U.S. patent application number 10/006163 was filed with the patent office on 2002-07-25 for human short-chain dehydrogenase.
This patent application is currently assigned to Incyte Pharmaceuticals, Inc.. Invention is credited to Corley, Neil C., Lal, Preeti.
Application Number | 20020098474 10/006163 |
Document ID | / |
Family ID | 21792046 |
Filed Date | 2002-07-25 |
United States Patent
Application |
20020098474 |
Kind Code |
A1 |
Lal, Preeti ; et
al. |
July 25, 2002 |
Human short-chain dehydrogenase
Abstract
The invention provides a human short-chain dehydrogenase (HSCD)
and polynucleotides which identify and encode HSCD. The invention
also provides expression vectors, host cells, antibodies, agonists,
and antagonists. The invention also provides methods for treating
or preventing disorders associated with expression of HSCD.
Inventors: |
Lal, Preeti; (Sunnyvale,
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: |
21792046 |
Appl. No.: |
10/006163 |
Filed: |
December 4, 2001 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10006163 |
Dec 4, 2001 |
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09249241 |
Feb 11, 1999 |
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09249241 |
Feb 11, 1999 |
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09019216 |
Feb 5, 1998 |
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Current U.S.
Class: |
435/4 ; 435/190;
435/252.3; 435/320.1; 435/325; 435/6.14; 435/69.1; 536/23.2;
800/8 |
Current CPC
Class: |
C12N 9/001 20130101;
A61K 38/00 20130101 |
Class at
Publication: |
435/4 ; 435/6;
435/69.1; 435/190; 435/320.1; 435/325; 435/252.3; 800/8;
536/23.2 |
International
Class: |
C12Q 001/00; C12Q
001/68; A01K 067/00; C07H 021/04; C12N 009/04; C12P 021/02; C12N
005/06 |
Claims
What is claimed is:
1. An isolated polypeptide selected from the group consisting of:
a) a polypeptide comprising the amino acid sequence of SEQ ID NO:1,
b) a polypeptide comprising a naturally occurring amino acid
sequence at least 90% identical to the amino acid sequence of SEQ
ID NO:1, c) a biologically active fragment of a polypeptide having
the amino acid sequence of SEQ ID NO:1, and d) an immunogenic
fragment of a polypeptide having the amino acid sequence of SEQ ID
NO:1.
2. An isolated polypeptide of claim 1 comprising the amino acid
sequence of SEQ ID NO:1.
3. An isolated polynucleotide encoding a polypeptide of claim
1.
4. An isolated polynucleotide encoding a polypeptide of claim
2.
5. An isolated polynucleotide of claim 4 comprising the
polynucleotide sequence of SEQ ID NO:2.
6. A recombinant polynucleotide comprising a promoter sequence
operably linked to a polynucleotide of claim 3.
7. A cell transformed with a recombinant polynucleotide of claim
6.
8. A transgenic organism comprising a recombinant polynucleotide of
claim 6.
9. A method of producing a polypeptide of claim 1, the method
comprising: a) culturing a cell under conditions suitable for
expression of the polypeptide, wherein said cell is transformed
with a recombinant polynucleotide, and said recombinant
polynucleotide comprises a promoter sequence operably linked to a
polynucleotide encoding the polypeptide of claim 1, and b)
recovering the polypeptide so expressed.
10. A method of claim 9, wherein the polypeptide comprises the
amino acid sequence of SEQ ID NO:1.
11. An isolated antibody which specifically binds to a polypeptide
selected from the group consisting of: a) a polypeptide comprising
the amino acid sequence of SEQ ID NO:1, b) a polypeptide comprising
a naturally occurring amino acid sequence at least 90% identical to
the amino acid sequence of SEQ ID NO:1, c) a biologically active
fragment of a polypeptide having the amino acid sequence of SEQ ID
NO:1, and d) an immunogenic fragment of a polypeptide having the
amino acid sequence of SEQ ID NO:1.
12. An isolated polynucleotide selected from the group consisting
of: a) a polynucleotide comprising the polynucleotide sequence of
SEQ ID NO:2, b) a polynucleotide comprising a naturally occurring
polynucleotide sequence at least 90% identical to the
polynucleotide sequence of SEQ ID NO:2, c) a polynucleotide
complementary to a polynucleotide of a), d) a polynucleotide
complementary to a polynucleotide of b), and e) an RNA equivalent
of a)-d).
13. An isolated polynucleotide comprising at least 60 contiguous
nucleotides of a polynucleotide of claim 12.
14. A method of detecting a target polynucleotide in a sample, said
target polynucleotide having a sequence of a polynucleotide of
claim 12, the method comprising: a) hybridizing the sample with a
probe comprising at least 20 contiguous nucleotides comprising a
sequence complementary to said target polynucleotide in the sample,
and which probe specifically hybridizes to said target
polynucleotide, under conditions whereby a hybridization complex is
formed between said probe and said target polynucleotide or
fragments thereof, and b) detecting the presence or absence of said
hybridization complex, and, optionally, if present, the amount
thereof.
15. A method of claim 14, wherein the probe comprises at least 60
contiguous nucleotides.
16. A method of detecting a target polynucleotide in a sample, said
target polynucleotide having a sequence of a polynucleotide of
claim 12, the method comprising: a) amplifying said target
polynucleotide or fragment thereof using polymerase chain reaction
amplification, and b) detecting the presence or absence of said
amplified target polynucleotide or fragment thereof, and,
optionally, if present, the amount thereof.
17. A composition comprising a polypeptide of claim 1 and a
pharmaceutically acceptable excipient.
18. A composition of claim 17, wherein the polypeptide comprises
the amino acid sequence of SEQ ID NO:1.
19. A method for treating a disease or condition associated with
decreased expression of functional HSCD, comprising administering
to a patient in need of such treatment the composition of claim
17.
20. A method of screening a compound for effectiveness as an
agonist of a polypeptide of claim 1, the method comprising: a)
exposing a sample comprising a polypeptide of claim 1 to a
compound, and b) detecting agonist activity in the sample.
21. A composition comprising an agonist compound identified by a
method of claim 20 and a pharmaceutically acceptable excipient.
22. A method for treating a disease or condition associated with
decreased expression of functional HSCD, comprising administering
to a patient in need of such treatment a composition of claim
21.
23. A method of screening a compound for effectiveness as an
antagonist of a polypeptide of claim 1, the method comprising: a)
exposing a sample comprising a polypeptide of claim 1 to a
compound, and b) detecting antagonist activity in the sample.
24. A composition comprising an antagonist compound identified by a
method of claim 23 and a pharmaceutically acceptable excipient.
25. A method for treating a disease or condition associated with
overexpression of functional HSCD, comprising administering to a
patient in need of such treatment a composition of claim 24.
26. A method of screening for a compound that specifically binds to
the polypeptide of claim 1, the method comprising: a) combining the
polypeptide of claim 1 with at least one test compound under
suitable conditions, and b) detecting binding of the polypeptide of
claim 1 to the test compound, thereby identifying a compound that
specifically binds to the polypeptide of claim 1.
27. A method of screening for a compound that modulates the
activity of the polypeptide of claim 1, the method comprising: a)
combining the polypeptide of claim 1 with at least one test
compound under conditions permissive for the activity of the
polypeptide of claim 1, b) assessing the activity of the
polypeptide of claim 1 in the presence of the test compound, and c)
comparing the activity of the polypeptide of claim 1 in the
presence of the test compound with the activity of the polypeptide
of claim 1 in the absence of the test compound, wherein a change in
the activity of the polypeptide of claim 1 in the presence of the
test compound is indicative of a compound that modulates the
activity of the polypeptide of claim 1.
28. A method of screening a compound for effectiveness in altering
expression of a target polynucleotide, wherein said target
polynucleotide comprises a sequence of claim 5, the method
comprising: a) exposing a sample comprising the target
polynucleotide to a compound, under conditions suitable for the
expression of the target polynucleotide, b) detecting altered
expression of the target polynucleotide, and c) comparing the
expression of the target polynucleotide in the presence of varying
amounts of the compound and in the absence of the compound.
29. A method of assessing toxicity of a test compound, the method
comprising: a) treating a biological sample containing nucleic
acids with the test compound, b) hybridizing the nucleic acids of
the treated biological sample with a probe comprising at least 20
contiguous nucleotides of a polynucleotide of claim 12 under
conditions whereby a specific hybridization complex is formed
between said probe and a target polynucleotide in the biological
sample, said target polynucleotide comprising a polynucleotide
sequence of a polynucleotide of claim 12 or fragment thereof, c)
quantifying the amount of hybridization complex, and d) comparing
the amount of hybridization complex in the treated biological
sample with the amount of hybridization complex in an untreated
biological sample, wherein a difference in the amount of
hybridization complex in the treated biological sample is
indicative of toxicity of the test compound.
30. A diagnostic test for a condition or disease associated with
the expression of HSCD in a biological sample, the method
comprising: a) combining the biological sample with an antibody of
claim 11, under conditions suitable for the antibody to bind the
polypeptide and form an antibody:polypeptide complex, and b)
detecting the complex, wherein the presence of the complex
correlates with the presence of the polypeptide in the biological
sample.
31. The antibody of claim 11, wherein the antibody is: a) a
chimeric antibody, b) a single chain antibody, c) a Fab fragment,
d) a F(ab').sub.2 fragment, or e) a humanized antibody.
32. A composition comprising an antibody of claim 11 and an
acceptable excipient.
33. A method of diagnosing a condition or disease associated with
the expression of HSCD in a subject, comprising administering to
said subject an effective amount of the composition of claim
32.
34. A composition of claim 32, wherein the antibody is labeled.
35. A method of diagnosing a condition or disease associated with
the expression of HSCD in a subject, comprising administering to
said subject an effective amount of the composition of claim
34.
36. A method of preparing a polyclonal antibody with the
specificity of the antibody of claim 11, the method comprising: a)
immunizing an animal with a polypeptide consisting of the amino
acid sequence of SEQ ID NO:1, or an immunogenic fragment thereof,
under conditions to elicit an antibody response, b) isolating
antibodies from said animal, and c) screening the isolated
antibodies with the polypeptide, thereby identifying a polyclonal
antibody which binds specifically to a polypeptide comprising the
amino acid sequence of SEQ ID NO:1.
37. A polyclonal antibody produced by a method of claim 36.
38. A composition comprising the polyclonal antibody of claim 37
and a suitable carrier.
39. A method of making a monoclonal antibody with the specificity
of the antibody of claim 11, the method comprising: a) immunizing
an animal with a polypeptide consisting of the amino acid sequence
of SEQ ID NO:1, or an immunogenic fragment thereof, under
conditions to elicit an antibody response, b) isolating antibody
producing cells from the animal, c) fusing the antibody producing
cells with immortalized cells to form monoclonal antibody-producing
hybridoma cells, d) culturing the hybridoma cells, and e) isolating
from the culture monoclonal antibody which binds specifically to a
polypeptide comprising the amino acid sequence of SEQ ID NO:1.
40. A monoclonal antibody produced by a method of claim 39.
41. A composition comprising the monoclonal antibody of claim 40
and a suitable carrier.
42. The antibody of claim 11, wherein the antibody is produced by
screening a Fab expression library.
43. The antibody of claim 11, wherein the antibody is produced by
screening a recombinant immunoglobulin library.
44. A method of detecting a polypeptide comprising the amino acid
sequence of SEQ ID NO:1 in a sample, the method comprising: a)
incubating the antibody of claim 11 with a sample under conditions
to allow specific binding of the antibody and the polypeptide, and
b) detecting specific binding, wherein specific binding indicates
the presence of a polypeptide comprising the amino acid sequence of
SEQ ID NO:1 in the sample.
45. A method of purifying a polypeptide comprising the amino acid
sequence of SEQ ID NO:1 from a sample, the method comprising: a)
incubating the antibody of claim 11 with a sample under conditions
to allow specific binding of the antibody and the polypeptide, and
b) separating the antibody from the sample and obtaining the
purified polypeptide comprising the amino acid sequence of SEQ ID
NO:1.
46. A microarray wherein at least one element of the microarray is
a polynucleotide of claim 13.
47. A method of generating an expression profile of a sample which
contains polynucleotides, the method comprising: a) labeling the
polynucleotides of the sample, b) contacting the elements of the
microarray of claim 46 with the labeled polynucleotides of the
sample under conditions suitable for the formation of a
hybridization complex, and c) quantifying the expression of the
polynucleotides in the sample.
48. An array comprising different nucleotide molecules affixed in
distinct physical locations on a solid substrate, wherein at least
one of said nucleotide molecules comprises a first oligonucleotide
or polynucleotide sequence specifically hybridizable with at least
30 contiguous nucleotides of a target polynucleotide, and wherein
said target polynucleotide is a polynucleotide of claim 12.
49. An array of claim 48, wherein said first oligonucleotide or
polynucleotide sequence is completely complementary to at least 30
contiguous nucleotides of said target polynucleotide.
50. An array of claim 48, wherein said first oligonucleotide or
polynucleotide sequence is completely complementary to at least 60
contiguous nucleotides of said target polynucleotide.
51. An array of claim 48, wherein said first oligonucleotide or
polynucleotide sequence is completely complementary to said target
polynucleotide.
52. An array of claim 48, which is a microarray.
53. An array of claim 48, further comprising said target
polynucleotide hybridized to a nucleotide molecule comprising said
first oligonucleotide or polynucleotide sequence.
54. An array of claim 48, wherein a linker joins at least one of
said nucleotide molecules to said solid substrate.
55. An array of claim 48, wherein each distinct physical location
on the substrate contains multiple nucleotide molecules, and the
multiple nucleotide molecules at any single distinct physical
location have the same sequence, and each distinct physical
location on the substrate contains nucleotide molecules having a
sequence which differs from the sequence of nucleotide molecules at
another distinct physical location on the substrate.
56. A polypeptide of claim 1, comprising the amino acid sequence of
SEQ ID NO:1.
57. A polynucleotide of claim 12, comprising the polynucleotide
sequence of SEQ ID NO:2.
Description
[0001] This application is a divisional application of U.S.
application Ser. No. 09/249,241, filed Feb. 11, 1999, entitled
HUMAN SHORT-CHAIN DEHYDROGENASE, which is a divisional application
of U.S. application Ser. No. 09/019,216, filed Feb. 5, 1998, which
issued on Jul. 27, 1999 as U.S. Pat. No. 5,928,923, entitled HUMAN
SHORT-CHAIN DEHYDROGENASE. Both of these applications are hereby
expressly incorporated by reference herein.
FIELD OF THE INVENTION
[0002] This invention relates to nucleic acid and amino acid
sequences of a human short-chain dehydrogenase and to the use of
these sequences in the diagnosis, treatment, and prevention of
immune disorders and cancer.
BACKGROUND OF THE INVENTION
[0003] Acetyl CoA is a key intermediate in the mitochondrial
metabolism of pyruvate and fatty acids. Pyruvate, which is
generated in the cytosol during glycolysis, is transported across
the mitochondrial membranes to the interior mitochondrial matrix.
The complete oxidation of pyruvate to form CO.sub.2 and H.sub.2O
occurs in the mitochondrion and utilizes O.sub.2 as the final
electron acceptor (oxidizer). Immediately on entering the matrix,
pyruvate reacts with coenzyme A to form CO.sub.2 and the
intermediate acetyl CoA, a reaction catalyzed by the enzyme
pyruvate dehydrogenase. This reaction is highly exergonic
(.DELTA.G.degree.=-8.0 kcal/mol) and is essentially irreversible.
Pyruvate dehydrogenase is one of the most complex enzymes known.
The molecule is 30 nm in diameter and contains 60 subunits composed
of three different enzymes, several regulatory polypeptides, and
five different coenzymes. Fatty acids are also oxidized in the
mitochondrion to produce acetyl CoA; the energy released is used to
synthesize ATP form ADP and phosphate ion. In eucaryotic cells,
fatty acids containing approximately 20 CH.sub.2 groups are
degraded chiefly in peroxisomes and converted to acetyl CoA.
[0004] Fatty acids are stored as triglycerols, primarily as
droplets in adipose cells. In response to hormones such as
adrenaline, triglycerols are hydrolyzed in the cytosol to free
fatty acids and glycerol. Fatty acids are released into the blood,
where they are taken up and used by most cells. They are the major
energy source for many tissues, in particular, heart muscle. In
humans, the oxidation of fats is quantitatively more important than
the oxidation of glucose as a source of ATP, due to the fact that
oxidation of 1 gram of triacylglycerol to CO.sub.2 generates about
six times as much ATP as does the oxidation of 1 gram of hydrated
glycogen.
[0005] Nicotinamide adenine dinucleotides are involved in a very
large number of oxidoreduction reactions both in the cytosol and in
mitochondria, including the oxidation of the acetyl group of acetyl
CoA to CO.sub.2. In general, nicotinamide adenine dinucleotides are
not tightly bound to enzymes and may function as substrates,
although they are often referred to as coenzymes. Nicotinamide
adenine dinucleotide (NAD.sup.+) and nicotinamide adenine
dinucleotide phosphate (NADP.sup.+) undergo reversible reduction to
NADH and NADPH, respectively, but have different activities in the
cell. The major role of NADH is to transfer electrons from
metabolic intermediates in a large number of biosynthetic processes
into the electron transfer chain. NADPH acts as a reducing agent in
a large number of biosynthetic processes.
[0006] In the cytosol, free fatty acids are linked to coenzyme A to
form an acyl CoA in an energetic reaction coupled to the hydrolysis
of ATP to AMP and inorganic pyrophosphate. The fatty acyl group is
then transported across the inner mitochondrial membrane by a
transporter protein and is reattached to another CoA molecule on
the matrix side. Each molecule of acyl CoA in the mitochondrion is
oxidized to form one molecule of acetyl CoA and an acyl CoA
shortened by two carbon atoms. Concomitantly, NAD.sup.+ and FAD are
reduced to NADH and FADH.sub.2, respectively. This set of reactions
is repeated on the shortened acyl CoA until all carbon atoms are
converted to acetyl CoA. Short-chain acyl-CoA dehydrogenase (SCAD)
is a homotetrameric mitochondrial flavoenzyme that catalyzes the
initial reaction in short-chain fatty acid beta-oxidation. Defects
in the SCAD enzyme are associated with neuromuscular dysfunction.
(See, e.g., Corydon, M. J. et al. (1997) Mamm. Genome
8(12):922-926.)
[0007] The discovery of a new human short-chain dehydrogenase and
the polynucleotides encoding it satisfies a need in the art by
providing new compositions which are useful in the diagnosis,
treatment, and prevention of immune disorders and cancer.
SUMMARY OF THE INVENTION
[0008] The invention features a substantially purified polypeptide,
human short-chain dehydrogenase (HSCD), comprising the amino acid
sequence of SEQ ID NO:1 or a fragment of SEQ ID NO:1.
[0009] The invention further provides a substantially purified
variant having at least 90% amino acid sequence identity to the
amino acid sequence of SEQ ID NO:1 or a fragment of SEQ ID NO:1.
The invention also provides an isolated and purified polynucleotide
encoding the polypeptide comprising the sequence of SEQ ID NO:1 or
a fragment of SEQ ID NO:1. The invention also includes an isolated
and purified polynucleotide variant having at least 90%
polynucleotide sequence identity to the polynucleotide encoding the
polypeptide comprising the amino acid sequence of SEQ ID NO:1 or a
fragment of SEQ ID NO:1.
[0010] Additionally, the invention provides a composition
comprising a polynucleotide encoding the polypeptide comprising the
amino acid sequence of SEQ ID NO:1 or a fragment of SEQ ID NO:1.
The invention further provides an isolated and purified
polynucleotide which hybridizes under stringent conditions to the
polynucleotide encoding the polypeptide comprising the amino acid
sequence of SEQ ID NO:1 or a fragment of SEQ ID NO:1, as well as an
isolated and purified polynucleotide which is complementary to the
polynucleotide encoding the polypeptide comprising the amino acid
sequence of SEQ ID NO:1 or a fragment of SEQ ID NO:1.
[0011] The invention also provides an isolated and purified
polynucleotide comprising the polynucleotide sequence of SEQ ID
NO:2 or a fragment of SEQ ID NO:2, and an isolated and purified
polynucleotide variant having at least 90% polynucleotide sequence
identity to the polynucleotide comprising the polynucleotide
sequence of SEQ ID NO:2 or a fragment of SEQ ID NO:2. The invention
also provides an isolated and purified polynucleotide having a
sequence complementary to the polynucleotide comprising the
polynucleotide sequence of SEQ ID NO:2 or a fragment of SEQ ID
NO:2.
[0012] The invention further provides an expression vector
containing at least a fragment of the polynucleotide encoding the
polypeptide comprising the sequence of SEQ ID NO:1 or a fragment of
SEQ ID NO:1. In another aspect, the expression vector is contained
within a host cell.
[0013] The invention also provides a method for producing a
polypeptide comprising the amino acid sequence of SEQ ID NO:1 or a
fragment of SEQ ID NO:1, the method comprising the steps of: (a)
culturing the host cell containing an expression vector containing
at least a fragment of a polynucleotide encoding the polypeptide
comprising the amino acid sequence of SEQ ID NO:1 or a fragment of
SEQ ID NO:1 under conditions suitable for the expression of the
polypeptide; and (b) recovering the polypeptide from the host cell
culture.
[0014] The invention also provides a pharmaceutical composition
comprising a substantially purified polypeptide having the sequence
of SEQ ID NO:1 or a fragment of SEQ ID NO:1 in conjunction with a
suitable pharmaceutical carrier.
[0015] The invention further includes a purified antibody which
binds to a polypeptide comprising the sequence of SEQ ID NO:1 or a
fragment of SEQ ID NO:1, as well as a purified agonist and a
purified antagonist of the polypeptide.
[0016] The invention also provides a method for treating or
preventing a cancer, the method comprising administering to a
subject in need of such treatment an effective amount of an
antagonist of the polypeptide having the amino acid sequence of SEQ
ID NO:1 or a fragment of SEQ ID NO:1.
[0017] The invention also provides a method for treating or
preventing an immune disorder, the method comprising administering
to a subject in need of such treatment an effective amount of a
pharmaceutical composition comprising substantially purified
polypeptide having the amino acid sequence of SEQ ID NO:1 or a
fragment of SEQ ID NO:1, an antagonist of the polypeptide having
the amino acid sequence of SEQ ID NO:1 or a fragment of SEQ ID
NO:1.
[0018] The invention also provides a method for detecting a
polynucleotide encoding a polypeptide comprising the amino acid
sequence of SEQ ID NO:1 or a fragment of SEQ ID NO:1 in a
biological sample containing nucleic acids, the method comprising
the steps of: (a) hybridizing the complement of the polynucleotide
encoding the polypeptide comprising the amino acid sequence of SEQ
ID NO:1 or a fragment of SEQ ID NO:1 to at least one of the nucleic
acids of the biological sample, thereby forming a hybridization
complex; and (b) detecting the hybridization complex, wherein the
presence of the hybridization complex correlates with the presence
of a polynucleotide encoding the polypeptide comprising the amino
acid sequence of SEQ ID NO:1 or a fragment of SEQ ID NO:1 in the
biological sample. In one aspect, the nucleic acids of the
biological sample are amplified by the polymerase chain reaction
prior to the hybridizing step.
BRIEF DESCRIPTION OF THE FIGURES
[0019] FIGS. 1A, 1B, 1C, and 1D show the amino acid sequence (SEQ
ID NO:1) and nucleic acid sequence (SEQ ID NO:2) of HSCD. The
alignment was produced using MACDNASIS PRO software (Hitachi
Software Engineering Co. Ltd., San Bruno, Calif.).
[0020] FIG. 2 shows the amino acid sequence alignments between HSCD
(356351; SEQ ID NO:1) and short-chain acyl-CoA dehydrogenase from
Caenorhabditis elegans (GI 2315796; SEQ ID NO:3), produced using
the multisequence alignment program of DNASTAR software (DNASTAR
Inc., Madison Wis.).
DESCRIPTION OF THE INVENTION
[0021] Before the present proteins, nucleotide sequences, and
methods are described, it is understood that this invention is not
limited to the particular methodology, protocols, cell lines,
vectors, and reagents described, as these may vary. It is also to
be understood that the terminology used herein is for the purpose
of describing particular embodiments only, and is not intended to
limit the scope of the present invention which will be limited only
by the appended claims.
[0022] It must be noted that as used herein and in the appended
claims, the singular forms "a," "an," and "the" include plural
reference unless the context clearly dictates otherwise. Thus, for
example, a reference to "a host cell" includes a plurality of such
host cells, and a reference to "an antibody" is a reference to one
or more antibodies and equivalents thereof known to those skilled
in the art, and so forth.
[0023] Unless defined otherwise, all technical and scientific terms
used herein have the same meanings as commonly understood by one of
ordinary skill in the art to which this invention belongs. Although
any methods and materials similar or equivalent to those described
herein can be used in the practice or testing of the present
invention, the preferred methods, devices, and materials are now
described. All publications mentioned herein are cited for the
purpose of describing and disclosing the cell lines, vectors, 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.
[0024] Definitions
[0025] "HSCD," as used herein, refers to the amino acid sequences
of substantially purified HSCD obtained from any species,
particularly a mammalian species, including bovine, ovine, porcine,
murine, equine, and preferably the human species, from any source,
whether natural, synthetic, semi-synthetic, or recombinant.
[0026] The term "agonist," as used herein, refers to a molecule
which, when bound to HSCD, increases or prolongs the duration of
the effect of HSCD. Agonists may include proteins, nucleic bib
acids, carbohydrates, or any other molecules which bind to and
modulate the effect of HSCD.
[0027] An "allele" or an "allelic sequence," as these terms are
used herein, is an alternative form of the gene encoding HSCD.
Alleles may result from at least one mutation in the nucleic acid
sequence and may result in altered mRNAs or in polypeptides whose
structure or function may or may not be altered. Any given natural
or recombinant gene may have none, one, or many allelic forms.
Common mutational changes which give rise to alleles are generally
ascribed to natural deletions, additions, 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.
[0028] "Altered" nucleic acid sequences encoding HSCD, as described
herein, include those sequences with deletions, insertions, or
substitutions of different nucleotides, resulting in a
polynucleotide the same HSCD or a polypeptide with at least one
functional characteristic of HSCD. Included within this definition
are polymorphisms which may or may not be readily detectable using
a particular oligonucleotide probe of the polynucleotide encoding
HSCD, and improper or unexpected hybridization to alleles, with a
locus other than the normal chromosomal locus for the
polynucleotide sequence encoding HSCD. The encoded protein may also
be "altered," and may contain deletions, insertions, or
substitutions of amino acid residues which produce a silent change
and result in a functionally equivalent HSCD. Deliberate amino acid
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 HSCD is retained. For example, negatively
charged amino acids may include aspartic acid and glutamic acid,
positively charged amino acids may include lysine and arginine, and
amino acids with uncharged polar head groups having similar
hydrophilicity values may include leucine, isoleucine, and valine;
glycine and alanine; asparagine and glutamine; serine and
threonine; and phenylalanine and tyrosine.
[0029] The terms "amino acid" or "amino acid sequence," as used
herein, refer to an oligopeptide, peptide, polypeptide, or protein
sequence, or a fragment of any of these, and to naturally occurring
or synthetic molecules. In this context, "fragments", "immunogenic
fragments", or "antigenic fragments" refer to fragments of HSCD
which are preferably about 5 to about 15 amino acids in length and
which retain some biological activity or immunological activity of
HSCD. Where "amino acid sequence" is recited herein to refer to an
amino acid sequence of a naturally occurring protein molecule,
"amino acid sequence" and like terms are not meant to limit the
amino acid sequence to the complete native amino acid sequence
associated with the recited protein molecule.
[0030] "Amplification," as used herein, relates to the production
of additional copies of a nucleic acid sequence. Amplification is
generally carried out using polymerase chain reaction (PCR)
technologies well known in the art. (See, e.g., Dieffenbach, C. W.
and G. S. Dveksler (1995) PCR Primer, a Laboratory Manual, Cold
Spring Harbor Press, Plainview, N.Y., pp.1-5.)
[0031] The term "antagonist," as it is used herein, refers to a
molecule which, when bound to HSCD, decreases the amount or the
duration of the effect of the biological or immunological activity
of HSCD. Antagonists may include proteins, nucleic acids,
carbohydrates, antibodies, or any other molecules which decrease
the effect of HSCD.
[0032] As used herein, the term "antibody" refers to intact
molecules as well as to fragments thereof, such as Fab,
F(ab').sub.2, and Fv fragments, which are capable of binding the
epitopic determinant. Antibodies that bind HSCD polypeptides can be
prepared using intact polypeptides or using fragments containing
small peptides of interest as the immunizing antigen. The
polypeptide or oligopeptide used to immunize an animal (e.g., a
mouse, a rat, or a rabbit) can be derived from the translation of
RNA, or synthesized chemically, and can be conjugated to a carrier
protein if desired. Commonly used carriers that are chemically
coupled to peptides include bovine serum albumin, thyroglobulin,
and keyhole limpet hemocyanin (KLH). The coupled peptide is then
used to immunize the animal.
[0033] The term "antigenic determinant," as used herein, refers to
that fragment of a molecule (i.e., an epitope) that makes contact
with a particular antibody. When a protein or a fragment of a
protein is used to immunize a host animal, numerous regions of the
protein may induce the production of antibodies which bind
specifically to antigenic determinants (given regions or
three-dimensional structures on the protein). An antigenic
determinant may compete with the intact antigen (i.e., the
immunogen used to elicit the immune response) for binding to an
antibody.
[0034] The term "antisense," as used herein, refers to any
composition containing a nucleic acid sequence which is
complementary to a specific nucleic acid sequence. The term
"antisense strand" is used in reference to a nucleic acid strand
that is complementary to the "sense" strand. Antisense molecules
may be produced by any method including synthesis or transcription.
Once introduced into a cell, the complementary nucleotides combine
with natural sequences produced by the cell to form duplexes and to
block either transcription or translation. The designation
"negative" can refer to the antisense strand, and the designation
"positive" can refer to the sense strand.
[0035] As used herein, the term "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
HSCD, or of any oligopeptide thereof, to induce a specific immune
response in appropriate animals or cells and to bind with specific
antibodies.
[0036] The terms "complementary" or "complementarity," as used
herein, refer 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." Complementarity between two single-stranded molecules may
be "partial," such that only some of the nucleic acids bind, or it
may be "complete," such that total complementarity exists between
the single stranded molecules. The degree of complementarity
between nucleic acid strands has significant effects on the
efficiency and strength of the hybridization between the nucleic
acid strands. This is of particular importance in amplification
reactions, which depend upon binding between nucleic acids strands,
and in the design and use of peptide nucleic acid (PNA)
molecules.
[0037] A "composition comprising a given polynucleotide sequence"
or a "composition comprising a given amino acid sequence," as these
terms are used herein, refer broadly to any composition containing
the given polynucleotide or amino acid sequence. The composition
may comprise a dry formulation, an aqueous solution, or a sterile
composition. Compositions comprising polynucleotide sequences
encoding HSCD or fragments of HSCD may be employed as hybridization
probes. The probes may be stored in freeze-dried form and may be
associated with a stabilizing agent such as a carbohydrate. In
hybridizations, the probe may be deployed in an aqueous solution
containing salts (e.g., NaCl), detergents (e.g., SDS), and other
components (e.g., Denhardt's solution, dry milk, salmon sperm DNA,
etc.).
[0038] The phrase "consensus sequence," as used herein, refers to a
nucleic acid sequence which has been resequenced to resolve
uncalled bases, extended using XL-PCR (Perkin Elmer, Norwalk,
Conn.) in the 5' and/or the 3' direction, and resequenced, or which
has been assembled from the overlapping sequences of more than one
Incyte Clone using a computer program for fragment assembly, such
as the GELVIEW fragment assembly system (GCG, Madison, Wis.). Some
sequences have been both extended and assembled to produce the
consensus sequence.
[0039] As used herein, the term "correlates with expression of a
polynucleotide" indicates that the detection of the presence of
nucleic acids, the same or related to a nucleic acid sequence
encoding HSCD, by northern analysis is indicative of the presence
of nucleic acids encoding HSCD in a sample, and thereby correlates
with expression of the transcript from the polynucleotide encoding
HSCD.
[0040] A "deletion," as the term is used herein, refers to a change
in the amino acid or nucleotide sequence that results in the
absence of one or more amino acid residues or nucleotides.
[0041] The term "derivative," as used herein, refers to the
chemical modification of HSCD, of a polynucleotide sequence
encoding HSCD, or of a polynucleotide sequence complementary to a
polynucleotide sequence encoding HSCD. Chemical modifications of a
polynucleotide sequence can include, for example, replacement of
hydrogen by an alkyl, acyl, or amino group. A derivative
polynucleotide encodes a polypeptide which retains at least one
biological or immunological function of the natural molecule. A
derivative polypeptide is one modified by glycosylation,
pegylation, or any similar process that retains at least one
biological or immunological function of the polypeptide from which
it was derived.
[0042] The term "homology," as used herein, refers to a degree of
complementarity. There may be partial homology or complete
homology. The word "identity" may substitute for the word
"homology." A partially complementary sequence that at least
partially inhibits an identical sequence from hybridizing to a
target nucleic acid is referred to as "substantially homologous."
The inhibition of hybridization of the completely complementary
sequence to the target sequence may be examined using a
hybridization assay (Southern or northern blot, solution
hybridization, and the like) under conditions of reduced
stringency. A substantially homologous sequence or hybridization
probe will compete for and inhibit the binding of a completely
homologous sequence to the target sequence under conditions of
reduced stringency. This is not to say that conditions of reduced
stringency are such that non-specific binding is permitted, as
reduced stringency conditions require that the binding of two
sequences to one another be a specific (i.e., a selective)
interaction. The absence of non-specific binding may be tested by
the use of a second target sequence which lacks even a partial
degree of complementarity (e.g., less than about 30% homology or
identity). In the absence of non-specific binding, the
substantially homologous sequence or probe will not hybridize to
the second non-complementary target sequence.
[0043] The phrases "percent identity" or "% identity" refer to the
percentage of sequence similarity found in a comparison of two or
more amino acid or nucleic acid sequences. Percent identity can be
determined electronically, e.g., by using the MEGALIGN program
(DNASTAR, Inc., Madison Wis.). The MEGALIGN program can create
alignments between two or more sequences according to different
methods, e.g., the Clustal method. (See, e.g., Higgins, D. G. and
P. M. Sharp (1988) Gene 73:237-244.) The Clustal algorithm groups
sequences into clusters by examining the distances between all
pairs. The clusters are aligned pairwise and then in groups. The
percentage similarity between two amino acid sequences, e.g.,
sequence A and sequence B, is calculated by dividing the length of
sequence A, minus the number of gap residues in sequence A, minus
the number of gap residues in sequence B, into the sum of the
residue matches between sequence A and sequence B, times one
hundred. Gaps of low or of no homology between the two amino acid
sequences are not included in determining percentage similarity.
Percent identity between nucleic acid sequences can also be counted
or calculated by other methods known in the art, e.g., the Jotun
Hein method. (See, e.g., Hein, J. (1990) Methods Enzymol.
183:626-645.) Identity between sequences can also be determined by
other methods known in the art, e.g., by varying hybridization
conditions.
[0044] "Human artificial chromosomes" (HACs), as described herein,
are linear microchromosomes which may contain DNA sequences of
about 6 kb to 10 Mb in size, and which contain all of the elements
required for stable mitotic chromosome segregation and maintenance.
(See, e.g., Harrington, J. J. et al. (1997) Nat. Genet.
15:345-355.)
[0045] The term "humanized antibody," as used herein, refers to
antibody molecules in which the amino acid sequence in the
non-antigen binding regions has been altered so that the antibody
more closely resembles a human antibody, and still retains its
original binding ability.
[0046] "Hybridization," as the term is used herein, refers to any
process by which a strand of nucleic acid binds with a
complementary strand through base pairing.
[0047] As used herein, the term "hybridization complex" as used
herein, refers to a complex formed between two nucleic acid
sequences by virtue of the formation of hydrogen bonds between
complementary bases. A hybridization complex may be formed in
solution (e.g., C.sub.0t or R.sub.0t analysis) or formed between
one nucleic acid sequence present in solution and another nucleic
acid sequence immobilized on a solid support (e.g., paper,
membranes, filters, chips, pins or glass slides, or any other
appropriate substrate to which cells or their nucleic acids have
been fixed).
[0048] The words "insertion" or "addition," as used herein, refer
to changes in an amino acid or nucleotide sequence resulting in the
addition of one or more amino acid residues or nucleotides,
respectively, to the sequence found in the naturally occurring
molecule.
[0049] "Immune response" can refer to conditions associated with
inflammation, trauma, immune disorders, or infectious or genetic
disease, etc. These conditions can be characterized by expression
of various factors, e.g., cytokines, chemokines, and other
signaling molecules, which may affect cellular and systemic defense
systems.
[0050] The term "microarray," as used herein, refers to an
arrangement of distinct polynucleotides arrayed on a substrate,
e.g., paper, nylon or any other type of membrane, filter, chip,
glass slide, or any other suitable solid support.
[0051] The terms "element" or "array element" as used herein in a
microarray context, refer to hybridizable polynucleotides arranged
on the surface of a substrate.
[0052] The term "modulate," as it appears herein, refers to a
change in the activity of HSCD. For example, modulation may cause
an increase or a decrease in protein activity, binding
characteristics, or any other biological, functional, or
immunological properties of HSCD.
[0053] The phrases "nucleic acid" or "nucleic acid sequence," as
used herein, refer to an oligonucleotide, nucleotide,
polynucleotide, or any fragment thereof, to DNA or RNA of genomic
or synthetic origin which may be single-stranded or double-stranded
and may represent the sense or the antisense strand, to peptide
nucleic acid (PNA), or to any DNA-like or RNA-like material. In
this context, "fragments" refers to those nucleic acid sequences
which are greater than about 60 nucleotides in length, and most
preferably are at least about 100 nucleotides, at least about 1000
nucleotides, or at least about 10,000 nucleotides in length.
[0054] The terms "operably associated" or "operably linked," as
used herein, refer to functionally related nucleic acid sequences.
A promoter is operably associated or operably linked with a coding
sequence if the promoter controls the transcription of the encoded
polypeptide. While operably associated or operably linked nucleic
acid sequences can be contiguous and in reading frame, certain
genetic elements, e.g., repressor genes, are not contiguously
linked to the encoded polypeptide but still bind to operator
sequences that control expression of the polypeptide.
[0055] The term "oligonucleotide," as used herein, refers to a
nucleic acid sequence of at least about 6 nucleotides to 60
nucleotides, preferably about 15 to 30 nucleotides, and most
preferably about 20 to 25 nucleotides, which can be used in PCR
amplification or in a hybridization assay or microarray. As used
herein, the term "oligonucleotide" is substantially equivalent to
the terms "amplimer," "primer," "oligomer," and "probe," as these
terms are commonly defined in the art.
[0056] "Peptide nucleic acid" (PNA), as used herein, refers to an
antisense molecule or anti-gene agent which comprises an
oligonucleotide of at least about 5 nucleotides in length linked to
a peptide backbone of amino acid residues ending in lysine. The
terminal lysine confers solubility to the composition. PNAs
preferentially bind complementary single stranded DNA and RNA and
stop transcript elongation, and may be pegylated to extend their
lifespan in the cell. (See, e.g., Nielsen, P. E. et al. (1993)
Anticancer Drug Des. 8:53-63.)
[0057] The term "sample," as used herein, is used in its broadest
sense. A biological sample suspected of containing nucleic acids
encoding HSCD, or fragments thereof, or HSCD itself, may comprise a
bodily fluid; an 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;
etc.
[0058] As used herein, the terms "specific binding" or
"specifically binding" refer to that interaction between a protein
or peptide and an agonist, an antibody, or an antagonist. The
interaction is dependent upon the presence of a particular
structure of the protein, e.g., the antigenic determinant or
epitope, recognized by the binding molecule. For example, if an
antibody is specific for epitope "A," the presence of a polypeptide
containing the epitope A, or the presence of free unlabeled A, in a
reaction containing free labeled A and the antibody will reduce the
amount of labeled A that binds to the antibody.
[0059] As used herein, the term "stringent conditions" refers to
conditions which permit hybridization between polynucleotide
sequences and the claimed polynucleotide sequences. Suitably
stringent conditions can be defined by, for example, the
concentrations of salt or formamide in the prehybridization and
hybridization solutions, or by the hybridization temperature, and
are well known in the art. In particular, stringency can be
increased by reducing the concentration of salt, increasing the
concentration of formamide, or raising the hybridization
temperature.
[0060] For example, hybridization under high stringency conditions
could occur in about 50% formamide at about 37.degree. C. to
42.degree. C. Hybridization could occur under reduced stringency
conditions in about 35% to 25% formamide at about 30.degree. C. to
35.degree. C. In particular, hybridization could occur under high
stringency conditions at 42.degree. C. in 50% formamide,
5.times.SSPE, 0.3% SDS, and 200 .mu.g/ml sheared and denatured
salmon sperm DNA. Hybridization could occur under reduced
stringency conditions as described above, but in 35% formamide at a
reduced temperature of 35.degree. C. The temperature range
corresponding to a particular level of stringency can be further
narrowed by calculating the purine to pyrimidine ratio of the
nucleic acid of interest and adjusting the temperature accordingly.
Variations on the above ranges and conditions are well known in the
art.
[0061] The term "substantially purified," as used herein, refers to
nucleic acid or amino acid sequences that are removed from their
natural environment and are isolated or separated, and are at least
about 60% free, preferably about 75% free, and most preferably
about 90% free from other components with which they are naturally
associated.
[0062] A "substitution," as used herein, refers to the replacement
of one or more amino acids or nucleotides by different amino acids
or nucleotides, respectively.
[0063] "Transformation," as defined herein, describes a process by
which exogenous DNA enters and changes a recipient cell.
Transformation may occur under natural or artificial conditions
according to various methods well known in the art, and may rely on
any known method for the insertion of foreign nucleic acid
sequences into a prokaryotic or eukaryotic host cell. The method
for transformation is selected based on the type of host cell being
transformed and may include, but is not limited to, viral
infection, electroporation, heat shock, lipofection, and particle
bombardment. The term "transformed" cells includes stably
transformed cells in which the inserted DNA is capable of
replication either as an autonomously replicating plasmid or as
part of the host chromosome, as well as transiently transformed
cells which express the inserted DNA or RNA for limited periods of
time.
[0064] A "variant" of HSCD, as used herein, refers to an amino acid
sequence that is altered by one or more amino acids. The variant
may have "conservative" changes, wherein a substituted amino acid
has similar structural or chemical properties (e.g., replacement of
leucine with isoleucine). More rarely, a variant may have
"nonconservative" changes (e.g., replacement of glycine with
tryptophan). Analogous minor variations may also include amino acid
deletions or insertions, or both. Guidance in determining which
amino acid residues may be substituted, inserted, or deleted
without abolishing biological or immunological activity may be
found using computer programs well known in the art, for example,
DNASTAR software.
[0065] The Invention
[0066] The invention is based on the discovery of a new human
short-chain dehydrogenase (HSCD), the polynucleotides encoding
HSCD, and the use of these compositions for the diagnosis,
treatment, or prevention of immune disorders and cancer.
[0067] Nucleic acids encoding the HSCD of the present invention
were first identified in Incyte Clone 356351 from the prostate cDNA
library (PROSNOT01) using a computer search for amino acid sequence
alignments. A consensus sequence, SEQ ID NO:2, was derived from the
following overlapping and/or extended nucleic acid sequences:
Incyte Clones 356351 (PROSNOT01), 1852929 (LUNGFET03), 2118849 and
2117677 (BRSTTUT02), and 1233166 (LUNGFET03).
[0068] In one embodiment, the invention encompasses a polypeptide
comprising the amino acid sequence of SEQ ID NO:1, as shown in
FIGS. 1A, 1B, 1C, and 1D. HSCD is 313 amino acids in length and has
four potential casein kinase II phosphorylation sites at residues
S.sub.65, T.sub.73, S.sub.114, and S.sub.224; one potential
glycosaminoglycan attachment site at residue S.sub.286; one
potential microbodies C-terminal targeting signal site at residue
S.sub.311; four potential N-myristoylation sites at residues
G.sub.14, G.sub.18, G.sub.164, and G.sub.194; and five potential
protein kinase C phosphorylation sites at residues T.sub.37,
T.sub.43, S.sub.232, S.sub.249, and T.sub.310. As shown in FIG. 2,
HSCD has chemical and structural homology with short-chain acyl CoA
dehydrogenase (GI 2315796; SEQ ID NO:3). In particular, HSCD and
short-chain acyl-CoA dehydrogenase share 43% identity, the
N-myristoylation sites at residues G.sub.14 and G.sub.18, and the
protein kinase C phosphorylation sites at residues T.sub.37 and
S.sub.249. The fragments of SEQ ID NO:2 from about C.sub.277 to
about G.sub.286 and from about C.sub.277 to about G.sub.286 are
useful as hybridization probes. Northern analysis shows the
expression of this sequence in various libraries, at least 50% of
which are immortalized or cancerous and at least 27% of which
involve the immune response. Of particular note is the expression
of HSCD in reproductive tissue libraries.
[0069] The invention also encompasses HSCD variants. A preferred
HSCD variant is one which has at least about 80%, more preferably
at least about 90%, and most preferably at least about 95% amino
acid sequence identity to the HSCD amino acid sequence, and which
contains at least one functional or structural characteristic of
HSCD.
[0070] The invention also encompasses polynucleotides which encode
HSCD. In a particular embodiment, the invention encompasses a
polynucleotide sequence comprising the sequence of SEQ ID NO:2,
which encodes an HSCD.
[0071] The invention also encompasses a variant of a polynucleotide
sequence encoding HSCD. In particular, such a variant
polynucleotide sequence will have at least about 80%, more
preferably at least about 90%, and most preferably at least about
95% polynucleotide sequence identity to the polynucleotide sequence
encoding HSCD. A particular aspect of the invention encompasses a
variant of SEQ ID NO:2 which has at least about 80%, more
preferably at least about 90%, and most preferably at least about
95% polynucleotide sequence identity to SEQ ID NO:2. Any one of the
polynucleotide variants described above can encode an amino acid
sequence which contains at least one functional or structural
characteristic of HSCD.
[0072] It will be appreciated by those skilled in the art that as a
result of the degeneracy of the genetic code, a multitude of
polynucleotide sequences encoding HSCD, some bearing minimal
homology to the polynucleotide sequences of any known and naturally
occurring gene, may be produced. Thus, the invention contemplates
each and every possible variation of polynucleotide sequence 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
sequence of naturally occurring HSCD, and all such variations are
to be considered as being specifically disclosed.
[0073] Although nucleotide sequences which encode HSCD and its
variants are preferably capable of hybridizing to the nucleotide
sequence of the naturally occurring HSCD under appropriately
selected conditions of stringency, it may be advantageous to
produce nucleotide sequences encoding HSCD or its derivatives
possessing a substantially 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 substantially altering the nucleotide
sequence encoding HSCD 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.
[0074] The invention also encompasses production of DNA sequences
which encode HSCD and HSCD derivatives, or fragments thereof,
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 HSCD or any fragment
thereof.
[0075] Also encompassed by the invention are polynucleotide
sequences that are capable of hybridizing to the claimed
polynucleotide sequences, and, in particular, to those shown in SEQ
ID NO:2, or a fragment of SEQ ID NO:2, under various conditions of
stringency. (See, e.g., Wahl, G. M. and S. L. Berger (1987) Methods
Enzymol. 152:399-407; and Kimmel, A. R. (1987) Methods Enzymol.
152:507-511.)
[0076] Methods for DNA sequencing 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 (US
Biochemical Corp., Cleveland, Ohio), Taq polymerase (Perkin Elmer),
thermostable T7 polymerase (Amersham, Chicago, Ill.), or
combinations of polymerases and proofreading exonucleases such as
those found in the ELONGASE amplification system (GIBCO/BRL,
Gaithersburg, Md.). Preferably, the process is automated with
machines such as the MICROLAB 2200 (Hamilton, Reno, Nev.), Peltier
thermal cycler (PTC200; M J Research, Watertown, Mass.), and the
ABI Catalyst and 373 and 377 DNA sequencers (Perkin Elmer).
[0077] The nucleic acid sequences encoding HSCD 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. (See, e.g.,
Sarkar, G. (1993) PCR Methods Applic. 2:318-322.) In particular,
genomic DNA is first amplified in the presence of a primer which is
complementary to a linker sequence within the vector and a primer
specific to a region of the nucleotide sequenc. 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
appropriate RNA polymerase and sequenced using reverse
transcriptase.
[0078] Inverse PCR may also be used to amplify or extend sequences
using divergent primers based on a known region. (See, e.g.,
Triglia, T. et al. (1988) Nucleic Acids Res. 16:8186.) The primers
may be designed using commercially available software such as OLIGO
4.06 primer analysis software (National Biosciences Inc., Plymouth,
Minn.) or another appropriate program to be about 22 to 30
nucleotides in length, to have a GC content of about 50% or more,
and to anneal to the target sequence at temperatures of about
68.degree. C. to 72.degree. C. The method uses several restriction
enzymes to generate a suitable fragment in the known region of a
gene. The fragment is then circularized by intramolecular ligation
and used as a PCR template.
[0079] 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. (See, e.g.,
Lagerstrom, M. et al. (1991) PCR Methods Applic. 1:111-119.) In
this method, multiple restriction enzyme digestions and ligations
may be used to place an engineered double-stranded sequence into an
unknown fragment of the DNA molecule before performing PCR. Other
methods which may be used to retrieve unknown sequences are known
in the art. (See, e.g., Parker, J. D. et al. (1991) Nucleic Acids
Res. 19:3055-3060.) Additionally, one may use PCR, nested primers,
and PROMOTERFINDER libraries to walk genomic DNA (Clontech, Palo
Alto, Calif.). This process avoids the need to screen libraries and
is useful in finding intron/exon junctions.
[0080] 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
include 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.
[0081] Capillary electrophoresis systems which are commercially
available may be used to analyze if the size or confirm the
nucleotide 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 a charge
coupled device camera for detection of the emitted wavelengths.
Output/light intensity may be converted to electrical signal using
appropriate software (e.g., GENOTYPER and SEQUENCE NAVIGATOR,
Perkin Elmer), 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.
[0082] In another embodiment of the invention, polynucleotide
sequences or fragments thereof which encode HSCD may be used in
recombinant DNA molecules to direct expression of HSCD, or
fragments or functional equivalents thereof, in appropriate host
cells. Due to the inherent degeneracy of the genetic code, other
DNA sequences which encode substantially the same or a functionally
equivalent amino acid sequence may be produced, and these sequences
may be used to clone and express HSCD.
[0083] As will be understood by those of skill in the art, it may
be advantageous to produce HSCD-encoding nucleotide sequences
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.
[0084] The nucleotide sequences of the present invention can be
engineered using methods generally known in the art in order to
alter HSCD-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 nucleotide
sequences. 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.
[0085] In another embodiment of the invention, natural, modified,
or recombinant nucleic acid sequences encoding HSCD may be ligated
to a heterologous sequence to encode a fusion protein. For example,
to screen peptide libraries for inhibitors of HSCD activity, it may
be useful to encode a chimeric HSCD protein that can be recognized
by a commercially available antibody. A fusion protein may also be
engineered to contain a cleavage site located between the HSCD
encoding sequence and the heterologous protein sequence, so that
HSCD may be cleaved and purified away from the heterologous
moiety.
[0086] In another embodiment, sequences encoding HSCD may be
synthesized, in whole or in part, using chemical methods well known
in the art. (See, e.g., Caruthers, M. H. et al. (1980) Nucleic
Acids Symp. Ser. 7:215-223, and Horn, T. 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 HSCD, or a fragment thereof. For example, peptide
synthesis can be performed using various solid-phase techniques.
(See, e.g., Roberge, J. Y. et al. (1995) Science 25 269:202-204.)
Automated synthesis may be achieved using the ABI 431A peptide
synthesizer (Perkin Elmer). Additionally, the amino acid sequence
of HSCD, or any part thereof, may be altered during direct
synthesis and/or combined with sequences from other proteins, or
any part thereof, to produce a variant polypeptide.
[0087] The peptide may be substantially purified by preparative
high performance liquid chromatography. (See, e.g, Chiez, R. M. and
F. Z. Regnier (1990) Methods Enzymol. 182:392-421.) The composition
of the synthetic peptides may be confirmed by amino acid analysis
or by sequencing. (See, e.g., Creighton, T. (1983) Proteins,
Structures and Molecular Properties, WH Freeman and Co., New York,
N.Y.)
[0088] In order to express a biologically active HSCD, the
nucleotide sequences encoding HSCD or derivatives thereof may be
inserted into appropriate expression vector, i.e., a vector which
contains the necessary elements for the transcription and
translation of the inserted coding sequence.
[0089] Methods which are well known to those skilled in the art may
be used to construct expression vectors containing sequences
encoding HSCD and appropriate transcriptional and translational
control elements. These methods include in vitro recombinant DNA
techniques, synthetic techniques, and in vivo genetic
recombination. (See, e.g., Sambrook, J. et al. (1989) Molecular
Cloning, A Laboratory Manual, Cold Spring Harbor Press, Plainview,
N.Y., ch. 4, 8, and 16-17; and Ausubel, F. M. et al. (1995, and
periodic supplements) Current Protocols in Molecular Biology, John
Wiley & Sons, New York, N.Y., ch. 9, 13, and 16.)
[0090] A variety of expression vector/host systems may be utilized
to contain and express sequences encoding HSCD. 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 virus expression vectors (e.g.,
baculovirus); plant cell systems transformed with virus expression
vectors (e.g., cauliflower mosaic virus (CaMV) or tobacco mosaic
virus (TMV)) or with bacterial expression vectors (e.g., Ti or
pBR322 plasmids); or animal cell systems. The invention is not
limited by the host cell employed.
[0091] The "control elements" or "regulatory sequences" are those
non-translated regions, e.g., enhancers, promoters, and 5' and 3'
untranslated regions, of the vector and polynucleotide sequences
encoding HSCD 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 suitable transcription and translation
elements, including constitutive and inducible promoters, may be
used. For example, when cloning in bacterial systems, inducible
promoters, e.g., hybrid lacZ promoter of the BLUESCRIPT phagemid
(Stratagene, La Jolla, Calif.) or PSPORT1 plasmid (GIBCO/BRL), 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. 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 HSCD, vectors based on SV40 or EBV
may be used with an appropriate selectable marker.
[0092] In bacterial systems, a number of expression vectors may be
selected depending upon the use intended for HSCD. For example,
when large quantities of HSCD 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, multifunctional E. coli cloning
and expression vectors such as BLUESCRIPT (Stratagene), in which
the sequence encoding HSCD 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, and pIN vectors. (See, e.g., Van Heeke, G. and S. M.
Schuster (1989) J. Biol. Chem. 264:5503-5509.) pGEX vectors
(Pharmacia Biotech, Uppsala, Sweden) may also be used to express
foreign polypeptides 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 polypeptide of interest can be released from the
GST moiety at will.
[0093] 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. (See, e.g., Ausubel,
supra; and Bitter, G. A. et al. (1987) Methods Enzymol.
153:516-544.)
[0094] In cases where plant expression vectors are used, the
expression of sequences encoding HSCD 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, N. (1987) EMBO J.
6:307-311). Alternatively, plant promoters such as the small
subunit of RUBISCO or heat shock promoters may be used. (See, e.g.,
Coruzzi, G. et al. (1984) EMBO J. 3:1671-1680; Broglie, R. et al.
(1984) Science 224:838-843; and Winter, J. 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, e.g., Hobbs, S. or Murry, L. E.
in McGraw Hill Yearbook of Science and Technology (1992) McGraw
Hill, New York, N.Y.; pp. 191-196.)
[0095] An insect system may also be used to express HSCD. 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 HSCD 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 sequences
encoding HSCD 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 HSCD may be expressed. (See, e.g.,
Engelhard, E. K. et al. (1994) Proc. Natl. Acad. Sci. USA
91:3224-3227.)
[0096] 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 HSCD may be ligated into an
adenovirus transcription/translation complex consisting of the late
promoter and tripartite leader sequence. Insertion in a
non-essential E1 or E3 region of the viral genome may be used to
obtain a viable virus which is capable of expressing HSCD in
infected host cells. (See, e.g., Logan, J. and T. Shenk (1984)
Proc. Natl. Acad. Sci. USA 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.
[0097] 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 about 6 kb to 10 Mb are constructed and
delivered via conventional delivery methods (liposomes,
polycationic amino polymers, or vesicles) for therapeutic
purposes.
[0098] Specific initiation signals may also be used to achieve more
efficient translation of sequences encoding HSCD. Such signals
include the ATG initiation codon and adjacent sequences. In cases
where sequences encoding HSCD and its initiation codon and upstream
sequences are inserted into the appropriate 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 appropriate for the particular cell
system used. (See, e.g., Scharf, D. et al. (1994) Results Probl.
Cell Differ. 20:125-162.)
[0099] In addition, a host cell strain may be chosen for its
ability to modulate expression of the inserted sequences or to
process the expressed protein in the desired fashion. Such
modifications of the polypeptide 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 American
Type Culture Collection (ATCC, Bethesda, Md.) and may be chosen to
ensure the correct modification and processing of the foreign
protein.
[0100] For long term, high yield production of recombinant
proteins, stable expression is preferred. For example, cell lines
capable of stably expressing HSCD can 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 about 1 to 2 days in
enriched media before being 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 appropriate to the cell type.
[0101] 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 genes and adenine
phosphoribosyltransferase genes, which can be employed in tk.sup.-
and apr.sup.- cells, respectively. (See, e.g., Wigler, M. et al.
(1977) Cell 11:223-232; and Lowy, I. et al. (1980) Cell 22:817-823)
Also, antimetabolite, antibiotic, or herbicide resistance can be
used as the basis for selection. For example, dhfr confers
resistance to methotrexate; npt confers resistance to the
aminoglycosides neomycin and G-418; and als and pat confer
resistance to chlorsulfuron and phosphinotricin acetyltransferase,
respectively. (See, e.g., Wigler, M. et al. (1980) Proc. Natl.
Acad. Sci. USA 77:3567-3570; Colbere-Garapin, F. et al (1981) J.
Mol. Biol. 150:1-14; and Murry, supra.) Additional selectable genes
have been described, e.g., trpB, which allows cells to utilize
indole in place of tryptophan, or hisD, which allows cells to
utilize histinol in place of histidine. (See, e.g., Hartman, S. C.
and R. C. Mulligan (1988) Proc. Natl. Acad. Sci. USA 85:8047-8051.)
Visible markers, e.g., anthocyanins, .beta. glucuronidase and its
substrate GUS, luciferase and its substrate luciferin may be used.
Green fluorescent proteins (GFP) (Clontech, Palo Alto, Calif.) can
also be used. These markers can be used not only to identify
transformants, but also to quantify the amount of transient or
stable protein expression attributable to a specific vector system.
(See, e.g., Rhodes, C. A. et al. (1995) Methods Mol. Biol.
55:121-131.)
[0102] Although the presence/absence of marker gene expression
suggests that the gene of interest is also present, the presence
and expression of the gene may need to be confirmed. For example,
if the sequence encoding HSCD is inserted within a marker gene
sequence, transformed cells containing sequences encoding HSCD can
be identified by the absence of marker gene function.
Alternatively, a marker gene can be placed in tandem with a
sequence encoding HSCD 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.
[0103] Alternatively, host cells which contain the nucleic acid
sequence encoding HSCD and express HSCD 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
sequences.
[0104] The presence of polynucleotide sequences encoding HSCD can
be detected by DNA-DNA or DNA-RNA hybridization or amplification
using probes or fragments or fragments of polynucleotides encoding
HSCD. Nucleic acid amplification based assays involve the use of
oligonucleotides or oligomers based on the sequences encoding HSCD
to detect transformants containing DNA or RNA encoding HSCD.
[0105] A variety of protocols for detecting and measuring the
expression of HSCD, using either polyclonal or monoclonal
antibodies specific for the protein, are known in the art. Examples
of such techniques include enzyme-linked immunosorbent assays
(ELISAs), radioimmunoassays (RIAs), and fluorescence activated cell
sorting (FACS). A two-site, monoclonal-based immunoassay utilizing
monoclonal antibodies reactive to two non-interfering epitopes on
HSCD is preferred, but a competitive binding assay may be employed.
These and other assays are well described in the art. (See, e.g.,
Hampton, R. et al. (1990) Serological Methods, a Laboratory Manual,
APS Press, St. Paul, Minn., Section IV; and Maddox, D. E. et al.
(1983) J. Exp. Med. 158:1211-1216).
[0106] 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 HSCD include oligolabeling, nick
translation, end-labeling, or PCR amplification using a labeled
nucleotide. Alternatively, the sequences encoding HSCD, 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 appropriate RNA polymerase such as T7, T3,
or SP6 and labeled nucleotides. These procedures may be conducted
using a variety of commercially available kits, such as those
provided by Pharmacia & Upjohn (Kalamazoo, Mich.), Promega
(Madison, Wis.), and U.S. Biochemical Corp. (Cleveland, Ohio).
Suitable reporter molecules or labels which may be used for ease of
detection include radionuclides, enzymes, fluorescent,
chemiluminescent, or chromogenic agents, as well as substrates,
cofactors, inhibitors, magnetic particles, and the like.
[0107] Host cells transformed with nucleotide sequences encoding
HSCD may be cultured under conditions suitable 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 HSCD may be designed to
contain signal sequences which direct secretion of HSCD through a
prokaryotic or eukaryotic cell membrane. Other constructions may be
used to join sequences encoding HSCD to nucleotide sequences
encoding a polypeptide 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 Corp., Seattle,
Wash.). The inclusion of cleavable linker sequences, such as those
specific for Factor XA or enterokinase (Invitrogen, San Diego,
Calif.), between the purification domain and the HSCD encoding
sequence may be used to facilitate to purification. One such
expression vector provides for expression of a fusion protein
containing HSCD and a nucleic acid encoding 6 histidine residues
preceding a thioredoxin or an enterokinase cleavage site. The
histidine residues facilitate purification on immobilized metal ion
affinity chromatography (IMIAC). (See, e.g., Porath, J. et al.
(1992) Prot. Exp. Purif. 3:263-281.) The enterokinase cleavage site
provides a means for purifying HSCD from the fusion protein. (See,
e.g., Kroll, D. J. et al. (1993) DNA Cell Biol. 12:441-453.)
[0108] Fragments of HSCD may be produced not only by recombinant
production, but also by direct peptide synthesis using solid-phase
techniques. (See, e.g., Creighton, T. E. (1984) Proteins:
Structures and Molecular Properties, pp. 55-60, W. H. Freeman and
Co., New York, N.Y.) Protein synthesis may be performed by manual
techniques or by automation. Automated synthesis may be achieved,
for example, using the Applied Biosystems 431A peptide synthesizer
(Perkin Elmer). Various fragments of HSCD may be synthesized
separately and then combined to produce the full length
molecule.
[0109] Therapeutics
[0110] Chemical and structural homology exists between HSCD and
short-chain acyl-CoA dehydrogenase from C. elegans (GI2315796). In
addition, HSCD is expressed in tissues associated with immune
disorders and cancer. Therefore, HSCD appears to play a role in
immune disorders and cancer.
[0111] Therefore, in one embodiment, an antagonist of HSCD or a
fragment or derivative thereof may be administered to a subject to
treat or prevent a cancer. Such cancers may include, but are not
limited to, adenocarcinoma, leukemia, lymphoma, melanoma, myeloma,
sarcoma, and teratocarcinoma; and, in particular, 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, an antibody which specifically binds HSCD may be
used directly as an antagonist or indirectly as a targeting or
delivery mechanism for bringing a pharmaceutical agent to cells or
tissues which express HSCD.
[0112] In another embodiment, a vector expressing the complement of
the polynucleotide encoding HSCD may be administered to a subject
to treat or prevent a cancer including, but not limited to, those
described above.
[0113] Therefore, in another embodiment, an antagonist of HSCD may
be administered to a subject to prevent or treat an immune
disorder. Immune disorders may include, but are not limited to
AIDS, Addison's disease, adult respiratory distress syndrome,
allergies, anemia, asthma, atherosclerosis, bronchitis,
cholecystitis, Crohn's disease, ulcerative colitis, atopic
dermatitis, dermatomyositis, diabetes mellitus, emphysema, erythema
nodosum, 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 autoimmune thyroiditis; complications of
cancer, hemodialysis, and extracorporeal circulation; viral,
bacterial, fungal, parasitic, protozoal, and helminthic infections;
and trauma. In one aspect, an antibody which specifically binds
HSCD may be used directly as an antagonist or indirectly as a
targeting or delivery mechanism for bringing a pharmaceutical agent
to cells or tissues which express HSCD.
[0114] In another embodiment, a vector expressing the complement of
the polynucleotide encoding HSCD may be administered to a subject
to treat or prevent an immune disorder including, but not limited
to, those described above.
[0115] In other embodiments, any of the proteins, antagonists,
antibodies, agonists, complementary sequences, or vectors of the
invention may be administered in combination with other appropriate
therapeutic agents. Selection of the appropriate 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 or prevention 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.
[0116] An antagonist of HSCD may be produced using methods which
are generally known in the art. In particular, purified HSCD may be
used to produce antibodies or to screen libraries of pharmaceutical
agents to identify those which specifically bind HSCD. Antibodies
to HSCD may also be generated using methods that are well known in
the art. Such antibodies may include, but are not limited to,
polyclonal, monoclonal, chimeric, and single chain antibodies, 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.
[0117] For the production of antibodies, various hosts including
goats, rabbits, rats, mice, humans, and others may be immunized by
injection with HSCD or with any fragment 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, KLH, and dinitrophenol. Among adjuvants used in humans,
BCG (bacilli Calmette-Guerin) and Corynebacterium parvum are
especially preferable.
[0118] It is preferred that the oligopeptides, peptides, or
fragments used to induce antibodies to HSCD have an amino acid
sequence consisting of at least about 5 amino acids, and, more
preferably, of at least about 10 amino acids. It is also preferable
that these oligopeptides, peptides, or fragments are identical to a
portion of the amino acid sequence of the natural protein and
contain the entire amino acid sequence of a small, naturally
occurring molecule. Short stretches of HSCD amino acids may be
fused with those of another protein, such as KLH, and antibodies to
the chimeric molecule may be produced.
[0119] Monoclonal antibodies to HSCD 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. (See, e.g., Kohler, G.
et al. (1975) Nature 256:495-497; Kozbor, D. et al. (1985) J.
Immunol. Methods 81:31-42; Cote, R. J. et al. (1983) Proc. Natl.
Acad. Sci. USA 80:2026-2030; and Cole, S. P. et al. (1984) Mol.
Cell Biol. 62:109-120.)
[0120] In addition, techniques developed for the production of
"chimeric antibodies," such as the splicing of mouse antibody genes
to human antibody genes to obtain a molecule with appropriate
antigen specificity and biological activity, can be used. (See,
e.g., Morrison, S. L. et al. (1984) Proc. Natl. Acad. Sci. USA
81:6851-6855; Neuberger, M. S. et al. (1984) Nature 312:604-608;
and Takeda, S. 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
HSCD-specific single chain antibodies. Antibodies with related
specificity, but of distinct idiotypic composition, may be
generated by chain shuffling from random combinatorial
immunoglobulin libraries. (See, e.g., Burton, D. R. (1991) Proc.
Natl. Acad. Sci. USA 88:10134-10137.)
[0121] 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. (See, e.g., Orlandi, R. et
al. (1989) Proc. Natl. Acad. Sci. USA 86: 3833-3837; and Winter, G.
et al. (1991) Nature 349:293-299.)
[0122] Antibody fragments which contain specific binding sites for
HSCD may also be generated. For example, such fragments include,
but are not limited to, F(ab')2 fragments produced by pepsin
digestion of the antibody molecule and Fab fragments 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. (See, e.g., Huse, W. D. et al. (1989) Science
246:1275-1281.)
[0123] 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 HSCD and its specific
antibody. A two-site, monoclonal-based immunoassay utilizing
monoclonal antibodies reactive to two non-interfering HSCD epitopes
is preferred, but a competitive binding assay may also be employed
(Maddox, supra).
[0124] In another embodiment of the invention, the polynucleotides
encoding HSCD, or any fragment or complement thereof, may be used
for therapeutic purposes. In one aspect, the complement of the
polynucleotide encoding HSCD 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 HSCD. Thus, complementary molecules or
fragments may be used to modulate HSCD 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 HSCD.
[0125] Expression vectors derived from retroviruses, adenoviruses,
or herpes or vaccinia viruses, or from various bacterial plasmids,
may be used for delivery of nucleotide sequences 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 sequences complementary to the
polynucleotides of the gene encoding HSCD. (See, e.g., Sambrook,
supra; and Ausubel, supra.)
[0126] Genes encoding HSCD can be turned off by transforming a cell
or tissue with expression vectors which express high levels of a
polynucleotide, or fragment thereof, encoding HSCD. 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 may
last even longer if appropriate replication elements are part of
the vector system.
[0127] 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 HSCD. Oligonucleotides derived from
the transcription initiation site, e.g., between about 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 sufficiently
for the binding of polymerases, transcription factors, or
regulatory molecules. Recent therapeutic advances using triplex DNA
have been described in the literature. (See, e.g., Gee, J. E. et
al. (1994) in Huber, B. E. and B. I. Carr, Molecular and
Immunologic Approaches, Futura Publishing Co., Mt. Kisco, N.Y., pp.
163-177.) A complementary sequence or antisense molecule may also
be designed to block translation of mRNA by preventing the
transcript from binding to ribosomes.
[0128] 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. For example, engineered hammerhead motif ribozyme
molecules may specifically and efficiently catalyze endonucleolytic
cleavage of sequences encoding HSCD.
[0129] Specific ribozyme cleavage sites within any potential RNA
target are initially identified by scanning the target molecule for
ribozyme cleavage sites, including 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.
[0130] 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 HSCD. Such DNA sequences may be incorporated
into a wide variety of vectors with suitable 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.
[0131] 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.
[0132] Many methods for introducing vectors into cells or tissues
are available and equally suitable 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 by polycationic amino polymers may be
achieved using methods which are well known in the art. (See, e.g.,
Goldman, C. K. et al. (1997) Nat. Biotechnol. 15:462-466.)
[0133] 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.
[0134] An additional embodiment of the invention relates to the
administration of a pharmaceutical or sterile composition, in
conjunction with a pharmaceutically acceptable carrier, for any of
the therapeutic effects discussed above. Such pharmaceutical
compositions may consist of HSCD, antibodies to HSCD, and mimetics,
agonists, antagonists, or inhibitors of HSCD. The compositions may
be administered alone or in combination with at least one other
agent, such as a 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.
[0135] 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.
[0136] In addition to the active ingredients, these pharmaceutical
compositions may contain suitable 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 (Maack Publishing Co.,
Easton, Pa.).
[0137] Pharmaceutical compositions for oral administration can be
formulated using pharmaceutically acceptable carriers well known in
the art in dosages suitable 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.
[0138] Pharmaceutical preparations for oral use can be obtained
through combining active compounds with solid excipient and
processing the resultant mixture of granules (optionally, after
grinding) to obtain tablets or dragee cores. Suitable auxiliaries
can be added, if desired. Suitable excipients include carbohydrate
or protein fillers, such as sugars, including lactose, sucrose,
mannitol, and 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, and alginic acid or a salt thereof, such as
sodium alginate.
[0139] Dragee cores may be used in conjunction with suitable
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 suitable 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.
[0140] 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 fillers
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
suitable liquids, such as fatty oils, liquid, or liquid
polyethylene glycol with or without stabilizers.
[0141] Pharmaceutical formulations suitable for parenteral
administration may be formulated in aqueous solutions, preferably
in physiologically compatible buffers such as Hanks's 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 appropriate oily injection
suspensions. Suitable lipophilic solvents or vehicles include fatty
oils, such as sesame oil, or synthetic fatty acid esters, such as
ethyl oleate, triglycerides, or liposomes. Non-lipid polycationic
amino polymers may also be used for delivery. Optionally, the
suspension may also contain suitable stabilizers or agents to
increase the solubility of the compounds and allow for the
preparation of highly concentrated solutions.
[0142] For topical or nasal administration, penetrants appropriate
to the particular barrier to be permeated are used in the
formulation. Such penetrants are generally known in the art.
[0143] 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.
[0144] 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, and
succinic acid. 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 mM to 50 mM
histidine, 0. 1% to 2% sucrose, and 2% to 7% mannitol, at a pH
range of 4.5 to 5.5, that is combined with buffer prior to use.
[0145] After pharmaceutical compositions have been prepared, they
can be placed in an appropriate container and labeled for treatment
of an indicated condition. For administration of HSCD, such
labeling would include amount, frequency, and method of
administration.
[0146] Pharmaceutical compositions suitable 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.
[0147] 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 such as mice, rats, rabbits,
dogs, or pigs. An animal model may also be used to determine the
appropriate concentration range and route of administration. Such
information can then be used to determine useful doses and routes
for administration in humans.
[0148] A therapeutically effective dose refers to that amount of
active ingredient, for example HSCD or fragments thereof,
antibodies of HSCD, and agonists, antagonists or inhibitors of
HSCD, which ameliorates the symptoms or condition. Therapeutic
efficacy and toxicity may be determined by standard pharmaceutical
procedures in cell cultures or with experimental animals, such as
by calculating the ED50 (the dose therapeutically effective in 50%
of the population) or LD50 (the dose lethal to 50% of the
population) statistics. The dose ratio of therapeutic to toxic
effects is the therapeutic index, which can be expressed as the
ED50/LD50 ratio. Pharmaceutical compositions which exhibit large
therapeutic indices are preferred. The data obtained from cell
culture assays and animal studies are used to formulate a range of
dosage for human use. The dosage contained in such compositions is
preferably within a range of circulating concentrations that
includes the ED50 with little or no toxicity. The dosage varies
within this range depending upon the dosage form employed, the
sensitivity of the patient, and the route of administration.
[0149] The exact dosage will be determined by the practitioner, in
light of factors related to the subject requiring treatment. Dosage
and administration are adjusted to provide sufficient levels of the
active moiety or to maintain the desired effect. Factors which may
be taken into account include the severity of the disease state,
the general health of the subject, the age, weight, and gender of
the subject, time and frequency of administration, drug
combination(s), reaction sensitivities, and response to therapy.
Long-acting pharmaceutical compositions may be administered every 3
to 4 days, every week, or biweekly depending on the half-life and
clearance rate of the particular formulation.
[0150] Normal dosage amounts may vary from about 0.1 .mu.g to
100,000 .mu.g, up to a total dose of about 1 gram, 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 polypeptides will be specific to particular
cells, conditions, locations, etc.
[0151] Diagnostics
[0152] In another embodiment, antibodies which specifically bind
HSCD may be used for the diagnosis of disorders characterized by
expression of HSCD, or in assays to monitor patients being treated
with HSCD or agonists, antagonists, or inhibitors of HSCD.
Antibodies useful for diagnostic purposes may be prepared in the
same manner as described above for therapeutics. Diagnostic assays
for HSCD include methods which utilize the antibody and a label to
detect HSCD in human body fluids or in extracts of cells or
tissues. The antibodies may be used with or without modification,
and may be labeled by covalent or non-covalent attachment of a
reporter molecule. A wide variety of reporter molecules, several of
which are described above, are known in the art and may be
used.
[0153] A variety of protocols for measuring HSCD, including ELISAs,
RIAs, and FACS, are known in the art and provide a basis for
diagnosing altered or abnormal levels of HSCD expression. Normal or
standard values for HSCD expression are established by combining
body fluids or cell extracts taken from normal mammalian subjects,
preferably human, with antibody to HSCD under conditions suitable
for complex formation The amount of standard complex formation may
be quantitated by various methods, preferably by photometric means.
Quantities of HSCD expressed in subject, control, and disease
samples from biopsied tissues are compared with the standard
values. Deviation between standard and subject values establishes
the parameters for diagnosing disease.
[0154] In another embodiment of the invention, the polynucleotides
encoding HSCD 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 HSCD may be
correlated with disease. The diagnostic assay may be used to
determine absence, presence, and excess expression of HSCD, and to
monitor regulation of HSCD levels during therapeutic
intervention.
[0155] In one aspect, hybridization with PCR probes which are
capable of detecting polynucleotide sequences, including genomic
sequences, encoding HSCD or closely related molecules may be used
to identify nucleic acid sequences which encode HSCD. The
specificity of the probe, whether it is made from a highly specific
region, e.g., the 5' regulatory region, or from a less specific
region, e.g., a conserved motif, and the stringency of the
hybridization or amplification (maximal, high, intermediate, or
low), will determine whether the probe identifies only naturally
occurring sequences encoding HSCD, alleles, or related
sequences.
[0156] Probes may also be used for the detection of related
sequences, and should preferably have at least 50% sequence
identity to any of the HSCD encoding sequences. The hybridization
probes of the subject invention may be DNA or RNA and may be
derived from the sequence of SEQ ID NO:2 or from genomic sequences
including promoters, enhancers, and introns of the HSCD gene.
[0157] Means for producing specific hybridization probes for DNAs
encoding HSCD include the cloning of polynucleotide sequences
encoding HSCD or HSCD derivatives into vectors for the production
of mRNA probes. Such vectors are known in the art, are commercially
available, and may be used to synthesize RNA probes in vitro by
means of the addition of the appropriate RNA polymerases and the
appropriate labeled nucleotides. Hybridization probes may be
labeled by a variety of reporter groups, for example, by
radionuclides such as .sup.32P or 35S, or by enzymatic labels, such
as alkaline phosphatase coupled to the probe via avidin/biotin
coupling systems, and the like.
[0158] Polynucleotide sequences encoding HSCD may be used for the
diagnosis of a disorder associated with expression of HSCD.
Examples of such a disorder include, but are not limited to,
cancers such as adenocarcinoma, leukemia, lymphoma, melanoma,
myeloma, sarcoma, and teratocarcinoma; and, in particular, 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; and immune disorders such as AIDS, Addison's disease,
adult respiratory distress syndrome, allergies, anemia, asthma,
atherosclerosis, bronchitis, cholecystitis, Crohn's disease,
ulcerative colitis, atopic dermatitis, dermatomyositis, diabetes
mellitus, emphysema, erythema nodosum, 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
autoimmune thyroiditis; complications of cancer, hemodialysis, and
extracorporeal circulation; viral, bacterial, fungal, parasitic,
protozoal, and helminthic infections; and trauma. The
polynucleotide sequences encoding HSCD may be used in Southern or
northern analysis, dot blot, or other membrane-based technologies;
in PCR technologies; or in dipstick, pin, ELISA assays or
microarrays utilizing fluids or tissues from patient biopsies to
detect altered HSCD expression. Such qualitative or quantitative
methods are well known in the art. The polynucleotide sequences
encoding HSCD may be used in Southern or northern analysis, dot
blot, or other membrane-based technologies; in PCR technologies; in
dipstick, pin, and ELISA assays; and in microarrays utilizing
fluids or tissues from patients to detect altered HSCD expression.
Such qualitative or quantitative methods are well known in the art.
The polynucleotide sequences encoding HSCD may be used in Southern
or northern analysis, dot blot, or other membrane-based
technologies; in PCR technologies; in dipstick, pin, and ELISA
assays; and in microarrays utilizing fluids or tissues from
patients to detect altered HSCD expression. Such qualitative or
quantitative methods are well known in the art.
[0159] In a particular aspect, the nucleotide sequences encoding
HSCD may be useful in assays that detect the presence of associated
disorders, particularly those mentioned above. The nucleotide
sequences encoding HSCD may be labeled by standard methods and
added to a fluid or tissue sample from a patient under conditions
suitable for the formation of hybridization complexes. After a
suitable incubation period, the sample is washed and the signal is
quantitated and compared with a standard value. If the amount of
signal in the patient sample is significantly altered in comparison
to a control sample then the presence of altered levels of
nucleotide sequences encoding HSCD in the sample indicates the
presence of the associated disorder. Such assays may also be used
to evaluate the efficacy of a particular therapeutic treatment
regimen in animal studies, in clinical trials, or to monitor the
treatment of an individual patient.
[0160] In order to provide a basis for the diagnosis of a disorder
associated with expression of HSCD, 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,
encoding HSCD, under conditions suitable for hybridization or
amplification. Standard hybridization may be quantified by
comparing the values obtained from normal subjects with values from
an experiment in which a known amount of a substantially purified
polynucleotide is used. Standard values obtained in this manner may
be compared with values obtained from samples from patients who are
symptomatic for a disorder. Deviation from standard values is used
to establish the presence of a disorder.
[0161] Once the presence of a disorder is established and a
treatment protocol is initiated, hybridization assays may be
repeated on a regular basis to determine if the level of expression
in the patient begins to approximate that which is observed in the
normal subject. The results obtained from successive assays may be
used to show the efficacy of treatment over a period ranging from
several days to months.
[0162] 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 preventative
measures or aggressive treatment earlier thereby preventing the
development or further progression of the cancer.
[0163] Additional diagnostic uses for oligonucleotides designed
from the sequences encoding HSCD may involve the use of PCR. These
oligomers may be chemically synthesized, generated enzymatically,
or produced in vitro. Oligomers will preferably contain a fragment
of a polynucleotide encoding HSCD, or a fragment of a
polynucleotide complementary to the polynucleotide encoding HSCD,
and will be employed under optimized conditions for identification
of a specific gene or condition. Oligomers may also be employed
under less stringent conditions for detection or quantitation of
closely related DNA or RNA sequences.
[0164] Methods which may also be used to quantitate the expression
of HSCD include radiolabeling or biotinylating nucleotides,
coamplification of a control nucleic acid, and interpolating
results from standard curves. (See, e.g., Melby, P. C. et al.
(1993) J. Immunol. Methods 159:235-244; and Duplaa, C. et al.
(1993) Anal. Biochem. 212:229-236.) The speed of quantitation of
multiple samples may be accelerated by running the assay in an
ELISA format where the oligomer of interest is presented in various
dilutions and a spectrophotometric or calorimetric response gives
rapid quantitation.
[0165] In further embodiments, oligonucleotides or longer fragments
derived from any of the polynucleotide sequences described herein
may be used as targets in a microarray. The microarray can be used
to monitor the expression level of large numbers of genes
simultaneously and to identify genetic variants, mutations, and
polymorphisms. This information may be used to determine gene
function, to understand the genetic basis of a disorder, to
diagnose a disorder, and to develop and monitor the activities of
therapeutic agents.
[0166] Microarrays may be prepared, used, and analyzed using
methods known in the art. (See, e.g., Brennan, T. M. et al. (1995)
U.S. Pat. No. 5,474,796; Schena, M. et al. (1996) Proc. Natl. Acad.
Sci. USA 93:10614-10619; Baldeschweileret al. (1995) PCT
application WO95/251116; Shalon, D. et al. (1995) PCT application
WO95/35505; Heller, R. A. et al. (1997) Proc. Natl. Acad. Sci. USA
94:2150-2155; and Heller, M. J. et al. (1997) U.S. Pat. No.
5,605,662.)
[0167] In another embodiment of the invention, nucleic acid
sequences encoding HSCD may be used to generate hybridization
probes useful in 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, e.g., human artificial chromosomes (HACs), yeast
artificial chromosomes (YACs), bacterial artificial chromosomes
(BACs), bacterial P1 constructions, or single chromosome cDNA
libraries. (See, e.g., Price, C. M. (1993) Blood Rev. 7:127-134;
and Trask, B. J. (1991) Trends Genet. 7:149-154.)
[0168] Fluorescent in situ hybridization (FISH) may be correlated
with other physical chromosome mapping techniques and genetic map
data. (See, e.g., Heinz-Ulrich, et al. (1995) in Meyers, R. A.
(ed.) Molecular Biology and Biotechnology, VCH Publishers New York,
N.Y., pp. 965-968.) Examples of genetic map data can be found in
various scientific journals or at the Online Mendelian Inheritance
in Man (OMIM) site. Correlation between the location of the gene
encoding HSCD on a physical chromosomal map and a specific
disorder, or a predisposition to a specific disorder, may help
define the region of DNA associated with that disorder. The
nucleotide sequences of the invention may be used to detect
differences in gene sequences among normal, carrier, and affected
individuals.
[0169] 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 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, e.g., AT to 11q22-23, any sequences mapping to that
area may represent associated or regulatory genes for further
investigation. (See, e.g., Gatti, R. A. et al. (1988) Nature
336:577-580.) The nucleotide sequence of the subject invention may
also be used to detect differences in the chromosomal location due
to translocation, inversion, etc., among normal, carrier, or
affected individuals.
[0170] In another embodiment of the invention, HSCD, its catalytic
or immunogenic fragments, or oligopeptides thereof can be used for
screening libraries of compounds in any of a variety of drug
screening techniques. The fragment 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 HSCD and the agent being tested may be
measured.
[0171] Another technique for drug screening provides for high
throughput screening of compounds having suitable binding affinity
to the protein of interest. (See, e.g., Geysen, et al. (1984) 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 HSCD, or fragments thereof, and washed. Bound HSCD is then
detected by methods well known in the art. Purified HSCD 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.
[0172] In another embodiment, one may use competitive drug
screening assays in which neutralizing antibodies capable of
binding HSCD specifically compete with a test compound for binding
HSCD. In this manner, antibodies can be used to detect the presence
of any peptide which shares one or more antigenic determinants with
HSCD.
[0173] In additional embodiments, the nucleotide sequences which
encode HSCD may be used in any molecular biology techniques that
have yet to be developed, provided the new techniques rely on
properties of nucleotide sequences that are currently known,
including, but not limited to, such properties as the triplet
genetic code and specific base pair interactions.
[0174] The examples below are provided to illustrate the subject
invention and are not included for the purpose of limiting the
invention.
EXAMPLES
[0175] I. PROSNOT01 cDNA Library Construction
[0176] The prostate tissue used for library construction was
obtained from a 78 year-old Caucasian male with leukemia (Lot No.
94-039, International Institute for the Advancement of Medicine,
Exton PA). The tissue was flash frozen, ground in a mortar and
pestle, lysed immediately in buffer containing guanidinium
isothiocyanate and spun through cesium chloride. The lysate was
extracted twice with phenol chloroform at pH 8.0 and centrifuged
over a CsCl cushion using an Beckman SW28 rotor in a Beckman L8-70M
Ultracentrifuge (Beckman Instruments). The RNA was precipitated
using 0.3 M sodium acetate and 2.5 volumes of ethanol, resuspended
in water and DNase treated for 15 min at 37.degree. C. The RNA was
isolated using the OLIGOTEX kit (QIAGEN Inc., Chatsworth Calif.)
and used to construct the cDNA library.
[0177] First strand cDNA synthesis was accomplished using an oligo
d(T) primer/linker which also contained an Xho I restriction site.
Second strand synthesis was performed using a combination of DNA
polymerase I, E. coli ligase and RNase H, followed by the addition
of an EcoRI adaptor to the blunt ended cDNA. The EcoRI adapted,
double-stranded cDNA was then digested with Xho I restriction
enzyme and fractionated on SEPHACRYL S400 to obtain sequences which
exceeded 1000 bp in size. The size selected cDNAs were inserted
into the LAMBDAZAP vector system (Stratagene, La Jolla Calif.); and
the vector, which contains the PBLUESCRIPT phagemid (Stratagene),
was transformed into cells of E. coli, strain XL1-BLUEMRF
(Stratagene).
[0178] The phagemid forms of individual cDNA clones were obtained
by the in vivo excision process. Enzymes from both pBluescript and
a cotransformed f1 helper phage nicked the DNA, initiated new DNA
synthesis, and created the smaller, single-stranded circular
phagemid DNA molecules which contained the cDNA insert. The
phagemid DNA was released, purified, and used to reinfect fresh
host cells (SOLR, Stratagene). Presence of the phagemid which
carries the gene for .beta.-lactamase allowed transformed bacteria
to grow on medium containing ampicillin.
[0179] II. Isolation and Sequencing of cDNA Clones
[0180] Plasmid DNA was released from the cells and purified using
the miniprep kit (Catalogue # 77468; Advanced Genetic Technologies
Corporation, Gaithersburg Md.). This kit consists of a 96 well
block with reagents for 960 purifications. The recommended protocol
was employed except for the following changes: 1) the 96 wells were
each filled with only 1 ml of sterile Terrific Broth (Catalog #
22711, GIBCO/BRL, Gaithersburg Md.) with carbenicillin at 25 mg/L
and glycerol at 0.4%; 2) the bacteria were cultured for 24 hours
after the wells were inoculated and then lysed with 60 .mu.l of
lysis buffer; 3) a centrifugation step employing the Beckman GS-6R
@2900 rpm for 5 min was performed before the contents of the block
were added to the primary filter plate; and 4) the optional step of
adding isopropanol to TRIS buffer was not routinely performed.
After the last step in the protocol, samples were transferred to a
Beckman 96-well block for storage.
[0181] Alternative methods of purifying plasmid DNA include the use
of MAGIC MINIPREPS DNA purification system (Catalogue #A7100,
Promega, Madison Wis.), or QIAWELL-8 plasmid, QIAWELL PLUS DNA, and
QIAWELL ULTRA DNA purification systems (QIAGEN Chatsworth
Calif.).
[0182] The cDNAs were sequenced by the method of Sanger F and AR
Coulson (1975; J Mol Biol 94:441f), using a MICROLAB 2200
(Hamilton, Reno Nev.) in combination with four Peltier thermal
cyclers (PTC200 from M J Research, Watertown Mass.) and Applied
Biosystems 377 or 373 DNA sequencing systems (Perkin Elmer) and the
reading frame was determined.
[0183] III. Homology Searching of cDNA Clones and Their Deduced
Proteins
[0184] Each cDNA was compared to sequences in GenBank using a
search algorithm developed by Applied Biosystems and incorporated
into the INHERIT 670 sequence analysis system. In this algorithm,
Pattern Specification Language (TRW Inc, Los Angeles, Calif.) was
used to determine regions of homology. The three parameters that
determine how the sequence comparisons run were window size, window
offset, and error tolerance. Using a combination of these three
parameters, the DNA database was searched for sequences containing
regions of homology to the query sequence, and the appropriate
sequences were scored with an initial value. Subsequently, these
homologous regions were examined using dot matrix homology plots to
distinguish regions of homology from chance matches. Smith-Waterman
alignments were used to display the results of the homology
search.
[0185] Peptide and protein sequence homologies were ascertained
using the INHERIT 670 sequence analysis system using the methods
similar to those used in DNA sequence homologies. Pattern
Specification Language and parameter windows were used to search
protein databases for sequences containing regions of homology
which were scored with an initial value. Dot-matrix homology plots
were examined to distinguish regions of significant homology from
chance matches.
[0186] BLAST, which stands for Basic Local Alignment Search Tool
(Altschul, S. F. (1993) J. Mol. Evol. 36:290-300; Altschul et al.
(1990) J. Mol. Biol. 215:403-410), was used to search for local
sequence alignments. BLAST produces alignments of both nucleotide
and amino acid sequences to determine sequence similarity. Because
of the local nature of the alignments, BLAST is especially useful
in determining exact matches or in identifying homologs. BLAST is
useful for matches which do not contain gaps. The fundamental unit
of BLAST algorithm output is the High-scoring Segment Pair
(HSP).
[0187] An HSP consists of two sequence fragments of arbitrary but
equal lengths whose alignment is locally maximal and for which the
alignment score meets or exceeds a threshold or cutoff score set by
the user. The BLAST approach is to look for HSPs between a query
sequence and a database sequence, to evaluate the statistical
significance of any matches found, and to report only those matches
which satisfy the user-selected threshold of significance. The
parameter E establishes the statistically significant threshold for
reporting database sequence matches. E is interpreted as the upper
bound of the expected frequency of chance occurrence of an HSP (or
set of HSPs) within the context of the entire database search. Any
database sequence whose match satisfies E is reported in the
program output.
[0188] IV. Northern Analysis
[0189] Northern analysis is a laboratory technique used to detect
the presence of a transcript of a gene and involves the
hybridization of a labeled nucleotide sequence to a membrane on
which RNAs from a particular cell type or tissue have been bound.
(See, e.g., Sambrook, supra, ch. 7; and Ausubel, F. M. et al.
supra, ch. 4 and 16.)
[0190] Analogous computer techniques applying BLAST are used to
search for identical or related molecules in nucleotide databases
such as the GenBank or LIFESEQ (Incyte Pharmaceuticals) databases.
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.
[0191] The basis of the search is the product score, which is
defined as: 1 % sequence identity .times. % maximum BLAST score
100
[0192] 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% to 2% error, and, with a product score of 70, the
match will be exact. Homologous i0 molecules are usually identified
by selecting those which show product scores between 15 and 40,
although lower scores may identify related molecules.
[0193] The results of northern analysis are reported as a list of
libraries in which the transcript encoding HSCD 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.
[0194] V. Extension of HSCD Encoding Polynucleotides
[0195] The nucleic acid sequence of Incyte Clone 356351 was used to
design oligonucleotide primers for extending a partial nucleotide
sequence to full length. One primer was synthesized to initiate
extension of an antisense polynucleotide, and the other was
synthesized to initiate extension of a sense polynucleotide.
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 4.06 software (National
Biosciences, Plymouth, Minn.), or another appropriate program, to
be about 22 to 30 nucleotides in length, to have a GC content of
about 50% or more, and to anneal to the target sequence at
temperatures of about 68.degree. C. to about 72.degree. C. Any
stretch of nucleotides which would result in hairpin structures and
primer-primer dimerizations was avoided.
[0196] Selected human cDNA libraries (GIBCO/BRL) 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.
[0197] High fidelity amplification was obtained by following the
instructions for the XL-PCR kit (Perkin Elmer) and thoroughly
mixing the enzyme and reaction mix. PCR was performed using the
Peltier thermal cycler (PTC200; M. J. Research, Watertown, Mass.),
beginning with 40 pmol of each primer and the recommended
concentrations of all other components of the kit, with the
following parameters:
[0198] Step 1 94.degree. C. for 1 min (initial denaturation)
[0199] Step 2 65.degree. C. for 1 min
[0200] Step 3 68.degree. C. for 6 min
[0201] Step 4 94.degree. C. for 15 sec
[0202] Step 5 65.degree. C. for 1 min
[0203] Step 6 68.degree. C. for 7 min
[0204] Step 7 Repeat steps 4 through 6 for an additional 15
cycles
[0205] Step 8 94.degree. C. for 15 sec
[0206] Step 9 65.degree. C. for 1 min
[0207] Step 10 68.degree. C. for 7:15 min
[0208] Step 11 Repeat steps 8 through 10 for an additional 12
cycles
[0209] Step 12 72.degree. C. for 8 min
[0210] Step 13 4.degree. C. (and holding)
[0211] A 5 .mu.l to 10 .mu.l aliquot of the reaction mixture was
analyzed by electrophoresis on a low concentration (about 0.6% to
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 (QIAGEN
Inc., Chatsworth, Calif.), and trimmed of overhangs using Klenow
enzyme to facilitate religation and cloning.
[0212] After ethanol precipitation, the products were redissolved
in 13 .mu.l of ligation buffer, 1 .mu.l T4-DNA ligase (15 units)
and 1 .mu.l T4 polynucleotide kinase were added, and the mixture
was incubated at room temperature for 2 to 3 hours, or overnight at
16.degree. C. Competent E. coli cells (in 40 .mu.l of appropriate
media) were transformed with 3 .mu.l of ligation mixture and
cultured in 80 .mu.l of SOC medium. (See, e.g., Sambrook, supra,
Appendix A, p. 2.) After incubation for one hour at 37.degree. C.,
the E. coli mixture was plated on Luria Bertani (LB) agar (See,
e.g., Sambrook, supra, Appendix A, p. 1) containing 2.times.Carb.
The following day, several colonies were randomly picked from each
plate and cultured in 150 .mu.l of liquid LB/2.times.Carb medium
placed in an individual well of an appropriate
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 from each sample was transferred into a PCR
array.
[0213] For PCR amplification, 18 .mu.l of concentrated PCR reaction
mix (3.3.times.) 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:
[0214] Step 1 94.degree. C. for 60 sec
[0215] Step 2 94.degree. C. for 20 sec
[0216] Step 3 55.degree. C. for 30 sec
[0217] Step 4 72.degree. C. for 90 sec
[0218] Step 5 Repeat steps 2 through 4 for an additional 29
cycles
[0219] Step 6 72.degree. C. for 180 sec
[0220] Step 7 4.degree. C. (and holding)
[0221] 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
appropriate clones were selected, ligated into plasmid, and
sequenced.
[0222] In like manner, the nucleotide sequence of SEQ ID NO:2 is
used to obtain 5' regulatory sequences using the procedure above,
oligonucleotides designed for 5' extension, and an appropriate
genomic library.
[0223] VI. Labeling and Use of Individual Hybridization Probes
[0224] Hybridization probes derived from SEQ ID NO:2 are employed
to screen cDNAs, genomic DNAs, or mRNAs. Although the labeling of
oligonucleotides, consisting of about 20 base pairs, is
specifically described, essentially the same procedure is used with
larger nucleotide fragments. Oligonucleotides are designed using
state-of-the-art software such as OLIGO 4.06 software (National
Biosciences) and labeled by combining 50 pmol of each oligomer, 250
.mu.Ci of [.gamma.-.sup.32P] adenosine triphosphate (Amersham,
Chicago, Ill.), and T4 polynucleotide kinase (DuPont NEN, Boston,
Mass.). The labeled oligonucleotides are substantially purified
using a SEPHADEX G-25 superfine resin column (Pharmacia &
Upjohn, Kalamazoo, Mich.). An 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 I,
or Pvu II (DuPont NEN, Boston, Mass.).
[0225] The DNA from each digest is fractionated on a 0.7 percent
agarose gel and transferred to nylon membranes (Nytran Plus,
Schleicher & Schuell, Durham, N.H.). Hybridization is carried
out for 16 hours at 40.degree. 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
(Kodak, Rochester, N.Y.) is exposed to blots or the blots are
exposed to film, hybridization patterns are compared visually.
[0226] VII. Microarrays
[0227] A chemical coupling procedure and an ink jet device can be
used to synthesize array elements on the surface of a substrate.
(See, e.g., Baldeschweiler, supra.) An array analogous to a dot or
slot blot may also be used to arrange and link elements to the
surface of a substrate using or thermal, UV, mechanical, or
chemical bonding procedures, or a vacuum system. A typical array
may be produced by hand or using available methods and machines and
contain any appropriate number of elements. After hybridization,
nonhybridized probes are removed and a scanner used to determine
the levels and patterns of fluorescence. The degree of
complementarity and the relative abundance of each probe which
hybridizes to an element on the microarray may be assessed through
analysis of the scanned images.
[0228] In another alternative, full-length cDNAs or Expressed
Sequence Tags (ESTs) comprise the elements of the microarray.
Full-length cDNAs or ESTs corresponding to one of the nucleotide
sequences of the present invention, or selected at random from a
cDNA library relevent to the present invention, are arranged on an
appropriate substrate, e.g., a glass slide. The cDNA is fixed to
the slide using, e.g., U.V. cross-linking followed, by thermal and
chemical and subsequent drying. (See, e.g., Schena, M. et al.
(1995) Science 270:467-470; and Shalon, D. et al. (1996) Genome
Res. 6:639-645.) Fluorescent probes are prepared and used for
hybridization to the elements on the substrate. The substrate is
analyzed by procedures described above.
[0229] Probe sequences for microarrays may be selected by screening
a large number of clones from a variety of cDNA libraries in order
to find sequences with conserved protein motifs common to genes
coding for signal sequence containing polypeptides. In one
embodiment, sequences identified from cDNA libraries, are analyzed
to identify those gene sequences with conserved protein motifs
using an appropriate analysis program, e.g., the Block 2
Bioanalysis Program (Incyte, Palo Alto, Calif.). This motif
analysis program, based on sequence information contained in the
Swiss-Prot Database and PROSFIE, is a method of determining the
function of uncharacterized proteins translated from genomic or
cDNA sequences. (See, e.g., Bairoch, A. et al. (1997) Nucleic Acids
Res. 25:217-221; and Attwood, T. K. et al. (1997) J. Chem. Inf.
Comput. Sci. 37:417-424.) PROSITE may be used to identify
functional or structural domains that cannot be detected using
conserved motifs due to extreme sequence divergence. The method is
based on weight matrices. Motifs identified by this method are then
calibrated against the SWISS-PROT database in order to obtain a
measure of the chance distribution of the matches.
[0230] In another embodiment, Hidden Markov models (HBMMs) may be
used to find shared motifs, specifically consensus sequences. (See,
e.g., Pearson, W. R. and D. J. Lipman (1988) Proc. Natl. Acad. Sci.
USA 85:2444-2448; and Smith, T. F. and M. S. Waterman (1981) J.
Mol. Biol. 147:195-197.) HMMs were initially developed to examine
speech recognition patterns, but are now being used in a biological
context to analyze protein and nucleic acid sequences as well as to
model protein structure. (See, e.g., Krogh, A. et al. (1994) J.
Mol. Biol. 235:1501-1531; and Collin, M. et al. (1993) Protein Sci.
2:305-314.) HMMs have a formal probabilistic basis and use
position-specific scores for amino acids or nucleotides. The
algorithm continues to incorporate information from newly
identified sequences to increase its motif analysis
capabilities.
[0231] VIII. Complementary Polynucleotides
[0232] Sequences complementary to the HSCD-encoding sequences, or
any parts thereof, are used to detect, decrease, or inhibit
expression of naturally occurring HSCD. Although use of
oligonucleotides comprising from about 15 to 30 base pairs is
described, essentially the same procedure is used with smaller or
with larger sequence fragments. Appropriate oligonucleotides are
designed using OLIGO 4.06 software and the coding sequence of HSCD.
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 HSCD-encoding transcript.
[0233] IX. Expression of HSCD
[0234] Expression of HSCD is accomplished by subcloning the cDNA
into an appropriate vector and transforming the vector into host
cells. This vector contains an appropriate promoter, e.g.,
.beta.-galactosidase, upstream of the cloning site, operably
associated with the cDNA of interest. (See, e.g., Sambrook, supra,
pp. 404-433; and Rosenberg, M. et al. (1983) Methods Enzymol.
101:123-138.)
[0235] Induction of an isolated, transformed bacterial strain with
isopropyl beta-D-thiogalactopyranoside (IPTG) using standard
methods produces a fusion protein which consists of the first 8
residues of .beta.-galactosidase, about 5 to 15 residues of linker,
and the full length protein. The signal residues direct the
secretion of HSCD into bacterial growth media which can be used
directly in the following assay for activity.
[0236] X. Demonstration of HSCD Activity
[0237] The oxidative and reductive CoA dehydrogenase activity is
measured with 100 .mu.g of protein, 200 pmol of
[6,7-.sup.3H]17.sup.beta-estradiol (or [6,7-.sup.3H]estrone for the
reduction) acetyl-CoA as a substrate in 100 mM phosphate buffer, pH
7.8 (pH 6.6) with 1 uM NAD.sup.+ as cofactor. Products of the
reaction are separated on a reversed phase (C18) high performance
liquid chromatography with mobile phase of acetonitrile:water 1:1
(v/v) as described in (See, e.g., Adamski J. et. al (1989) Acta
Endocr. 121:161-167.) Acyl CoA dehydrogenase activity is measured
by monitoring NAD.sup.+ formation at 340 nm using an ultraviolet
spectrophotometer. Michaelis-Menten K.sub.m values are estimated
from initial velocities (conversions of substrate less than 15%) of
the corresponding reactions. SDS-PAGE and western blotting is
performed as described in, e.g., Adamski, J. et al. (1992; Biochem.
J. 288:375-381).
[0238] XI. Production of HSCD Specific Antibodies
[0239] HSCD substantially purified using PAGE electrophoresis (see,
e.g., Harrington, M. G. (1990) Methods Enzymol. 182:488-495), or
other purification techniques, is used to immunize rabbits and to
produce antibodies using standard protocols. The HSCD amino acid
sequence is analyzed using DNASTAR software (DNASTAR Inc.) to
determine regions of high immunogenicity, and a corresponding
oligopeptide is synthesized and used to raise antibodies by to
means known to those of skill in the art. Methods for selection of
appropriate epitopes, such as those near the C-terminus or in
hydrophilic regions are well described in the art. (See, e.g.,
Ausubel et al. supra, ch. 11.)
[0240] Typically, the oligopeptides are 15 residues in length, and
are synthesized using an Applied Biosystems 431A peptide
synthesizer using fmoc-chemistry and coupled to KLH (Sigma, St.
Louis, Mo.) by reaction with
N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase
immunogenicity. (See, e.g., Ausubel et al. supra.) Rabbits are
immunized with the oligopeptide-KLH complex in complete Freund's
adjuvant. Resulting antisera are tested for antipeptide activity,
for example, by binding the peptide to plastic, blocking with 1%
BSA, reacting with rabbit antisera, washing, and reacting with
radio-iodinated goat anti-rabbit IgG.
[0241] XII. Purification of Naturally Occurring HSCD Using Specific
Antibodies
[0242] Naturally occurring or recombinant HSCD is substantially
purified by immunoaffinity chromatography using antibodies specific
for HSCD. An immunoaffinity column is constructed by covalently
coupling anti-HSCD antibody to an activated chromatographic resin,
such as CNBr-activated SEPHAROSE (Pharmacia & Upjohn). After
the coupling, the resin is blocked and washed according to the
manufacturer's instructions.
[0243] Media containing HSCD are passed over the immunoaffinity
column, and the column is washed under conditions that allow the
preferential absorbance of HSCD (e.g., high ionic strength buffers
in the presence of detergent). The column is eluted under
conditions that disrupt antibody/HSCD binding (e.g., a buffer of pH
2 to pH 3, or a high concentration of a chaotrope, such as urea or
thiocyanate ion), and HSCD is collected.
[0244] XIII. Identification of Molecules Which Interact with
HSCD
[0245] HSCD, or biologically active fragments thereof, are labeled
with .sup.125I Bolton-Hunter reagent. (See, e.g., Bolton, A. E. and
W. M. Hunter (1973) Biochem. J. 133:529-539.) Candidate molecules
previously arrayed in the wells of a multi-well plate are incubated
with the labeled HSCD, washed, and any wells with labeled HSCD
complex are assayed. Data obtained using different concentrations
of HSCD are used to calculate values for the number, affinity, and
association of HSCD with the candidate molecules.
[0246] Various modifications and variations of the described
methods and systems 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
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