, T3, or SP6 and labeled
nucleotides. These procedures may be conducted using a variety of
commercially available kits (APB; Promega, Madison WI).
[0196] Host cells transformed with polynucleotides encoding HRM may
be cultured under conditions for the expression and recovery of the
protein from cell culture. The protein produced by a transformed
cell may be secreted or contained intracellularly depending on the
sequence and/or the vector used. As will be understood by those of
skill in the art, expression vectors containing polynucleotides
which encode HRM may be designed to contain signal sequences which
direct secretion of HRM through a prokaryotic or eukaryotic cell
membrane. Other constructions may be used to join sequences
encoding HRM to polynucleotide encoding a protein domain which will
facilitate purification of soluble proteins. Such purification
facilitating domains include, but are not limited to, metal
chelating peptides such as histidine-tryptophan modules that allow
purification on immobilized metals, protein A domains that allow
purification on immobilized immunoglobulin, and the domain utilized
in the FLAGS extension/affinity purification system (Immunex,
Seattle WA). The inclusion of cleavable linker sequences such as
those specific for Factor XA or enterokinase (Invitrogen, San Diego
CA) between the purification domain and HRM may be used to
facilitate purification. One such expression vector provides for
expression of a fusion protein containing HRM and a nucleic acid
encoding 6 histidine residues preceding a thioredoxin or an
enterokinase cleavage site. The histidine residues facilitate
purification on IMAC (immobilized metal ion affinity
chromatography) as described in Porath et al. (1992, Prot Exp Purif
3:263-281) while the enterokinase cleavage site provides a means
for purifying HRM from the fusion protein. A discussion of vectors
which contain fusion proteins is provided in Kroll et al. (1993;
DNA Cell Biol 12:441-453).
[0197] In addition to recombinant production, portions of HRM may
be produced by direct peptide synthesis using solid-phase
techniques (Merrifield (1963) J Am Chem Soc 85:2149-2154). Protein
synthesis may be performed using manual techniques or by
automation. Automated synthesis may be achieved, for example, using
431A Peptide synthesizer (ABI). Various portions of HRM may be
chemically synthesized separately and combined using chemical
methods to produce the full length molecule.
[0198] Therapeutics
[0199] Chemical and structural homology exits among the human
regulatory proteins of the invention. The expression of HRM is
closely associated with cell proliferation. Therefore, in cancers
or immune disorders where HRM is an activator, transcription
factor, or enhancer, and is promoting cell proliferation; it is
desirable to decrease the expression of HRM. In cancers where HRM
is an inhibitor or suppressor and is controlling or decreasing cell
proliferation, it is desirable to provide the protein or to
increase the expression of HRM.
[0200] In one embodiment, where HRM is an inhibitor, HRM or a
portion or derivative thereof may be administered to a subject to
treat a cancer such as adenocarcinoma, leukemia, lymphoma,
melanoma, myeloma, sarcoma, and teratocarcinoma. Such cancers
include, but are not limited to, cancers of the adrenal gland,
bladder, bone, bone marrow, brain, breast, cervix, gall bladder,
ganglia, gastrointestinal tract, heart, kidney, liver, lung,
muscle, ovary, pancreas, parathyroid, penis, prostate, salivary
glands, skin, spleen, testis, thymus, thyroid, and uterus.
[0201] In another embodiment, an agonist which is specific for HRM
may be administered to a subject to treat a cancer including, but
not limited to, those cancers listed above.
[0202] In another further embodiment, a vector capable of
expressing HRM, or a portion or a derivative thereof, may be
administered to a subject to treat a cancer including, but not
limited to, those cancers listed above.
[0203] In a further embodiment where HRM is promoting cell
proliferation, antagonists which decrease the expression or
activity of HRM may be administered to a subject to treat a cancer
such as adenocarcinoma, leukemia, lymphoma, melanoma, myeloma,
sarcoma, and teratocarcinoma. Such cancers include, but are not
limited to, cancers of the adrenal gland, bladder, bone, bone
marrow, brain, breast, cervix, gall bladder, ganglia,
gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary,
pancreas, parathyroid, penis, prostate, salivary glands, skin,
spleen, testis, thymus, thyroid, and uterus. In one aspect,
antibodies which specifically bind HRM may be used directly as an
antagonist or indirectly as a targeting or delivery mechanism for
bringing a pharmaceutical agent to cells or tissue which express
HRM.
[0204] In another embodiment, a vector expressing the complement of
the polynucleotide encoding HRM may be administered to a subject to
treat a cancer including, but not limited to, those cancers listed
above.
[0205] In yet another embodiment where HRM is promoting leukocyte
activity or proliferation, antagonists which decrease the activity
of HRM may be administered to a subject to treat an immune
response. Such responses may be associated with AIDS, Addison's
disease, adult respiratory distress syndrome, allergies, anemia,
asthma, atherosclerosis, bronchitis, cholecystitus, Crohn's
disease, ulcerative colitis, atopic dermatitis, dermatomyositis,
diabetes mellitus, emphysema, atrophic gastritis,
glomerulonephritis, gout, Graves' disease, hypereosinophilia,
irritable bowel syndrome, lupus erythematosus, multiple sclerosis,
myasthenia gravis, myocardial or pericardial inflammation,
osteoarthritis, osteoporosis, pancreatitis, polymyositis,
rheumatoid arthritis, scleroderma, Sjbgren's syndrome, and
autoimmune thyroiditis, complications of cancer, hemodialysis,
extracorporeal circulation, viral, bacterial, fungal, parasitic,
protozoal, and helminthic infections, and trauma. In one aspect,
antibodies which specifically bind HRM may be used directly as an
antagonist or indirectly as a targeting or delivery mechanism for
bringing a pharmaceutical agent to cells or tissue which express
HRM.
[0206] In another embodiment, a vector expressing the complement of
the polynucleotide encoding HRM may be administered to a subject to
treat an immune response including, but not limited to, those
listed above In one further embodiment, HRM or a portion or
derivative thereof may be added to cells to stimulate cell
proliferation. In particular, HRM may be added to a cell in culture
or cells in vivo using delivery mechanisms such as liposomes, viral
based vectors, or electroinjection for the purpose of promoting
cell proliferation and tissue or organ regeneration. Specifically,
HRM may be added to a cell, cell line, tissue or organ culture in
vitro or ex vivo to stimulate cell proliferation for use in
heterologous or autologous transplantation. In some cases, the cell
will have been preselected for its ability to fight an infection or
a cancer or to correct a genetic defect in .alpha. disease such as
sickle cell anemia, , thalassemia, cystic fibrosis, or Huntington's
chorea.
[0207] In another embodiment, an agonist which is specific for HRM
may be administered to a cell to stimulate cell proliferation, as
described above.
[0208] In another embodiment, a vector capable of expressing HRM,
or a portion or a derivative thereof, may be administered to a cell
to stimulate cell proliferation, as described above.
[0209] In other embodiments, any of the therapeutic proteins,
antagonists, antibodies, agonists, complementary sequences or
vectors of the invention may be administered in combination with
other therapeutic agents. Selection of the agents for use in
combination therapy may be made by one of ordinary skill in the
art, according to conventional pharmaceutical principles. The
combination of therapeutic agents may act synergistically to effect
the treatment of the various disorders described above. Using this
approach, one may be able to achieve therapeutic efficacy with
lower dosages of each agent, thus reducing the potential for
adverse side effects.
[0210] Antagonists or inhibitors of HRM may be produced using
methods which are generally known in the art. In particular,
purified HRM may be used to produce antibodies or to screen
libraries of pharmaceutical agents to identify those which
specifically bind HRM.
[0211] Antibodies to HRM may be generated using methods that are
well known in the art. Such antibodies may include, but are not
limited to, polyclonal, monoclonal, chimeric, single chain, Fab
fragments, and fragments produced by a Fab expression library.
Neutralizing antibodies, (i.e., those which inhibit dimer
formation) are especially preferred for therapeutic use.
[0212] For the production of antibodies, various hosts including
goats, rabbits, rats, mice, humans, and others, may be immunized by
injection with HRM or any portion or oligopeptide thereof which has
immunogenic properties. Depending on the host species, various
adjuvants may be used to increase immunological response. Such
adjuvants include, but are not limited to, Freund's, mineral gels
such as aluminum hydroxide, and surface active substances such as
lysolecithin, pluronic polyols, polyanions, peptides, oil
emulsions, keyhole limpet hemocyanin, and dinitrophenol. Among
adjuvants used in humans, BCG (bacilli Calmette-Guerin) and
Corynebacterium parvum are especially preferable.
[0213] It is preferred that the oligopeptides, peptides, or
portions used to induce antibodies to HRM have an amino acid
sequence consisting of at least five amino acids and more
preferably at least 10 amino acids. It is also preferable that they
are identical to a portion of the amino acid sequence of the
natural protein, and they may contain the entire amino acid
sequence of a small, naturally occurring molecule. Short stretches
of HRM amino acids may be fused with those of another protein such
as keyhole limpet hemocyanin and antibody produced against the
chimeric molecule.
[0214] Monoclonal antibodies to HRM may be prepared using any
technique which provides for the production of antibody molecules
by continuous cell lines in culture. These include, but are not
limited to, the hybridoma technique, the human B-cell hybridoma
technique, and the EBV-hybridoma technique (Kohler et al. (1975)
Nature 256:495-497 Kozbor et al. (1985) J Immunol Methods 81:31-42
Cote et al. (1983) Pr Natl Acad Sci 80:2026-2030, Cole et al.
(1984) Mol Cell Biol 62:109-120).
[0215] In addition, techniques developed for the production of
"chimeric antibodies", the splicing of mouse antibody genes to
human antibody genes to obtain a molecule with antigen specificity
and biological activity can be used (Morrison et al. (1984) Proc
Natl Acad Sci 81:6851-6855, Neuberger et al. (1984) Nature
312:604-608, and Takeda et al. (1985) Nature 314:452-454).
Alternatively, techniques described for the production of single
chain antibodies may be adapted, using methods known in the art, to
produce HRM-specific single chain antibodies. Antibodies with
related specificity, but of distinct idiotypic composition, may be
generated by chain shuffling from random combinatorial
immunoglobulin libraries (Burton (1991) Proc Natl Acad Sci
88:11120-3).
[0216] Antibodies may also be produced by inducing in vivo
production in the lymphocyte population or by screening
immunoglobulin libraries or panels of highly specific binding
reagents as disclosed in the literature (Orlandi et al. (1989) Proc
Natl Acad Sci 86:3833-3837, Winter et al. (1991) Nature
349:293-299).
[0217] Antibody fragments which contain specific binding sites for
HRM may also be generated. For example, such fragments include, but
are not limited to, the F(ab')2 fragments which can be produced by
pepsin digestion of the antibody molecule and the Fab fragments
which can be generated by reducing the disulfide bridges of the
F(ab')2 fragments. Alternatively, Fab expression libraries may be
constructed to allow rapid and easy identification of monoclonal
Fab fragments with the desired specificity (Huse et al. (1989)
Science 254:1275-1281).
[0218] Various immunoassays may be used for screening to identify
antibodies having the desired specificity. Numerous protocols for
competitive binding or immunoradiometric assays using either
polyclonal or monoclonal antibodies with established specificities
are well known in the art. Such immunoassays typically involve the
measurement of complex formation between HRM and its specific
antibody. A two-site, monoclonal-based immunoassay utilizing
monoclonal antibodies reactive to two non-interfering HRM epitopes
is preferred, but a competitive binding assay may also be employed
(Maddox, supra).
[0219] In another embodiment of the invention, the polynucleotides
encoding HRM, or any fragment or complement thereof, may be used
for therapeutic purposes. In one aspect, the complement of the
polynucleotide encoding HRM may be used in situations in which it
would be desirable to block the transcription of the mRNA. In
particular, cells may be transformed with sequences complementary
to polynucleotides encoding HRM. Thus, complementary molecules or
fragments may be used to modulate HRM activity, or to achieve
regulation of gene function. Such technology is now well known in
the art, and sense or antisense oligonucleotides or larger
fragments, can be designed from various locations along the coding
or control regions of sequences encoding HRM.
[0220] Expression vectors derived from retroviruses, adenovirus,
herpes or vaccinia viruses, or from various bacterial plasmids may
be used for delivery of polynucleotides to the targeted organ,
tissue or cell population. Methods which are well known to those
skilled in the art can be used to construct vectors which will
express nucleic acid sequence which is complementary to the
polynucleotides of the gene encoding HRM. These techniques are
described both in Sambrook (ura and in Ausubel (supra).
[0221] Genes encoding HRM can be turned off by transforming a cell
or tissue with expression vectors which express high levels of a
polynucleotide or fragment thereof which encodes HRM. Such
constructs may be used to introduce untranslatable sense or
antisense sequences into a cell. Even in the absence of integration
into the DNA, such vectors may continue to transcribe RNA molecules
until they are disabled by endogenous nucleases. Transient
expression may last for a month or more with a non-replicating
vector and even longer if replication elements are part of the
vector system.
[0222] As mentioned above, modifications of gene expression can be
obtained by designing complementary sequences or antisense
molecules (DNA, RNA, or PNA) to the control, 5' or regulatory
regions of the gene encoding HRM (signal sequence, promoters,
enhancers, and introns). Oligonucleotides derived from the
transcription initiation site, e.g., between positions -10 and +10
from the start site, are preferred. Similarly, inhibition can be
achieved using "triple helix" base-pairing methodology. Triple
helix pairing is useful because it causes inhibition of the ability
of the double helix to open for the binding of polymerases,
transcription factors, or regulatory molecules. Recent therapeutic
advances using triplex DNA have been described in the literature
(Gee et al. (1994) In: Huber and Carr, Molecular and Immunologic
Approaches, Futura Publishing, Mt. Kisco N.Y.). The complementary
sequence or antisense molecule may also be designed to block
translation of mRNA by preventing the transcript from binding to
ribosomes.
[0223] Ribozymes, enzymatic RNA molecules, may also be used to
catalyze the specific cleavage of RNA. The mechanism of ribozyme
action involves sequence-specific hybridization of the ribozyme
molecule to complementary target RNA, followed by endonucleolytic
cleavage. Examples which may be used include engineered hammerhead
motif ribozyme molecules that can specifically and efficiently
catalyze endonucleolytic cleavage of sequences encoding HRM.
[0224] Specific ribozyme cleavage sites within any potential RNA
target are initially identified by scanning the target molecule for
ribozyme cleavage sites which include the following sequences: GUA,
GUU, and GUC. Once identified, short RNA sequences of between 15
and 20 ribonucleotides corresponding to the region of the target
gene containing the cleavage site may be evaluated for secondary
structural features which may render the oligonucleotide
inoperable. The suitability of candidate targets may also be
evaluated by testing accessibility to hybridization with
complementary oligonucleotides using ribonuclease protection
assays.
[0225] Complementary ribonucleic acid molecules and ribozymes of
the invention may be prepared by any method known in the art for
the synthesis of nucleic acid molecules. These include techniques
for chemically synthesizing oligonucleotides such as solid phase
phosphoramidite chemical synthesis. Alternatively, RNA molecules
may be generated by in vitro and in vivo transcription of DNA
sequences encoding HRM. Such DNA sequences may be incorporated into
a wide variety of vectors with RNA polymerase promoters such as T7
or SP6. Alternatively, these cDNA constructs that synthesize
complementary RNA constitutively or inducibly can be introduced
into cell lines, cells, or tissues.
[0226] RNA molecules may be modified to increase intracellular
stability and half-life. Possible modifications include, but are
not limited to, the addition of flanking sequences at the 5' and/or
3' ends of the molecule or the use of phosphorothioate or 2'
O-methyl rather than phosphodiesterase linkages within the backbone
of the molecule. This concept is inherent in the production of PNAs
and can be extended in all of these molecules by the inclusion of
nontraditional bases such as inosine, queosine, and wybutosine, as
well as acetyl-, methyl-, thio-, and similarly modified forms of
adenine, cytidine, guanine, thymine, and uridine which are not as
easily recognized by endogenous endonucleases.
[0227] Many methods for introducing vectors into cells or tissues
are available for use in vivo, in vitro, and ex vivo. For ex vivo
therapy, vectors may be introduced into stem cells taken from the
patient and clonally propagated for autologous transplant back into
that same patient. Delivery by transfection, by liposome injections
or polycationic amino polymers (Goldman et al. (1997) Nature
Biotechnol 15:462-66, incorporated herein by reference) may be
achieved using methods which are well known in the art.
[0228] Any of the therapeutic methods described above may be
applied to any subject in need of such therapy, including, for
example, mammals such as dogs, cats, cows, horses, rabbits,
monkeys, and most preferably, humans.
[0229] An additional embodiment of the invention relates to the
administration of a pharmaceutical composition, in conjunction with
a pharmaceutically acceptable carrier, for any of the therapeutic
effects discussed above. Such pharmaceutical compositions may
consist of HRM, antibodies to HRM, mimetics, agonists, antagonists,
or inhibitors of HRM. The compositions may be administered alone or
in combination with at least one other agent, such as stabilizing
compound, which may be administered in any sterile, biocompatible
pharmaceutical carrier, including, but not limited to, saline,
buffered saline, dextrose, and water. The compositions may be
administered to a patient alone, or in combination with other
agents, drugs or hormones.
[0230] The pharmaceutical compositions utilized in this invention
may be administered by any number of routes including, but not
limited to, oral, intravenous, intramuscular, intra-arterial,
intramedullary, intrathecal, intraventricular, transdermal,
subcutaneous, intraperitoneal, intranasal, enteral, topical,
sublingual, or rectal means.
[0231] In addition to the active ingredients, these pharmaceutical
compositions may contain pharmaceutically-acceptable carriers
comprising excipients and auxiliaries which facilitate processing
of the active compounds into preparations which can be used
pharmaceutically. Further details on techniques for formulation and
administration may be found in the latest edition of Remington's
Pharmaceutical Sciences (Mack Publishing, Easton PA).
[0232] Pharmaceutical compositions for oral administration can be
formulated using pharmaceutically acceptable carriers well known in
the art in dosages for oral administration. Such carriers enable
the pharmaceutical compositions to be formulated as tablets, pills,
dragees, capsules, liquids, gels, syrups, slurries, suspensions,
and the like, for ingestion by the patient.
[0233] Pharmaceutical preparations for oral use can be obtained
through combination of active compounds with solid excipient,
optionally grinding a resulting mixture, and processing the mixture
of granules, after adding auxiliaries, if desired, to obtain
tablets or dragee cores. Excipients include carbohydrate or protein
fillers, such as sugars, including lactose, sucrose, mannitol, or
sorbitol, starch from corn, wheat, rice, potato, or other plants,
cellulose, such as methyl cellulose, hydroxypropylmethyl-cellulose,
or sodium carboxymethylcellulose, gums including arabic and
tragacanth, and proteins such as gelatin and collagen. If desired,
disintegrating or solubilizing agents may be added, such as the
cross-linked polyvinyl pyrrolidone, agar, alginic acid, or a salt
thereof, such as sodium alginate.
[0234] Dragee cores may be used in conjunction with coatings, such
as concentrated sugar solutions, which may also contain gum arabic,
talc, polyvinylpyrrolidone, carbopol gel, polyethylene glycol,
and/or titanium dioxide, lacquer solutions, and organic solvents or
solvent mixtures. Dyestuffs or pigments may be added to the tablets
or dragee coatings for product identification or to characterize
the quantity of active compound, i.e., dosage.
[0235] Pharmaceutical preparations which can be used orally include
push-fit capsules made of gelatin, as well as soft, sealed capsules
made of gelatin and a coating, such as glycerol or sorbitol.
Push-fit capsules can contain active ingredients mixed with a
filler or binders, such as lactose or starches, lubricants, such as
talc or magnesium stearate, and, optionally, stabilizers. In soft
capsules, the active compounds may be dissolved or suspended in
liquids, such as fatty oils, liquid, or liquid polyethylene glycol
with or without stabilizers.
[0236] Pharmaceutical formulations for parenteral administration
may be formulated in aqueous solutions, preferably in
physiologically compatible buffers such as Hanks' solution.
Ringer's solution, or physiologically buffered saline. Aqueous
injection suspensions may contain substances which increase the
viscosity of the suspension, such as sodium carboxymethyl
cellulose, sorbitol, or dextran. Additionally, suspensions of the
active compounds may be prepared as oily injection suspensions.
Lipophilic solvents or vehicles include fatty oils such as sesame
oil, or synthetic fatty acid esters, such as ethyl oleate or
triglycerides, or liposomes. Non-lipid polycationic amino polymers
may also be used for delivery. Optionally, the suspension may also
contain stabilizers or agents which increase the solubility of the
compounds to allow for the preparation of highly concentrated
solutions.
[0237] For topical or nasal administration, penetrants to the
particular barrier to be permeated are used in the formulation.
Such penetrants are generally known in the art.
[0238] The pharmaceutical compositions of the present invention may
be manufactured in a manner that is known in the art, e.g., by
means of conventional mixing, dissolving, granulating,
dragee-making, levigating, emulsifying, encapsulating, entrapping,
or lyophilizing processes.
[0239] The pharmaceutical composition may be provided as a salt and
can be formed with many acids, including but not limited to,
hydrochloric, sulfuric, acetic, lactic, tartaric, malic, succinic,
etc. Salts tend to be more soluble in aqueous or other protonic
solvents than are the corresponding free base forms. In other
cases, the preferred preparation may be a lyophilized powder which
may contain any or all of the following: 1-50 mM histidine, 0.1%-2%
sucrose, and 2-7% mannitol, at a pH range of 4.5 to 5.5, that is
com buffer prior to use.
[0240] After pharmaceutical compositions have been prepared, they
can be placed in a container and labeled for treatment of an
indicated condition. For administration of HRM, such labeling would
include amount, frequency, and method of administration.
[0241] Pharmaceutical compositions for use in the invention include
compositions wherein the active ingredients are contained in an
effective amount to achieve the intended purpose. The determination
of an effective dose is well within the capability of those skilled
in the art.
[0242] For any compound, the therapeutically effective dose can be
estimated initially either in cell culture assays, e.g., of
neoplastic cells, or in animal models, usually mice, rabbits, dogs,
or pigs. The animal model may also be used to determine the
concentration range and route of administration. Such information
can then be used to determine useful doses and routes for
administration in humans.
[0243] A therapeutically effective dose refers to that amount of
active ingredient, for example HRM or portions thereof, antibodies
of HRM, agonists, antagonists or inhibitors of HRM, which
ameliorates the symptoms or condition. Therapeutic efficacy and
toxicity may be determined by standard pharmaceutical procedures in
cell cultures or experimental animals, e.g., ED50 (the dose
therapeutically effective in 50% of the population) and LD50 (the
dose lethal to 50% of the population). The dose ratio between
therapeutic and toxic effects is the therapeutic index, and it can
be expressed as the ratio, LD50/ED50.
[0244] Pharmaceutical compositions which exhibit large therapeutic
indices are preferred. The data obtained from cell culture assays
and animal studies is used in formulating a range of dosage for
human use. The dosage contained in such compositions is preferably
within a range of circulating concentrations that include the ED50
with little or no toxicity. The dosage varies within this range
depending upon the dosage form employed, sensitivity of the
patient, and the route of administration.
[0245] The exact dosage will be determined by the practitioner, in
light of factors related to the subject that requires treatment.
Dosage and administration are adjusted to provide levels of the
active moiety that produce or maintain the desired effect. Factors
which may be taken into account include the severity of the disease
state, general health of the subject, age, weight, and gender of
the subject, diet, time and frequency of administration, drug
combination(s), reaction sensitivities, and tolerance/response to
therapy. Long-acting pharmaceutical compositions may be
administered every 3 to 4 days, every week, or once every two weeks
depending on half-life and clearance rate of the particular
formulation.
[0246] Normal dosage amounts may vary from 0.1 to 100,000
micrograms, up to a total dose of about 1 g, depending upon the
route of administration. Guidance as to particular dosages and
methods of delivery is provided in the literature and generally
available to practitioners in the art. Those skilled in the art
will employ different formulations for nucleotides than for
proteins or their inhibitors. Similarly, delivery of
polynucleotides or proteins will be specific to particular cells,
conditions, locations, etc.
[0247] Diagnostic
[0248] In another embodiment, antibodies which specifically bind
HRM may be used for the diagnosis of conditions or diseases
characterized by expression of HRM, or in assays to monitor
patients being treated with HRM, agonists, antagonists or
inhibitors. The antibodies useful for diagnostic purposes may be
prepared in the same manner as those described above for
therapeutics. Diagnostic assays for HRM include methods which
utilize the antibody and a label to detect HRM in human body fluids
or extracts of cells or tissues. The antibodies may be used with or
without modification, and may be labeled by joining them, either
covalently or non-covalently, with a reporter molecule. A wide
variety of reporter molecules which are known in the art may be
used, several of which are described above.
[0249] A variety of protocols including ELISA, RIA, and FACS for
measuring HRM are known in the art and provide a basis for
diagnosing altered or abnormal levels of HRM expression. Normal or
standard values for HRM expression are established by combining
body fluids or cell extracts taken from normal mammalian subjects,
preferably human, with antibody to HRM under conditions for complex
formation. The amount of standard complex formation may be
quantified by various methods, but preferably by photometric means.
Quantities of HRM expressed in subject samples are compared with
the standard values from control and diseased samples. Deviation
between standard and subject values establishes the parameters for
diagnosing disease.
[0250] In another embodiment of the invention, the polynucleotides
encoding HRM may be used for diagnostic purposes. The
polynucleotides which may be used include oligonucleotide
sequences, complementary RNA and DNA molecules, and PNAs. The
polynucleotides may be used to detect and quantitate gene
expression in biopsied tissues in which expression of HRM may be
correlated with disease. The diagnostic assay may be used to
distinguish between absence, presence, and excess expression of
HRM, and to monitor regulation of HRM levels during therapeutic
intervention.
[0251] In one aspect, hybridization with PCR probes which are
capable of detecting polynucleotides, including genomic sequences,
encoding HRM or closely related molecules, may be used to identify
nucleic acid sequences which encode HRM. The specificity of the
probe, whether it is made from a highly specific region, e.g., 10
unique nucleotides in the 5' regulatory region, or a less specific
region, e.g., especially in the 3' coding region, and the
stringency of the hybridization or amplification (maximal, high,
intermediate, or low) will determine whether the probe identifies
only naturally occurring sequences encoding HRM, alleles, or
related sequences.
[0252] Probes may also be used for the detection of related
sequences, and should preferably contain at least 50% of the
nucleotides from any of the HRM encoding sequences. The
hybridization probes of the invention may be DNA or RNA and derived
from the polynucleotide of SEQ ID NOs:50-98 or from genomic
sequence including promoter, enhancer elements, and introns of the
naturally occurring HRM.
[0253] Means for producing specific hybridization probes for
polynucleotides encoding HRM include the cloning of nucleic acid
sequences encoding HRM or HRM derivatives into vectors for the
production of mRNA probes. Such vectors are known in the art,
commercially available, and may be used to synthesize RNA probes in
vitro by means of the addition of the RNA polymerases and the
labeled nucleotides. Hybridization probes may be labeled by a
variety of reporter groups, for example, radionuclides such as 32P
or 35S, or enzymatic labels, such as alkaline phosphatase coupled
to the probe via avidin/biotin coupling systems, and the like.
[0254] Polynucleotides encoding HRM may be used for the diagnosis
of conditions, disorders, or diseases which are associated with
either increased or decreased expression of HRM. Examples of such
conditions or diseases include adenocarcinoma, leukemia, lymphoma,
melanoma, myeloma, sarcoma, teratocarcinoma, and cancers of the
adrenal gland, bladder, bone, brain, breast, cervix, gall bladder,
ganglia, gastrointestinal tract, heart, kidney, liver, lung, bone
marrow, muscle, ovary, pancreas, parathyroid, penis, prostate,
salivary glands, skin, spleen, testis, thymus, thyroid, and uterus,
and immune disorders such as AIDS, Addison's disease, adult
respiratory distress syndrome, allergies, anemia, asthma,
atherosclerosis, bronchitis, cholecystitus, Crohn's disease,
ulcerative colitis, atopic dermatitis, dermatomyositis, diabetes
mellitus, emphysema, atrophic gastritis, glomerulonephritis, gout,
Graves' disease, hypereosinophilia, irritable bowel syndrome, lupus
erythematosus, multiple sclerosis, myasthenia gravis, myocardial or
pericardial inflammation, osteoarthritis, osteoporosis,
pancreatitis, polymyositis, rheumatoid arthritis, scleroderma,
Sjogren's syndrome, and thyroiditis. The polynucleotides encoding
HRM may be used in Southern or northern analysis, dot blot, or
other membrane-based technologies, in PCR technologies, or in
dipstick, pin, or other multiformat assays including microarrays to
analyze fluids or tissues from patient biopsies to detect altered
HRM expression. Such qualitative or quantitative methods are well
known in the art.
[0255] In a particular aspect, the polynucleotides encoding HRM may
be useful in assays that detect activation or induction of various
cancers, particularly those mentioned above. The polynucleotides
encoding HRM may be labeled by standard methods, and added to a
fluid or tissue sample from a patient under conditions for the
formation of hybridization complexes. After an incubation period,
the sample is washed, the signal is quantitated and compared with a
standard value. If the amount of signal in the biopsied or
extracted sample is significantly different from that of a
comparable control sample, the polynucleotides have hybridized with
nucleic acids in the sample, and the presence of differentially
expressed polynucleotides encoding HRM in the sample indicates the
presence of the disease. Such assays may also be used to evaluate
the efficacy of a particular therapeutic treatment regimen in
animal studies, in clinical trials, or in monitoring the treatment
of an individual patient.
[0256] In order to provide a basis for the diagnosis of disease
associated with expression of HRM, a normal or standard profile for
expression is established. This may be accomplished by combining
body fluids or cell extracts taken from normal subjects, either
animal or human, with a sequence, or a fragment thereof, which
encodes HRM, under conditions for hybridization or amplification.
Standard hybridization may be quantified by comparing the values
obtained from normal subjects with those from an experiment where a
known amount of an isolated polynucleotide is used. Standard values
obtained from normal samples may be compared with values obtained
from samples from patients who are symptomatic for disease.
Deviation between standard and subject values is used to establish
the presence of disease.
[0257] Once disease is established and a treatment protocol is
initiated, hybridization assays may be repeated on a regular basis
to evaluate whether the level of expression in the patient begins
to approximate that which is observed in the normal patient. The
results obtained from successive assays may be used to show the
efficacy of treatment over a period ranging from several days to
months.
[0258] With respect to cancer, the presence of a relatively high
amount of transcript in biopsied tissue from an individual may
indicate a predisposition for the development of the disease or may
provide a means for detecting the disease prior to the appearance
of actual clinical symptoms. A more definitive diagnosis of this
type may allow health professionals to employ aggressive treatment
earlier thereby preventing further progression of the cancer.
[0259] Additional diagnostic uses for oligonucleotides designed
from the sequences encoding HRM may involve the use of PCR. Such
oligomers may be chemically synthesized, generated enzymatically,
or produced in vitro. Oligomers will preferably consist of two
polynucleotides, one with sense orientation (5'->3') and another
with antisense (3'<-5'), employed under optimized conditions for
identification of a specific gene or condition. The same two
oligomers, nested sets of oligomers, or even a degenerate pool of
oligomers may be employed under less stringent conditions for
detection and/or quantitation of closely related DNA or RNA
sequences.
[0260] Methods which may also be used to quantitate the expression
of HRM include radiolabeling or biotinylating nucleotides,
coamplification of a control nucleic acid, and standard curves onto
which the experimental results are interpolated (Melby et al.
(1993) J Immunol Methods, 159:235-244, Duplaa et al. (1993) Anal
Biochem 229-236). The speed of quantitation of multiple samples may
be accelerated by running the assay in an multiwell format where
the oligomer of interest is presented in various dilutions and a
spectrophotometric or colorimetric response gives rapid
quantitation.
[0261] In further embodiments, oligonucleotides or longer fragments
derived from any of the polynucleotides may be used as targets on a
microarray. The microarray can be used to monitor the expression
level of large numbers of genes simultaneously (to produce a
transcript image), and to identify genetic variants, mutations and
polymorphisms. This information may be used to determine gene
function, understanding the genetic basis of disease, diagnosing
disease, and in developing and in monitoring the activities of
therapeutic agents.
[0262] In one embodiment, the microarray is prepared and used
according to the methods described in PCT application WO95/11995,
Lockhart et al. (1996, Nature Biotechnol 14:1675-1680) and Schena
et al. (1996, Proc Natl Acad Sci 93:10614-10619), all of which are
incorporated herein in their entirety by reference.
[0263] The microarray is preferably composed of a large number of
unique, single-stranded nucleic acid sequences, usually either
synthetic antisense oligonucleotides or fragments of cDNAs, fixed
to a solid support. The oligonucleotides are preferably about 6-60
nucleotides in length, more preferably 15-30 nucleotides in length,
and most preferably about 20-25 nucleotides in length. For a
certain type of microarray, it may be preferable to use
oligonucleotides which are only 7-10 nucleotides in length. The
microarray may contain oligonucleotides which cover the known 5',
or 3', sequence, or contain sequential oligonucleotides which cover
the full length sequence, or unique oligonucleotides selected from
particular areas along the length of the sequence. Polynucleotides
used in the microarray may be oligonucleotides that are specific to
a gene or genes of interest in which at least a fragment of the
sequence is known or that are specific to one or more unidentified
cDNAs which are common to a particular cell or tissue type or to a
normal, developmental, or disease state. In certain situations it
may be to use pairs of oligonucleotides on a microarray. The
"pairs" will be identical, except for one nucleotide which is
located in the center of the sequence. The second oligonucleotide
in the pair (mismatched by one) serves as a control. The number of
oligonucleotide pairs may range from 2 to one million.
[0264] In order to produce oligonucleotides to a known sequence for
a microarray, the gene of interest is examined using a computer
algorithm which starts at the 5' or more preferably at the 3' end
of the polynucleotide. The algorithm identifies oligomers of
defined length that are unique to the gene, have a GC content
within a range for hybridization, and lack predicted secondary
structure that may interfere with hybridization. In one aspect, the
oligomers are synthesized at designated areas on a substrate using
a light-directed chemical process. The substrate may be paper,
nylon or other type of membrane, filter, chip, glass slide, or any
other solid support.
[0265] In another aspect, the oligonucleotides may be synthesized
on the surface of the substrate by using a chemical coupling
procedure and an ink jet application apparatus, as described in PCT
application WO95/251116 (Baldeschweiler et al.) which is
incorporated herein in its entirety by reference. In another
aspect, a gridded array analogous to a dot or slot blot apparatus
may be used to arrange and link cDNA fragments or oligonucleotides
to the surface of a substrate using a vacuum system, thermal, UV,
mechanical or chemical bonding procedures. In yet another aspect,
an array may be produced by hand or using available devices,
materials, and machines (including multichannel pipetters or
robotic instruments) and may contain 8, 24, 96, 384, 1536 or 6144
oligonucleotides, or any other multiple from 2 to one million which
lends itself to the efficient use of commercially available
instrumentation.
[0266] In order to conduct sample analysis using the microarrays,
polynucleotides are extracted from a biological sample. The
biological samples may be obtained from any bodily fluid (blood,
urine, saliva, phlegm, gastric juices, etc.), cultured cells,
biopsies, or other tissue preparations. To produce probes, the
polynucleotides extracted from the sample are used to produce
nucleic acid sequences which are complementary to the nucleic acids
on the microarray. If the microarray consists of cDNAs, antisense
RNAs (aRNA) are probes. Therefore, in one aspect, mRNA is used to
produce cDNA which, in turn and in the presence of fluorescent
nucleotides, is used to produce fragment or oligonucleotide aRNA
probes. These fluorescently labeled probes are incubated with the
microarray so that the probe sequences hybridize to the cDNA
oligonucleotides of the microarray. In another aspect,
complementary nucleic acid sequences are used as probes and can
also include polynucleotides, fragments, complementary, or
antisense sequences produced using restriction enzymes, PCR
technologies, and oligolabeling kits which are well known in the
art.
[0267] Incubation conditions are adjusted so that hybridization
occurs with precise complementary matches or with various degrees
of less complementarity. After removal of nonhybridized probes, a
scanner is used to determine the levels and patterns of
fluorescence. The scanned images are examined to determine degree
of complementarity and the relative abundance of each
oligonucleotide sequence on the microarray. A detection system may
be used to measure the absence, presence, and amount of
hybridization for all of the distinct sequences simultaneously.
This data may be used for large scale correlation studies or
functional analysis of the sequences, mutations, variants, or
polymorphisms among samples (Heller et al. (1997) Proc Natl Acad
Sci 94:2150-55).
[0268] In another embodiment of the invention, the nucleic acid
sequences which encode HRM may also be used to generate
hybridization probes which are useful for mapping the naturally
occurring genomic sequence. The sequences may be mapped to a
particular chromosome, to a specific region of a chromosome or to
artificial chromosome constructions, such as human artificial
chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial
artificial chromosomes (BACs), bacterial PI constructions, or
single chromosome cDNA libraries as reviewed in Price (1993, Blood
Rev 7:127-134) and Trask (1991, Trends Genet 7:149-154).
[0269] Fluorescent in situ hybridization (FISH as described in
Verma et al. (1988) Human Chromosomes: A Manual of Basic
Techniques, Pergamon Press, New York N.Y.) may be correlated with
other physical chromosome mapping techniques and genetic map data.
Examples of genetic map data can be found in various scientific
journals or at Online Mendelian Inheritance in Man (OMIM).
Correlation between the location of the gene encoding HRM on a
physical chromosomal map and a specific disease, or predisposition
to a specific disease, may help delimit the region of DNA
associated with that genetic disease. The polynucleotides of the
invention may be used to detect differences in gene sequences
between normal, carrier, or affected individuals.
[0270] In situ hybridization of chromosomal preparations and
physical mapping techniques such as linkage analysis using
established chromosomal markers may be used for extending genetic
maps. Often the placement of a gene on the chromosome of another
mammalian species, such as mouse, may reveal associated markers
even if the number or arm of a particular human chromosome is not
known. New sequences can be assigned to chromosomal arms, or parts
thereof, by physical mapping. This provides valuable information to
investigators searching for disease genes using positional cloning
or other gene discovery techniques. Once the disease or syndrome
has been crudely localized by genetic linkage to a particular
genomic region, for example, AT to 11q22-23 (Gatti et al. (1988)
Nature 336:577-580), any sequences mapping to that area may
represent associated or regulatory genes for further investigation.
The polynucleotide of the invention may also be used to detect
differences in the chromosomal location due to translocation,
inversion, etc. among normal, carrier, or affected individuals.
[0271] In another embodiment of the invention, HRM, its catalytic
or immunogenic portions or oligopeptides thereof, can be used for
screening libraries of compounds in any of a variety of drug
screening techniques. The portion employed in such screening may be
free in solution, affixed to a solid support, borne on a cell
surface, or located intracellularly. The formation of binding
complexes, between HRM and the agent being tested, may be
measured.
[0272] Another technique for drug screening which may be used
provides for high throughput screening of compounds having binding
affinity to the protein of interest as described in published PCT
application WO84/03564. In this method, large numbers of different
small test compounds are synthesized on a solid substrate, such as
plastic pins or some other surface. The test compounds are reacted
with HRM, or portions thereof, and washed. Bound HRM is then
detected by methods well known in the art. Purified HRM can also be
coated directly onto plates for use in the aforementioned drug
screening techniques. Alternatively, non-neutralizing antibodies
can be used to capture the peptide and immobilize it on a solid
support.
[0273] In another embodiment, one may use competitive drug
screening assays in which neutralizing antibodies capable of
binding HRM specifically compete with a test compound for binding
HRM. In this manner, the antibodies can be used to detect the
presence of any peptide which shares one or more antigenic
determinants with HRM.
[0274] In additional embodiments, the polynucleotides which encode
HRM may be used in any molecular biology techniques that have yet
to be developed, provided the new techniques rely on properties of
polynucleotides that are currently known, including, but not
limited to, such properties as the triplet genetic code and
specific base pair interactions.
[0275] The examples below are provided to illustrate the invention
and are not included for the purpose of limiting the invention.
EXAMPLES
[0276] For purposes of example, the preparation and sequencing of
the LNODNOT03 cDNA library, from which Incyte Clones 1572888,
1573677, 1574624, and 1577239 were isolated, is described.
Preparation and sequencing of cDNAs in libraries in the LIFESEQ
database (Incyte Genomics, Palo Alto CA) have varied over time, and
the gradual changes involved use of kits, plasmids, and machinery
available at the particular time the library was made and
analyzed.
I LNODNOT03 cDNA Library Construction
[0277] The LNODNOT03 cDNA library was constructed using 1 .mu.g of
polyA RNA isolated from lymph node tissue removed from a
67-year-old Caucasian male during a segmental lung resection and
bronchoscopy. Microscopic examination showed that the tissue was
extensively necrotic with 10% viable tumor. The invasive grade 3/4
squamous cell carcinoma had formed a mass in the right lower lobe
of the lung which had invaded into, but not through, the visceral
pleura. Focally, the tumor had obliterated the bronchial lumen
although the bronchial margin was negative for dysplasia/neoplasm.
One of two intrapulmonary, one of four inferior mediastinal
(subcarinal), and two of eight superior mediastinal lymph nodes
were metastatically involved. Patient history included hemangioma
and tobacco use, the patient was taking Doxycycline, a
tetracycline, to treat an infection.
[0278] The frozen tissue was homogenized and lysed in guanidinium
isothiocyanate solution using a POLYTRON homogenizer (Brinkmann
Instruments, Westbury N.Y.). The lysate was centrifuged over a 5.7
M CsCl cushion using an SW28 rotor in a L8-70M ultracentrifuge
(Beckman Coulter, Fullerton Calif.) for 18 hours at 25,000 rpm at
ambient temperature. The RNA was extracted with acid phenol, pH
4.7, precipitated using 0.3 M sodium acetate and 2.5 volumes of
ethanol, resuspended in RNAse-free water, and treated with DNAse at
37C. Extraction and precipitation were repeated as before. The MRNA
was isolated using the OLIGOTEX kit (Qiagen, Chatsworth Calif.) and
used to construct the cDNA library.
[0279] The mRNA was handled according to the recommended protocols
in the SUPERSCRIPT plasmid system (Life Technologies). The cDNAs
were fractionated on a SEPHAROSE CL4B column (APB), and those cDNAs
exceeding 400 bp were ligated into pINCY plasmid (Incyte Genomics).
The plasmid was subsequently transformed into DH5.alpha. competent
cells (Life Technologies).
II Isolation and Sequencing of cDNA Clones
[0280] Plasmid DNA was released from the cells and purified using
the REAL Prep 96 plasmid kit (Qiagen). This kit enabled the
simultaneous purification of 96 samples in a 96-well block using
multi-channel reagent dispensers. The recommended protocol was
employed except for the following changes: 1) the bacteria were
cultured in 1 ml of sterile TERRIFIC BROTH (BD Biosciences, Sparks
MD) with carbenicillin at 25 mg/L and glycerol at 0.4%, 2) after
incubation for 19 hours, the cells were lysed with 0.3 ml of lysis
buffer and precipitated using isopropanol, and 3) the plasmid
pellet was resuspended in 0.1 ml of distilled water. After the last
step in the protocol, samples were transferred to a 96-well block
for storage at 4 C.
[0281] The cDNAs were prepared using a MICROLAB system (Hamilton)
in combination with DNA ENGINE thermal cyclers (MJ Research),
sequenced by the method of Sanger and Coulson (1975, J Mol Biol
94:441f) using 377 PRISM DNA sequencing systems (ABI), and reading
frame was determined.
III Homology Searching of cDNA Clones and Their Deduced
Proteins
[0282] The polynucleotides and/or amino acid sequences of the
Sequence Listing were used to query sequences in the GenBank,
SwissProt, BLOCKS, and Pima II databases. These databases, which
contain previously identified and annotated sequences, were
searched for regions of homology using BLAST, which stands for
Basic Local Alignment Search Tool (Altschul (1993) J Mol Evol
36:290-300, Altschul et al. (1990) J Mol Biol 215:403-410).
[0283] BLAST produced alignments of both nucleotide and amino acid
sequences to determine sequence similarity. Because of the local
nature of the alignments, BLAST was especially useful in
determining exact matches or in identifying homologs which may be
of prokaryotic (bacterial) or eukaryotic (animal, fungal, or plant)
origin. Other algorithms such as the one described in Smith et al.
(1992, Protein Engineering 5:35-51) could have been used when
dealing with primary sequence patterns and secondary structure gap
penalties. The sequences disclosed in this application have lengths
of at least 49 nucleotides, and no more than 12% uncalled bases
(where N is recorded rather than A, C, G, or T).
[0284] The BLAST approach searched for matches between a query
sequence and a database sequence. BLAST evaluated the statistical
significance of any matches found and reported only those matches
that satisfy the user-selected threshold of significance. In this
application, threshold was set at 10.sup.-25 for nucleotides and
10.sup.-14 for peptides.
[0285] Incyte polynucleotides were searched against the GenBank
databases for primate (pri), rodent (rod), and other mammalian
sequences (mam), and deduced amino acid sequences from the same
clones were then searched against GenBank functional protein
databases, mammalian (mamp), vertebrate (vrtp), and eukaryote
(eukp) for homology.
IV Northern Analysis
[0286] Northern analysis is a laboratory technique used to detect
the presence of a transcript of a gene and involves the
hybridization of a labeled polynucleotide to a membrane on which
RNAs from a particular cell type or tissue have been bound
(Sambrook, supra).
[0287] Analogous computer techniques use BLAST to search for
identical or related molecules in nucleotide databases such as
GenBank or the LIFESEQ database (Incyte Genomics). This analysis is
much faster than multiple, membrane-based hybridizations. In
addition, the sensitivity of the computer search can be modified to
determine whether any particular match is categorized as exact or
homologous.
[0288] The basis of the search is the product score which is
defined as:
% sequence identitv .times.% maximum BLAST score/100
[0289] The product score takes into account both the degree of
similarity between two sequences and the length of the sequence
match. For example, with a product score of 40, the match will be
exact within a 1-2% error, and at 70, the match will be exact.
Homologous molecules are usually identified by selecting those
which show product scores between 15 and 40, although lower scores
may identify related molecules.
[0290] The results of northern analysis are reported as a list of
libraries in which the transcript encoding HRM occurs. Abundance
and percent abundance are also reported. Abundance directly
reflects the number of times a particular transcript is represented
in a cDNA library, and percent abundance is abundance divided by
the total number of sequences examined in the cDNA library.
V Extension of HRM Encoding Polynucleotides
[0291] The nucleic acid sequence of an Incyte Clone disclosed in
the Sequence Listing was used to design oligonucleotide primers for
extending a partial sequence to full length. One primer was
synthesized to initiate extension in the antisense direction, and
the other was synthesized to extend sequence in the sense
direction. Primers were used to facilitate the extension of the
known sequence "outward" generating amplicons containing new,
unknown nucleotide sequence for the region of interest. The initial
primers were designed from the cDNA using OLIGO software (Molecular
Insights), or another program, to be about 22 to about 30
nucleotides in length, to have a GC content of 50% or more, and to
anneal to the target sequence at temperatures of about 68 to about
72 C. Any stretch of nucleotides which would result in hairpin
structures and primer-primer dimerizations was avoided.
[0292] Selected human cDNA libraries (Life Technologies) were used
to extend the sequence. If more than one extension is necessary or
desired, additional sets of primers are designed to further extend
the known region.
[0293] High fidelity amplification was obtained by following the
instructions for the XL-PCR kit (ABI) and thoroughly mixing the
enzyme and reaction mix. Beginning with 40 pmol of each primer and
the recommended concentrations of all other components of the kit,
PCR was performed using the DNA ENGINE thermal cycler (MJ Research)
and the following parameters: Step 1, 94C for 1 min (initial
denaturation); Step 2, 65C for 1 min; Step 3, 68C for 6 min; Step
4, 94C for 15 sec; Step 5, 65C for 1 min; Step 6, 68C for 7 min;
Step 7, repeat step 4-6 for 15 additional cycles; Step 8, 94C for
15 sec 1 min; Step 10, 68C for 7:15 min; Step 11, repeat step 8-10
for 12 cycles; Step 12, 72C for 13, hold at 4 C.
[0294] A 5-10 .mu.l aliquot of the reaction mixture was analyzed by
electrophoresis on a low concentration (about 0.6-0.8%) agarose
mini-gel to determine which reactions were successful in extending
the sequence. Bands thought to contain the largest products were
excised from the gel, purified using QIAQUICK kit (Qiagen), and
trimmed of overhangs using Klenow enzyme to facilitate religation
and cloning.
[0295] After ethanol precipitation, the products were redissolved
in 13 .mu.l of ligation buffer, 1.mu. iul T4-DNA ligase (15 units)
and 1.mu.l T4 polynucleotide kinase were added, and the mixture was
incubated at room temperature for 2-3 hours or overnight at 16 C.
Competent E. coli cells (in 40 .mu.l of media) were transformed
with 3 .mu.l of ligation mixture and cultured in 80 .mu.l of SOC
medium (Sambrook, supra). After incubation for one hour at 37 C,
the E coli mixture was plated on Luria Bertani (LB)-agar (Sambrook,
supra) containing 2x carbenicillin (Carb). The following day,
several colonies were randomly picked from each plate and cultured
in 150 .mu.l of liquid LB/2= Carb medium placed in an individual
well of a commercially-available, sterile 96-well microtiter plate.
The following day, 5 ,.mu.l of each overnight culture was
transferred into a non-sterile 96-well plate and after dilution
1:10 with water, 5 .mu.l of each sample was transferred into a PCR
array.
[0296] For PCR amplification, 18 ,.mu.l of concentrated PCR
reaction mix (3.3x) containing 4 units of rTth DNA polymerase, a
vector primer, and one or both of the gene specific primers used
for the extension reaction were added to each well. Amplification
was performed using the following conditions: Step 1, 94 C for 60
sec; Step 2, 94 C for 20 sec; Step 3, 55 C for 30 sec; Step 4, 72 C
for 90 sec; Step 5, repeat steps 2-4 for an additional 29 cycles,
Step 6, 72 C for 180 sec, and Step 7, hold at 4 C.
[0297] Aliquots of the PCR reactions were run on agarose gels
together with molecular weight markers. The sizes of the PCR
products were compared to the original partial cDNAs, and clones
were selected, ligated into plasmid, and sequenced.
[0298] In like manner, a genomic library and a polynucleotide
selected from SEQ ID NOs:50-98 is used to obtain 5' regulatory
sequences using the procedure above.
VI Labeling and Use of Individual Hybridization Probes
[0299] Hybridization probes derived from SEQ ID NOs:50-98 are
employed to screen cDNAs, genomic DNAs, or mRNAs. Although the
labeling of oligonucleotides, consisting of about 20 base-pairs, is
specifically described, the same procedure is used with larger
nucleotide fragments. Oligonucleotides are designed using
state-of-the-art software such as OLIGO software (Molecular
Insights), labeled by combining 50 pmol of each oligomer and 250
.mu.Ci of [.gamma.-.sup.32P] adenosine triphosphate (APB) and T4
polynucleotide kinase (NEN Life Science Products, Acton Mass.). The
labeled oligonucleotides are purified using SEPHADEX G-25 superfine
resin column (APB). A aliquot containing 10.sup.7 counts per minute
of the labeled probe is used in a typical membrane-based
hybridization analysis of human genomic DNA digested with one of
the following endonucleases (Ase I, Bgl II, Eco RI, Pst I, Xba 1,
or Pvu II, NEN Life Science Products).
[0300] The DNA from each digest is fractionated on a 0.7 percent
agarose gel and transferred to NYTRANPLUS membranes (Schleicher
& Schuell, Durham NH). Hybridization is carried out for 16
hours at 40 C. To remove nonspecific signals, blots are
sequentially washed at room temperature under increasingly
stringent conditions up to 0.1 .times. saline sodium citrate and
0.5% sodium dodecyl sulfate. After XOMAT AR film (Eastman Kodak,
Rochester N.Y.) is exposed to the blots in a PHOSPHOIMAGER cassette
(APB) for several hours, hybridization patterns are compared
visually.
VII Microarrays
[0301] To produce oligonucleotides for a microarray, SEQ ID
NOs:50-98 are examined using a computer algorithm which starts at
the 3' end of the polynucleotide. The algorithm identified
oligomers of defined length that are unique to the gene, have a GC
content within a range for hybridization, and lack predicted
secondary structure that would interfere with hybridization. The
algorithm identifies approximately 20 sequence-specific
oligonucleotides of 20 nucleotides in length (20-mers). A matched
set of oligonucleotides are created in which one nucleotide in the
center of each sequence is altered. This process is repeated for
each gene in the microarray, and double sets of twenty 20 mers are
synthesized and arranged on the surface of the silicon chip using a
light-directed chemical process (described in PCT/WO95/11995).
[0302] In the alternative, a chemical coupling procedure and an ink
jet device are used to synthesize oligomers on the surface of a
substrate (PCT/WO95/251116). In another alternative, a gridded
array is used to arrange and link cDNA fragments or
oligonucleotides to the surface of a substrate using a vacuum
system, thermal, UV, mechanical, or chemical bonding procedures. A
typical array may be produced by hand or using available materials
and machines and contain grids of 8 dots, 24 dots, 96 dots, 384
dots, 1536 dots or 6144 dots. After hybridization, the microarray
is washed to remove nonhybridized probes, and a scanner is used to
determine the levels and patterns of fluorescence. The scanned
image is examined to determine degree of complementarity and the
relative abundance/expression level of each sequence in the
microarray.
VIII Complementary Polynucleotides
[0303] Sequence complementary to the sequence encoding HRM, or any
part thereof, is used to detect, decrease or inhibit expression of
naturally occurring HRM. Although use of oligonucleotides
comprising from about 15 to about 30 base-pairs is described, the
same procedure is used with smaller or larger sequence fragments.
Oligonucleotides are designed using OLIGO software (Molecular
Insights) and the coding sequence of SEQ ID NOs:50-98. To inhibit
transcription, a complementary oligonucleotide is designed from the
most unique 5' sequence and used to prevent promoter binding to the
coding sequence. To inhibit translation, a complementary
oligonucleotide is designed to prevent ribosomal binding to the
transcript encoding HRM.
IX Expression of HRM
[0304] Expression of HRM is accomplished by subcloning the cDNAs
into vectors and transforming the vectors into host cells. In this
case, the cloning vector is also used to express HRM in E. coli.
Upstream of the cloning site, this vector contains a promoter for
.beta.-galactosidase, followed by sequence containing the
amino-terminal Met, and the subsequent seven residues of
.beta.-galactosidase. Immediately following these eight residues is
a bacteriophage promoter useful for transcription and a linker
containing a number of unique restriction sites.
[0305] Induction of an isolated, transformed bacterial strain with
IPTG using standard methods produces a fusion protein which
consists of the first eight residues of .beta.-galactosidase, about
5 to 15 residues of linker, and the full length protein. The signal
residues direct the secretion of HRM into the bacterial growth
media which can be used directly in the following assay for
activity.
X Demonstration of HRM Activity
[0306] HRM can be expressed in a mammalian cell line such as DLD-1
or HCT116 (ATCC) by transforming the cells with a eukaryotic
expression vector encoding HRM. Eukaryotic expression vectors are
commercially available and the techniques to introduce them into
cells are well known to those skilled in the art. The effect of HRM
on cell morphology may be visualized by microscopy, the effect on
cell growth may be determined by measuring cell doubling-time, and
the effect on tumorigenicity may be assessed by the ability of
transformed cells to grow in a soft agar growth assay (Groden
(1995) Cancer Res 55:1531-1539).
XI Production of HRM Specific Antibodies
[0307] HRM that is purified using PAGE electrophoresis (Sambrook,
supra), or other purification techniques, is used to immunize
rabbits and to produce antibodies using standard protocols. In the
alternative, an amino acid sequence deduced from SEQ ID NOs:50-98
is analyzed using LASERGENE software (DNASTAR, Madison Wis.) to
determine regions of high immunogenicity, and an oligopeptide is
synthesized and used to raise antibodies by means known to those of
skill in the art. Selection of epitope, such as those near the
C-terminus or in hydrophilic regions, is described by Ausubel
(supra).
[0308] Typically, the oligopeptides are 15 residues in length,
synthesized using a 43 1A Peptide synthesizer (ABI) using
Fmoc-chemistry, and coupled to keyhole limpet hemocyanin
(Sigma-Aldrich, St. Louis Mo.) by reaction with
N-maleimidobenzoyl-N-hydroxysuccinimide ester (Ausubel supra).
Rabbits are immunized with the oligopeptide-KLH complex in complete
Freund's adjuvant. The resulting antisera are tested for
antipeptide activity, for example, by binding the protein to a
substrate, blocking with 1% BSA, reacting with rabbit antisera,
washing, and reacting with radio iodinated, goat anti-rabbit
IgG.
XII Purification of Naturally Occurring HRM Using Specific
Antibodies
[0309] Naturally occurring or recombinant HRM is substantially
purified by immunoaffinity chromatography using antibodies specific
for HRM. An immunoaffinity column is constructed by covalently
coupling HRM antibody to an activated chromatographic resin, such
as CNBr-activated SEPHAROSE resin (APB). After the coupling, the
resin is blocked and washed according to the manufacturer's
instructions.
[0310] Media containing HRM is passed over the immunoaffinity
column, and the column is washed under conditions that allow the
preferential absorbance of HRM (e.g., high ionic strength buffers
in the presence of detergent). The column is eluted under
conditions that disrupt antibody/protein binding (eg, a buffer of
pH 2-3 or a high concentration of a chaotrope, such as urea or
thiocyanate ion), and HRM is collected.
XIII Identification of Molecules Which Interact with HRM
[0311] HRM, or biologically active portions thereof, are labeled
with .sup.125I Bolton-Hunter reagent (Bolton et al. (1973) Biochem
J 133:529-39). Candidate molecules previously arrayed in the wells
of a multi-well plate are incubated with the labeled HRM, washed
and any wells with labeled HRM complex are assayed. Data obtained
using different concentrations of HRM are used to calculate values
for the number, affinity, and association of HRM with the candidate
molecules.
[0312] All publications and patents mentioned in the above
specification are herein incorporated by reference. Various
modifications and variations of the described method and system of
the invention will be apparent to those skilled in the art without
departing from the scope and spirit of the invention. Although the
invention has been described in connection with specific preferred
embodiments, it should be understood that the invention as claimed
should not be unduly limited to such specific embodiments. Indeed,
various modifications of the described modes for carrying out the
invention which are obvious to those skilled in molecular biology
or related fields are intended to be within the scope of the
following claims.
Sequence CWU 1
1
* * * * *