U.S. patent application number 11/333838 was filed with the patent office on 2006-05-18 for 17867, a novel human aminopeptidase.
This patent application is currently assigned to Millennium Pharmaceuticals, Inc.. Invention is credited to Rosana Kapeller-Libermann, Mark Williamson.
Application Number | 20060105386 11/333838 |
Document ID | / |
Family ID | 23355903 |
Filed Date | 2006-05-18 |
United States Patent
Application |
20060105386 |
Kind Code |
A1 |
Kapeller-Libermann; Rosana ;
et al. |
May 18, 2006 |
17867, a novel human aminopeptidase
Abstract
The present invention relates to a newly identified human
aminopeptidase. The invention also relates to polynucleotides
encoding the aminopeptidase. The invention further relates to
methods using the aminopeptidase polypeptides and polynucleotides
as a target for diagnosis and treatment in aminopeptidase-related
disorders. The invention further relates to drug-screening methods
using the aminopeptidase polypeptides and polynucleotides to
identify agonists and antagonists for diagnosis and treatment. The
invention further encompasses agonists and antagonists based on the
aminopeptidase polypeptides and polynucleotides. The invention
further relates to procedures for producing the aminopeptidase
polypeptides and polynucleotides.
Inventors: |
Kapeller-Libermann; Rosana;
(Chestnut Hill, MA) ; Williamson; Mark; (Saugus,
MA) |
Correspondence
Address: |
MILLENNIUM PHARMACEUTICALS, INC.
40 Landsdowne Street
CAMBRIDGE
MA
02139
US
|
Assignee: |
Millennium Pharmaceuticals,
Inc.
|
Family ID: |
23355903 |
Appl. No.: |
11/333838 |
Filed: |
January 17, 2006 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10039073 |
Dec 31, 2001 |
|
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11333838 |
Jan 17, 2006 |
|
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09345650 |
Jun 30, 1999 |
6362324 |
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10039073 |
Dec 31, 2001 |
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Current U.S.
Class: |
435/6.11 ;
435/226; 435/320.1; 435/325; 435/6.16; 435/69.1; 435/7.23;
530/388.26; 536/23.2 |
Current CPC
Class: |
A61P 15/00 20180101;
A61P 35/00 20180101; A61P 1/00 20180101; G01N 2500/00 20130101;
A61P 43/00 20180101; A61P 11/00 20180101; Y02A 50/30 20180101; Y02A
50/475 20180101; C12N 9/48 20130101; A61P 3/10 20180101; C12Q 1/37
20130101; A61K 38/00 20130101 |
Class at
Publication: |
435/006 ;
435/007.23; 435/069.1; 435/226; 435/320.1; 435/325; 530/388.26;
536/023.2 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68; G01N 33/574 20060101 G01N033/574; C07H 21/04 20060101
C07H021/04; C12P 21/06 20060101 C12P021/06 |
Claims
1. An isolated nucleic acid molecule that encodes a polypeptide
having an amino peptidase protein activity, selected from the group
consisting of: a) a nucleic acid molecule comprising a nucleotide
sequence which is at least 70% identical to the nucleotide sequence
of SEQ ID NO:2, SEQ ID NO:3, or the nucleotide sequence of the DNA
insert of the plasmid deposited with ATCC as Accession Number
PTA-1642; b) a nucleic acid molecule comprising a nucleotide
sequence which is at least 80% identical to the nucleotide sequence
of SEQ ID NO:2, SEQ ID NO:3, or the nucleotide sequence of the DNA
insert of the plasmid deposited with ATCC as Accession Number
PTA-1642; c) a nucleic acid molecule comprising a nucleotide
sequence which is at least 90% identical to the nucleotide sequence
of SEQ ID NO:2, SEQ ID NO:3, or the nucleotide sequence of the DNA
insert of the plasmid deposited with ATCC as Accession Number
PTA-1642; d) a nucleic acid molecule that hybridizes to a nucleic
acid molecule comprising SEQ ID NO:2, SEQ ID NO:3, or a complement
thereof, under stringent conditions, said stringent conditions
comprising hybridization in 6.times.sodium chloride/sodium citrate
(SSC) at about 45.degree. C., followed by one or more washes in
0.2.times.SSC., 0.1% SDS at 50-65.degree. C.
2. The nucleic acid molecule of claim 1 further comprising vector
nucleic acid sequences.
3. The nucleic acid molecule of claim 1 further comprising nucleic
acid sequences encoding a heterologous polypeptide.
4. A host cell which contains the nucleic acid molecule of claim
2.
5. The host cell of claim 4 which is a mammalian host cell.
6. A non-human mammalian host cell containing the nucleic acid
molecule of claim 1.
7. An isolated polypeptide having an amino peptidase protein
activity, selected from the group consisting of: a) a polypeptide
which is encoded by a nucleic acid molecule comprising a nucleotide
sequence which is at least 70% identical to a nucleic acid
comprising the nucleotide sequence of SEQ ID NO:2, SEQ ID NO:3, or
the nucleotide sequence of the DNA insert of the plasmid deposited
with ATCC as Accession Number PTA- 1642; b) a polypeptide which is
encoded by a nucleic acid molecule comprising a nucleotide sequence
which is at least 80% identical to the nucleotide sequence of SEQ
ID NO:2, SEQ ID NO:3, or the nucleotide sequence of the DNA insert
of the plasmid deposited with ATCC as Accession Number PTA-1642; c)
a polypeptide which is encoded by a nucleic acid molecule
comprising a nucleotide sequence which is at least 90% identical to
the nucleotide sequence of SEQ ID NO:2, SEQ ID NO:3, or the
nucleotide sequence of the DNA insert of the plasmid deposited with
ATCC as Accession Number PTA-1642; d) a polypeptide encoded by a
nucleic acid molecule which hybridizes to a nucleic acid molecule
comprising SEQ ID NO:2, SEQ ID NO:3, or a complement thereof under
stringent conditions, said stringent conditions comprising
hybridization in 6.times.sodium chloride/sodium citrate (SSC) at
about 45.degree. C., followed by one or more washes in
0.2.times.SSC., 0.1% SDS at 50-65.degree. C; and e) a fragment of a
polypeptide comprising the amino acid sequence of SEQ ID NO:1, or
the amino acid sequence encoded by the cDNA insert of the plasmid
deposited with the ATCC as Accession Number PTA-1642, wherein the
fragment comprises at least 50 contiguous amino acids of SEQ ID
NO:2.
8. The isolated polypeptide of claim 7 comprising the amino acid
sequence of SEQ ID NO:1.
9. The polypeptide of claim 7 further comprising heterologous amino
acid sequences.
10. An antibody which selectively binds to a polypeptide of claim
7.
11. A method for producing a polypeptide comprising culturing the
host cell of claim 4 under conditions in which the nucleic acid
molecule is expressed.
12. A method for detecting the presence of a polypeptide of claim 7
in a sample, comprising: a) contacting the sample with a compound
which selectively binds to a polypeptide of claim 7; and b)
determining whether the compound binds to the polypeptide in the
sample.
13. A method for detecting the presence of a polypeptide of claim 8
in a sample, comprising: a) contacting the sample with a compound
which selectively binds to a polypeptide of claim 8; and b)
determining whether the compound binds to the polypeptide in the
sample.
14. The method of claim 13, wherein the compound which binds to the
polypeptide is an antibody.
15. A kit comprising a compound which selectively binds to a
polypeptide of claim 8 and instructions for use.
16. A method for detecting the presence of a nucleic acid molecule
of claim 1 in a sample, comprising the steps of: a) contacting the
sample with a nucleic acid probe or primer which selectively
hybridizes to the nucleic acid molecule; and b) determining whether
the nucleic acid probe or primer binds to a nucleic acid molecule
in the sample.
17. The method of claim 16, wherein the sample comprises mRNA
molecules and is contacted with a nucleic acid probe.
18. A kit comprising a compound which selectively hybridizes to a
nucleic acid molecule of claim 1 and instructions for use.
19. A method for identifying a compound which binds to a
polypeptide of claim 8 comprising the steps of: a) contacting a
polypeptide, or a cell expressing a polypeptide of claim 8 with a
test compound; and b) determining whether the polypeptide binds to
the test compound.
20. The method of claim 19, wherein the binding of the test
compound to the polypeptide is detected by a method selected from
the group consisting of: a) detection of binding by direct
detecting of test compound/polypeptide binding; b) detection of
binding using a competition binding assay; c) detection of binding
using an assay for aminopeptidase protein activity.
21. A method for modulating the activity of a polypeptide of claim
8 comprising contacting a polypeptide or a cell expressing a
polypeptide of claim 8 with a compound which binds to the
polypeptide in a sufficient concentration to modulate the activity
of the polypeptide.
22. A method for identifying a compound which modulates the
activity of a polypeptide of claim 8, comprising: a) contacting a
polypeptide of claim 8 with a test compound; and b) determining the
effect of the test compound on the activity of the polypeptide to
thereby identify a compound which modulates the activity of the
polypeptide.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a divisional of U.S. Ser. No.
10/039,073, filed Dec. 31, 2001 (pending), which is a continuation
of U.S. Ser. No. 09/345,650, filed Jun. 30, 1999, now U.S. Pat. No.
6,362,324, which are hereby incorporated in their entirety by
reference herein.
FIELD OF THE INVENTION
[0002] The present invention relates to a newly identified human
arninopeptidase. The invention also relates to polynucleotides
encoding the aminopeptidase. The invention further relates to
methods using the aminopeptidase polypeptides and polynucleotides
as a target for diagnosis and treatment in aminopeptidase-related
disorders. The invention further relates to drug-screening methods
using the aminopeptidase polypeptides and polynucleotides to
identify agonists and antagonists for diagnosis and treatment. The
invention further encompasses agonists and antagonists based on the
aminopeptidase polypeptides and polynucleotides. The invention
further relates to procedures for producing the aminopeptidase
polypeptides and polynucleotides.
BACKGROUND OF THE INVENTION
[0003] Proteases may function in carcinogenesis by inactivating or
activating regulators of the cell cycle, differentiation,
programmed cell death, or other processes affecting cancer
development and/or progression. Consistent with the model involving
protease activity and tumor progression, certain protease
inhibitors have been shown to be effective inhibitors of
carcinogenesis both in vitro and in vivo.
[0004] Aminopeptidases (APs) are a group of widely distributed
exopeptidases that catalyse the hydrolysis of amino acid residues
from the amino-terminus of polypeptides and proteins. The enzymes
are found in plant and animal tissue, in eukaryotes and
prokaryotes, and in secreted and soluble forms. Biological
functions of aminopeptidases include protein maturation, terminal
degradation of proteins, hormone level regulation, and cell-cycle
control.
[0005] The enzymes are implicated in a host of conditions and
disorders including aging, cancers, cataracts, cystic fibrosis and
leukemias. In eukaryotes, APs are associated with removal of the
initiator methionine. In prokaryotes the methionine is removed by
methionine aminopeptidase subsequent to removal of the N-formyl
group from the initiator N-formyl methionine, facilitating
subsequent modifications such as N-acetylation and
N-myristoylation. In E. coli AP-A (pepA), the xerB gene product is
required for stabilization of unstable plasmid multimers.
[0006] APs are also involved in the metabolism of secreted
regulatory molecules, such as hormones and neurotransmitters, and
modulation of cell-cell interactions. In mammalian cells and
tissues, the enzymes are apparently required for terminal stages of
protein degradation, and EGF-induced cell-cycle control; and may
have a role in protein turnover and selective elimination of
obsolete or defective proteins. Furthermore, the enzymes are
implicated in the supply of amino acids and energy during
starvation and/or differentiation, and degradation of transported
exogenous peptides to amino acids for nutrition. As leukotriene A4
hydrolase may be an aminopeptidase, APs may further have a role in
inflammation. Industrial uses of the enzymes include modification
of amino termini in recombinantly expressed proteins. See A. Taylor
(1993) TIBS 18: 1993:167-172.
[0007] A variety of aminopeptidases have been identified from a
wide variety of tissues and organisms, including zinc
aminopeptidase and aminopeptidase M from rat kidney membrane;
arginine aminopeptidase from liver; aminopeptidase N.sup.b from
muscle; leucine aminopeptidase (LAP) from bovine and hog lens and
kidney; aminopeptidase A (xerB gene product) from E. coli; yscl
APE1/LAP4 and aminopeptidase A (pep4 gene product) from S.
cerevisiae; LAP from aeromonas; dipeptidase from mouse ascites;
methionine aminopeptidase from salmonella, E. coli, S. cerevisiae
and hog liver; and D-amino acid aminopeptidase from ochrobactrum
anthropi SCRC C1-38.
[0008] Of these aminopeptidases, the structure of bovine lens
leucine aminopeptidase (blLAP) is well characterized and consists
of a homohexamer synthesized as a large precursor, each monomer
containing two thirds of the protein in a major lobe and one third
in a minor lobe. The minor lobe contains the N-terminal 150
residues. All putative active site residues, presumably also the
inhibitor bestatin-binding site, are found in the C-terminal lobe
and include Ala-333, Asn-330, Leu360, Asp332, Asp255, Glu-334,
Lys250, Asp273, Met454, Ala-451, Gly362, Thr-359, Met270, Lys262,
Gly362 and Ile-421.
[0009] Many aminopeptidases are metalloenzymes, requiring divalent
cations, with specificities for Zn.sup.2+ or Co.sup.2+; however,
particular sites of certain aminopeptidases can readily utilize
Mn.sup.2+ and Mg.sup.2+. Residues used to ligand Zn.sup.2+ include
the His His Glu and Asp Glu Lys configurations. In addition to
bestatin, boronic and phosphonic acids, .alpha.-methylleucine and
isoamylthioamide are identified as competitive inhibitors for most
aminopeptidases. See A. Taylor (1993) TIBS 18: 1993:167-172; Burley
et al. (1992) J. Mol. Biol. 224:113-140; Taylor et al. (1993)
Biochemistry 32:784-790.
[0010] Aminopeptidases from various organisms and various tissues
within an organism have high degrees of primary sequence homology,
as indicated by immunological assays. Some enzymes also exhibit
very similar kinetic profiles. Direct amino acids sequence
comparison of blLAP and aminopeptidase-A from E. coli shows 18, 44
and 35% identity for the amino- and carboxy-terminals, and the
entire protein, respectively. The comparison shows 46, 66, and 60%
identity for the respective regions. See Burley et al. (1992) J.
Mol. Biol. 224:113-140.
[0011] Bovine lens leucine aminopeptidase (biLAP), bovine kidney
LAP, human lens and liver LAPs, hog, lens, kidney and intestine
LAPs, proline-AP, E. coli AP-A, AP-I and the S. typhimurium pepA
gene product have been categorized as belonging to the family of
zinc aminopeptidases which utilize the residues Asp Glu Lys for
zinc binding and the active site amino acid configuration described
above for bovine LAP for substrate binding. This family, possibly
also including Aeromonas LAP, is suggested to be distinguished from
zinc proteases which utilize His His Glu in zinc binding and Arg in
substrate binding. The Saccharomyces methionine-AP is characterized
to contain two zinc finger like motifs in the amino-terminus and
shares little homology with biLAP. See A. Taylor (1993) TIBS 18:
MAY 1993:167-171; Watt et al. (1989) J. Biol. Chem.
264:5480-5487.
[0012] Leucine aminopeptidase expression is regulated at the
transcriptional level, evidenced by enhancement of both activity
and mRNA upon removal of serum in in vitro aged and/or transforming
lens epithelial cells. Furthermore, LAP mRNA and protein is induced
by interferon y in human ACHN renal carcinoma, A549 lung carcinoma,
HS1 53 fibroblasts and A375 melanoma. Regulation by development and
growth is also implicated. The E. coli pepN gene is
transcriptionally regulated upon anaerobiosis and phosphate
starvation. Membrane bound AP-N (CD13) is expressed in a
lineage-restricted manner by subsets of normal and malignant cells,
apparently through regulation by physically distinct promoters.
Expression of the yeast yscl product APEI is dependent upon the
levels of yscA and PEP4 gene products. Synthesis of APE1 is
sensitive to media glucose levels, and the activity of yeast
aminopeptidase is sensitive to substitution of ammonia rather than
peptone as the source of nitrogen. See Harris et al. (1992) J.
Biol. Chem. 267:6865-6869; Jones et al. (1982) Genetics
102:665-677.
[0013] Accordingly, aminopeptidases are a major target for drug
action and development. Therefore, it is valuable to the field of
pharmaceutical development to identify and characterize previously
unknown aminopeptidases. The present invention advances the state
of the art by providing a previously unidentified human
aminopeptidase.
SUMMARY OF THE INVENTION
[0014] It is an object of the invention to identify novel
aminopeptidases.
[0015] It is a further object of the invention to provide novel
aminopeptidase polypeptides that are useful as reagents or targets
in aminopeptidase assays applicable to treatment and diagnosis of
aminopeptidase-related disorders.
[0016] It is a further object of the invention to provide
polynucleotides corresponding to the novel aminopeptidase
polypeptides that are useful as targets and reagents in
aminopeptidase assays applicable to treatment and diagnosis of
aminopeptidase-related disorders and useful for producing novel
aminopeptidase polypeptides by recombinant methods.
[0017] A specific object of the invention is to identify compounds
that act as agonists and antagonists and modulate the expression of
the novel aminopeptidase.
[0018] A further specific object of the invention is to provide
compounds that modulate expression of the aminopeptidase for
treatment and diagnosis of aminopeptidase-related disorders.
[0019] The invention is thus based on the identification of a novel
human aminopeptidase. The amino acid sequence is shown in SEQ ID NO
1. The nucleotide sequence is shown as SEQ ID NO 2.
[0020] The invention provides isolated arninopeptidase
polypeptides, including a polypeptide having the amino acid
sequence shown in SEQ ID NO 1 or the amino acid sequence encoded by
the cDNA deposited as ATCC Patent Deposit No. PTA-1642 on Apr. 5,
2000 ("the deposited cDNA").
[0021] The invention also provides isolated aminopeptidase nucleic
acid molecules having the sequence shown in SEQ ID NO 2 or in the
deposited cDNA.
[0022] The invention also provides variant polypeptides having an
amino acid sequence that is substantially homologous to the amino
acid sequence shown in SEQ ID NO 1 or encoded by the deposited
cDNA.
[0023] The invention also provides variant nucleic acid sequences
that are substantially homologous to the nucleotide sequence shown
in SEQ ID NO 2 or in the deposited cDNA.
[0024] The invention also provides fragments of the polypeptide
shown in SEQ ID NO 1 and nucleotide sequence shown in SEQ ID NO 2,
as well as substantially homologous fragments of the polypeptide or
nucleic acid.
[0025] The invention further provides nucleic acid constructs
comprising the nucleic acid molecules described herein. In a
preferred embodiment, the nucleic acid molecules of the invention
are operatively linked to a regulatory sequence.
[0026] The invention also provides vectors and host cells for
expressing the aminopeptidase nucleic acid molecules and
polypeptides, and particularly recombinant vectors and host
cells.
[0027] The invention also provides methods of making the vectors
and host cells and methods for using them to produce the
aminopeptidase nucleic acid molecules and polypeptides.
[0028] The invention also provides antibodies or antigen-binding
fragments thereof that selectively bind the aminopeptidase
polypeptides and fragments.
[0029] The invention also provides methods of screening for
compounds that modulate expression or activity of the
aminopeptidase polypeptides or nucleic acid (RNA or DNA).
[0030] The invention also provides a process for modulating
aminopeptidase polypeptide or nucleic acid expression or activity,
especially using the screened compounds. Modulation may be used to
treat conditions related to aberrant activity or expression of the
aminopeptidase polypeptides or nucleic acids.
[0031] The invention also provides assays for determining the
activity of or the presence or absence of the arninopeptidase
polypeptides or nucleic acid molecules in a biological sample,
including for disease diagnosis.
[0032] The invention also provides assays for determining the
presence of a mutation in the polypeptides or nucleic acid
molecules, including for disease diagnosis.
[0033] In still a further embodiment, the invention provides a
computer readable means containing the nucleotide and/or amino acid
sequences of the nucleic acids and polypeptides of the invention,
respectively.
DESCRIPTION OF THE DRAWINGS
[0034] FIG. 1A-C shows the aminopeptidase nucleotide sequence (SEQ
ID NO 2), the coding region (nucleotides 146-3028 of SEQ ID NO:2;
nucleotides 1-2883 of SEQ ID NO:3) and the deduced amino acid
sequence (SEQ ID NO 1).
[0035] FIG. 2 shows an analysis of the aminopeptidase amino acid
sequence: ottum and coil regions; hydrophilicity; amphipathic
regions; flexible regions; antigenic index; and surface probability
plot.
[0036] FIG. 3 shows a hydrophobicity plot of the
aminopeptidase.
[0037] FIG. 4A-C shows an analysis of the aminopeptidase open
reading frame for amino acids corresponding to specific functional
sites. The protein also contains a zinc binding region signature
found in neutral zinc metallopeptidases.
[0038] FIG. 5 shows RNA expression of the aminopeptidase in normal
human tissues and in carcinomas.
[0039] FIG. 6 shows RNA expression of the aminopeptidase in human
tissues and cells.
DETAILED DESCRIPTION OF THE INVENTION
Polypeptides
[0040] The invention is based on the discovery of a novel human
aminopeptidase. Specifically, an expressed sequence tag (EST) was
selected based on homology to aminopeptidase sequences. This EST
was used to design primers based on sequences that it contains and
used to identify a cDNA from endothelial cell cDNA library.
Positive clones were sequenced and the overlapping fragments were
assembled. Analysis of the assembled sequence revealed that the
cloned cDNA molecule encodes an aminopeptidase.
[0041] The invention thus relates to a novel aminopeptidase having
the deduced amino acid sequence shown in FIG. 1 (SEQ ID NO 1) or
having the amino acid sequence encoded by the cDNA deposited in a
bacterial host with the Patent Depository of the American Type
Culture Collection (ATCC), Manassas, Va., on Apr. 5, 2000 and
assigned Patent Deposit No. PTA-1642.
[0042] The deposit will be maintained under the terms of the
Budapest Treaty on the International Recognition of the Deposit of
Microorganisms. The deposit is provided as a convenience to those
of skill in the art and is not an admission that a deposit is
required under 35 U.S.C. .sctn. 112. The deposited sequence, as
well as the polypeptides encoded by the sequence, is incorporated
herein by reference and controls in the event of any conflict, such
as a sequencing error, with description in this application.
[0043] "Aminopeptidase polypeptide" or "aminopeptidase protein"
refers to the polypeptide in SEQ ID NO 1 or encoded by the
deposited cDNA. The term "aminopeptidase protein" or
"aminopeptidase polypeptide", however, further includes the
numerous variants described herein, as well as fragments derived
from the full-length aminopeptidase and variants.
[0044] Tissues and/or cells in which the aminopeptidase is found
include, but are not limited to, the tissues shown in FIGS. 5 and
6. In addition to these tissues, expression has also been found in
colon and breast carcinoma and in lung carcinoma, especially
squamous cell carcinoma.
[0045] The present invention thus provides an isolated or purified
aminopeptidase polypeptide and variants and fragments thereof.
[0046] Based on a BLAST search, highest homology was shown to an
insulin-regulated membrane aminopeptidase.
[0047] As used herein, a polypeptide is said to be "isolated" or
"purified" when it is substantially free of cellular material when
it is isolated from recombinant and non-recombinant cells, or free
of chemical precursors or other chemicals when it is chemically
synthesized. A polypeptide, however, can be joined to another
polypeptide with which it is not normally associated in a cell and
still be considered "isolated" or "purified."
[0048] The aminopeptidase polypeptides can be purified to
homogeneity. It is understood, however, that preparations in which
the polypeptide is not purified to homogeneity are useful and
considered to contain an isolated form of the polypeptide. The
critical feature is that the preparation allows for the desired
function of the polypeptide, even in the presence of considerable
amounts of other components. Thus, the invention encompasses
various degrees of purity.
[0049] In one embodiment, the language "substantially free of
cellular material" includes preparations of the aminopeptidase
having less than about 30% (by dry weight) other proteins (i.e.,
contaminating protein), less than about 20% other proteins, less
than about 10% other proteins, or less than about 5% other
proteins. When the polypeptide is recombinantly produced, it can
also be substantially free of culture medium, i.e., culture medium
represents less than about 20%, less than about 10%, or less than
about 5% of the volume of the protein preparation.
[0050] An aminopeptidase polypeptide is also considered to be
isolated when it is part of a membrane preparation or is purified
and then reconstituted with membrane vesicles or liposomes.
[0051] The language "substantially free of chemical precursors or
other chemicals" includes preparations of the aminopeptidase
polypeptide in which it is separated from chemical precursors or
other chemicals that are involved in its synthesis. In one
embodiment, the language "substantially free of chemical precursors
or other chemicals" includes preparations of the polypeptide having
less than about 30% (by dry weight) chemical precursors or other
chemicals, less than about 20% chemical precursors or other
chemicals, less than about 10% chemical precursors or other
chemicals, or less than about 5% chemical precursors or other
chemicals.
[0052] In one embodiment, the aminopeptidase polypeptide comprises
the amino acid sequence shown in SEQ ID NO 1. However, the
invention also encompasses sequence variants. Variants include a
substantially homologous protein encoded by the same genetic locus
in an organism, i.e., an allelic variant. Variants also encompass
proteins derived from other genetic loci in an organism, but having
substantial homology to the aminopeptidase of SEQ ID NO 1. Variants
also include proteins substantially homologous to the
aminopeptidase but derived from another organism, i.e., an
ortholog. Variants also include proteins that are substantially
homologous to the aminopeptidase that are produced by chemical
synthesis. Variants also include proteins that are substantially
homologous to the aminopeptidase that are produced by recombinant
methods. It is understood, however, that variants exclude any amino
acid sequences disclosed prior to the invention.
[0053] As used herein, two proteins (or a region of the proteins)
are substantially homologous when the amino acid sequences are at
least about 60-65%, 65-70%, 70-75%, typically at least about
80-85%, and most typically at least about 90-95% or more
homologous. A substantially homologous amino acid sequence,
according to the present invention, will be encoded by a nucleic
acid sequence hybridizing to the nucleic acid sequence, or portion
thereof, of the sequence shown in SEQ ID NO 2 under stringent
conditions as more fully described below.
[0054] To determine the percent identity of two amino acid
sequences or of two nucleic acid sequences, the sequences are
aligned for optimal comparison purposes (e.g., gaps can be
introduced in one or both of a first and a second amino acid or
nucleic acid sequence for optimal alignment and non-homologous
sequences can be disregarded for comparison purposes). In a
preferred embodiment, the length of a reference sequence aligned
for comparison purposes is at least 30%, preferably at least 40%,
more preferably at least 50%, even more preferably at least 60%,
and even more preferably at least 70%, 80%, or 90% of the length of
the reference sequence (e.g., when aligning a second sequence to
the amino acid sequences herein having 502 amino acid residues, at
least 165, preferably at least 200, more preferably at least 250,
even more preferably at least 300, and even more preferably at
least 350, 400, 450, and 500 amino acid residues are aligned). The
amino acid residues or nucleotides at corresponding amino acid
positions or nucleotide positions are then compared. When a
position in the first sequence is occupied by the same amino acid
residue or nucleotide as the corresponding position in the second
sequence, then the molecules are identical at that position (as
used herein amino acid or nucleic acid "identity" is equivalent to
amino acid or nucleic acid "homology"). The percent identity
between the two sequences is a function of the number of identical
positions shared by the sequences, taking into account the number
of gaps, and the length of each gap, which need to be introduced
for optimal alignment of the two sequences.
[0055] The invention also encompasses polypeptides having a lower
degree of identity but having sufficient similarity so as to
perform one or more of the same functions performed by the
aminopeptidase. Similarity is determined by conserved amino acid
substitution. Such substitutions are those that substitute a given
amino acid in a polypeptide by another amino acid of like
characteristics. Conservative substitutions are likely to be
phenotypically silent. Typically seen as conservative substitutions
are the replacements, one for another, among the aliphatic amino
acids Ala, Val, Leu, and Ile; interchange of the hydroxyl residues
Ser and Thr, exchange of the acidic residues Asp and Glu,
substitution between the amide residues Asn and Gln, exchange of
the basic residues Lys and Arg and replacements among the aromatic
residues Phe, Tyr. Guidance concerning which amino acid changes are
likely to be phenotypically silent are found in Bowie et al.,
Science 247:1306-1310 (1990). TABLE-US-00001 TABLE 1 Conservative
Amino Acid Substitutions. Aromatic Phenylalanine Tryptophan
Tyrosine Hydrophobic Leucine Isoleucine Valine Polar Glutamine
Asparagine Basic Arginine Lysine Histidine Acidic Aspartic Acid
Glutamic Acid Small Alanine Serine Threonine Methionine Glycine
[0056] The comparison of sequences and determination of percent
identity and similarity between two sequences can be accomplished
using a mathematical algorithm. (Computational Molecular Biology,
Lesk, A. M., ed., Oxford University Press, New York, 1988;
Biocomputing: Informatics and Genome Projects, Smith, D. W., ed.,
Academic Press, New York, 1993; Computer Analysis of Sequence Data,
Part 1, Griffin, A. M., and Griffin, H. G., eds., Humana Press, New
Jersey, 1994; Sequence Analysis in Molecular Biology, von Heinje,
G., Academic Press, 1987; and Sequence Analysis Primer, Gribskov,
M. and Devereux, J., eds., M Stockton Press, New York, 1991).
[0057] A preferred, non-limiting example of such a mathematical
algorithm is described in Karlin et al. (1993) Proc. Natl. Acad.
Sci. USA 90:5873-5877. Such an algorithm is incorporated into the
NBLAST and XBLAST programs (version 2.0) as described in Altschul
et al. (1997) Nucleic Acids Res. 25:3389-3402. When utilizing BLAST
and Gapped BLAST programs, the default parameters of the respective
programs (e.g., NBLAST) can be used. See www.ncbi.nlm.nih.gov. In
one embodiment, parameters for sequence comparison can be set at
score=100, wordlength=12, or can be varied (e.g., W=5or W=20).
[0058] In a preferred embodiment, the percent identity between two
amino acid sequences is determined using the Needleman et al.
(1970) (J. Mol. Biol. 48:444-453) algorithm which has been
incorporated into the GAP program in the GCG software package
(available at www.gcg.com), using either a BLOSUM 62 matrix or a
PAM250 matrix, and a gap weight of 16, 14, 12, 10, 8, 6, or 4 and a
length weight of 1, 2, 3, 4, 5, or 6. In yet another preferred
embodiment, the percent identity between two nucleotide sequences
is determined using the GAP program in the GCG software package
(Devereux et al. (1984) Nucleic Acids Res. 12(1):387) (available at
www.gcg.com), using a NWSgapdna.CMP matrix and a gap weight of 40,
50, 60, 70, or 80 and a length weight of 1, 2, 3, 4, 5, or 6.
[0059] Another preferred, non-limiting example of a mathematical
algorithm utilized for the comparison of sequences is the algorithm
of Myers and Miller, CABIOS (1989). Such an algorithm is
incorporated into the ALIGN program (version 2.0) which is part of
the CGC sequence alignment software package. When utilizing the
ALIGN program for comparing amino acid sequences, a PAM120 weight
residue table, a gap length penalty of 12, and a gap penalty of 4
can be used. Additional algorithms for sequence analysis are known
in the art and include ADVANCE and ADAM as described in Torellis et
al. (1994) Comput. Appl. Biosci. 10:3-5; and FASTA described in
Pearson et al. (1988) PNAS 85:2444-8.
[0060] A variant polypeptide can differ in amino acid sequence by
one or more substitutions, deletions, insertions, inversions,
fusions, and truncations or a combination of any of these.
[0061] Variant polypeptides can be fully functional or can lack
function in one or more activities. Thus, in the present case,
variations can affect the function, for example, of one or more of
the regions corresponding to the catalytic region, regulatory
regions, substrate binding regions, zinc binding regions, regions
involved in membrane association, and regions involved in enzyme
modification, for example, by phosphorylation.
[0062] Fully functional variants typically contain only
conservative variation or variation in non-critical residues or in
non-critical regions. Functional variants can also contain
substitution of similar amino acids, which results in no change or
an insignificant change in function. Alternatively, such
substitutions may positively or negatively affect function to some
degree.
[0063] Non-functional variants typically contain one or more
non-conservative amino acid substitutions, deletions, insertions,
inversions, or truncation or a substitution, insertion, inversion,
or deletion in a critical residue or critical region.
[0064] As indicated, variants can be naturally-occurring or can be
made by recombinant means or chemical synthesis to provide useful
and novel characteristics for the aminopeptidase polypeptide. This
includes preventing immunogenicity from pharmaceutical formulations
by preventing protein aggregation.
[0065] Useful variations further include alteration of catalytic
activity. For example, one embodiment involves a variation at the
peptide binding site that results in binding but not hydrolysis of
the peptide substrate. A further useful variation at the same site
can result in altered affinity for the peptide substrate. Useful
variations also include changes that provide for affinity for
another peptide substrate. Another useful variation provides a
fusion protein in which one or more domains or subregions are
operationally fused to one or more domains or subregions from
another aminopeptidase.
[0066] Amino acids that are essential for function can be
identified by methods known in the art, such as site-directed
mutagenesis or alanine-scanning mutagenesis (Cunningham et al.
(1985) Science 244:1081-1085). The latter procedure introduces
single alanine mutations at every residue in the molecule. The
resulting mutant molecules are then tested for biological activity,
such as peptide bond hydrolysis in vitro or related biological
activity, such as proliferative activity. Sites that are critical
for binding can also be determined by structural analysis such as
crystallization, nuclear magnetic resonance or photoaffinity
labeling (Smith et al. (1992) J. Mol. Biol. 224:899-904; de Vos et
al. (1992) Science 255:306-312).
[0067] Substantial homology can be to the entire nucleic acid or
amino acid sequence or to fragments of these sequences.
[0068] The invention thus also includes polypeptide fragments of
the aminopeptidase. Fragments can be derived from the amino acid
sequence shown in SEQ ID NO. 1. However, the invention also
encompasses fragments of the variants of the aminopeptidase as
described herein.
[0069] The fragments to which the invention pertains, however, are
not to be construed as encompassing fragments that may be disclosed
prior to the present invention.
[0070] Accordingly, a fragment can comprise at least about 10, 15,
20, 25, 30, 35, 40, 45, 50 or more contiguous amino acids.
Fragments can retain one or more of the biological activities of
the protein, for example the ability to bind to or hydrolyze target
peptides, as well as fragments that can be used as an immunogen to
generate aminopeptidase antibodies.
[0071] Biologically active fragments (peptides which are, for
example, 5, 7, 10, 12, 15, 20, 30, 35, 36, 37, 38, 39, 40, 50, 100
or more amino acids in length) can comprise a functional site. Such
sites include but are not limited to the catalytic site, regulatory
sites, sites important for substrate recognition or binding, zinc
binding region, the region containing a metalloprotease motif
(IAHELAHQW), sites containing the motif characteristic of
aminopeptidases in the M1 family (GAMEN), the site contributing to
exopeptidase specificity, the peptidase domain from about amino
acid 69 to about amino acid 458, phosphorylation sites,
glycosylation sites, and other functional sites disclosed
herein.
[0072] Such sites or motifs can be identified by means of routine
computerized homology searching procedures.
[0073] Fragments, for example, can extend in one or both directions
from the functional site to encompass 5, 10, 15, 20, 30, 40, 50, or
up to 100 amino acids. Further, fragments can include sub-fragments
of the specific sites or regions disclosed herein, which
sub-fragments retain the function of the site or region from which
they are derived.
[0074] These regions can be identified by well-known methods
involving computerized homology analysis.
[0075] The invention also provides fragments with immunogenic
properties. These contain an epitope-bearing portion of the
aminopeptidase and variants. These epitope-bearing peptides are
useful to raise antibodies that bind specifically to an
aminopeptidase polypeptide or region or fragment. These peptides
can contain at least 10, 12, at least 14, or between at least about
15 to about 30 amino acids.
[0076] Non-limiting examples of antigenic polypeptides that can be
used to generate antibodies include but are not limited to peptides
derived from extracellular regions. Regions having a high
antigenicity index are shown in FIG. 2. However,
intracellularly-made antibodies ("intrabodies") are also
encompassed, which would recognize intracellular peptide
regions.
[0077] The epitope-bearing aminopeptidase polypeptides may be
produced by any conventional means (Houghten, R. A. (1985) Proc.
Natl. Acad. Sci. USA 82:5131-5135). Simultaneous multiple peptide
synthesis is described in U.S. Pat. No. 4,631,211.
[0078] Fragments can be discrete (not fused to other amino acids or
polypeptides) or can be within a larger polypeptide. Further,
several fragments can be comprised within a single larger
polypeptide. In one embodiment a fragment designed for expression
in a host can have heterologous pre- and pro-polypeptide regions
fused to the amino terminus of the aminopeptidase fragment and an
additional region fused to the carboxyl terminus of the
fragment.
[0079] The invention thus provides chimeric or fusion proteins.
These comprise an aminopeptidase peptide sequence operatively
linked to a heterologous peptide having an amino acid sequence not
substantially homologous to the aminopeptidase. "Operatively
linked" indicates that the aminopeptidase peptide and the
heterologous peptide are fused in-frame. The heterologous peptide
can be fused to the N-terminus or C-terminus of the aminopeptidase
or can be internally located.
[0080] In one embodiment the fusion protein does not affect
aminopeptidase function per se. For example, the fusion protein can
be a GST-fusion protein in which the aminopeptidase sequences are
fused to the C-terminus of the GST sequences. Other types of fusion
proteins include, but are not limited to, enzymatic fusion
proteins, for example beta-galactosidase fusions, yeast two-hybrid
GALA fusions, poly-His fusions and Ig fusions. Such fusion
proteins, particularly poly-His fusions, can facilitate the
purification of recombinant aminopeptidase. In certain host cells
(e.g., mammalian host cells), expression and/or secretion of a
protein can be increased by using a heterologous signal sequence.
Therefore, in another embodiment, the fusion protein contains a
heterologous signal sequence at its N-terminus.
[0081] EP-A-O 464 533 discloses fusion proteins comprising various
portions of immunoglobulin constant regions. The Fc is useful in
therapy and diagnosis and thus results, for example, in improved
pharmacokinetic properties (EP-A 0232 262). In drug discovery, for
example, human proteins have been fused with Fc portions for the
purpose of high-throughput screening assays to identify antagonists
(Bennett et al. (1995) J. Mol. Recog. 8:52-58 (1995) and Johanson
et al. J. Biol. Chem. 270:9459-9471). Thus, this invention also
encompasses soluble fusion proteins containing an aminopeptidase
polypeptide and various portions of the constant regions of heavy
or light chains of immunoglobulins of various subclass (IgG, IgM,
IgA, IgE). Preferred as immunoglobulin is the constant part of the
heavy chain of human IgG, particularly IgG1, where fusion takes
place at the hinge region. For some uses it is desirable to remove
the Fc after the fusion protein has been used for its intended
purpose, for example when the fusion protein is to be used as
antigen for immunizations. In a particular embodiment, the Fc part
can be removed in a simple way by a cleavage sequence, which is
also incorporated and can be cleaved with factor Xa.
[0082] A chimeric or fusion protein can be produced by standard
recombinant DNA techniques. For example, DNA fragments coding for
the different protein sequences are ligated together in-frame in
accordance with conventional techniques. In another embodiment, the
fusion gene can be synthesized by conventional techniques including
automated DNA synthesizers. Alternatively, PCR amplification of
gene fragments can be carried out using anchor primers which give
rise to complementary overhangs between two consecutive gene
fragments which can subsequently be annealed and re-amplified to
generate a chimeric gene sequence (see Ausubel et al. (1992)
Current Protocols in Molecular Biology). Moreover, many expression
vectors are commercially available that already encode a fusion
moiety (e.g., a GST protein). An aminopeptidase-encoding nucleic
acid can be cloned into such an expression vector such that the
fusion moiety is linked in-frame to the aminopeptidase.
[0083] Another form of fusion protein is one that directly affects
aminopeptidase functions. Accordingly, an aminopeptidase
polypeptide is encompassed by the present invention in which one or
more of the aminopeptidase regions (or parts thereof) has been
replaced by homologous regions (or parts thereof) from another
aminopeptidase. Accordingly, various permutations are possible.
Thus, chimeric aminopeptidases can be formed in which one or more
of the native domains or subregions has been replaced by
another.
[0084] Additionally, chimeric aminopeptidase proteins can be
produced in which one or more functional sites is derived from a
different aminopeptidase. It is understood however that sites could
be derived from aminopeptidases that occur in the mammalian genome
but which have not yet been discovered or characterized.
[0085] The isolated aminopeptidase protein can be purified from
cells that naturally express it, such as from any of those tissues
shown in FIGS. 5 and 6, especially purified from cells that have
been altered to express it (recombinant), or synthesized using
known protein synthesis methods.
[0086] In one embodiment, the protein is produced by recombinant
DNA techniques. For example, a nucleic acid molecule encoding the
aminopeptidase polypeptide is cloned into an expression vector, the
expression vector introduced into a host cell and the protein
expressed in the host cell. The protein can then be isolated from
the cells by an appropriate purification scheme using standard
protein purification techniques. Polypeptides often contain amino
acids other than the 20 amino acids commonly referred to as the 20
naturally-occurring amino acids. Further, many amino acids,
including the terminal amino acids, may be modified by natural
processes, such as processing and other post-translational
modifications, or by chemical modification techniques well known in
the art. Common modifications that occur naturally in polypeptides
are described in basic texts, detailed monographs, and the research
literature, and they are well known to those of skill in the
art.
[0087] Accordingly, the polypeptides also encompass derivatives or
analogs in which a substituted amino acid residue is not one
encoded by the genetic code, in which a substituent group is
included, in which the mature polypeptide is fused with another
compound, such as a compound to increase the half-life of the
polypeptide (for example, polyethylene glycol), or in which the
additional amino acids are fused to the mature polypeptide, such as
a leader or secretory sequence or a sequence for purification of
the mature polypeptide or a pro-protein sequence.
[0088] Known modifications include, but are not limited to,
acetylation, acylation, ADP-ribosylation, amidation, covalent
attachment of flavin, covalent attachment of a heme moiety,
covalent attachment of a nucleotide or nucleotide derivative,
covalent attachment of a lipid or lipid derivative, covalent
attachment of phosphatidylinositol, cross-linking, cyclization,
disulfide bond formation, demethylation, formation of covalent
crosslinks, formation of cystine, formation of pyroglutamate,
formylation, gamma carboxylation, glycosylation, GPI anchor
formation, hydroxylation, iodination, methylation, myristoylation,
oxidation, proteolytic processing, phosphorylation, prenylation,
racemization, selenoylation, sulfation, transfer-RNA mediated
addition of amino acids to proteins such as arginylation, and
ubiquitination.
[0089] Such modifications are well-known to those of skill in the
art and have been described in great detail in the scientific
literature. Several particularly common modifications,
glycosylation, lipid attachment, sulfation, gamma-carboxylation of
glutamic acid residues, hydroxylation and ADP-ribosylation, for
instance, are described in most basic texts, such as
Proteins-Structure and Molecular Properties, 2nd ed., T.E.
Creighton, W. H. Freeman and Company, New York (1993). Many
detailed reviews are available on this subject, such as by Wold,
F., Posttranslational Covalent Modification of Proteins, B. C.
Johnson, Ed., Academic Press, New York 1-12 (1983); Seifter et al.
(1990) Meth. Enzymol. 182: 626-646) and Rattan et al. (1992) Ann.
N.Y Acad. Sci. 663:48-62).
[0090] As is also well known, polypeptides are not always entirely
linear. For instance, polypeptides may be branched as a result of
ubiquitination, and they may be circular, with or without
branching, generally as a result of post-translation events,
including natural processing events and events brought about by
human manipulation which do not occur naturally. Circular, branched
and branched circular polypeptides may be synthesized by
non-translational natural processes and by synthetic methods.
[0091] Modifications can occur anywhere in a polypeptide, including
the peptide backbone, the amino acid side-chains and the amino or
carboxyl termini. Blockage of the amino or carboxyl group in a
polypeptide, or both, by a covalent modification, is common in
naturally-occurring and synthetic polypeptides. For instance, the
aminoterminal residue of polypeptides made in E. coli, prior to
proteolytic processing, almost invariably will be
N-formylmethionine.
[0092] The modifications can be a function of how the protein is
made. For recombinant polypeptides, for example, the modifications
will be determined by the host cell posttranslational modification
capacity and the modification signals in the polypeptide amino acid
sequence. Accordingly, when glycosylation is desired, a polypeptide
should be expressed in a glycosylating host, generally a eukaryotic
cell. Insect cells often carry out the same posttranslational
glycosylations as mammalian cells and, for this reason, insect cell
expression systems have been developed to efficiently express
mammalian proteins having native patterns of glycosylation. Similar
considerations apply to other modifications.
[0093] The same type of modification may be present in the same or
varying degree at several sites in a given polypeptide. Also, a
given polypeptide may contain more than one type of
modification.
Polypeptide Uses
[0094] The protein sequences of the present invention can be used
as a "query sequence" to perform a search against public databases
to, for example, identify other family members or related
sequences. Such searches can be performed using the NBLAST and
XBLAST programs (version 2.0) of Altschul et al. (1990) J. Mol.
Biol. 215:403-10. BLAST nucleotide searches can be performed with
the NBLAST program, score=100, wordlength=12 to obtain nucleotide
sequences homologous to the nucleic acid molecules of the
invention. BLAST protein searches can be performed with the XBLAST
program, score=50, wordlength=3 to obtain amino acid sequences
homologous to the proteins of the invention. To obtain gapped
alignments for comparison purposes, Gapped BLAST can be utilized as
described in Altschul et al., (1997) Nucleic Acids Res.
25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs,
the default parameters of the respective programs (e.g., XBLAST and
NBLAST) can be used. See www.ncbi.nlm.nih.gov.
[0095] The aminopeptidase polypeptides are useful for producing
antibodies specific for the aminopeptidase, regions, or fragments.
Regions having a high antigenicity index score are shown in FIG.
2.
[0096] The aminopeptidase polypeptides are useful for biological
assays related to aminopeptidases. Such assays involve any of the
known aminopeptidase functions or activities or properties useful
for diagnosis and treatment of aminopeptidase-related
conditions.
[0097] The aminopeptidase polypeptides are also useful in drug
screening assays, in cell-based or cell-free systems. Cell-based
systems can be native, i.e., cells that normally express the
aminopeptidase, as a biopsy or expanded in cell culture. In one
embodiment, however, cell-based assays involve recombinant host
cells expressing the aminopeptidase.
[0098] Determrining the ability of the test compound to interact
with the aminopeptidase can also comprise determining the ability
of the test compound to preferentially bind to the polypeptide as
compared to the ability of a known binding molecule to bind to the
polypeptide.
[0099] The polypeptides can be used to identify compounds that
modulate aminopeptidase activity. Such compounds, for example, can
increase or decrease affinity or rate of binding to peptide
substrate, compete with peptide substrate for binding to the
aminopeptidase, or displace peptide substrate bound to the
aminopeptidase. Both aminopeptidase and appropriate variants and
fragments can be used in high-throughput screens to assay candidate
compounds for the ability to bind to the aminopeptidase. These
compounds can be further screened against a functional
aminopeptidase to determine the effect of the compound on the
aminopeptidase activity. Compounds can be identified that activate
(agonist) or inactivate (antagonist) the aminopeptidase to a
desired degree. Modulatory methods can be performed in vitro (e.g.,
by culturing the cell with the agent) or, alternatively, in vivo
(e.g., by administering the agent to a subject.
[0100] The aminopeptidase polypeptides can be used to screen a
compound for the ability to stimulate or inhibit interaction
between the aminopeptidase protein and a target molecule that
normally interacts with the aminopeptidase protein, for example,
substrate-peptide or zinc component. The assay includes the steps
of combining the aminopeptidase protein with a candidate compound
under conditions that allow the aminopeptidase protein or fragment
to interact with the target molecule, and to detect the formation
of a complex between the aminopeptidase protein and the target or
to detect the biochemical consequence of the interaction with the
aminopeptidase and the target.
[0101] Determining the ability of the aminopeptidase to bind to a
target molecule can also be accomplished using a technology such as
real-time Bimolecular Interaction Analysis (BIA). Sjolander et al.
(1991) Anal. Chem. 63:2338-2345 and Szabo et al (1995) Curr. Opin.
Struct. Biol. 5:699-705. As used herein, "BIA" is a technology for
studying biospecific interactions in real time, without labeling
any of the interactants (e.g., BIAcore.TM.). Changes in the optical
phenomenon surface plasmon resonance (SPR) can be used as an
indication of real-time reactions between biological molecules.
[0102] The test compounds of the present invention can be obtained
using any of the numerous approaches in combinatorial library
methods known in the art, including: biological libraries;
spatially addressable parallel solid phase or solution phase
libraries; synthetic library methods requiring deconvolution; the
`one-bead one-compound` library method; and synthetic library
methods using affinity chromatography selection. The biological
library approach is limited to polypeptide libraries, while the
other four approaches are applicable to polypeptide, non-peptide
oligomer or small molecule libraries of compounds (Lam, K. S.
(1997) Anticancer Drug Des. 12:145).
[0103] Examples of methods for the synthesis of molecular libraries
can be found in the art, for example in DeWitt et al. (1993) Proc.
Natl. Acad. Sci. USA 90:6909; Erb et al. (1994) Proc. Natl. Acad.
Sci. USA 91:11422; Zuckermann et al. (1994). J. Med. Chem. 37:2678;
Cho et al. (1993) Science 261:1303; Carell et al. (1994) Angew.
Chem. Int. Ed. Engl. 33:2059; Carell et al. (1994) Angew. Chem.
Int. Ed. Engl. 33:2061; and in Gallop et al. (1994) J. Med. Chem.
37:1233. Libraries of compounds may be presented in solution (e.g.,
Houghten (1992) Biotechniques 13:412-421), or on beads (Lam (1991)
Nature 354:82-84), chips (Fodor (1993) Nature 364:555-556),
bacteria (Ladner U.S. Pat. No. 5,223,409), spores (Ladner U.S. Pat.
No. '409), plasmids (Cull et al. (1992) Proc. Natl. Acad. Sci. USA
89:1865-1869) or on phage (Scott and Smith (1990) Science
249:386-390); (Devlin (1990) Science 249:404-406); (Cwirla et al.
(1990) Proc. Natl. Acad. Sci. 97:6378-6382); (Felici (1991) J. Mol.
Biol. 222:301-310); (Ladner supra).
[0104] Candidate compounds include, for example, 1) peptides such
as soluble peptides, including Ig-tailed fusion peptides and
members of random peptide libraries (see, e.g., Lam et al. (1991)
Nature 354:82-84; Houghten et al. (1991) Nature 354:84-86) and
combinatorial chemistry-derived molecular libraries made of D-
and/or L- configuration amino acids; 2) phosphopeptides (e.g.,
members of random and partially degenerate, directed phosphopeptide
libraries, see, e.g., Songyang et al. (1993) Cell 72:767-778); 3)
antibodies (e.g., polyclonal, monoclonal, humanized,
anti-idiotypic, chimeric, and single chain antibodies as well as
Fab, F(ab').sub.2, Fab expression library fragments, and
epitope-binding fragments of antibodies); and 4) small organic and
inorganic molecules (e.g., molecules obtained from combinatorial
and natural product libraries).
[0105] One candidate compound is a soluble full-length
aminopeptidase or fragment that competes for peptide binding. Other
candidate compounds include mutant aminopeptidases or appropriate
fragments containing mutations that affect aminopeptidase function
and compete for peptide substrate. Accordingly, a fragment that
competes for substrate, for example with a higher affinity, or a
fragment that binds substrate but does not degrade it, is
encompassed by the invention.
[0106] The invention provides other end points to identify
compounds that modulate (stimulate or inhibit) aminopeptidase
activity. The assays typically involve an assay of cellular events
that indicate aminopeptidase activity. Thus, the expression of
genes that are up- or down-regulated in response to the
aminopeptidase activity can be assayed. In one embodiment, the
regulatory region of such genes can be operably linked to a marker
that is easily detectable, such as luciferase. Alternatively,
modification of the aminopeptidase could also be measured.
[0107] Any of the biological or biochemical functions mediated by
the arninopeptidase can be used as an endpoint assay. These include
all of the biochemical or biochemical/biological events described
herein, in the references cited herein, incorporated by reference
for these endpoint assay targets, and other functions known to
those of ordinary skill in the art.
[0108] In the case of the aminopeptidase, specific end points can
include peptide bond hydrolysis.
[0109] Binding and/or activating compounds can also be screened by
using chimeric aminopeptidase proteins in which one or more
regions, segments, sites, and the like, as disclosed herein, or
parts thereof, can be replaced by their heterologous counterparts
derived from other arninopeptidases. For example, a catalytic
region can be used that interacts with a different peptide sequence
specificity and/or affinity than the native aminopeptidase.
Accordingly, a different set of components is available as an
end-point assay for activation. As a further alternative, the site
of modification by an effector protein, for example
phosphorylation, can be replaced with the site for a different
effector protein. Activation can also be detected by a reporter
gene containing an easily detectable coding region operably linked
to a transcriptional regulatory sequence that is part of the native
pathway in which the aminopeptidase is involved.
[0110] The aminopeptidase polypeptides are also useful in
competition binding assays in methods designed to discover
compounds that interact with the aminopeptidase. Thus, a compound
is exposed to an aminopeptidase polypeptide under conditions that
allow the compound to bind or to otherwise interact with the
polypeptide. Soluble aminopeptidase polypeptide is also added to
the mixture. If the test compound interacts with the soluble
aminopeptidase polypeptide, it decreases the amount of complex
formed or activity from the aminopeptidase target. This type of
assay is particularly useful in cases in which compounds are sought
that interact with specific regions of the aminopeptidase. Thus,
the soluble polypeptide that competes with the target
aminopeptidase region is designed to contain peptide sequences
corresponding to the region of interest.
[0111] Another type of competition-binding assay can be used to
discover compounds that interact with specific functional sites. As
an example, bindable zinc and a candidate compound can be added to
a sample of the aminopeptidase. Compounds that interact with the
aminopeptidase at the same site as the zinc will reduce the amount
of complex formed between the aminopeptidase and the zinc.
Accordingly, it is possible to discover a compound that
specifically prevents interaction between the aminopeptidase and
the zinc component. Another example involves adding a candidate
compound to a sample of aminopeptidase and substrate peptide. A
compound that competes with the peptide will reduce the amount of
hydrolysis or binding of the peptide to the aminopeptidase.
Accordingly, compounds can be discovered that directly interact
with the aminopeptidase and compete with the peptide. Such assays
can involve any other component that interacts with the
aminopeptidase.
[0112] To perform cell free drug screening assays, it is desirable
to immobilize either the aminopeptidase, or fragment, or its target
molecule to facilitate separation of complexes from uncomplexed
forms of one or both of the proteins, as well as to accommodate
automation of the assay.
[0113] Techniques for immobilizing proteins on matrices can be used
in the drug screening assays. In one embodiment, a fusion protein
can be provided which adds a domain that allows the protein to be
bound to a matrix. For example,
glutathione-S-transferase/aminopeptidase fusion proteins can be
adsorbed onto glutathione sepharose beads (Sigma Chemical, St.
Louis, Mo.) or glutathione derivatized microtitre plates, which are
then combined with the cell lysates (e.g., .sup.35S-labeled) and
the candidate compound, and the mixture incubated under conditions
conducive to complex formation (e.g., at physiological conditions
for salt and pH). Following incubation, the beads are washed to
remove any unbound label, and the matrix immobilized and radiolabel
determined directly, or in the supernatant after the complexes is
dissociated. Alternatively, the complexes can be dissociated from
the matrix, separated by SDS-PAGE, and the level of
aminopeptidase-binding protein found in the bead fraction
quantitated from the gel using standard electrophoretic techniques.
For example, either the polypeptide or its target molecule can be
immobilized utilizing conjugation of biotin and streptavidin using
techniques well known in the art. Alternatively, antibodies
reactive with the protein but which do not interfere with binding
of the protein to its target molecule can be derivatized to the
wells of the plate, and the protein trapped in the wells by
antibody conjugation. Preparations of an aminopeptidase-binding
target component, such as a peptide or zinc component, and a
candidate compound are incubated in the aminopeptidase-presenting
wells and the amount of complex trapped in the well can be
quantitated. Methods for detecting such complexes, in addition to
those described above for the GST-immobilized complexes, include
immunodetection of complexes using antibodies reactive with the
aminopeptidase target molecule, or which are reactive with
aminopeptidase and compete with the target molecule; as well as
enzyme-linked assays which rely on detecting an enzymatic activity
associated with the target molecule.
[0114] Modulators of aminopeptidase activity identified according
to these drug screening assays can be used to treat a subject with
a disorder related to the aminopeptidase, by treating cells that
express the aminopeptidase, such as any of those shown in FIGS. 5
and 6. These methods of treatment include the steps of
administering the modulators of aminopeptidase activity in a
pharmaceutical composition as described herein, to a subject in
need of such treatment.
[0115] Disorders involving the lung include, but are not limited
to, congenital anomalies; atelectasis; diseases of vascular origin,
such as pulmonary congestion and edema, including hemodynamic
pulmonary edema and edema caused by microvascular injury, adult
respiratory distress syndrome (diffuse alveolar damage), pulmonary
embolism, hemorrhage, and infarction, and pulmonary hypertension
and vascular sclerosis; chronic obstructive pulmonary disease, such
as emphysema, chronic bronchitis, bronchial asthma, and
bronchiectasis; diffuse interstitial (infiltrative, restrictive)
diseases, such as pneumoconioses, sarcoidosis, idiopathic pulmonary
fibrosis, desquamative interstitial pneumonitis, hypersensitivity
pneumonitis, pulmonary eosinophilia (pulmonary infiltration with
eosinophilia), Bronchiolitis obliterans-organizing pneumonia,
diffuse pulmonary hemorrhage syndromes, including Goodpasture
syndrome, idiopathic pulmonary hemosiderosis and other hemorrhagic
syndromes, pulmonary involvement in collagen vascular disorders,
and pulmonary alveolar proteinosis; complications of therapies,
such as drug-induced lung disease, radiation-induced lung disease,
and lung transplantation; tumors, such as bronchogenic carcinoma,
including paraneoplastic syndromes, bronchioloalveolar carcinoma,
neuroendocrine tumors, such as bronchial carcinoid, miscellaneous
tumors, and metastatic tumors; pathologies of the pleura, including
inflammatory pleural effusions, noninflammatory pleural effusions,
pneumothorax, and pleural tumors, including solitary fibrous tumors
(pleural fibroma) and malignant mesothelioma.
[0116] Disorders involving the colon include, but are not limited
to, congenital anomalies, such as atresia and stenosis, Meckel
diverticulum, congenital aganglionic megacolon-Hirschsprung
disease; enterocolitis, such as diarrhea and dysentery, infectious
enterocolitis, including viral gastroenteritis, bacterial
enterocolitis, necrotizing enterocolitis, antibiotic-associated
colitis (pseudomembranous colitis), and collagenous and lymphocytic
colitis, miscellaneous intestinal inflammatory disorders, including
parasites and protozoa, acquired immunodeficiency syndrome,
transplantation, drug-induced intestinal injury, radiation
enterocolitis, neutropenic colitis (typhlitis), and diversion
colitis; idiopathic inflammatory bowel disease, such as Crohn
disease and ulcerative colitis; tumors of the colon, such as
non-neoplastic polyps, adenomas, familial syndromes, colorectal
carcinogenesis, colorectal carcinoma, and carcinoid tumors.
[0117] Disorders in which aminopeptidase expression is especially
relevant include, but are not limited to, breast and colon
carcinoma, lung carcinoma, especially squamous cell carcinoma, and
insulin related disorders such as diabetes.
[0118] The aminopeptidase is overexpressed in both lung, breast,
and colon cancer. As such, the gene is particularly relevant for
the treatment of these disorders, where inhibiting expression of
the gene could affect tumor development and/or progression.
[0119] The aminopeptidase is also expressed in the tissues shown in
FIGS. 5 and 6, and as such is specifically involved in disorders
relating to these tissues.
[0120] The aminopeptidase polypeptides are thus useful for treating
an aminopeptidase-associated disorder characterized by aberrant
expression or activity of an aminopeptidase. In one embodiment, the
method involves administering an agent (e.g., an agent identified
by a screening assay described herein), or combination of agents
that modulates (e.g., upregulates or downregulates) expression or
activity of the protein. In another embodiment, the method involves
administering the aminopeptidase as therapy to compensate for
reduced or aberrant expression or activity of the protein.
[0121] Methods for treatment include but are not limited to the use
of soluble aminopeptidase or fragments of the aminopeptidase
protein that compete for substrate or any other component that
directly interacts with the aminopeptidase, such as zinc or any of
the enzymes that modify the aminopeptidase. These aminopeptidases
or fragments can have a higher affinity for the target so as to
provide effective competition.
[0122] Stimulation of activity is desirable in situations in which
the protein is abnormally downregulated and/or in which increased
activity is likely to have a beneficial effect. Likewise,
inhibition of activity is desirable in situations in which the
protein is abnormally upregulated and/or in which decreased
activity is likely to have a beneficial effect. In one example of
such a situation, a subject has a disorder characterized by
aberrant development or cellular differentiation. In another
example, the subject has a proliferative disease (e.g., cancer) or
a disorder characterized by an aberrant hematopoietic response. In
another example, it is desirable to achieve tissue regeneration in
a subject (e.g., where a subject has undergone brain or spinal cord
injury and it is desirable to regenerate neuronal tissue in a
regulated manner).
[0123] In yet another aspect of the invention, the proteins of the
invention can be used as "bait proteins" in a two-hybrid assay or
three-hybrid assay (see, e.g., U.S. Pat. No. 5,283,317; Zervos et
al. (1993) Cell 72:223-232; Madura et al. (1993) J. Biol. Chem.
268:12046-12054; Bartel et al. (1993) Biotechniques 14:920-924;
Iwabuchi et al. (1993) Oncogene 8:1693-1696; and Brent WO
94/10300), to identify other proteins (captured proteins) which
bind to or interact with the proteins of the invention and modulate
their activity.
[0124] The aminopeptidase polypeptides also are useful to provide a
target for diagnosing a disease or predisposition to disease
mediated by the aminopeptidase, including, but not limited to,
those diseases discussed herein, and particularly lung, breast, and
colon carcinoma and insulin-related disorders, such as diabetes.
Targets are useful for diagnosing a disease or predisposition to
disease mediated by the aminopeptidase, in the tissues shown in
FIGS. 5 and 6. Accordingly, methods are provided for detecting the
presence, or levels of, the aminopeptidase in a cell, tissue, or
organism. The method involves contacting a biological sample with a
compound capable of interacting with the aminopeptidase such that
the interaction can be detected.
[0125] One agent for detecting aminopeptidase is an antibody
capable of selectively binding to aminopeptidase. A biological
sample includes tissues, cells and biological fluids isolated from
a subject, as well as tissues, cells and fluids present within a
subject.
[0126] The aminopeptidase also provides a target for diagnosing
active disease, or predisposition to disease, in a patient having a
variant aminopeptidase. Thus, aminopeptidase can be isolated from a
biological sample and assayed for the presence of a genetic
mutation that results in an aberrant protein. This includes amino
acid substitution, deletion, insertion, rearrangement, (as the
result of aberrant splicing events), and inappropriate
post-translational modification. Analytic methods include altered
electrophoretic mobility, altered tryptic peptide digest, altered
aminopeptidase activity in cell-based or cell-free assay,
alteration in peptide binding or degradation, zinc binding or
antibody-binding pattern, altered isoelectric point, direct amino
acid sequencing, and any other of the known assay techniques useful
for detecting mutations in a protein in general or in an
aminopeptidase specifically.
[0127] In vitro techniques for detection of aminopeptidase include
enzyme linked immunosorbent assays (ELISAs), Western blots,
immunoprecipitations and immunofluorescence. Alternatively, the
protein can be detected in vivo in a subject by introducing into
the subject a labeled anti-aminopeptidase antibody. For example,
the antibody can be labeled with a radioactive marker whose
presence and location in a subject can be detected by standard
imaging techniques. Particularly useful are methods, which detect
the allelic variant of the aminopeptidase expressed in a subject,
and methods, which detect fragments of the aminopeptidase in a
sample.
[0128] The aminopeptidase polypeptides are also useful in
pharmacogenomic analysis. Pharmacogenomics deal with clinically
significant hereditary variations in the response to drugs due to
altered drug disposition and abnormal action in affected persons.
See, e.g., Eichelbaum, M. (1996) Clin. Exp. Pharmacol. Physiol.
23(10-11):983-985, and Linder, M. W. (1997) Clin. Chem.
43(2):254-266. The clinical outcomes of these variations result in
severe toxicity of therapeutic drugs in certain individuals or
therapeutic failure of drugs in certain individuals as a result of
individual variation in metabolism. Thus, the genotype of the
individual can determine the way a therapeutic compound acts on the
body or the way the body metabolizes the compound. Further, the
activity of drug metabolizing enzymes affects both the intensity
and duration of drug action. Thus, the pharmacogenomics of the
individual permit the selection of effective compounds and
effective dosages of such compounds for prophylactic or therapeutic
treatment based on the individual's genotype. The discovery of
genetic polymorphisms in some drug metabolizing enzymes has
explained why some patients do not obtain the expected drug
effects, show an exaggerated drug effect, or experience serious
toxicity from standard drug dosages. Polymorphisms can be expressed
in the phenotype of the extensive metabolizer and the phenotype of
the poor metabolizer. Accordingly, genetic polymorphism may lead to
allelic protein variants of the aminopeptidase in which one or more
of the aminopeptidase functions in one population is different from
those in another population. The polypeptides thus allow a target
to ascertain a genetic predisposition that can affect treatment
modality. Thus, in a peptide-based treatment, polymorphism may give
rise to catalytic regions that are more or less active.
Accordingly, dosage would necessarily be modified to maximize the
therapeutic effect within a given population containing the
polymorphism. As an alternative to genotyping, specific polymorphic
polypeptides could be identified.
[0129] The aminopeptidase polypeptides are also useful for
monitoring therapeutic effects during clinical trials and other
treatment. Thus, the therapeutic effectiveness of an agent that is
designed to increase or decrease gene expression, protein levels or
aminopeptidase activity can be monitored over the course of
treatment using the aminopeptidase polypeptides as an end-point
target. The monitoring can be, for example, as follows: (i)
obtaining a pre-administration sample from a subject prior to
administration of the agent; (ii) detecting the level of expression
or activity of the protein in the pre-administration sample; (iii)
obtaining one. or more post-administration samples from the
subject; (iv) detecting the level of expression or activity of the
protein in the post-administration samples; (v) comparing the level
of expression or activity of the protein in the pre-administration
sample with the protein in the post-administration sample or
samples; and (vi) increasing or decreasing the administration of
the agent to the subject accordingly.
Antibodies
[0130] The invention also provides antibodies that selectively bind
to the aminopeptidase and its variants and fragments. An antibody
is considered to selectively bind, even if it also binds to other
proteins that are not substantially homologous with the
aminopeptidase. These other proteins share homology with a fragment
or domain of the aminopeptidase. This conservation in specific
regions gives rise to antibodies that bind to both proteins by
virtue of the homologous sequence. In this case, it would be
understood that antibody binding to the aminopeptidase is still
selective.
[0131] To generate antibodies, an isolated aminopeptidase
polypeptide is used as an immunogen to generate antibodies using
standard techniques for polyclonal and monoclonal antibody
preparation. Either the full-length protein or antigenic peptide
fragment can be used. Regions having a high antigenicity index are
shown in FIG. 2.
[0132] Antibodies are preferably prepared from these regions or
from discrete fragments in these regions. However, antibodies can
be prepared from any region of the peptide as described herein. A
preferred fragment produces an antibody that diminishes or
completely prevents peptide hydrolysis or binding. Antibodies can
be developed against the entire aminopeptidase or domains of the
aminopeptidase as described herein, for example, the zinc binding
region, matalloprotease motif (IAHELAHQW), the GAMEN motif, sites
contributing to exopeptidase specificity, and the peptidase domain
or subregions thereof. Antibodies can also be developed against
specific functional sites as disclosed herein.
[0133] The antigenic peptide can comprise a contiguous sequence of
at least 12, 14, 15, or 30 amino acid residues. In one embodiment,
fragments correspond to regions that are located on the surface of
the protein, e.g., hydrophilic regions. These fragments are not to
be construed, however, as encompassing any fragments, which may be
disclosed prior to the invention.
[0134] Antibodies can be polyclonal or monoclonal. An intact
antibody, or a fragment thereof (e.g. Fab or F(ab').sub.2) can be
used.
[0135] Detection can be facilitated by coupling (i.e., physically
linking) the antibody to a detectable substance. Examples of
detectable substances include various enzymes, prosthetic groups,
fluorescent materials, luminescent materials, bioluminescent
materials, and radioactive materials. Examples of suitable enzymes
include horseradish peroxidase, alkaline phosphatase,
.beta.-galactosidase, or acetylcholinesterase; examples of suitable
prosthetic group complexes include streptavidin/biotin and
avidinibiotin; examples of suitable fluorescent materials include
umbelliferone, fluorescein, fluorescein isothiocyanate, rhodamine,
dichlorotriazinylamine fluorescein, dansyl chloride or
phycoerythrin; an example of a luminescent material includes
luminol; examples of bioluminescent materials include luciferase,
luciferin, and aequorin, and examples of suitable radioactive
material include .sup.125I, .sup.131I, .sup.35S or .sup.3H.
[0136] An appropriate immunogenic preparation can be derived from
native, recombinantly expressed, or chemically synthesized
peptides.
Antibody Uses
[0137] The antibodies can be used to isolate an aminopeptidase by
standard techniques, such as affinity chromatography or
immunoprecipitation. The antibodies can facilitate the purification
of the natural aminopeptidase from cells and recombinantly produced
aminopeptidase expressed in host cells.
[0138] The antibodies are useful to detect the presence of
aminopeptidase in cells or tissues to determine the pattern of
expression of the aminopeptidase among various tissues in an
organism and over the course of normal development.
[0139] The antibodies can be used to detect aminopeptidase in situ,
in vitro, or in a cell lysate or supernatant in order to evaluate
the abundance and pattern of expression.
[0140] The antibodies can be used to assess abnormal tissue
distribution or abnormal expression during development.
[0141] Antibody detection of circulating fragments of the full
length aminopeptidase can be used to identify aminopeptidase
turnover.
[0142] Further, the antibodies can be used to assess aminopeptidase
expression in disease states such as in active stages of the
disease or in an individual with a predisposition toward disease
related to aminopeptidase function. When a disorder is caused by an
inappropriate tissue distribution, developmental expression, or
level of expression of the aminopeptidase protein, the antibody can
be prepared against the normal aminopeptidase protein. If a
disorder is characterized by a specific mutation in the
aminopeptidase, antibodies specific for this mutant protein can be
used to assay for the presence of the specific mutant
aminopeptidase. However, intracellularly-made antibodies
("intrabodies") are also encompassed, which would recognize
intracellular aminopeptidase peptide regions.
[0143] The antibodies can also be used to assess normal and
aberrant subcellular localization of cells in the various tissues
in an organism. Antibodies can be developed against the whole
aminopeptidase or portions of the aminopeptidase, for example,
portions of the peptidase domain from amino acid 69-458, including
substrate recognition site.
[0144] The diagnostic uses can be applied, not only in genetic
testing, but also in monitoring a treatment modality. Accordingly,
where treatment is ultimately aimed at correcting aminopeptidase
expression level or the presence of aberrant aminopeptidases and
aberrant tissue distribution or developmental expression,
antibodies directed against the aminopeptidase or relevant
fragments can be used to monitor therapeutic efficacy.
[0145] Antibodies accordingly can be used diagnostically to monitor
protein levels in tissue as part of a clinical testing procedure,
e.g., to, for example, determine the efficacy of a given treatment
regimen.
[0146] Additionally, antibodies are useful in pharmacogenomic
analysis. Thus, antibodies prepared against polymorphic
arninopeptidase can be used to identify individuals that require
modified treatment modalities.
[0147] The antibodies are also useful as diagnostic tools as an
immunological marker for aberrant aminopeptidase analyzed by
electrophoretic mobility, isoelectric point, tryptic peptide
digest, and other physical assays known to those in the art.
[0148] The antibodies are also useful for tissue typing. Thus,
where a specific aminopeptidase has been correlated with expression
in a specific tissue, antibodies that are specific for this
aminopeptidase can be used to identify a tissue type.
[0149] The antibodies are also useful in forensic identification.
Accordingly, where an individual has been correlated with a
specific genetic polymorphism resulting in a specific polymorphic
protein, an antibody specific for the polymorphic protein can be
used as an aid in identification.
[0150] The antibodies are also useful for inhibiting aminopeptidase
function, for example, zinc binding, and peptide binding and/or
hydrolysis.
[0151] These uses can also be applied in a therapeutic context in
which treatment involves inhibiting aminopeptidase function. An
antibody can be used, for example, to block peptide binding.
Antibodies can be prepared against specific fragments containing
sites required for function or against intact aminopeptidase
associated with a cell.
[0152] Completely human antibodies are particularly desirable for
therapeutic treatment of human patients. For an overview of this
technology for producing human antibodies, see Lonberg et al.
(1995) Int. Rev. Immunol. 13:65-93. For a detailed discussion of
this technology for producing human antibodies and human monoclonal
antibodies and protocols for producing such antibodies, e.g., U.S.
Pat. No. 5,625,126; U.S. Pat. No. 5,633,425; U.S. Pat. No.
5,569,825; U.S. Pat. No. 5,661,016; and U.S. Pat. No.
5,545,806.
[0153] The invention also encompasses kits for using antibodies to
detect the presence of an aminopeptidase protein in a biological
sample. The kit can comprise antibodies such as a labeled or
labelable antibody and a compound or agent for detecting
aminopeptidase in a biological sample; means for determining the
amount of aminopeptidase in the sample; and means for comparing the
amount of aminopeptidase in the sample with a standard. The
compound or agent can be packaged in a suitable container. The kit
can further comprise instructions for using the kit to detect
aminopeptidase.
Polynucleotides
[0154] The nucleotide sequence in SEQ ID NO 2 was obtained by
sequencing the deposited human cDNA. Accordingly, the sequence of
the deposited clone is controlling as to any discrepancies between
the two and any reference to the sequence of SEQ ID NO 2 includes
reference to the sequence of the deposited cDNA.
[0155] The specifically disclosed cDNA comprises the coding region
and 5' and 3' untranslated sequences in SEQ ID NO 2.
[0156] The invention provides isolated polynucleotides encoding the
novel aminopeptidase. The term "aminopeptidase polynucleotide" or
"aminopeptidase nucleic acid" refers to the sequence shown in SEQ
ID NO 2 or in the deposited cDNA. The term "aminopeptidase
polynucleotide" or "aminopeptidase nucleic acid" further includes
variants and fragments of the amninopeptidase polynucleotides.
[0157] An "isolated" aminopeptidase nucleic acid is one that is
separated from other nucleic acid present in the natural source of
the aminopeptidase nucleic acid. Preferably, an "isolated" nucleic
acid is free of sequences which naturally flank the aminopeptidase
nucleic acid (i.e., sequences located at the 5' and 3' ends of the
nucleic acid) in the genomic DNA of the organism from which the
nucleic acid is derived. However, there can be some flanking
nucleotide sequences, for example up to about 5 KB. The important
point is that the aminopeptidase nucleic acid is isolated from
flanking sequences such that it can be subjected to the specific
manipulations described herein, such as recombinant expression,
preparation of probes and primers, and other uses specific to the
aminopeptidase nucleic acid sequences.
[0158] Moreover, an "isolated" nucleic acid molecule, such as a
cDNA or RNA molecule, can be substantially free of other cellular
material, or culture medium when produced by recombinant
techniques, or chemical precursors or other chemicals when
chemically synthesized. However, the nucleic acid molecule can be
fused to other coding or regulatory sequences and still be
considered isolated.
[0159] In some instances, the isolated material will form part of a
composition (for example, a crude extract containing other
substances), buffer system or reagent mix. In other circumstances,
the material may be purified to essential homogeneity, for example
as determined by PAGE or column chromatography such as HPLC.
Preferably, an isolated nucleic acid comprises at least about 50,
80 or 90% (on a molar basis) of all macromolecular species
present.
[0160] For example, recombinant DNA molecules contained in a vector
are considered isolated. Further examples of isolated DNA molecules
include recombinant DNA molecules maintained in heterologous host
cells or purified (partially or substantially) DNA molecules in
solution. Isolated RNA molecules include in vivo or in vitro RNA
transcripts of the isolated DNA molecules of the present invention.
Isolated nucleic acid molecules according to the present invention
further include such molecules produced synthetically.
[0161] In some instances, the isolated material will form part of a
composition (or example, a crude extract containing other
substances), buffer system or reagent mix. In other circumstances,
the material may be purified to essential homogeneity, for example
as determined by PAGE or column chromatography such as HPLC.
Preferably, an isolated nucleic acid comprises at least about 50,
80 or 90% (on a molar basis) of all macromolecular species
present.
[0162] The aminopeptidase polynucleotides can encode the mature
protein plus additional amino or carboxyterminal amino acids, or
amino acids interior to the mature polypeptide (when the mature
form has more than one polypeptide chain, for instance). Such
sequences may play a role in processing of a protein from precursor
to a mature form, facilitate protein trafficking, prolong or
shorten protein half-life or facilitate manipulation of a protein
for assay or production, among other things. As generally is the
case in situ, the additional amino acids may be processed away from
the mature protein by cellular enzymes.
[0163] The aminopeptidase polynucleotides include, but are not
limited to, the sequence encoding the mature polypeptide alone, the
sequence encoding the mature polypeptide and additional coding
sequences, such as a leader or secretory sequence (e.g., a pre-pro
or pro-protein sequence), the sequence encoding the mature
polypeptide, with or without the additional coding sequences, plus
additional non-coding sequences, for example introns and non-coding
5' and 3' sequences such as transcribed but non-translated
sequences that play a role in transcription, mRNA processing
(including splicing and polyadenylation signals), ribosome binding
and stability of mRNA. In addition, the polynucleotide may be fused
to a marker sequence encoding, for example, a peptide that
facilitates purification.
[0164] Aminopeptidase polynucleotides can be in the form of RNA,
such as mRNA, or in the form DNA, including cDNA and genomic DNA
obtained by cloning or produced by chemical synthetic techniques or
by a combination thereof. The nucleic acid, especially DNA, can be
double-stranded or single-stranded. Single-stranded nucleic acid
can be the coding strand (sense strand) or the non-coding strand
(anti-sense strand).
[0165] Aminopeptidase nucleic acid can comprise the nucleotide
sequences shown in SEQ ID NO 2, corresponding to human endothelial
cell cDNA
[0166] In one embodiment, the aminopeptidase nucleic acid comprises
only the coding region.
[0167] The invention further provides variant aminopeptidase
polynucleotides, and fragments thereof, that differ from the
nucleotide sequence shown in SEQ ID NO 2 due to degeneracy of the
genetic code and thus encode the same protein as that encoded by
the nucleotide sequence shown in SEQ ID NO 2.
[0168] The invention also provides aminopeptidase nucleic acid
molecules encoding the variant polypeptides described herein. Such
polynucleotides may be naturally occurring, such as allelic
variants (same locus), homologs (different locus), and orthologs
(different organism), or may be constructed by recombinant DNA
methods or by chemical synthesis. Such non-naturally occurring
variants may be made by mutagenesis techniques, including those
applied to polynucleotides, cells, or organisms. Accordingly, as
discussed above, the variants can contain nucleotide substitutions,
deletions, inversions and insertions.
[0169] Typically, variants have a substantial identity with a
nucleic acid molecules of SEQ ID NO 2 and the complements thereof.
Variation can occur in either or both the coding and non-coding
regions. The variations can produce both conservative and
non-conservative amino acid substitutions.
[0170] Orthologs, homologs, and allelic variants can be identified
using methods well known in the art. These variants comprise a
nucleotide sequence encoding an aminopeptidase that is typically at
least about 60-65%, 65-70%, 70-75%, more typically at least about
80-85%, and most typically at least about 90-95% or more homologous
to the nucleotide sequence shown in SEQ ID NO 2 or a fragment of
this sequence. Such nucleic acid molecules can readily be
identified as being able to hybridize under stringent conditions,
to the nucleotide sequence shown in SEQ ID NO 2 or a fragment of
the sequence. It is understood that stringent hybridization does
not indicate substantial homology where it is due to general
homology, such as poly A sequences, or sequences common to all or
most proteins, metalloproteases, all zinc binding proteins, all
proteins in the M1 family, or all aminopeptidases. Moreover, it is
understood that variants do not include any of the nucleic acid
sequences that may have been disclosed prior to the invention.
[0171] As used herein, the term "hybridizes under stringent
conditions" is intended to describe conditions for hybridization
and washing under which nucleotide sequences encoding a polypeptide
at least 50-55%, 55% homologous to each other typically remain
hybridized to each other. The conditions can be such that sequences
at least about 65%, at least about 70%, at least about 75%, at
least about 80%, at least about 90%, at least about 95% or more
identical to each other remain hybridized to one another. Such
stringent conditions are known to those skilled in the art and can
be found in Current Protocols in Molecular Biology, John Wiley
& Sons, N.Y. (1989), 6.3.1-6.3.6, incorporated by reference.
One example of stringent hybridization conditions are hybridization
in 6.times.sodium chloride/sodium citrate (SSC) at about 45.degree.
C., followed by one or more washes in 0.2.times.SSC, 0.1% SDS at
50-65.degree. C. In another non-limiting example, nucleic acid
molecules are allowed to hybridize in 6.times.sodium
chloride/sodium citrate (SSC) at about 45.degree. C., followed by
one or more low stringency washes in 0.2.times.SSC/0.1% SDS at room
temperature, or by one or more moderate stringency washes in
0.2.times.SSC/0.1% SDS at 42.degree. C., or washed in
0.2.times.SSC/0.1% SDS at 65.degree. C. for high stringency. In one
embodiment, an isolated nucleic acid molecule that hybridizes under
stringent conditions to the sequence of SEQ ID NO 2 corresponds to
a naturally-occurring nucleic acid molecule. As used herein, a
"naturally-occurring" nucleic acid molecule refers to an RNA or DNA
molecule having a nucleotide sequence that occurs in nature (e.g.,
encodes a natural protein).
[0172] As understood by those of ordinary skill, the exact
conditions can be determined empirically and depend on ionic
strength, temperature and the concentration of destabilizing agents
such as formamide or denaturing agents such as SDS. Other factors
considered in determining the desired hybridization conditions
include the length of the nucleic acid sequences, base composition,
percent mismatch between the hybridizing sequences and the
frequency of occurrence of subsets of the sequences within other
non-identical sequences. Thus, equivalent conditions can be
determined by varying one or more of these parameters while
maintaining a similar degree of identity or similarity between the
two nucleic acid molecules.
[0173] The present invention also provides isolated nucleic acids
that contain a single or double stranded fragment or portion that
hybridizes under stringent conditions to the nucleotide sequence of
SEQ ID NO 2 or the complement of SEQ ID NO 2. In one embodiment,
the nucleic acid consists of a portion of the nucleotide sequence
of SEQ ID NO 2 and the complement of SEQ ID NO 2. The nucleic acid
fragments of the invention are at least about 15, preferably at
least about 18, 20, 23 or 25 nucleotides, and can be 30, 40, 50,
100, 200, 500 or more nucleotides in length. Longer fragments, for
example, 30 or more nucleotides in length, which encode antigenic
proteins or polypeptides described herein are useful.
[0174] Furthermore, the invention provides polynucleotides that
comprise a fragment of the full-length aminopeptidase
polynucleotides. The fragment can be single or double-stranded and
can comprise DNA or RNA. The fragment can be derived from either
the coding or the non-coding sequence.
[0175] In another embodiment an isolated aminopeptidase nucleic
acid encodes the entire coding region. In another embodiment the
isolated aminopeptidase nucleic acid encodes a sequence
corresponding to the mature protein that may be from about amino
acid 6 to the last amino acid. Other fragments include nucleotide
sequences encoding the amino acid fragments described herein.
[0176] Thus, aminopeptidase nucleic acid fragments further include
sequences corresponding to the regions described herein, subregions
also described, and specific functional sites. Aminopeptidase
nucleic acid fragments also include combinations of the regions,
segments, motifs, and other functional sites described above. A
person of ordinary skill in the art would be aware of the many
permutations that are possible.
[0177] Where the location of the regions or sites have been
predicted by computer analysis, one of ordinary sill would
appreciate that the amino acid residues constituting these regions
can vary depending on the criteria used to define the regions.
[0178] However, it is understood that an aminopeptidase fragment
includes any nucleic acid sequence that does not include the entire
gene.
[0179] The invention also provides aminopeptidase nucleic acid
fragments that encode epitope bearing regions of the aminopeptidase
proteins described herein.
[0180] Nucleic acid fragments, according to the present invention,
are not to be construed as encompassing those fragments that may
have been disclosed prior to the invention.
Polynucleotide Uses
[0181] The nucleotide sequences of the present invention can be
used as a "query sequence" to perform a search against public
databases, for example, to identify other family members or related
sequences. Such searches can be performed using the NBLAST and
XBLAST programs (version 2.0) of Altschul et al. (1990) J. Mol.
Biol. 215:403-10. BLAST protein searches can be performed with the
XBLAST program, score=50, wordlength=3 to obtain amino acid
sequences homologous to the proteins of the invention. To obtain
gapped alignments for comparison purposes, Gapped BLAST can be
utilized as described in Altschul et al. (1997) Nucleic Acids Res.
25(17):3389-3402. When utilizing BLAST and Gapped BLAST programs,
the default parameters of the respective programs (e.g., XBLAST and
NBLAST) can be used. See www.ncbi.nlm.nih.gov.
[0182] The nucleic acid fragments of the invention provide probes
or primers in assays such as those described below. "Probes" are
oligonucleotides that hybridize in a base-specific manner to a
complementary strand of nucleic acid. Such probes include
polypeptide nucleic acids, as described in Nielsen et al. (1991)
Science 254:1497-1500. Typically, a probe comprises a region of
nucleotide sequence that hybridizes under highly stringent
conditions to at least about 15, typically about 20-25, and more
typically about 40, 50 or 75 consecutive nucleotides of the nucleic
acid sequence shown in SEQ ID NO 2 and the complements thereof.
More typically, the probe further comprises a label, e.g.,
radioisotope, fluorescent compound, enzyme, or enzyme
co-factor.
[0183] As used herein, the term "primer" refers to a
single-stranded oligonucleotide which acts as a point of initiation
of template-directed DNA synthesis using well-known methods (e.g.,
PCR, LCR) including, but not limited to those described herein. The
appropriate length of the primer depends on the particular use, but
typically ranges from about 15 to 30 nucleotides. The term "primer
site" refers to the area of the target DNA to which a primer
hybridizes. The term "primer pair" refers to a set of primers
including a 5' (upstream) primer that hybridizes with the 5' end of
the nucleic acid sequence to be amplified and a 3' (downstream)
primer that hybridizes with the complement of the sequence to be
amplified.
[0184] The aminopeptidase polynucleotides are thus useful for
probes, primers, and in biological assays.
[0185] Where the polynucleotides are used to assess aminopeptidase
properties or functions, such as in the assays described herein,
all or less than all of the entire cDNA can be useful. Assays
specifically directed to aminopeptidase functions, such as
assessing agonist or antagonist activity, encompass the use of
known fragments. Further, diagnostic methods for assessing
aminopeptidase function can also be practiced with any fragment,
including those fragments that may have been known prior to the
invention. Similarly, in methods involving treatment of
aminopeptidase dysfunction, all fragments are encompassed including
those, which may have been known in the art.
[0186] The aminopeptidase polynucleotides are useful as a
hybridization probe for cDNA and genomic DNA to isolate a
full-length cDNA and genomic clones encoding the polypeptides
described in SEQ ID NO 1 and to isolate cDNA and genomic clones
that correspond to variants producing the same polypeptides shown
in SEQ ID NO 1 or the other variants described herein. Variants can
be isolated from the same tissue and organism from which the
polypeptides shown in SEQ ID NO 1 were isolated, different tissues
from the same organism, or from different organisms. This method is
useful for isolating genes and cDNA that are
developmentally-controlled and therefore may be expressed in the
same tissue or different tissues at different points in the
development of an organism.
[0187] The probe can correspond to any sequence along the entire
length of the gene encoding the aminopeptidase. Accordingly, it
could be derived from 5' noncoding regions, the coding region, and
3' noncoding regions.
[0188] The nucleic acid probe can be, for example, the full-length
cDNA of SEQ ID NO 2, or a fragment thereof, such as an
oligonucleotide of at least 12, 15, 30, 50, 100, 250 or 500
nucleotides in length and sufficient to specifically hybridize
under stringent conditions to mRNA or DNA.
[0189] Fragments of the polynucleotides described herein are also
useful to synthesize larger fragments or full-length
polynucleotides described herein. For example, a fragment can be
hybridized to any portion of an mRNA and a larger or full-length
cDNA can be produced.
[0190] The fragments are also useful to synthesize antisense
molecules of desired length and sequence.
[0191] Antisense nucleic acids of the invention can be designed
using the nucleotide sequences of SEQ ID NO 2, and constructed
using chemical synthesis and enzymatic ligation reactions using
procedures known in the art. For example, an antisense nucleic acid
(e.g., an antisense oligonucleotide) can be chemically synthesized
using naturally occurring nucleotides or variously modified
nucleotides designed to increase the biological stability of the
molecules or to increase the physical stability of the duplex
formed between the antisense and sense nucleic acids, e.g.,
phosphorothioate derivatives and acridine substituted nucleotides
can be used. Examples of modified nucleotides which can be used to
generate the antisense nucleic acid include 5-fluorouracil,
5-bromouracil, 5-chlorouracil, 5-iodouracil, hypoxanthine,
xanthine, 4-acetylcytosine, 5-(carboxyhydroxylmethyl) uracil,
5-carboxymethylaminomethyl-2-thiouridine,
5-carboxymethylaminomethyluracil, dihydrouracil,
beta-D-galactosylqueosine, inosine, N6-isopentenyladenine,
1-methylguanine, 1-methylinosine, 2,2-dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine,
5-methylcytosine, N6-adenine, 7-methylguanine,
5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil,
beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil,
5-methoxyuracil, 2-methylthio-N6-isopentenyladenine,
uracil-5-oxyacetic acid (v), wybutoxosine, pseudouracil, queosine,
2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil,
5-methyluracil, uracil-5-oxyacetic acid methylester,
uracil-5-oxyacetic acid (v), 5-methyl-2-thiouracil,
3-(3-amino-3-N-2-carboxypropyl) uracil, (acp3)w, and
2,6-diaminopurine. Alternatively, the antisense nucleic acid can be
produced biologically using an expression vector into which a
nucleic acid has been subcloned in an antisense orientation (i.e.,
RNA transcribed from the inserted nucleic acid will be of an
antisense orientation to a target nucleic acid of interest).
[0192] Additionally, the nucleic acid molecules of the invention
can be modified at the base moiety, sugar moiety or phosphate
backbone to improve, e.g., the stability, hybridization, or
solubility of the molecule. For example, the deoxyribose phosphate
backbone of the nucleic acids can be modified to generate peptide
nucleic acids (see Hyrup et al. (1996) Bioorganic & Medicinal
Chemistry 4:5). As used herein, the terms "peptide nucleic acids"
or "PNAs" refer to nucleic acid mimics, e.g., DNA mimics, in which
the deoxyribose phosphate backbone is replaced by a pseudopeptide
backbone and only the four natural nucleobases are retained. The
neutral backbone of PNAs has been shown to allow for specific
hybridization to DNA and RNA under conditions of low ionic
strength. The synthesis of PNA oligomers can be performed using
standard solid phase peptide synthesis protocols as described in
Hyrup et al. (1996), supra; Perry-O'Keefe et al. (1996) Proc. Natl.
Acad. Sci. USA 93:14670. PNAs can be further modified, e.g., to
enhance their stability, specificity or cellular uptake, by
attaching lipophilic or other helper groups to PNA, by the
formation of PNA-DNA chimeras, or by the use of liposomes or other
techniques of drug delivery known in the art. The synthesis of
PNA-DNA chimeras can be performed as described in Hyrup (1996),
supra, Finn et al. (1996) Nucleic Acids Res. 24(17):3357-63, Mag et
al. (1989) Nucleic Acids Res. 17:5973, and Peterser et al. (1975)
Bioorganic Med. Chem. Lett. 5:1119.
[0193] The nucleic acid molecules and fragments of the invention
can also include other appended groups such as peptides (e.g., for
targeting host cell aminopeptidases in vivo), or agents
facilitating transport across the cell membrane (see, e.g.,
Letsinger et al. (1989) Proc. Natl. Acad. Sci. USA 86:6553-6556;
Lemaitre et al. (1987) Proc. Natl. Acad. Sci. USA 84:648-652; PCT
Publication No. WO 88/0918) or the blood brain barrier (see, e.g.,
PCT Publication No. WO 89/10134). In addition, oligonucleotides can
be modified with hybridization-triggered cleavage agents (see,
e.g., Krol et al. (1988) Bio-Techniques 6:958-976) or intercalating
agents (see, e.g., Zon (1988) Pharm Res. 5:539-549).
[0194] The aminopeptidase polynucleotides are also useful as
primers for PCR to amplify any given region of an aminopeptidase
polynucleotide.
[0195] The aminopeptidase polynucleotides are also useful for
constructing recombinant vectors. Such vectors include expression
vectors that express a portion of, or all of, the aminopeptidase
polypeptides. Vectors also include insertion vectors, used to
integrate into another polynucleotide sequence, such as into the
cellular genome, to alter in situ expression of aminopeptidase
genes and gene products. For example, an endogenous aminopeptidase
coding sequence can be replaced via homologous recombination with
all or part of the coding region containing one or more
specifically introduced mutations.
[0196] The aminopeptidase polynucleotides are also useful for
expressing antigenic portions of the aminopeptidase proteins.
[0197] The aminopeptidase polynucleotides are also useful as probes
for determining the chromosomal positions of the aminopeptidase
polynucleotides by means of in situ hybridization methods, such as
FISH. (For a review of this technique, see Verma et al. (1988)
Human Chromosomes: A Manual of Basic Techniques (Pergamon Press,
New York), and PCR mapping of somatic cell hybrids. The mapping of
the sequences to chromosomes is an important first step in
correlating these sequences with genes associated with disease.
[0198] Reagents for chromosome mapping can be used individually to
mark a single chromosome or a single site on that chromosome, or
panels of reagents can be used for marking multiple sites and/or
multiple chromosomes. Reagents corresponding to noncoding regions
of the genes actually are preferred for mapping purposes. Coding
sequences are more likely to be conserved within gene families,
thus increasing the chance of cross hybridizations during
chromosomal mapping.
[0199] Once a sequence has been mapped to a precise chromosomal
location, the physical position of the sequence on the chromosome
can be correlated with genetic map data. (Such data are found, for
example, in V. McKusick, Mendelian Inheritance in Man, available
on-line through Johns Hopkins University Welch Medical Library).
The relationship between a gene and a disease mapped to the same
chromosomal region, can then be identified through linkage analysis
(co-inheritance of physically adjacent genes), described in, for
example, Egeland et al. ((1987) Nature 325:783-787).
[0200] Moreover, differences in the DNA sequences between
individuals affected and unaffected with a disease associated with
a specified gene, can be determined. If a mutation is observed in
some or all of the affected individuals but not in any unaffected
individuals, then the mutation is likely to be the causative agent
of the particular disease. Comparison of affected and unaffected
individuals generally involves first looking for structural
alterations in the chromosomes, such as deletions or
translocations, that are visible from chromosome spreads, or
detectable using PCR based on that DNA sequence. Ultimately,
complete sequencing of genes from several individuals can be
performed to confirm the presence of a mutation and to distinguish
mutations from polymorphisms.
[0201] The aminopeptidase polynucleotide probes are also useful to
determine patterns of the presence of the gene encoding the
aminopeptidases and their variants with respect to tissue
distribution, for example, whether gene duplication has occurred
and whether the duplication occurs in all or only a subset of
tissues. The genes can be naturally occurring or can have been
introduced into a cell, tissue, or organism exogenously.
[0202] The aminopeptidase polynucleotides are also useful for
designing ribozymes corresponding to all, or a part, of the mRNA
produced from genes encoding the polynucleotides described
herein.
[0203] The aminopeptidase polynucleotides are also useful for
constructing host cells expressing a part, or all, of the
aminopeptidase polynucleotides and polypeptides.
[0204] The aminopeptidase polynucleotides are also useful for
constructing transgenic animals expressing all, or a part, of the
aminopeptidase polynucleotides and polypeptides.
[0205] The aminopeptidase polynucleotides are also useful for
making vectors that express part, or all, of the aminopeptidase
polypeptides.
[0206] The aminopeptidase polynucleotides are also useful as
hybridization probes for determining the level of aminopeptidase
nucleic acid expression. Accordingly, the probes can be used to
detect the presence of, or to determine levels of, aminopeptidase
nucleic acid in cells, tissues, and in organisms. The nucleic acid
whose level is determined can be DNA or RNA. Accordingly, probes
corresponding to the polypeptides described herein can be used to
assess gene copy number in a given cell, tissue, or organism. This
is particularly relevant in cases in which there has been an
amplification of the aminopeptidase genes.
[0207] Alternatively, the probe can be used in an in situ
hybridization context to assess the position of extra copies of the
aminopeptidase genes, as on extrachromosomal elements or as
integrated into chromosomes in which the aminopeptidase gene is not
normally found, for example as a homogeneously staining region.
[0208] These uses are relevant for diagnosis of disorders involving
an increase or decrease in aminopeptidase expression relative to
normal, such as a proliferative disorder, a differentiative or
developmental disorder, or a hematopoietic disorder.
[0209] Disorders in which the aminopeptidase expression is relevant
include, but are not limited to, lung and colon carcinomas and
insulin-related disorders, such as diabetes.
[0210] The aminopeptidase is expressed in the tissues shown in
FIGS. 5 and 6. As such, the gene is particularly relevant for the
treatment of disorders involving these tissues, especially lung,
breast, and colon.
[0211] Thus, the present invention provides a method for
identifying a disease or disorder associated with aberrant
expression or activity of aminopeptidase nucleic acid, in which a
test sample is obtained from a subject and nucleic acid (e.g.,
mRNA, genomic DNA) is detected, wherein the presence of the nucleic
acid is diagnostic for a subject having or at risk of developing a
disease or disorder associated with aberrant expression or activity
of the nucleic acid.
[0212] One aspect of the invention relates to diagnostic assays for
determining nucleic acid expression as well as activity in the
context of a biological sample (e.g., blood, serum, cells, tissue)
to determine whether an individual has a disease or disorder, or is
at risk of developing a disease or disorder, associated with
aberrant nucleic acid expression or activity. Such assays can be
used for prognostic or predictive purpose to thereby
prophylactically treat an individual prior to the onset of a
disorder characterized by or associated with expression or activity
of the nucleic acid molecules.
[0213] In vitro techniques for detection of mRNA include Northern
hybridizations and in situ hybridizations. In vitro techniques for
detecting DNA includes Southern hybridizations and in situ
hybridization.
[0214] Probes can be used as a part of a diagnostic test kit for
identifying cells or tissues that express the aminopeptidase, such
as by measuring the level of an aminopeptidase-encoding nucleic
acid in a sample of cells from a subject e.g., mRNA or genomic DNA,
or determining if the aminopeptidase gene has been mutated.
[0215] Nucleic acid expression assays are useful for drug screening
to identify compounds that modulate aminopeptidase nucleic acid
expression (e.g., antisense, polypeptides, peptidomimetics, small
molecules or other drugs). A cell is contacted with a candidate
compound and the expression of mRNA determined. The level of
expression of the mRNA in the presence of the candidate compound is
compared to the level of expression of the mRNA in the absence of
the candidate compound. The candidate compound can then be
identified as a modulator of nucleic acid expression based on this
comparison and be used, for example to treat a disorder
characterized by aberrant nucleic acid expression. The modulator
can bind to the nucleic acid or indirectly modulate expression,
such as by interacting with other cellular components that affect
nucleic acid expression
[0216] Modulatory methods can be performed in vitro (e.g., by
culturing the cell with the agent) or, alternatively, in vivo
(e.g., by administering the gent to a subject) in patients or in
transgenic animals.
[0217] The invention thus provides a method for identifying a
compound that can be used to treat a disorder associated with
nucleic acid expression of the aminopeptidase gene. The method
typically includes assaying the ability of the compound to modulate
the expression of the aminopeptidase nucleic acid and thus
identifying a compound that can be used to treat a disorder
characterized by undesired aminopeptidase nucleic acid
expression.
[0218] The assays can be performed in cell-based and cell-free
systems. Cell-based assays include cells naturally expressing the
aminopeptidase nucleic acid or recombinant cells genetically
engineered to express specific nucleic acid sequences.
[0219] Alternatively, candidate compounds can be assayed in vivo in
patients or in transgenic animals.
[0220] The assay for aminopeptidase nucleic acid expression can
involve direct assay of nucleic acid levels, such as mRNA levels,
or on collateral compounds (such as peptide hydrolysis). Further,
the expression of genes that are up- or down-regulated in response
to the aminopeptidase activity can also be assayed. In this
embodiment the regulatory regions of these genes can be operably
linked to a reporter gene such as luciferase.
[0221] Thus, modulators of aminopeptidase gene expression can be
identified in a method wherein a cell is contacted with a candidate
compound and the expression of mRNA determnined. The level of
expression of aminopeptidase mRNA in the presence of the candidate
compound is compared to the level of expression of aminopeptidase
mRNA in the absence of the candidate compound. The candidate
compound can then be identified as a modulator of nucleic acid
expression based on this comparison and be used, for example to
treat a disorder characterized by aberrant nucleic acid expression.
When expression of mRNA is statistically significantly greater in
the presence of the candidate compound than in its absence, the
candidate compound is identified as a stimulator of nucleic acid
expression. When nucleic acid expression is statistically
significantly less in the presence of the candidate compound than
in its absence, the candidate compound is identified as an
inhibitor of nucleic acid expression.
[0222] Accordingly, the invention provides methods of treatment,
with the nucleic acid as a target, using a compound identified
through drug screening as a gene modulator to modulate
aminopeptidase nucleic acid expression. Modulation includes both
up-regulation (i.e. activation or agonization) or down-regulation
(suppression or antagonization) or effects on nucleic acid activity
(e.g. when nucleic acid is mutated or improperly modified).
Treatment is of disorders characterized by aberrant expression or
activity of the nucleic acid.
[0223] Disorders in which the aminopeptidase expression is relevant
include, but are not limited to, those discussed herein and
particularly in lung and colon carcinoma and insulin-related
disorder, such as diabetes.
[0224] Alternatively, a modulator for aminopeptidase nucleic acid
expression can be a small molecule or drug identified using the
screening assays described herein as long as the drug or small
molecule inhibits the aminopeptidase nucleic acid expression.
[0225] The aminopeptidase polynucleotides are also useful for
monitoring the effectiveness of modulating compounds on the
expression or activity of the aminopeptidase gene in clinical
trials or in a treatment regimen. Thus, the gene expression pattern
can serve as a barometer for the continuing effectiveness of
treatment with the compound, particularly with compounds to which a
patient can develop resistance. The gene expression pattern can
also serve as a marker indicative of a physiological response of
the affected cells to the compound. Accordingly, such monitoring
would allow either increased administration of the compound or the
administration of alternative compounds to which the patient has
not become resistant. Similarly, if the level of nucleic acid
expression falls below a desirable level, administration of the
compound could be commensurately decreased.
[0226] Monitoring can be, for example, as follows: (i) obtaining a
pre-administration sample from a subject prior to administration of
the agent; (ii) detecting the level of expression of a specified
mRNA or genomic DNA of the invention in the pre-administration
sample; (iii) obtaining one or more post-administration samples
from the subject; (iv) detecting the level of expression or
activity of the mRNA or genomic DNA in the post-administration
samples; (v) comparing the level of expression or activity of the
mRNA or genomic DNA in the pre-administration sample with the mRNA
or genomic DNA in the post-administration sample or samples; and
(vi) increasing or decreasing the administration of the agent to
the subject accordingly.
[0227] The aminopeptidase polynucleotides are also useful in
diagnostic assays for qualitative changes in aminopeptidase nucleic
acid, and particularly in qualitative changes that lead to
pathology. The polynucleotides can be used to detect mutations in
aminopeptidase genes and gene expression products such as mRNA. The
polynucleotides can be used as hybridization probes to detect
naturally-occurring genetic mutations in the anninopeptidase gene
and thereby to determine whether a subject with the mutation is at
risk for a disorder caused by the mutation. Mutations include
deletion, addition, or substitution of one or more nucleotides in
the gene, chromosomal rearrangement, such as inversion or
transposition, modification of genoric DNA, such as aberrant
methylation patterns or changes in gene copy number, such as
amplification. Detection of a mutated form of the aminopeptidase
gene associated with a dysfunction provides a diagnostic tool for
an active disease or susceptibility to disease when the disease
results from overexpression, underexpression, or altered expression
of an aminopeptidase.
[0228] Mutations in the aminopeptidase gene can be detected at the
nucleic acid level by a variety of techniques. Genomic DNA can be
analyzed directly or can be amplified by using PCR prior to
analysis. RNA or cDNA can be used in the same way.
[0229] In certain embodiments, detection of the mutation involves
the use of a probe/primer in a polymerase chain reaction (PCR)
(see, e.g. U.S. Pat. Nos. 4,683,195 and 4,683,202), such as anchor
PCR or RACE PCR, or, alternatively, in a ligation chain reaction
(LCR) (see, e.g., Landegran et al. (1988) Science 241:1077-1080;
and Nakazawa et al. (1994) PNAS 91:360-364), the latter of which
can be particularly useful for detecting point mutations in the
gene (see Abravaya et al. (1995) Nucleic Acids Res. 23:675-682).
This method can include the steps of collecting a sample of cells
from a patient, isolating nucleic acid (e.g., genomic, mRNA or
both) from the cells of the sample, contacting the nucleic acid
sample with one or more primers which specifically hybridize to a
gene under conditions such that hybridization and amplification of
the gene (if present) occurs, and detecting the presence or absence
of an amplification product, or detecting the size of the
amplification product and comparing the length to a control sample.
Deletions and insertions can be detected by a change in size of the
amplified product compared to the normal genotype. Point mutations
can be identified by hybridizing amplified DNA to normal RNA or
antisense DNA sequences.
[0230] It is anticipated that PCR and/or LCR may be desirable to
use as a preliminary amplification step in conjunction with any of
the techniques used for detecting mutations described herein.
[0231] Alternative amplification methods include: self sustained
sequence replication (Guatelli et al. (1990) Proc. Natl. Acad. Sci.
USA 87:1874-1878), transcriptional amplification system (Kwoh et
al. (1989) Proc. Natl. Acad. Sci. USA 86:1173-1177), Q-Beta
Replicase (Lizardi et al. (1988) Bio/Technology 6:1197), or any
other nucleic acid amplification method, followed by the detection
of the amplified molecules using techniques well-known to those of
skill in the art. These detection schemes are especially useful for
the detection of nucleic acid molecules if such molecules are
present in very low numbers.
[0232] Alternatively, mutations in an aminopeptidase gene can be
directly identified, for example, by alterations in restriction
enzyme digestion patterns determined by gel electrophoresis.
[0233] Further, sequence-specific ribozymes (U.S. Pat. No.
5,498,531) can be used to score for the presence of specific
mutations by development or loss of a ribozyme cleavage site.
[0234] Perfectly matched sequences can be distinguished from
mismatched sequences by nuclease cleavage digestion assays or by
differences in melting temperature.
[0235] Sequence changes at specific locations can also be assessed
by nuclease protection assays such as RNase and S1 protection or
the chemical cleavage method.
[0236] Furthermore, sequence differences between a mutant
aminopeptidase gene and a wild-type gene can be determined by
direct DNA sequencing. A variety of automated sequencing procedures
can be utilized when performing the diagnostic assays ((1995)
Biotechniques 19:448), including sequencing by mass spectrometry
(see, e.g., PCT International Publication No. WO 94/16101; Cohen et
al. (1996) Adv. Chromatogr. 36:127-162; and Griffin et al. (1993)
Appl. Biochem. Biotechnol. 38:147-159).
[0237] Other methods for detecting mutations in the gene include
methods in which protection from cleavage agents is used to detect
mismatched bases in RNA/RNA or RNA/DNA duplexes (Myers et al.
(1985) Science 230:1242); Cotton et al. (1988) PNAS 85:4397;
Saleeba et al. (1992) Meth. Enzymol. 217:286-295), electrophoretic
mobility of mutant and wild type nucleic acid is compared (Orita et
al. (1989) PNAS 86:2766; Cotton et al. (1993) Mutat. Res.
285:125-144; and Hayashi et al. (1992) Genet. Anal. Tech. Appl.
9:73-79), and movement of mutant or wild-type fragments in
polyacrylamide gels containing a gradient of denaturant is assayed
using denaturing gradient gel electrophoresis (Myers et al. (1985)
Nature 313:495). The sensitivity of the assay may be enhanced by
using RNA (rather than DNA), in which the secondary structure is
more sensitive to a change in sequence. In one embodiment, the
subject method utilizes heteroduplex analysis to separate double
stranded heteroduplex molecules on the basis of changes in
electrophoretic mobility (Keen et al. (1991) Trends Genet. 7:5).
Examples of other techniques for detecting point mutations include,
selective oligonucleotide hybridization, selective amplification,
and selective primer extension.
[0238] In other embodiments, genetic mutations can be identified by
hybridizing a sample and control nucleic acids, e.g., DNA or RNA,
to high density arrays containing hundreds or thousands of
oligonucleotide probes (Cronin et al. (1996) Human Mutation
7:244-255; Kozal et al. (1996) Nature Medicine 2:753-759). For
example, genetic mutations can be identified in two dimensional
arrays containing light-generated DNA probes as described in Cronin
et al. supra. Briefly, a first hybridization array of probes can be
used to scan through long stretches of DNA in a sample and control
to identify base changes between the sequences by making linear
arrays of sequential overlapping probes. This step allows the
identification of point mutations. This step is followed by a
second hybridization array that allows the characterization of
specific mutations by using smaller, specialized probe arrays
complementary to all variants or mutations detected. Each mutation
array is composed of parallel probe sets, one complementary to the
wild-type gene and the other complementary to the mutant gene.
[0239] The aminopeptidase polynucleotides are also useful for
testing an individual for a genotype that while not necessarily
causing the disease, nevertheless affects the treatment modality.
Thus, the polynucleotides can be used to study the relationship
between an individual's genotype and the individual's response to a
compound used for treatment (pharmacogenomic relationship). In the
present case, for example, a mutation in the aminopeptidase gene
that results in altered affinity for zinc could result in an
excessive or decreased drug effect with standard concentrations of
zinc. Accordingly, the aminopeptidase polynucleotides described
herein can be used to assess the mutation content of the gene in an
individual in order to select an appropriate compound or dosage
regimen for treatment.
[0240] Thus polynucleotides displaying genetic variations that
affect treatment provide a diagnostic target that can be used to
tailor treatment in an individual. Accordingly, the production of
recombinant cells and animals containing these polymorphisms allow
effective clinical design of treatment compounds and dosage
regimens.
[0241] The methods can involve obtaining a control biological
sample from a control subject, contacting the control sample with a
compound or agent capable of detecting mRNA, or genomic DNA, such
that the presence of mRNA or genomic DNA is detected in the
biological sample, and comparing the presence of mRNA or genomic
DNA in the control sample with the presence of mRNA or genomic DNA
in the test sample.
[0242] The aminopeptidase polynucleotides are also useful for
chromosome identification when the sequence is identified with an
individual chromosome and to a particular location on the
chromosome. First, the DNA sequence is matched to the chromosome by
in situ or other chromosome-specific hybridization. Sequences can
also be correlated to specific chromosomes by preparing PCR primers
that can be used for PCR screening of somatic cell hybrids
containing individual chromosomes from the desired species. Only
hybrids containing the chromosome containing the gene homologous to
the primer will yield an amplified fragment. Sublocalization can be
achieved using chromosomal fragments. Other strategies include
prescreening with labeled flow-sorted chromosomes and preselection
by hybridization to chromosome-specific libraries. Further mapping
strategies include fluorescence in situ hybridization, which allows
hybridization with probes shorter than those traditionally used.
Reagents for chromosome mapping can be used individually to mark a
single chromosome or a single site on the chromosome, or panels of
reagents can be used for marking multiple sites and/or multiple
chromosomes. Reagents corresponding to noncoding regions of the
genes actually are preferred for mapping purposes. Coding sequences
are more likely to be conserved within gene families, thus
increasing the chance of cross hybridizations during chromosomal
mapping.
[0243] The aminopeptidase polynucleotides can also be used to
identify individuals from small biological samples. This can be
done for example using restriction fragment-length polymorphism
(RFLP) to identify an individual. Thus, the polynucleotides
described herein are useful as DNA markers for RFLP (See U.S. Pat.
No. 5,272,057).
[0244] Furthermore, the aminopeptidase sequence can be used to
provide an alternative technique, which determines the actual DNA
sequence of selected fragments in the genome of an individual.
Thus, the aminopeptidase sequences described herein can be used to
prepare two PCR primers from the 5' and 3' ends of the sequences.
These primers can then be used to amplify DNA from an individual
for subsequent sequencing.
[0245] Panels of corresponding DNA sequences from individuals
prepared in this manner can provide unique individual
identifications, as each individual will have a unique set of such
DNA sequences. It is estimated that allelic variation in humans
occurs with a frequency of about once per each 500 bases. Allelic
variation occurs to some degree in the coding regions of these
sequences, and to a greater degree in the noncoding regions. The
aminopeptidase sequences can be used to obtain such identification
sequences from individuals and from tissue. The sequences represent
unique fragments of the human genome. Each of the sequences
described herein can, to some degree, be used as a standard against
which DNA from an individual can be compared for identification
purposes.
[0246] If a panel of reagents from the sequences is used to
generate a unique identification database for an individual, those
same reagents can later be used to identify tissue from that
individual. Using the unique identification database, positive
identification of the individual, living or dead, can be made from
extremely small tissue samples.
[0247] The aminopeptidase polynucleotides can also be used in
forensic identification procedures. PCR technology can be used to
amplify DNA sequences taken from very small biological samples,
such as a single hair follicle, body fluids (e.g. blood, saliva, or
semen). The amplified sequence can then be compared to a standard
allowing identification of the origin of the sample.
[0248] The aminopeptidase polynucleotides can thus be used to
provide polynucleotide reagents, e.g., PCR primers, targeted to
specific loci in the human genome, which can enhance the
reliability of DNA-based forensic identifications by, for example,
providing another "identification marker" (i.e. another DNA
sequence that is unique to a particular individual). As described
above, actual base sequence information can be used for
identification as an accurate alternative to patterns formed by
restriction enzyme generated fragments. Sequences targeted to the
noncoding region are particularly useful since greater polymorphism
occurs in the noncoding regions, making it easier to differentiate
individuals using this technique.
[0249] The aminopeptidase polynucleotides can further be used to
provide polynucleotide reagents, e.g., labeled or labelable probes
which can be used in, for example, an in situ hybridization
technique, to identify a specific tissue. This is useful in cases
in which a forensic pathologist is presented with a tissue of
unknown origin. Panels of aminopeptidase probes can be used to
identify tissue by species and/or by organ type.
[0250] In a similar fashion, these primers and probes can be used
to screen tissue culture for contamination (i.e. screen for the
presence of a mixture of different types of cells in a
culture).
[0251] Alternatively, the aminopeptidase polynucleotides can be
used directly to block transcription or translation of
aminopeptidase gene sequences by means of antisense or ribozyme
constructs. Thus, in a disorder characterized by abnormally high or
undesirable aminopeptidase gene expression, nucleic acids can be
directly used for treatment.
[0252] The aminopeptidase polynucleotides are thus useful as
antisense constructs to control aminopeptidase gene expression in
cells, tissues, and organisms. A DNA antisense polynucleotide is
designed to be complementary to a region of the gene involved in
transcription, preventing transcription and hence production of
aminopeptidase protein. An antisense RNA or DNA polynucleotide
would hybridize to the mRNA and thus block translation of mRNA into
aminopeptidase protein.
[0253] Examples of antisense molecules useful to inhibit nucleic
acid expression include antisense molecules complementary to a
fragment of the 5' untranslated region of SEQ ID NO 2 which also
includes the start codon and antisense molecules which are
complementary to a fragment of the 3' untranslated region of SEQ ID
NO 2.
[0254] Alternatively, a class of antisense molecules can be used to
inactivate mRNA in order to decrease expression of aminopeptidase
nucleic acid. Accordingly, these molecules can treat a disorder
characterized by abnormal or undesired aminopeptidase nucleic acid
expression. This technique involves cleavage by means of ribozymes
containing nucleotide sequences complementary to one or more
regions in the mRNA that attenuate the ability of the mRNA to be
translated. Possible regions include coding regions and
particularly coding regions corresponding to the catalytic and
other functional activities of the aminopeptidase protein.
[0255] The aminopeptidase polynucleotides also provide vectors for
gene therapy in patients containing cells that are aberrant in
aminopeptidase gene expression. Thus, recombinant cells, which
include the patient's cells that have been engineered ex vivo and
returned to the patient, are introduced into an individual where
the cells produce the desired aminopeptidase protein to treat the
individual.
[0256] The invention also encompasses kits for detecting the
presence of an aminopeptidase nucleic acid in a biological sample.
For example, the kit can comprise reagents such as a labeled or
labelable nucleic acid or agent capable of detecting aminopeptidase
nucleic acid in a biological sample; means for determining the
amount of aminopeptidase nucleic acid in the sample; and means for
comparing the amount of aminopeptidase nucleic acid in the sample
with a standard. The compound or agent can be packaged in a
suitable container. The kit can further comprise instructions for
using the kit to detect aminopeptidase mRNA or DNA.
Computer Readable Means
[0257] The nucleotide or amino acid sequences of the invention are
also provided in a variety of mediums to facilitate use thereof. As
used herein, "provided" refers to a manufacture, other than an
isolated nucleic acid or amino acid molecule, which contains a
nucleotide or amino acid sequence of the present invention. Such a
manufacture provides the nucleotide or amino acid sequences, or a
subset thereof (e.g., a subset of open reading frames (ORFs)) in a
form which allows a skilled artisan to examine the manufacture
using means not directly applicable to examining the nucleotide or
amino acid sequences, or a subset thereof, as they exists in nature
or in purified form.
[0258] In one application of this embodiment, a nucleotide or amino
acid sequence of the present invention can be recorded on computer
readable media. As used herein, "computer readable media" refers to
any medium that can be read and accessed directly by a computer.
Such media include, but are not limited to: magnetic storage media,
such as floppy discs, hard disc storage medium, and magnetic tape;
optical storage media such as CD-ROM; electrical storage media such
as RAM and ROM; and hybrids of these categories such as
magnetic/optical storage media. The skilled artisan will readily
appreciate how any of the presently known computer readable mediums
can be used to create a manufacture comprising computer readable
medium having recorded thereon a nucleotide or amino acid sequence
of the present invention.
[0259] As used herein, "recorded" refers to a process for storing
information on computer readable medium. The skilled artisan can
readily adopt any of the presently known methods for recording
information on computer readable medium to generate manufactures
comprising the nucleotide or amino acid sequence information of the
present invention.
[0260] A variety of data storage structures are available to a
skilled artisan for creating a computer readable medium having
recorded thereon a nucleotide or amino acid sequence of the present
invention. The choice of the data storage structure will generally
be based on the means chosen to access the stored information. In
addition, a variety of data processor programs and formats can be
used to store the nucleotide sequence information of the present
invention on computer readable medium. The sequence information can
be represented in a word processing text file, formatted in
commercially-available software such as WordPerfect and Microsoft
Word, or represented in the form of an ASCII file, stored in a
database application, such as DB2, Sybase, Oracle, or the like. The
skilled artisan can readily adapt any number of dataprocessor
structuring formats (e.g., text file or database) in order to
obtain computer readable medium having recorded thereon the
nucleotide sequence information of the present invention.
[0261] By providing the nucleotide or amino acid sequences of the
invention in computer readable form, the skilled artisan can
routinely access the sequence information for a variety of
purposes. For example, one skilled in the art can use the
nucleotide or amino acid sequences of the invention in computer
readable form to compare a target sequence or target structural
motif with the sequence information stored within the data storage
means. Search means are used to identify fragments or regions of
the sequences of the invention which match a particular target
sequence or target motif.
[0262] As used herein, a "target sequence" can be any DNA or amino
acid sequence of six or more nucleotides or two or more amino
acids. A skilled artisan can readily recognize that the longer a
target sequence is, the less likely a target sequence will be
present as a random occurrence in the database. The most preferred
sequence length of a target sequence is from about 10 to 100 amino
acids or from about 30 to 300 nucleotide residues. However, it is
well recognized that commercially important fragments, such as
sequence fragments involved in gene expression and protein
processing, may be of shorter length.
[0263] As used herein, "a target structural motif," or "target
motif," refers to any rationally selected sequence or combination
of sequences in which the sequence(s) are chosen based on a
three-dimensional configuration which is formed upon the folding of
the target motif. There are a variety of target motifs known in the
art. Protein target motifs include, but are not limited to, enzyme
active sites and signal sequences. Nucleic acid target motifs
include, but are not limited to, promoter sequences, hairpin
structures and inducible expression elements (protein binding
sequences).
[0264] Computer software is publicly available which allows a
skilled artisan to access sequence information provided in a
computer readable medium for analysis and comparison to other
sequences. A variety of known algorithms are disclosed publicly and
a variety of commercially available software for conducting search
means are and can be used in the computer-based systems of the
present invention. Examples of such software includes, but is not
limited to, MacPattern (EMBL), BLASTN and BLASTX (NCBIA).
[0265] For example, software which implements the BLAST (Altschul
et al. (1990) J. Mol. Biol. 215:403-410) and BLAZE (Brutlag et al.
(1993) Comp. Chem. 17:203-207) search algorithms on a Sybase system
can be used to identify open reading frames (ORFs) of the sequences
of the invention which contain homology to ORFs or proteins from
other libraries. Such ORFs are protein encoding fragments and are
useful in producing commercially important proteins such as enzymes
used in various reactions and in the production of commercially
useful metabolites.
Vectors/Host Cells
[0266] The invention also provides vectors containing the
aminopeptidase polynucleotides. The term "vector" refers to a
vehicle, preferably a nucleic acid molecule that can transport the
aminopeptidase polynucleotides. When the vector is a nucleic acid
molecule, the aminopeptidase polynucleotides are covalently linked
to the vector nucleic acid. With this aspect of the invention, the
vector includes a plasmid, single or double stranded phage, a
single or double stranded RNA or DNA viral vector, or artificial
chromosome, such as a BAC, PAC, YAC, OR MAC.
[0267] A vector can be maintained in the host cell as an
extrachromosomal element where it replicates and produces
additional copies of the aminopeptidase polynucleotides.
Alternatively, the vector may integrate into the host cell genome
and produce additional copies of the anrinopeptidase
polynucleotides when the host cell replicates.
[0268] The invention provides vectors for the maintenance (cloning
vectors) or vectors for expression (expression vectors) of the
aminopeptidase polynucleotides. The vectors can function in
procaryotic or eukaryotic cells or in both (shuttle vectors).
[0269] Expression vectors contain cis-acting regulatory regions
that are operably linked in the vector to the arninopeptidase
polynucleotides such that transcription of the polynucleotides is
allowed in a host cell. The polynucleotides can be introduced into
the host cell with a separate polynucleotide capable of affecting
transcription. Thus, the second polynucleotide may provide a
trans-acting factor interacting with the cis-regulatory control
region to allow transcription of the aminopeptidase polynucleotides
from the vector.
[0270] Alternatively, a trans-acting factor may be supplied by the
host cell. Finally, a trans-acting factor can be produced from the
vector itself.
[0271] It is understood, however, that in some embodiments,
transcription and/or translation of the aminopeptidase
polynucleotides can occur in a cell-free system.
[0272] The regulatory sequence to which the polynucleotides
described herein can be operably linked include promoters for
directing mRNA transcription. These include, but are not limited
to, the left promoter from bacteriophage .lamda., the lac, TRP, and
TAC promoters from E. coli, the early and late promoters from SV40,
the CMV immediate early promoter, the adenovirus early and late
promoters, and retrovirus long-terminal repeats.
[0273] In addition to control regions that promote transcription,
expression vectors may also include regions that modulate
transcription, such as repressor binding sites and enhancers.
Examples include the SV40 enhancer, the cytomegalovirus immediate
early enhancer, polyoma enhancer, adenovirus enhancers, and
retrovirus LTR enhancers.
[0274] In addition to containing sites for transcription initiation
and control, expression vectors can also contain sequences
necessary for transcription termination and, in the transcribed
region a ribosome binding site for translation. Other regulatory
control elements for expression include initiation and termination
codons as well as polyadenylation signals. The person of ordinary
skill in the art would be aware of the numerous regulatory
sequences that are useful in expression vectors. Such regulatory
sequences are described, for example, in Sambrook et al. (1989)
Molecular Cloning: A Laboratory Manual 2nd. ed., Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y.).
[0275] A variety of expression vectors can be used to express an
aminopeptidase polynucleotide. Such vectors include chromosomal,
episomal, and virus-derived vectors, for example vectors derived
from bacterial plasmids, from bacteriophage, from yeast episomes,
from yeast chromosomal elements, including yeast artificial
chromosomes, from viruses such as baculoviruses, papovaviruses such
as SV40, Vaccinia viruses, adenoviruses, poxviruses, pseudorabies
viruses, and retroviruses. Vectors may also be derived from
combinations of these sources such as those derived from plasmid
and bacteriophage genetic elements, e.g. cosmids and phagemids.
Appropriate cloning and expression vectors for prokaryotic and
eukaryotic hosts are described in Sambrook et al. (1989) Molecular
Cloning: A Laboratory Manual 2nd. ed., Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y.
[0276] The regulatory sequence may provide constitutive expression
in one or more host cells (i.e. tissue specific) or may provide for
inducible expression in one or more cell types such as by
temperature, nutrient additive, or exogenous factor such as a
hormone or other ligand. A variety of vectors providing for
constitutive and inducible expression in prokaryotic and eukaryotic
hosts are well known to those of ordinary skill in the art.
[0277] The aminopeptidase polynucleotides can be inserted into the
vector nucleic acid by well-known methodology. Generally, the DNA
sequence that will ultimately be expressed is joined to an
expression vector by cleaving the DNA sequence and the expression
vector with one or more restriction enzymes and then ligating the
fragments together. Procedures for restriction enzyme digestion and
ligation are well known to those of ordinary skill in the art.
[0278] The vector containing the appropriate polynucleotide can be
introduced into an appropriate host cell for propagation or
expression using well-known techniques. Bacterial cells include,
but are not limited to, E. coli, Streptomyces, and Salmonella
typhimurium. Eukaryotic cells include, but are not limited to,
yeast, insect cells such as Drosophila, animal cells such as COS
and CHO cells, and plant cells.
[0279] As described herein, it may be desirable to express the
polypeptide as a fusion protein. Accordingly, the invention
provides fusion vectors that allow for the production of the
aminopeptidase polypeptides. Fusion vectors can increase the
expression of a recombinant protein, increase the solubility of the
recombinant protein, and aid in the purification of the protein by
acting for example as a ligand for affinity purification. A
proteolytic cleavage site may be introduced at the junction of the
fusion moiety so that the desired polypeptide can ultimately be
separated from the fusion moiety. Proteolytic enzymes include, but
are not limited to, factor Xa, thrombin, and enterokinase. Typical
fusion expression vectors include pGEX (Smith et al. (1988) Gene
67:31-40), pMAL (New England Biolabs, Beverly, Mass.) and pRIT5
(Pharmacia, Piscataway, N.J.) which fuse glutathione S-transferase
(GST), maltose E binding protein, or protein A, respectively, to
the target recombinant protein. Examples of suitable inducible
non-fusion E. coli expression vectors include pTrc (Amann et al.
(1988) Gene 69:301-315) and pET 11d (Studier et al. (1990) Gene
Expression Technology: Methods in Enzymology 185:60-89).
[0280] Recombinant protein expression can be maximized in a host
bacteria by providing a genetic background wherein the host cell
has an impaired capacity to proteolytically cleave the recombinant
protein. (Gottesman, S. (1990) Gene Expression Technology: Methods
in Enzymology 185, Academic Press, San Diego, Calif. 119-128).
Alternatively, the sequence of the polynucleotide of interest can
be altered to provide preferential codon usage for a specific host
cell, for example E. coli. (Wada et al. (1992) Nucleic Acids Res.
20:2111-2118).
[0281] The aminopeptidase polynucleotides can also be expressed by
expression vectors that are operative in yeast. Examples of vectors
for expression in yeast e.g., S. cerevisiae include pYepSec1
(Baldari et al. (1987) EMBO J. 6:229-234 ), pMFa (Kurjan et al.
(1982) Cell 30:933-943), pJRY88 (Schultz et al. (1987) Gene
54:113-123), and pYES2 (Invitrogen Corporation, San Diego,
Calif.).
[0282] The aminopeptidase polynucleotides can also be expressed in
insect cells using, for example, baculovirus expression vectors.
Baculovirus vectors available for expression of proteins in
cultured insect cells (e.g., Sf 9 cells) include the pAc series
(Smith et al. (1983) Mol. Cell Biol. 3:2156-2165) and the pVL
series (Lucklow et al. (1989) Virology 170:31-39).
[0283] In certain embodiments of the invention, the polynucleotides
described herein are expressed in mammalian cells using mammalian
expression vectors. Examples of mammalian expression vectors
include pCDM8 (Seed, B. (1987) Nature 329:840) and pMT2PC (Kaufman
et al. (1987) EMBO J. 6:187-195).
[0284] The expression vectors listed herein are provided by way of
example only of the well-known vectors available to those of
ordinary skill in the art that would be useful to express the
aminopeptidase polynucleotides. The person of ordinary skill in the
art would be aware of other vectors suitable for maintenance
propagation or expression of the polynucleotides described herein.
These are found for example in Sambrook et al. (1989) Molecular
Cloning: A Laboratory Manual 2nd, ed., Cold Spring Harbor
Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring
Harbor, N.Y.
[0285] The invention also encompasses vectors in which the nucleic
acid sequences described herein are cloned into the vector in
reverse orientation, but operably linked to a regulatory sequence
that permits transcription of antisense RNA. Thus, an antisense
transcript can be produced to all, or to a portion, of the
polynucleotide sequences described herein, including both coding
and non-coding regions. Expression of this antisense RNA is subject
to each of the parameters described above in relation to expression
of the sense RNA (regulatory sequences, constitutive or inducible
expression, tissue-specific expression).
[0286] The invention also relates to recombinant host cells
containing the vectors described herein. Host cells therefore
include prokaryotic cells, lower eukaryotic cells such as yeast,
other eukaryotic cells such as insect cells, and higher eukaryotic
cells such as mammalian cells.
[0287] The recombinant host cells are prepared by introducing the
vector constructs described herein into the cells by techniques
readily available to the person of ordinary skill in the art. These
include, but are not limited to, calcium phosphate transfection,
DEAE-dextran-mediated transfection, cationic lipid-mediated
transfection, electroporation, transduction, infection,
lipofection, and other techniques such as those found in Sambrook
et al. (Molecular Cloning: A Laboratory Manual, 2d ed., Cold Spring
Harbor Laboratory, Cold Spring Harbor Laboratory Press, Cold Spring
Harbor, N.Y.).
[0288] Host cells can contain more than one vector. Thus, different
nucleotide sequences can be introduced on different vectors of the
same cell. Similarly, the aminopeptidase polynucleotides can be
introduced either alone or with other polynucleotides that are not
related to the aminopeptidase polynucleotides such as those
providing trans-acting factors for expression vectors. When more
than one vector is introduced into a cell, the vectors can be
introduced independently, co-introduced or joined to the
aminopeptidase polynucleotide vector.
[0289] In the case of bacteriophage and viral vectors, these can be
introduced into cells as packaged or encapsulated virus by standard
procedures for infection and transduction. Viral vectors can be
replication-competent or replication-defective. In the case in
which viral replication is defective, replication will occur in
host cells providing functions that complement the defects.
[0290] Vectors generally include selectable markers that enable the
selection of the subpopulation of cells that contain the
recombinant vector constructs. The marker can be contained in the
same vector that contains the polynucleotides described herein or
may be on a separate vector. Markers include tetracycline or
ampicillin-resistance genes for prokaryotic host cells and
dihydrofolate reductase or neomycin resistance for eukaryotic host
cells. However, any marker that provides selection for a phenotypic
trait will be effective.
[0291] While the mature proteins can be produced in bacteria,
yeast, mammalian cells, and other cells under the control of the
appropriate regulatory sequences, cell-free transcription and
translation systems can also be used to produce these proteins
using RNA derived from the DNA constructs described herein.
[0292] Where secretion of the polypeptide is desired, appropriate
secretion signals are incorporated into the vector. The signal
sequence can be endogenous to the aminopeptidase polypeptides or
heterologous to these polypeptides.
[0293] Where the polypeptide is not secreted into the medium, the
protein can be isolated from the host cell by standard disruption
procedures, including freeze thaw, sonication, mechanical
disruption, use of lysing agents and the like. The polypeptide can
then be recovered and purified by well-known purification methods
including ammonium sulfate precipitation, acid extraction, anion or
cationic exchange chromatography, phosphocellulose chromatography,
hydrophobic-interaction chromatography, affinity chromatography,
hydroxylapatite chromatography, lectin chromatography, or high
performance liquid chromatography.
[0294] It is also understood that depending upon the host cell in
recombinant production of the polypeptides described herein, the
polypeptides can have various glycosylation patterns, depending
upon the cell, or maybe non-glycosylated as when produced in
bacteria. In addition, the polypeptides may include an initial
modified methionine in some cases as a result of a host-mediated
process.
Uses of Vectors and Host Cells
[0295] It is understood that "host cells" and "recombinant host
cells" refer not only to the particular subject cell but also to
the progeny or potential progeny of such a cell. Because certain
modifications may occur in succeeding generations due to either
mutation or environmental influences, such progeny may not, in
fact, be identical to the parent cell, but are still included
within the scope of the term as used herein.
[0296] The host cells expressing the polypeptides described herein,
and particularly recombinant host cells, have a variety of uses.
First, the cells are useful for producing aminopeptidase proteins
or polypeptides that can be further purified to produce desired
amounts of aminopeptidase protein or fragments. Thus, host cells
containing expression vectors are useful for polypeptide
production.
[0297] Host cells are also useful for conducting cell-based assays
involving the aminopeptidase or aminopeptidase fragments. Thus, a
recombinant host cell expressing a native aminopeptidase is useful
to assay for compounds that stimulate or inhibit aminopeptidase
function. This includes zinc or peptide binding, gene expression at
the level of transcription or translation, and interaction with
other cellular components.
[0298] Host cells are also useful for identifying aminopeptidase
mutants in which these functions are affected. If the mutants
naturally occur and give rise to a pathology, host cells containing
the mutations are useful to assay compounds that have a desired
effect on the mutant aminopeptidase (for example, stimulating or
inhibiting function) which may not be indicated by their effect on
the native aminopeptidase.
[0299] Recombinant host cells are also useful for expressing the
chimeric polypeptides described herein to assess compounds that
activate or suppress activation by means of a heterologous domain,
segment, site, and the like, as disclosed herein.
[0300] Further, mutant aminopeptidases can be designed in which one
or more of the various functions is engineered to be increased or
decreased and used to augment or replace aminopeptidase proteins in
an individual. Thus, host cells can provide a therapeutic benefit
by replacing an aberrant aminopeptidase or providing an aberrant
aminopeptidase that provides a therapeutic result. In one
embodiment, the cells provide aminopeptidases that are abnormally
active.
[0301] In another embodiment, the cells provide aminopeptidases
that are abnormally inactive. These aminopeptidases can compete
with endogenous aminopeptidases in the individual.
[0302] In another embodiment, cells expressing aminopeptidases that
cannot be activated, are introduced into an individual in order to
compete with endogenous aminopeptidases for zinc or peptide. For
example, in the case in which excessive zinc is part of a treatment
modality, it may be necessary to effectively inactivate zinc at a
specific point in treatment. Providing cells that compete for the
molecule, but which cannot be affected by aminopeptidase activation
would be beneficial.
[0303] Homologously recombinant host cells can also be produced
that allow the in situ alteration of endogenous aminopeptidase
polynucleotide sequences in a host cell genome. This technology is
more fully described in WO 93/09222, WO 91/12650 and U.S. Pat. No.
5,641,670. Briefly, specific polynucleotide sequences corresponding
to the aminopeptidase polynucleotides or sequences proximal or
distal to an aminopeptidase gene are allowed to integrate into a
host cell genome by homologous recombination where expression of
the gene can be affected. In one embodiment, regulatory sequences
are introduced that either increase or decrease expression of an
endogenous sequence. Accordingly, an aminopeptidase protein can be
produced in a cell not normally producing it, or increased
expression of aminopeptidase protein can result in a cell normnally
producing the protein at a specific level. Alternatively, the
entire gene can be deleted. Still further, specific mutations can
be introduced into any desired region of the gene to produce mutant
aminopeptidase proteins. Such mutations could be introduced, for
example, into the specific regions disclosed herein.
[0304] In one embodiment, the host cell can be a fertilized oocyte
or embryonic stem cell that can be used to produce a transgenic
animal containing the altered aminopeptidase gene. Alternatively,
the host cell can be a stem cell or other early tissue precursor
that gives rise to a specific subset of cells and can be used to
produce transgenic tissues in an animal. See also Thomas et al.,
Cell 51:503 (1987) for a description of homologous recombination
vectors. The vector is introduced into an embryonic stem cell line
(e.g., by electroporation) and cells in which the introduced gene
has homologously recombined with the endogenous aminopeptidase gene
is selected (see e.g., Li, E. et al. (1992) Cell 69:915). The
selected cells are then injected into a blastocyst of an animal
(e.g., a mouse) to form aggregation chimeras (see e.g., Bradley, A.
in Teratocarcinomas and Embryonic Stem Cells: A Practical Approach,
E. J. Robertson, ed. (IRL, Oxford, 1987) pp. 113-152). A chimeric
embryo can then be implanted into a suitable pseudopregnant female
foster animal and the embryo brought to term. Progeny harboring the
homologously recombined DNA in their germ cells can be used to
breed animals in which all cells of the animal contain the
homologously recombined DNA by germline transmission of the
transgene. Methods for constructing homologous recombination
vectors and homologous recombinant animals are described further in
Bradley, A. (1991) Current Opinion in Biotechnology 2:823-829 and
in PCT International Publication Nos. WO 90/11354; WO 91/01140; and
WO 93/04169.
[0305] The genetically engineered host cells can be used to produce
non-human transgenic animals. A transgenic animal is preferably a
mammal, for example a rodent, such as a rat or mouse, in which one
or more of the cells of the animal include a transgene. A transgene
is exogenous DNA which is integrated into the genome of a cell from
which a transgenic animal develops and which remains in the genome
of the mature animal in one or more cell types or tissues of the
transgenic animal. These animals are useful for studying the
function of an aminopeptidase protein and identifying and
evaluating modulators of aminopeptidase protein activity.
[0306] Other examples of transgenic animals include non-human
primates, sheep, dogs, cows, goats, chickens, and amphibians.
[0307] In one embodiment, a host cell is a fertilized oocyte or an
embryonic stem cell into which aminopeptidase polynucleotide
sequences have been introduced.
[0308] A transgenic animal can be produced by introducing nucleic
acid into the male pronuclei of a fertilized oocyte, e.g., by
microinjection, retroviral infection, and allowing the oocyte to
develop in a pseudopregnant female foster animal. Any of the
aminopeptidase nucleotide sequences can be introduced as a
transgene into the genome of a non-human animal, such as a
mouse.
[0309] Any of the regulatory or other sequences useful in
expression vectors can form part of the transgenic sequence. This
includes intronic sequences and polyadenylation signals, if not
already included. A tissue-specific regulatory sequence(s) can be
operably linked to the transgene to direct expression of the
aminopeptidase protein to particular cells.
[0310] Methods for generating transgenic animals via embryo
manipulation and microinjection, particularly animals such as mice,
have become conventional in the art and are described, for example,
in U.S. Pat. Nos. 4,736,866 and 4,870,009, both by Leder et al.,
U.S. Pat. No. 4,873,191 by Wagner et al. and in Hogan, B.,
Manipulating the Mouse Embryo, (Cold Spring Harbor Laboratory
Press, Cold Spring Harbor, N.Y., 1986). Similar methods are used
for production of other transgenic animals. A transgenic founder
animal can be identified based upon the presence of the transgene
in its genome and/or expression of transgenic mRNA in tissues or
cells of the animals. A transgenic founder animal can then be used
to breed additional animals carrying the transgene. Moreover,
transgenic animals carrying a transgene can further be bred to
other transgenic animals carrying other transgenes. A transgenic
animal also includes animals in which the entire animal or tissues
in the animal have been produced using the homologously recombinant
host cells described herein.
[0311] In another embodiment, transgenic non-human animals can be
produced which contain selected systems, which allow for regulated
expression of the transgene. One example of such a system is the
cre/loxP recombinase system of bacteriophage P1. For a description
of the cre/loxP recombinase system, see, e.g., Lakso et al. (1992)
PNAS 89:6232-6236. Another example of a recombinase system is the
FLP recombinase system of S. cerevisiae (O'Gorman et al. (1991)
Science 251:1351-1355. If a cre/loxP recombinase system is used to
regulate expression of the transgene, animals containing transgenes
encoding both the Cre recombinase and a selected protein is
required. Such animals can be provided through the construction of
"double" transgenic animals, e.g., by mating two transgenic
animals, one containing a transgene encoding a selected protein and
the other containing a transgene encoding a recombinase.
[0312] Clones of the non-human transgenic animals described herein
can also be produced according to the methods described in Wilmut
et al. (1997) Nature 385:810-813 and PCT International Publication
Nos. WO 97/07668 and WO 97/07669. In brief, a cell, e.g., a somatic
cell, from the transgenic animal can be isolated and induced to
exit the growth cycle and enter G.sub.o phase. The quiescent cell
can then be fused, e.g., through the use of electrical pulses, to
an enucleated oocyte from an animal of the same species from which
the quiescent cell is isolated. The reconstructed oocyte is then
cultured such that it develops to morula or blastocyst and then
transferred to a pseudopregnant female foster animal. The offspring
born of this female foster animal will be a clone of the animal
from which the cell, e.g., the somatic cell, is isolated.
[0313] Transgenic animals containing recombinant cells that express
the polypeptides described herein are useful to conduct the assays
described herein in an in vivo context. Accordingly, the various
physiological factors that are present in vivo and that could
affect binding or activation, may not be evident from in vitro
cell-free or cell-based assays. Accordingly, it is useful to
provide non-human transgenic animals to assay in vivo
aminopeptidase function, including peptide interaction, the effect
of specific mutant aminopeptidases on aminopeptidase function and
peptide interaction, and the effect of chimeric aminopeptidases. It
is also possible to assess the effect of null mutations, that is
mutations that substantially or completely eliminate one or more
aminopeptidase functions.
Pharmaceutical Compositions
[0314] The aminopeptidase nucleic acid molecules, protein,
modulators of the protein, and antibodies (also referred to herein
as "active compounds") can be incorporated into pharmaceutical
compositions suitable for administration to a subject, e.g., a
human. Such compositions typically comprise the nucleic acid
molecule, protein, modulator, or antibody and a pharmaceutically
acceptable carrier.
[0315] The term "administer" is used in its broadest sense and
includes any method of introducing the compositions of the present
invention into a subject. This includes producing polypeptides or
polynucleotides in vivo by in vivo transcription or translation of
polynucleotides that have been exogenously introduced into a
subject. Thus, polypeptides or nucleic acids produced in the
subject from the exogenous compositions are encompassed in the term
"administer."
[0316] As used herein the language "pharmaceutically acceptable
carrier" is intended to include any and all solvents, dispersion
media, coatings, antibacterial and antifungal agents, isotonic and
absorption delaying agents, and the like, compatible with
pharmaceutical administration. The use of such media and agents for
pharmaceutically active substances is well known in the art. Except
insofar as any conventional media or agent is incompatible with the
active compound, such media can be used in the compositions of the
invention. Supplementary active compounds can also be incorporated
into the compositions. A pharmaceutical composition of the
invention is formulated to be compatible with its intended route of
administration. Examples of routes of administration include
parenteral, e.g., intravenous, intradermal, subcutaneous, oral
(e.g., inhalation), transdermal (topical), transmucosal, and rectal
administration. Solutions or suspensions used for parenteral,
intradermal, or subcutaneous application can include the following
components: a sterile diluent such as water for injection, saline
solution, fixed oils, polyethylene glycols, glycerine, propylene
glycol or other synthetic solvents; antibacterial agents such as
benzyl alcohol or methyl parabens; antioxidants such as ascorbic
acid or sodium bisulfite; chelating agents such as
ethylenediaminetetraacetic acid; buffers such as acetates, citrates
or phosphates and agents for the adjustment of tonicity such as
sodium chloride or dextrose. pH can be adjusted with acids or
bases, such as hydrochloric acid or sodium hydroxide. The
parenteral preparation can be enclosed in ampules, disposable
syringes or multiple dose vials made of glass or plastic.
[0317] Pharmaceutical compositions suitable for injectable use
include sterile aqueous solutions (where water soluble) or
dispersions and sterile powders for the extemporaneous preparation
of sterile injectable solutions or dispersion. For intravenous
administration, suitable carriers include physiological saline,
bacteriostatic water, Cremophor EL.TM. (BASF, Parsippany, N.J.) or
phosphate buffered saline (PBS). In all cases, the composition must
be sterile and should be fluid to the extent that easy
syringability exists. It must be stable under the conditions of
manufacture and storage and must be preserved against the
contaminating action of microorganisms such as bacteria and fungi.
The carrier can be a solvent or dispersion medium containing, for
example, water, ethanol, polyol (for example, glycerol, propylene
glycol, and liquid polyethylene glycol, and the like), and suitable
mixtures thereof. The proper fluidity can be maintained, for
example, by the use of a coating such as lecithin, by the
maintenance of the required particle size in the case of dispersion
and by the use of surfactants. Prevention of the action of
microorganisms can be achieved by various antibacterial and
antifungal agents, for example, parabens, chlorobutanol, phenol,
ascorbic acid, thimerosal, and the like. In many cases, it will be
preferable to include isotonic agents, for example, sugars,
polyalcohols such as mannitol, sorbitol, sodium chloride in the
composition. Prolonged absorption of the injectable compositions
can be brought about by including in the composition an agent which
delays absorption, for example, aluminum monostearate and
gelatin.
[0318] Sterile injectable solutions can be prepared by
incorporating the active compound (e.g., an aminopeptidase protein
or anti- aminopeptidase antibody) in the required amount in an
appropriate solvent with one or a combination of ingredients
enumerated above, as required, followed by filtered sterilization.
Generally, dispersions are prepared by incorporating the active
compound into a sterile vehicle which contains a basic dispersion
medium and the required other ingredients from those enumerated
above. In the case of sterile powders for the preparation of
sterile injectable solutions, the preferred methods of preparation
are vacuum drying and freeze-drying which yields a powder of the
active ingredient plus any additional desired ingredient from a
previously sterile-filtered solution thereof.
[0319] Oral compositions generally include an inert diluent or an
edible carrier. They can be enclosed in gelatin capsules or
compressed into tablets. For oral administration, the agent can be
contained in enteric forms to survive the stomach or further coated
or mixed to be released in a particular region of the GI tract by
known methods. For the purpose of oral therapeutic administration,
the active compound can be incorporated with excipients and used in
the form of tablets, troches, or capsules. Oral compositions can
also be prepared using a fluid carrier for use as a mouthwash,
wherein the compound in the fluid carrier is applied orally and
swished and expectorated or swallowed. Pharmaceutically compatible
binding agents, and/or adjuvant materials can be included as part
of the composition. The tablets, pills, capsules, troches and the
like can contain any of the following ingredients, or compounds of
a similar nature: a binder such as microcrystalline cellulose, gum
tragacanth or gelatin; an excipient such as starch or lactose, a
disintegrating agent such as alginic acid, Primogel, or corn
starch; a lubricant such as magnesium stearate or Sterotes; a
glidant such as colloidal silicon dioxide; a sweetening agent such
as sucrose or saccharin; or a flavoring agent such as peppermint,
methyl salicylate, or orange flavoring.
[0320] For administration by inhalation, the compounds are
delivered in the form of an aerosol spray from pressured container
or dispenser, which contains a suitable propellant, e.g., a gas
such as carbon dioxide, or a nebulizer.
[0321] Systemic administration can also be by transmucosal or
transdermal means. For transmucosal or transdermal administration,
penetrants appropriate to the barrier to be permeated are used in
the formulation. Such penetrants are generally known in the art,
and include, for example, for transmucosal administration,
detergents, bile salts, and fusidic acid derivatives. Transmucosal
administration can be accomplished through the use of nasal sprays
or suppositories. For transdermal administration, the active
compounds are formulated into ointments, salves, gels, or creams as
generally known in the art.
[0322] The compounds can also be prepared in the form of
suppositories (e.g., with conventional suppository bases such as
cocoa butter and other glycerides) or retention enemas for rectal
delivery.
[0323] In one embodiment, the active compounds are prepared with
carriers that will protect the compound against rapid elimination
from the body, such as a controlled release formulation, including
implants and microencapsulated delivery systems. Biodegradable,
biocompatible polymers can be used, such as ethylene vinyl acetate,
polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and
polylactic acid. Methods for preparation of such formulations will
be apparent to those skilled in the art. The materials can also be
obtained commercially from Alza Corporation and Nova
Pharmaceuticals, Inc. Liposomal suspensions (including liposomes
targeted to infected cells with monoclonal antibodies to viral
antigens) can also be used as pharmaceutically acceptable carriers.
These can be prepared according to methods known to those skilled
in the art, for example, as described in U.S. Pat. No.
4,522,811.
[0324] It is especially advantageous to formulate oral or
parenteral compositions in dosage unit form for ease of
administration and uniformity of dosage. "Dosage unit form" as used
herein refers to physically discrete units suited as unitary
dosages for the subject to be treated; each unit containing a
predetermined quantity of active compound calculated to produce the
desired therapeutic effect in association with the required
pharmaceutical carrier. The specification for the dosage unit forms
of the invention are dictated by and directly dependent on the
unique characteristics of the active compound and the particular
therapeutic effect to be achieved, and the limitations inherent in
the art of compounding such an active compound for the treatment of
individuals.
[0325] The nucleic acid molecules of the invention can be inserted
into vectors and used as gene therapy vectors. Gene therapy vectors
can be delivered to a subject by, for example, intravenous
injection, local administration (U.S. Pat. No. 5,328,470) or by
stereotactic injection (see e.g., Chen et al. (1994) PNAS
91:3054-3057). The pharmaceutical preparation of the gene therapy
vector can include the gene therapy vector in an acceptable
diluent, or can comprise a slow release matrix in which the gene
delivery vehicle is imbedded. Alternatively, where the complete
gene delivery vector can be produced intact from recombinant cells,
e.g. retroviral vectors, the pharmaceutical preparation can include
one or more cells which produce the gene delivery system.
[0326] The pharmaceutical compositions can be included in a
container, pack, or dispenser together with instructions for
administration.
[0327] This invention may be embodied in many different forms and
should not be construed as limited to the embodiments set forth
herein; rather, these embodiments are provided so that this
disclosure will fully convey the invention to those skilled in the
art. Many modifications and other embodiments of the invention will
come to mind in one skilled in the art to which this invention
pertains having the benefit of the teachings presented in the
foregoing description. Although specific terms are employed, they
are used as in the art unless otherwise indicated.
Sequence CWU 1
1
3 1 960 PRT Homo sapiens 1 Met Phe His Ser Ser Ala Met Val Asn Ser
His Arg Lys Pro Met Phe 1 5 10 15 Asn Ile His Arg Gly Phe Tyr Cys
Leu Thr Ala Ile Leu Pro Gln Ile 20 25 30 Cys Ile Cys Ser Gln Phe
Ser Val Pro Ser Ser Tyr His Phe Thr Glu 35 40 45 Asp Pro Gly Ala
Phe Pro Val Ala Thr Asn Gly Glu Arg Phe Pro Trp 50 55 60 Gln Glu
Leu Arg Leu Pro Ser Val Val Ile Pro Leu His Tyr Asp Leu 65 70 75 80
Phe Val His Pro Asn Leu Thr Ser Leu Asp Phe Val Ala Ser Glu Lys 85
90 95 Ile Glu Val Leu Val Ser Asn Ala Thr Gln Phe Ile Ile Leu His
Ser 100 105 110 Lys Asp Leu Glu Ile Thr Asn Ala Thr Leu Gln Ser Glu
Glu Asp Ser 115 120 125 Arg Tyr Met Lys Pro Gly Lys Glu Leu Lys Val
Leu Ser Tyr Pro Ala 130 135 140 His Glu Gln Ile Ala Leu Leu Val Pro
Glu Lys Leu Thr Pro His Leu 145 150 155 160 Lys Tyr Tyr Val Ala Met
Asp Phe Gln Ala Lys Leu Gly Asp Gly Phe 165 170 175 Glu Gly Phe Tyr
Lys Ser Thr Tyr Arg Thr Leu Gly Gly Glu Thr Arg 180 185 190 Ile Leu
Ala Val Thr Asp Phe Glu Pro Thr Gln Ala Arg Met Ala Phe 195 200 205
Pro Cys Phe Asp Glu Pro Leu Phe Lys Ala Asn Phe Ser Ile Lys Ile 210
215 220 Arg Arg Glu Ser Arg His Ile Ala Leu Ser Asn Met Pro Lys Val
Lys 225 230 235 240 Thr Ile Glu Leu Glu Gly Gly Leu Leu Glu Asp His
Phe Glu Thr Thr 245 250 255 Val Lys Met Ser Thr Tyr Leu Val Ala Tyr
Ile Val Cys Asp Phe His 260 265 270 Ser Leu Ser Gly Phe Thr Ser Ser
Gly Val Lys Val Ser Ile Tyr Ala 275 280 285 Ser Pro Asp Lys Arg Asn
Gln Thr His Tyr Ala Leu Gln Ala Ser Leu 290 295 300 Lys Leu Leu Asp
Phe Tyr Glu Lys Tyr Phe Asp Ile Tyr Tyr Pro Leu 305 310 315 320 Ser
Lys Leu Asp Leu Ile Ala Ile Pro Asp Phe Ala Pro Gly Ala Met 325 330
335 Glu Asn Trp Gly Leu Ile Thr Tyr Arg Glu Thr Ser Leu Leu Phe Asp
340 345 350 Pro Lys Thr Ser Ser Ala Ser Asp Lys Leu Trp Val Thr Arg
Val Ile 355 360 365 Ala His Glu Leu Ala His Gln Trp Phe Gly Asn Leu
Val Thr Met Glu 370 375 380 Trp Trp Asn Asp Ile Trp Leu Lys Glu Gly
Phe Ala Lys Tyr Met Glu 385 390 395 400 Leu Ile Ala Val Asn Ala Thr
Tyr Pro Glu Leu Gln Phe Asp Asp Tyr 405 410 415 Phe Leu Asn Val Cys
Phe Glu Val Ile Thr Lys Asp Ser Leu Asn Ser 420 425 430 Ser Arg Pro
Ile Ser Lys Pro Ala Glu Thr Pro Thr Gln Ile Gln Glu 435 440 445 Met
Phe Asp Glu Val Ser Tyr Asn Lys Gly Ala Cys Ile Leu Asn Met 450 455
460 Leu Lys Asp Phe Leu Gly Glu Glu Lys Phe Gln Lys Gly Ile Ile Gln
465 470 475 480 Tyr Leu Lys Lys Phe Ser Tyr Arg Asn Ala Lys Asn Asp
Asp Leu Trp 485 490 495 Ser Ser Leu Ser Asn Ser Cys Leu Glu Ser Asp
Phe Thr Ser Gly Gly 500 505 510 Val Cys His Ser Asp Pro Lys Met Thr
Ser Asn Met Leu Ala Phe Leu 515 520 525 Gly Glu Asn Ala Glu Val Lys
Glu Met Met Thr Thr Trp Thr Leu Gln 530 535 540 Lys Gly Ile Pro Leu
Leu Val Val Lys Gln Asp Gly Cys Ser Leu Arg 545 550 555 560 Leu Gln
Gln Glu Arg Phe Leu Gln Gly Val Phe Gln Glu Asp Pro Glu 565 570 575
Trp Arg Ala Leu Gln Glu Arg Tyr Leu Trp His Ile Pro Leu Thr Tyr 580
585 590 Ser Thr Ser Ser Ser Asn Val Ile His Arg His Ile Leu Lys Ser
Lys 595 600 605 Thr Asp Thr Leu Asp Leu Pro Glu Lys Thr Ser Trp Val
Lys Phe Asn 610 615 620 Val Asp Ser Asn Gly Tyr Tyr Ile Val His Tyr
Glu Gly His Gly Trp 625 630 635 640 Asp Gln Leu Ile Thr Gln Leu Asn
Gln Asn His Thr Leu Leu Arg Pro 645 650 655 Lys Asp Arg Val Gly Leu
Ile His Asp Val Phe Gln Leu Val Gly Ala 660 665 670 Gly Arg Leu Thr
Leu Asp Lys Ala Leu Asp Met Thr Tyr Tyr Leu Gln 675 680 685 His Glu
Thr Ser Ser Pro Ala Leu Leu Glu Gly Leu Ser Tyr Leu Glu 690 695 700
Ser Phe Tyr His Met Met Asp Arg Arg Asn Ile Ser Asp Ile Ser Glu 705
710 715 720 Asn Leu Lys Arg Tyr Leu Leu Gln Tyr Phe Lys Pro Val Ile
Asp Arg 725 730 735 Gln Ser Trp Ser Asp Lys Gly Ser Val Trp Asp Arg
Met Leu Arg Ser 740 745 750 Ala Leu Leu Lys Leu Ala Cys Asp Leu Asn
His Ala Pro Cys Ile Gln 755 760 765 Lys Ala Ala Glu Leu Phe Ser Gln
Trp Met Glu Ser Ser Gly Lys Leu 770 775 780 Asn Ile Pro Thr Asp Val
Leu Lys Ile Val Tyr Ser Val Gly Ala Gln 785 790 795 800 Thr Thr Ala
Gly Trp Asn Tyr Leu Leu Glu Gln Tyr Glu Leu Ser Met 805 810 815 Ser
Ser Ala Glu Gln Asn Lys Ile Leu Tyr Ala Leu Ser Thr Ser Lys 820 825
830 His Gln Glu Lys Leu Leu Lys Leu Ile Glu Leu Gly Met Glu Gly Lys
835 840 845 Val Ile Lys Thr Gln Asn Leu Ala Ala Leu Leu His Ala Ile
Ala Arg 850 855 860 Arg Pro Lys Gly Gln Gln Leu Ala Trp Asp Phe Val
Arg Glu Asn Trp 865 870 875 880 Thr His Leu Leu Lys Lys Phe Asp Leu
Gly Ser Tyr Asp Ile Arg Met 885 890 895 Ile Ile Ser Gly Thr Thr Ala
His Phe Ser Ser Lys Asp Lys Leu Gln 900 905 910 Glu Val Lys Leu Phe
Phe Glu Ser Leu Glu Ala Gln Gly Ser His Leu 915 920 925 Asp Ile Phe
Gln Thr Val Leu Glu Thr Ile Thr Lys Asn Ile Lys Trp 930 935 940 Leu
Glu Lys Asn Leu Pro Thr Leu Arg Thr Trp Leu Met Val Asn Thr 945 950
955 960 2 3366 DNA Homo sapiens CDS (146)...(3028) 2 ccccgcgtcc
ggcatgattt aagattaaat tcatgtattg aaaatattgt tcagacccca 60
tgtgacataa ctggagccag tgcagtgcca tgaagaacta cgagattagc ctggatatta
120 acttgtcttc tagagaatag atttc atg ttc cat tct tct gca atg gtt aat
172 Met Phe His Ser Ser Ala Met Val Asn 1 5 tca cac aga aaa cca atg
ttt aac att cac aga gga ttt tac tgc tta 220 Ser His Arg Lys Pro Met
Phe Asn Ile His Arg Gly Phe Tyr Cys Leu 10 15 20 25 aca gcc atc ttg
ccc caa ata tgc att tgt tct cag ttc tca gtg cca 268 Thr Ala Ile Leu
Pro Gln Ile Cys Ile Cys Ser Gln Phe Ser Val Pro 30 35 40 tct agt
tat cac ttc act gag gat cct ggg gct ttc cca gta gcc act 316 Ser Ser
Tyr His Phe Thr Glu Asp Pro Gly Ala Phe Pro Val Ala Thr 45 50 55
aat ggg gaa cga ttt cct tgg cag gag cta agg ctc ccc agt gtg gtc 364
Asn Gly Glu Arg Phe Pro Trp Gln Glu Leu Arg Leu Pro Ser Val Val 60
65 70 att cct ctc cat tat gac ctc ttt gtc cac ccc aat ctc acc tct
ctg 412 Ile Pro Leu His Tyr Asp Leu Phe Val His Pro Asn Leu Thr Ser
Leu 75 80 85 gac ttt gtt gca tct gag aag atc gaa gtc ttg gtc agc
aat gct acc 460 Asp Phe Val Ala Ser Glu Lys Ile Glu Val Leu Val Ser
Asn Ala Thr 90 95 100 105 cag ttt atc atc ttg cac agc aaa gat ctt
gaa atc acg aat gcc acc 508 Gln Phe Ile Ile Leu His Ser Lys Asp Leu
Glu Ile Thr Asn Ala Thr 110 115 120 ctt cag tca gag gaa gat tca aga
tac atg aaa cca gga aaa gaa ctg 556 Leu Gln Ser Glu Glu Asp Ser Arg
Tyr Met Lys Pro Gly Lys Glu Leu 125 130 135 aaa gtt ttg agt tac cct
gct cat gaa caa att gca ctg ctg gtt cca 604 Lys Val Leu Ser Tyr Pro
Ala His Glu Gln Ile Ala Leu Leu Val Pro 140 145 150 gag aaa ctt acg
cct cac ctg aaa tac tat gtg gct atg gac ttc caa 652 Glu Lys Leu Thr
Pro His Leu Lys Tyr Tyr Val Ala Met Asp Phe Gln 155 160 165 gcc aag
tta ggt gat ggc ttt gaa ggg ttt tat aaa agc aca tac aga 700 Ala Lys
Leu Gly Asp Gly Phe Glu Gly Phe Tyr Lys Ser Thr Tyr Arg 170 175 180
185 act ctt ggt ggt gaa aca aga att ctt gca gta aca gat ttt gag cca
748 Thr Leu Gly Gly Glu Thr Arg Ile Leu Ala Val Thr Asp Phe Glu Pro
190 195 200 acc cag gca cgc atg gct ttc cct tgc ttt gat gaa ccg ttg
ttc aaa 796 Thr Gln Ala Arg Met Ala Phe Pro Cys Phe Asp Glu Pro Leu
Phe Lys 205 210 215 gcc aac ttt tca atc aag ata cga aga gag agc agg
cat att gca cta 844 Ala Asn Phe Ser Ile Lys Ile Arg Arg Glu Ser Arg
His Ile Ala Leu 220 225 230 tcc aac atg cca aag gtt aag aca att gaa
ctt gaa gga ggt ctt ttg 892 Ser Asn Met Pro Lys Val Lys Thr Ile Glu
Leu Glu Gly Gly Leu Leu 235 240 245 gaa gat cac ttt gaa act act gta
aaa atg agt aca tac ctt gta gcc 940 Glu Asp His Phe Glu Thr Thr Val
Lys Met Ser Thr Tyr Leu Val Ala 250 255 260 265 tac ata gtt tgt gat
ttc cac tct ctg agt ggc ttc act tca tca ggg 988 Tyr Ile Val Cys Asp
Phe His Ser Leu Ser Gly Phe Thr Ser Ser Gly 270 275 280 gtc aag gtg
tcc atc tat gca tcc cca gac aaa cgg aat caa aca cat 1036 Val Lys
Val Ser Ile Tyr Ala Ser Pro Asp Lys Arg Asn Gln Thr His 285 290 295
tat gct ttg cag gca tca ctg aag cta ctt gat ttt tat gaa aag tac
1084 Tyr Ala Leu Gln Ala Ser Leu Lys Leu Leu Asp Phe Tyr Glu Lys
Tyr 300 305 310 ttt gat atc tac tat cca ctc tcc aaa ctg gat tta att
gct att cct 1132 Phe Asp Ile Tyr Tyr Pro Leu Ser Lys Leu Asp Leu
Ile Ala Ile Pro 315 320 325 gac ttt gca cct gga gcc atg gaa aat tgg
ggc ctc att aca tat agg 1180 Asp Phe Ala Pro Gly Ala Met Glu Asn
Trp Gly Leu Ile Thr Tyr Arg 330 335 340 345 gag acg tca ctg ctt ttt
gac ccc aag acc tct tct gct tcc gat aaa 1228 Glu Thr Ser Leu Leu
Phe Asp Pro Lys Thr Ser Ser Ala Ser Asp Lys 350 355 360 ctg tgg gtc
acc aga gtc ata gcc cat gaa ctg gcg cac cag tgg ttt 1276 Leu Trp
Val Thr Arg Val Ile Ala His Glu Leu Ala His Gln Trp Phe 365 370 375
ggc aac ctg gtc aca atg gaa tgg tgg aat gat att tgg ctt aag gag
1324 Gly Asn Leu Val Thr Met Glu Trp Trp Asn Asp Ile Trp Leu Lys
Glu 380 385 390 ggt ttt gca aaa tac atg gaa ctt atc gct gtt aat gct
aca tat cca 1372 Gly Phe Ala Lys Tyr Met Glu Leu Ile Ala Val Asn
Ala Thr Tyr Pro 395 400 405 gag ctg caa ttt gat gac tat ttt ttg aat
gtg tgt ttt gaa gta att 1420 Glu Leu Gln Phe Asp Asp Tyr Phe Leu
Asn Val Cys Phe Glu Val Ile 410 415 420 425 aca aaa gat tca ttg aat
tca tcc cgc cct atc tcc aaa cca gcg gaa 1468 Thr Lys Asp Ser Leu
Asn Ser Ser Arg Pro Ile Ser Lys Pro Ala Glu 430 435 440 acc ccg act
caa ata cag gaa atg ttt gat gaa gtt tcc tat aac aag 1516 Thr Pro
Thr Gln Ile Gln Glu Met Phe Asp Glu Val Ser Tyr Asn Lys 445 450 455
gga gct tgt att ttg aat atg ctc aag gat ttt ctg ggt gag gag aaa
1564 Gly Ala Cys Ile Leu Asn Met Leu Lys Asp Phe Leu Gly Glu Glu
Lys 460 465 470 ttc cag aaa gga ata att cag tac tta aag aag ttc agc
tat aga aat 1612 Phe Gln Lys Gly Ile Ile Gln Tyr Leu Lys Lys Phe
Ser Tyr Arg Asn 475 480 485 gct aag aat gat gac ttg tgg agc agt ctg
tca aat agt tgt tta gaa 1660 Ala Lys Asn Asp Asp Leu Trp Ser Ser
Leu Ser Asn Ser Cys Leu Glu 490 495 500 505 agt gat ttt aca tct ggt
gga gtt tgt cat tcg gat ccc aag atg aca 1708 Ser Asp Phe Thr Ser
Gly Gly Val Cys His Ser Asp Pro Lys Met Thr 510 515 520 agt aac atg
ctc gcc ttt ctg ggg gaa aat gca gag gtc aaa gag atg 1756 Ser Asn
Met Leu Ala Phe Leu Gly Glu Asn Ala Glu Val Lys Glu Met 525 530 535
atg act aca tgg act ctc cag aaa gga atc ccc ctg ctg gtg gtt aaa
1804 Met Thr Thr Trp Thr Leu Gln Lys Gly Ile Pro Leu Leu Val Val
Lys 540 545 550 caa gac ggg tgt tca ctc cga ctg caa cag gag cgc ttc
ctc cag ggg 1852 Gln Asp Gly Cys Ser Leu Arg Leu Gln Gln Glu Arg
Phe Leu Gln Gly 555 560 565 gtt ttc cag gaa gac cct gaa tgg agg gcc
ctg cag gag agg tac ctg 1900 Val Phe Gln Glu Asp Pro Glu Trp Arg
Ala Leu Gln Glu Arg Tyr Leu 570 575 580 585 tgg cat atc cca ttg acc
tac tcc acg agt tct tct aat gtg atc cac 1948 Trp His Ile Pro Leu
Thr Tyr Ser Thr Ser Ser Ser Asn Val Ile His 590 595 600 aga cac att
cta aaa tca aag aca gat act ctg gat cta cct gaa aag 1996 Arg His
Ile Leu Lys Ser Lys Thr Asp Thr Leu Asp Leu Pro Glu Lys 605 610 615
acc agt tgg gtg aaa ttt aat gtg gac tca aat ggt tac tac atc gtt
2044 Thr Ser Trp Val Lys Phe Asn Val Asp Ser Asn Gly Tyr Tyr Ile
Val 620 625 630 cac tat gag ggt cat gga tgg gac caa ctc att aca cag
ctg aat cag 2092 His Tyr Glu Gly His Gly Trp Asp Gln Leu Ile Thr
Gln Leu Asn Gln 635 640 645 aac cac aca ctt ctc aga cct aag gac aga
gta ggt ctg att cat gat 2140 Asn His Thr Leu Leu Arg Pro Lys Asp
Arg Val Gly Leu Ile His Asp 650 655 660 665 gtg ttt cag cta gtt ggt
gca ggg aga ctg acc cta gac aaa gct ctt 2188 Val Phe Gln Leu Val
Gly Ala Gly Arg Leu Thr Leu Asp Lys Ala Leu 670 675 680 gac atg act
tac tac ctc caa cat gaa aca agc agc ccc gca ctt ctc 2236 Asp Met
Thr Tyr Tyr Leu Gln His Glu Thr Ser Ser Pro Ala Leu Leu 685 690 695
gaa ggt ctg agt tac ttg gaa tcg ttt tac cac atg atg gac aga agg
2284 Glu Gly Leu Ser Tyr Leu Glu Ser Phe Tyr His Met Met Asp Arg
Arg 700 705 710 aat att tca gat atc tct gaa aac ctc aag cgt tac ctt
ctt cag tat 2332 Asn Ile Ser Asp Ile Ser Glu Asn Leu Lys Arg Tyr
Leu Leu Gln Tyr 715 720 725 ttt aag cca gtg att gac agg caa agc tgg
agt gac aag ggc tca gtc 2380 Phe Lys Pro Val Ile Asp Arg Gln Ser
Trp Ser Asp Lys Gly Ser Val 730 735 740 745 tgg gac agg atg ctc cgc
tcg gct ctc ttg aag ctg gcc tgt gac ctg 2428 Trp Asp Arg Met Leu
Arg Ser Ala Leu Leu Lys Leu Ala Cys Asp Leu 750 755 760 aac cat gct
cct tgc atc cag aaa gct gct gaa ctc ttc tcc cag tgg 2476 Asn His
Ala Pro Cys Ile Gln Lys Ala Ala Glu Leu Phe Ser Gln Trp 765 770 775
atg gaa tcc agt gga aaa tta aat ata cca aca gat gtt tta aag att
2524 Met Glu Ser Ser Gly Lys Leu Asn Ile Pro Thr Asp Val Leu Lys
Ile 780 785 790 gtg tat tct gtg ggt gct cag aca aca gca gga tgg aat
tac ctt tta 2572 Val Tyr Ser Val Gly Ala Gln Thr Thr Ala Gly Trp
Asn Tyr Leu Leu 795 800 805 gag caa tat gaa ctg tca atg tca agt gct
gaa caa aac aaa att ctg 2620 Glu Gln Tyr Glu Leu Ser Met Ser Ser
Ala Glu Gln Asn Lys Ile Leu 810 815 820 825 tat gct ttg tca acg agc
aag cat cag gaa aag tta ctg aag tta att 2668 Tyr Ala Leu Ser Thr
Ser Lys His Gln Glu Lys Leu Leu Lys Leu Ile 830 835 840 gaa cta gga
atg gaa gga aag gtt atc aag aca cag aac ttg gca gct 2716 Glu Leu
Gly Met Glu Gly Lys Val Ile Lys Thr Gln Asn Leu Ala Ala 845 850 855
ctc ctt cat gcg att gcc aga cgt cca aag ggg cag caa cta gca tgg
2764 Leu Leu His Ala Ile Ala Arg Arg Pro Lys Gly Gln Gln Leu Ala
Trp 860 865 870 gat ttt gta aga gaa aat tgg acc cat ctt ctg aaa aaa
ttt gac ttg 2812 Asp Phe Val Arg Glu Asn Trp Thr His Leu Leu Lys
Lys Phe Asp Leu 875 880 885 ggc tca tat gac ata agg atg atc atc tct
ggc aca aca gct cac ttt 2860 Gly Ser Tyr Asp Ile Arg Met Ile Ile
Ser Gly Thr Thr Ala His Phe 890
895 900 905 tct tcc aag gat aag ttg caa gag gtg aaa cta ttt ttt gaa
tct ctt 2908 Ser Ser Lys Asp Lys Leu Gln Glu Val Lys Leu Phe Phe
Glu Ser Leu 910 915 920 gag gct caa gga tca cat ctg gat att ttt caa
act gtt ctg gaa acg 2956 Glu Ala Gln Gly Ser His Leu Asp Ile Phe
Gln Thr Val Leu Glu Thr 925 930 935 ata acc aaa aat ata aaa tgg ctg
gag aag aat ctt ccg act ctg agg 3004 Ile Thr Lys Asn Ile Lys Trp
Leu Glu Lys Asn Leu Pro Thr Leu Arg 940 945 950 act tgg cta atg gtt
aat act taa atggtcaata gaaaaagtag gctgggcgcg 3058 Thr Trp Leu Met
Val Asn Thr * 955 960 gtggctcacg cctgtaatcc cagcactttg ggaggctgag
aagggcggat cacgaggtca 3118 ggagatggag accatcctgg ctaacacggt
gagaccccgt ctccgctaaa aatacaaaaa 3178 attagccggg catggtggca
ggtgcctgta gtcccagcta ctcggcaggc tgcagcagga 3238 aaatggcata
aacccgggag gtggagcttg cagtgagccg agattgcacc actgcattcc 3298
agcctgggtg actgagcgag actctgtctc aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa
3358 aaaaaaaa 3366 3 2883 DNA homo sapiens 3 atgttccatt cttctgcaat
ggttaattca cacagaaaac caatgtttaa cattcacaga 60 ggattttact
gcttaacagc catcttgccc caaatatgca tttgttctca gttctcagtg 120
ccatctagtt atcacttcac tgaggatcct ggggctttcc cagtagccac taatggggaa
180 cgatttcctt ggcaggagct aaggctcccc agtgtggtca ttcctctcca
ttatgacctc 240 tttgtccacc ccaatctcac ctctctggac tttgttgcat
ctgagaagat cgaagtcttg 300 gtcagcaatg ctacccagtt tatcatcttg
cacagcaaag atcttgaaat cacgaatgcc 360 acccttcagt cagaggaaga
ttcaagatac atgaaaccag gaaaagaact gaaagttttg 420 agttaccctg
ctcatgaaca aattgcactg ctggttccag agaaacttac gcctcacctg 480
aaatactatg tggctatgga cttccaagcc aagttaggtg atggctttga agggttttat
540 aaaagcacat acagaactct tggtggtgaa acaagaattc ttgcagtaac
agattttgag 600 ccaacccagg cacgcatggc tttcccttgc tttgatgaac
cgttgttcaa agccaacttt 660 tcaatcaaga tacgaagaga gagcaggcat
attgcactat ccaacatgcc aaaggttaag 720 acaattgaac ttgaaggagg
tcttttggaa gatcactttg aaactactgt aaaaatgagt 780 acataccttg
tagcctacat agtttgtgat ttccactctc tgagtggctt cacttcatca 840
ggggtcaagg tgtccatcta tgcatcccca gacaaacgga atcaaacaca ttatgctttg
900 caggcatcac tgaagctact tgatttttat gaaaagtact ttgatatcta
ctatccactc 960 tccaaactgg atttaattgc tattcctgac tttgcacctg
gagccatgga aaattggggc 1020 ctcattacat atagggagac gtcactgctt
tttgacccca agacctcttc tgcttccgat 1080 aaactgtggg tcaccagagt
catagcccat gaactggcgc accagtggtt tggcaacctg 1140 gtcacaatgg
aatggtggaa tgatatttgg cttaaggagg gttttgcaaa atacatggaa 1200
cttatcgctg ttaatgctac atatccagag ctgcaatttg atgactattt tttgaatgtg
1260 tgttttgaag taattacaaa agattcattg aattcatccc gccctatctc
caaaccagcg 1320 gaaaccccga ctcaaataca ggaaatgttt gatgaagttt
cctataacaa gggagcttgt 1380 attttgaata tgctcaagga ttttctgggt
gaggagaaat tccagaaagg aataattcag 1440 tacttaaaga agttcagcta
tagaaatgct aagaatgatg acttgtggag cagtctgtca 1500 aatagttgtt
tagaaagtga ttttacatct ggtggagttt gtcattcgga tcccaagatg 1560
acaagtaaca tgctcgcctt tctgggggaa aatgcagagg tcaaagagat gatgactaca
1620 tggactctcc agaaaggaat ccccctgctg gtggttaaac aagacgggtg
ttcactccga 1680 ctgcaacagg agcgcttcct ccagggggtt ttccaggaag
accctgaatg gagggccctg 1740 caggagaggt acctgtggca tatcccattg
acctactcca cgagttcttc taatgtgatc 1800 cacagacaca ttctaaaatc
aaagacagat actctggatc tacctgaaaa gaccagttgg 1860 gtgaaattta
atgtggactc aaatggttac tacatcgttc actatgaggg tcatggatgg 1920
gaccaactca ttacacagct gaatcagaac cacacacttc tcagacctaa ggacagagta
1980 ggtctgattc atgatgtgtt tcagctagtt ggtgcaggga gactgaccct
agacaaagct 2040 cttgacatga cttactacct ccaacatgaa acaagcagcc
ccgcacttct cgaaggtctg 2100 agttacttgg aatcgtttta ccacatgatg
gacagaagga atatttcaga tatctctgaa 2160 aacctcaagc gttaccttct
tcagtatttt aagccagtga ttgacaggca aagctggagt 2220 gacaagggct
cagtctggga caggatgctc cgctcggctc tcttgaagct ggcctgtgac 2280
ctgaaccatg ctccttgcat ccagaaagct gctgaactct tctcccagtg gatggaatcc
2340 agtggaaaat taaatatacc aacagatgtt ttaaagattg tgtattctgt
gggtgctcag 2400 acaacagcag gatggaatta ccttttagag caatatgaac
tgtcaatgtc aagtgctgaa 2460 caaaacaaaa ttctgtatgc tttgtcaacg
agcaagcatc aggaaaagtt actgaagtta 2520 attgaactag gaatggaagg
aaaggttatc aagacacaga acttggcagc tctccttcat 2580 gcgattgcca
gacgtccaaa ggggcagcaa ctagcatggg attttgtaag agaaaattgg 2640
acccatcttc tgaaaaaatt tgacttgggc tcatatgaca taaggatgat catctctggc
2700 acaacagctc acttttcttc caaggataag ttgcaagagg tgaaactatt
ttttgaatct 2760 cttgaggctc aaggatcaca tctggatatt tttcaaactg
ttctggaaac gataaccaaa 2820 aatataaaat ggctggagaa gaatcttccg
actctgagga cttggctaat ggttaatact 2880 taa 2883
* * * * *
References