U.S. patent application number 14/065587 was filed with the patent office on 2014-02-27 for breast endothelial cell expression patterns.
This patent application is currently assigned to Genzyme Corporation. The applicant listed for this patent is Genzyme Corporation, The Johns Hopkins University. Invention is credited to Stephen L. MADDEN, Saraswati SUKUMAR.
Application Number | 20140056911 14/065587 |
Document ID | / |
Family ID | 33299657 |
Filed Date | 2014-02-27 |
United States Patent
Application |
20140056911 |
Kind Code |
A1 |
SUKUMAR; Saraswati ; et
al. |
February 27, 2014 |
Breast Endothelial Cell Expression Patterns
Abstract
To gain a better understanding of breast tumor angiogenesis,
breast endothelial cells (ECs) were isolated and evaluated for gene
expression patterns. When transcripts from breast ECs derived from
normal and malignant breast tissues were compared, genes that were
specifically elevated in tumor-associated breast endothelium were
revealed. These results confirm that neoplastic and normal
endothelium in human breast are distinct at the molecular level,
and have significant implications for the development of
anti-angiogenic therapies in the future.
Inventors: |
SUKUMAR; Saraswati;
(Columbia, MD) ; MADDEN; Stephen L.; (Sudbury,
MA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Genzyme Corporation
The Johns Hopkins University |
Framingham
Baltimore |
MA
MD |
US
US |
|
|
Assignee: |
Genzyme Corporation
Framingham
MA
The Johns Hopkins University
Baltimore
MD
|
Family ID: |
33299657 |
Appl. No.: |
14/065587 |
Filed: |
October 29, 2013 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
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13176222 |
Jul 5, 2011 |
8568985 |
|
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14065587 |
|
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12269418 |
Nov 12, 2008 |
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13176222 |
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10551217 |
Dec 12, 2006 |
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PCT/US2004/009704 |
Mar 31, 2004 |
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12269418 |
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60458960 |
Apr 1, 2003 |
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Current U.S.
Class: |
424/158.1 ;
424/174.1; 424/277.1; 435/375; 435/6.11; 435/6.12; 435/6.13;
435/6.14; 435/7.1; 435/7.23; 435/7.4; 506/9 |
Current CPC
Class: |
C12Q 2600/136 20130101;
A61K 38/17 20130101; A61P 35/00 20180101; G01N 33/57415 20130101;
A61P 37/04 20180101; C07K 16/18 20130101; C12Q 1/6886 20130101;
G01N 33/5011 20130101; A61K 39/39558 20130101; A61K 51/1018
20130101; A61P 43/00 20180101; A61K 39/0011 20130101; C07K 2317/34
20130101 |
Class at
Publication: |
424/158.1 ;
435/7.1; 435/7.23; 435/7.4; 506/9; 424/174.1; 435/375; 435/6.13;
424/277.1; 435/6.12; 435/6.11; 435/6.14 |
International
Class: |
G01N 33/574 20060101
G01N033/574; C12Q 1/68 20060101 C12Q001/68; A61K 39/00 20060101
A61K039/00; A61K 39/395 20060101 A61K039/395; G01N 33/50 20060101
G01N033/50 |
Claims
1. A method to aid in diagnosing breast tumor, comprising the steps
of: detecting an expression product of at least one gene in a first
brain tissue sample suspected of being neoplastic wherein said at
least one gene is selected from the group consisting of
hypothetical protein DKFZp434G171; heat shock 70kDa protein 1A;
jagged 1 (Alagille syndrome); cyclin-dependent kinase 3;
6-phosphogluconolactonase; likely homolog of rat and mouse
retinoid-inducible serine carboxypeptidase; plasmalemma vesicle
associated protein; NADH:ubiquinone oxidoreductase MLRQ subunit
homolog; HIF-1 responsive RTP801; ribosomal protein L27; secreted
protein, acidic, cysteine-rich (osteonectin); hexokinase 1;
ribosomal protein L13a; collagen, type IV, alpha 1; insulin-like
growth factor binding protein 7; collagen, type III, alpha 1
(Ehlers-Danlos syndrome type IV, autosomal dominant); heat shock
10kDa protein 1 (chaperonin 10); calcium channel,
voltage-dependent, alpha 1H subunit; CD9 antigen (p24); TEM17;
TEM13, Thy-1 cell surface antigen; Tax interaction protein 1;
dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive);
hypothetical protein MGC34648; putative translation initiation
factor; insulin-like growth factor binding protein 4; matrix
metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV
collagenase); heterogeneous nuclear ribonucleoprotein R; bHLH
factor Hes4; collagen, type VI, alpha 2; T-box 2;
glyceraldehyde-3-phosphate dehydrogenase; G protein-coupled
receptor 4; collagen, type I, alpha 1; ras-related C3 botulinum
toxin substrate 1 (rho family, small GTP binding protein Rac1);
ribosomal protein, large, P1; TEM10, COL1A2 involved in tissue
remodeling; heat shock 70kDa protein 8; KIAA0152 gene product;
Ca2+-promoted Ras inactivator; serine/arginine repetitive matrix 2;
hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix
transcription factor); benzodiazapine receptor (peripheral);
ectonucleoside triphosphate diphosphohydrolase 1; heparan sulfate
proteoglycan 2 (perlecan); fibromodulin; hairy/enhancer-of-split
related with YRPW motif 1; collagen, type V, alpha 3;
hairy/enhancer-of-split related with YRPW motif-like; hypothetical
protein MGC2731; amino-terminal enhancer of split;
mitogen-activated protein kinase 9; regulator of G-protein
signalling 5; prothymosin, alpha (gene sequence 28); tubulin, beta,
2; protease, serine, 23; hypothetical protein FLJ20898; calpain 1,
(mu/I) large subunit; interferon, alpha-inducible protein (clone
IFI-6-16); ESTs, Weakly similar to T25031 hypothetical protein
T20D3.3--Caenorhabditis elegans [C. elegans]; major
histocompatibility complex, class I, C; hypoxia up-regulated 1;
complement component 4B; prefoldin 2; cytoskeleton-associated
protein 1; Rho GTPase activating protein 4; Homo sapiens clone
FLC1492 PRO3121 mRNA, complete cds; transducin-like enhancer of
split 2 (E(sp1) homolog, Drosophila); ribosomal protein L37;
hypothetical protein MGC4677; ESTs, Highly similar to MT1A_HUMAN
METALLOTHIONEIN-IA (MT-1A) [H. sapiens]; TEM11, nidogen (enactin);
guanine nucleotide binding protein (G protein), gamma 5; matrix Gla
protein; heat shock 105kD; GNAS complex locus; Homo sapiens cDNA
FLJ11658 fis, clone HEMBA1004577; H19, imprinted maternally
expressed untranslated mR NA; protein tyrosine phosphatase type
IVA, member 3; snail homolog 1 (Drosophila); integrin-binding
sialoprotein (bone sialoprotein, bone sialoprotein II); tissue
inhibitor of metalloproteinase 1 (erythroid potentiating activity,
collagenase inhibitor); peptidylprolyl isomerase B (cyclophilin B);
MARCKS-like protein; FAST kinase; protease, serine, 11 (IGF
binding); beta-2-microglobulin; delta sleep inducing peptide,
immunoreactor; collagen, type IV, alpha 2; immediate early response
3; cadherin 5, type 2, VE-cadherin (vascular epithelium); RGC32
protein; guanylate cyclase 1, soluble, beta 3; major
histocompatibility complex, class I, B; ribonuclease, RNase A
family, 1 (pancreatic); collagen, type XVIII, alpha 1; v-jun
sarcoma virus 17 oncogene homolog (avian); Homo sapiens mRNA; cDNA
DKFZp686G1610 (from clone DKFZp686G1610); nucleolin; lectin,
galactoside-binding, soluble, 3 binding protein;
Lysosomal-associated multispanning membrane protein-5; ribosomal
protein S16; guanine nucleotide binding protein (G protein), gamma
12; serine (or cysteine) proteinase inhibitor, Glade E (nexin,
plasminogen activator inhibitor type 1), member 1; biglycan; DnaJ
(Hsp40) homolog, subfamily B, member 1; tumor rejection antigen
(gp96) 1; interferon, alpha-inducible protein (clone IFI-15K);
solute carrier family 21 (prostaglandin transporter), member 2;
CD74 antigen (invariant polypeptide of major histocompatibility
complex, class II antigen-associated); serum/glucocorticoid
regulated kinase; mitogen-activated protein kinase; receptor
(calcitonin) activity modifying protein 3; sema domain,
immunoglobulin domain (Ig); benzodiazapine receptor
(peripheral)--mitochondrial; C1 domain-containing phosphatase &
tensin-like; and Notch homolog 3 (Drosophila); and comparing
expression of the at least one gene in the first breast tissue
sample with expression of the at least one gene in a second breast
tissue sample which is normal, wherein increased expression of the
at least one gene in the first breast tissue sample relative to the
second tissue sample identifies the first breast tissue sample as
likely to be neoplastic.
2. The method of claim 1 wherein the increased expression of the at
least one gene in the first breast tissue sample relative to the
second tissue sample is at least two-fold higher.
3. The method of claim 1 wherein the increased expression of the at
least one gene in the first breast tissue sample relative to the
second tissue sample is at least five-fold higher.
4. The method of claim 1 wherein the increased expression of the at
least one gene in the first breast tissue sample relative to the
second tissue sample is at least ten-fold higher.
5. The method of claim 1 wherein the expression product is RNA.
6. The method of claim 1 wherein the expression product is
protein.
7. The method of claim 1 wherein the first and second tissue
samples are from a human.
8. The method of claim 1 wherein the first and second tissue
samples are from the same human.
9. The method of claim 1 wherein the step of detecting is performed
using a Western blot.
10. The method of claim 1 wherein the step of detecting is
performed using an immunoassay.
11. The method of claim 1 wherein the step of detecting is
performed using an immunohistochemical assay.
12. The method of claim 1 wherein the step of detecting is
performed using SAGE.
13. The method of claim 1 wherein the step of detecting is
performed using hybridization to a microarray.
14. A method of treating a breast tumor, comprising the step of:
contacting cells of the breast tumor with an antibody, wherein the
antibody specifically binds to an extracellular epitope of a
protein selected from the group consisting of benzodiazapine
receptor (peripheral); cadherin 5, type 2, VE-cadherin (vascular
epithelium); calcium channel, voltage-dependent, alpha 1H subunit;
CD74 antigen (invariant polypeptide of major histocompatibility
complex, class II antigen-associated); CD9 antigen (p24);
dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive);
ectonucleoside triphosphate diphosphohydrolase 1; G protein-coupled
receptor 4; hypothetical protein FLJ20898; hypoxia up-regulated 1;
immediate early response 3; interferon, alpha-inducible protein
(clone IFI-6-16); jagged 1 (Alagille syndrome); KIAA0152 gene
product; Lysosomal-associated multispanning membrane protein-5;
major histocompatibility complex, class I, B; major
histocompatibility complex, class I, C; NADH:ubiquinone
oxidoreductase MLRQ subunit homolog; Notch homolog 3 (Drosophila);
plasmalemma vesicle associated protein; solute carrier family 21
(prostaglandin transporter), member 2; TEM13, Thy-1 cell surface
antigen; receptor (calcitonin) activity modifying protein 3; sema
domain, immunoglobulin domain (Ig); benzodiazapine receptor
(peripheral)--mitochondrial; and TEM17; whereby immune destruction
of cells of the breast tumor is triggered.
15. The method of claim 14 wherein the antibody is conjugated to a
diagnostic or therapeutic reagent.
16. The method of claim 14 wherein the breast tumor is
multidrug-sensitive.
17. The method of claim 14 wherein the reagent is a
chemotherapeutic agent.
18. The method of claim 14 wherein the reagent is a cytotoxin.
19. The method of claim 14 wherein the reagent is a non-radioactive
label.
20. The method of claim 14 wherein the reagent is a radioactive
compound.
21. The method of claim 14 wherein the breast tumor is in a
human.
22. A method of identifying a test compound as a potential
anti-cancer or anti-breast tumor drug, comprising the step of:
contacting a test compound with a cell which expresses at least one
gene selected from the group consisting of hypothetical protein
DKFZp434G171; heat shock 70kDa protein 1A; jagged 1 (Alagille
syndrome); cyclin-dependent kinase 3; 6-phosphogluconolactonase;
likely homolog of rat and mouse retinoid-inducible serine
carboxypeptidase; plasmalemma vesicle associated protein;
NADH:ubiquinone oxidoreductase MLRQ subunit homolog; HIF-1
responsive RTP801; ribosomal protein L27; secreted protein, acidic,
cysteine-rich (osteonectin); hexokinase 1; ribosomal protein L13a;
collagen, type IV, alpha 1; insulin-like growth factor binding
protein 7; collagen, type III, alpha 1 (Ehlers-Danlos syndrome type
IV, autosomal dominant); heat shock 10kDa protein 1 (chaperonin
10); calcium channel, voltage-dependent, alpha 1H subunit; CD9
antigen (p24); TEM17; TEM13, Thy-1 cell surface antigen; Tax
interaction protein 1; dysferlin, limb girdle muscular dystrophy 2B
(autosomal recessive); hypothetical protein MGC34648; putative
translation initiation factor; insulin-like growth factor binding
protein 4; matrix metalloproteinase 9 (gelatinase B, 92kDa
gelatinase, 92kDa type IV collagenase); heterogeneous nuclear
ribonucleoprotein R; bHLH factor Hes4; collagen, type VI, alpha 2;
T-box 2; glyceraldehyde-3-phosphate dehydrogenase; G
protein-coupled receptor 4; collagen, type I, alpha 1; ras-related
C3 botulinum toxin substrate 1 (rho family, small GTP binding
protein Rac1); ribosomal protein, large, P1; TEM10, COL1A2 involved
in tissue remodeling; heat shock 70kDa protein 8; KIAA0152 gene
product; Ca2+-promoted Ras inactivator; serine/arginine repetitive
matrix 2; hypoxia-inducible factor 1, alpha subunit (basic
helix-loop-helix transcription factor); benzodiazapine receptor
(peripheral); ectonucleoside triphosphate diphosphohydrolase 1;
heparan sulfate proteoglycan 2 (perlecan); fibromodulin;
hairy/enhancer-of-split related with YRPW motif 1; collagen, type
V, alpha 3; hairy/enhancer-of-split related with YRPW motif-like;
hypothetical protein MGC2731; amino-terminal enhancer of split;
mitogen-activated protein kinase 9; regulator of G-protein
signalling 5; prothymosin, alpha (gene sequence 28); tubulin, beta,
2; protease, serine, 23; hypothetical protein FLJ20898; calpain 1,
(mu/I) large subunit; interferon, alpha-inducible protein (clone
IFI-6-16); ESTs, Weakly similar to T25031 hypothetical protein
T20D3.3--Caenorhabditis elegans [C. elegans]; major
histocompatibility complex, class I, C; hypoxia up-regulated 1;
complement component 4B; prefoldin 2; cytoskeleton-associated
protein 1; Rho GTPase activating protein 4; Homo sapiens clone
FLC1492 PRO3121 mRNA, complete cds; transducin-like enhancer of
split 2 (E(sp1) homolog, Drosophila); ribosomal protein L37;
hypothetical protein MGC4677; ESTs, Highly similar to MT1A_HUMAN
METALLOTHIONEIN-IA (MT-1A) [H. sapiens]; TEM11, nidogen (enactin);
guanine nucleotide binding protein (G protein), gamma 5; matrix Gla
protein; heat shock 105kD; GNAS complex locus; Homo sapiens cDNA
FLJ11658 fis, clone HEMBA1004577; H19, imprinted maternally
expressed untranslated mR NA; protein tyrosine phosphatase type
IVA, member 3; snail homolog 1 (Drosophila); integrin-binding
sialoprotein (bone sialoprotein, bone sialoprotein II); tissue
inhibitor of metalloproteinase 1 (erythroid potentiating activity,
collagenase inhibitor); peptidylprolyl isomerase B (cyclophilin B);
MARCKS-like protein; FAST kinase; protease, serine, 11 (IGF
binding); beta-2-microglobulin; delta sleep inducing peptide,
immunoreactor; collagen, type IV, alpha 2; immediate early response
3; cadherin 5, type 2, VE-cadherin (vascular epithelium); RGC32
protein; guanylate cyclase 1, soluble, beta 3; major
histocompatibility complex, class I, B; ribonuclease, RNase A
family, 1 (pancreatic); collagen, type XVIII, alpha 1; v-jun
sarcoma virus 17 oncogene homolog (avian); Homo sapiens mRNA; cDNA
DKFZp686G1610 (from clone DKFZp686G1610); nucleolin; lectin,
galactoside-binding, soluble, 3 binding protein;
Lysosomal-associated multispanning membrane protein-5; ribosomal
protein S16; guanine nucleotide binding protein (G protein), gamma
12; serine (or cysteine) proteinase inhibitor, Glade E (nexin,
plasminogen activator inhibitor type 1), member 1; biglycan; DnaJ
(Hsp40) homolog, subfamily B, member 1; tumor rejection antigen
(gp96) 1; interferon, alpha-inducible protein (clone IFI-15K);
solute carrier family 21 (prostaglandin transporter), member 2;
CD74 antigen (invariant polypeptide of major histocompatibility
complex, class II antigen-associated); serum/glucocorticoid
regulated kinase; mitogen-activated protein kinase; receptor
(calcitonin) activity modifying protein 3; sema domain,
immunoglobulin domain (Ig); benzodiazapine receptor
(peripheral)--mitochondrial; C1 domain-containing phosphatase &
tensin-like; and Notch homolog 3 (Drosophila); monitoring an
expression product of the at least one gene; and identifying the
test compound as a potential anti-cancer drug if it decreases the
expression of the at least one gene.
23. The method of claim 22 wherein the cell is a human cell.
24. The method of claim 22 wherein the cell is a breast tumor
cell.
25. The method of claim 22 wherein the cell is a human breast tumor
cell.
26. The method of claim 22 wherein the expression product is
RNA.
27. The method of claim 22 wherein the expression product is
protein.
28. The method of claim 22 wherein the cell overexpresses the at
least one gene relative to a normal cell of the same tissue.
29. The method of claim 22 wherein expression of at least two of
said genes is monitored.
30. The method of claim 22 wherein expression of at least three of
said genes is monitored.
31. The method of claim 22 wherein expression of at least four of
said genes is monitored.
32. The method of claim 22 wherein the test compound is identified
if the decrease in expression is at least two-fold.
33. The method of claim 22 wherein the test compound is identified
if the decrease in expression is at least five-fold.
34. The method of claim 22 wherein the decrease in expression is at
least ten-fold.
35. The method of claim 22 wherein the test compound is identified
as an anti-breast tumor drug.
36. A method to induce an immune response to a breast tumor,
comprising: administering to a mammal a protein or nucleic acid
encoding a protein selected from the group consisting of:
hypothetical protein DKFZp434G171; heat shock 70kDa protein 1A;
jagged 1 (Alagille syndrome); cyclin-dependent kinase 3;
6-phosphogluconolactonase; likely homolog of rat and mouse
retinoid-inducible serine carboxypeptidase; plasmalemma vesicle
associated protein; NADH:ubiquinone oxidoreductase MLRQ subunit
homolog; HIF-1 responsive RTP801; ribosomal protein L27; secreted
protein, acidic, cysteine-rich (osteonectin); hexokinase 1;
ribosomal protein L13a; collagen, type IV, alpha 1; insulin-like
growth factor binding protein 7; collagen, type III, alpha 1
(Ehlers-Danlos syndrome type IV, autosomal dominant); heat shock
10kDa protein 1 (chaperonin 10); calcium channel,
voltage-dependent, alpha 1H subunit; CD9 antigen (p24); TEM17;
TEM13, Thy-1 cell surface antigen; Tax interaction protein 1;
dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive);
hypothetical protein MGC34648; putative translation initiation
factor; insulin-like growth factor binding protein 4; matrix
metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV
collagenase); heterogeneous nuclear ribonucleoprotein R; bHLH
factor Hes4; collagen, type VI, alpha 2; T-box 2;
glyceraldehyde-3-phosphate dehydrogenase; G protein-coupled
receptor 4; collagen, type I, alpha 1; ras-related C3 botulinum
toxin substrate 1 (rho family, small GTP binding protein Rac1);
ribosomal protein, large, P1; TEM10, COL1A2 involved in tissue
remodeling; heat shock 70kDa protein 8; KIAA0152 gene product;
Ca2+-promoted Ras inactivator; serine/arginine repetitive matrix 2;
hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix
transcription factor); benzodiazapine receptor (peripheral);
ectonucleoside triphosphate diphosphohydrolase 1; heparan sulfate
proteoglycan 2 (perlecan); fibromodulin; hairy/enhancer-of-split
related with YRPW motif 1; collagen, type V, alpha 3;
hairy/enhancer-of-split related with YRPW motif-like; hypothetical
protein MGC2731; amino-terminal enhancer of split;
mitogen-activated protein kinase 9; regulator of G-protein
signalling 5; prothymosin, alpha (gene sequence 28); tubulin, beta,
2; protease, serine, 23; hypothetical protein FLJ20898; calpain 1,
(mu/I) large subunit; interferon, alpha-inducible protein (clone
IFI-6-16); ESTs, Weakly similar to T25031 hypothetical protein
T20D3.3--Caenorhabditis elegans [C. elegans]; major
histocompatibility complex, class I, C; hypoxia up-regulated 1;
complement component 4B; prefoldin 2; cytoskeleton-associated
protein 1; Rho GTPase activating protein 4; Homo sapiens clone
FLC1492 PRO3121 mRNA, complete cds; transducin-like enhancer of
split 2 (E(sp1) homolog, Drosophila); ribosomal protein L37;
hypothetical protein MGC4677; ESTs, Highly similar to MT1A_HUMAN
METALLOTHIONEIN-IA (MT-1A) [H. sapiens]; TEM11, nidogen (enactin);
guanine nucleotide binding protein (G protein), gamma 5; matrix Gla
protein; heat shock 105kD; GNAS complex locus; Homo sapiens cDNA
FLJ11658 fis, clone HEMBA1004577; H19, imprinted maternally
expressed untranslated mR NA; protein tyrosine phosphatase type
IVA, member 3; snail homolog 1 (Drosophila); integrin-binding
sialoprotein (bone sialoprotein, bone sialoprotein II); tissue
inhibitor of metalloproteinase 1 (erythroid potentiating activity,
collagenase inhibitor); peptidylprolyl isomerase B (cyclophilin B);
MARCKS-like protein; FAST kinase; protease, serine, 11 (IGF
binding); beta-2-microglobulin; delta sleep inducing peptide,
immunoreactor; collagen, type IV, alpha 2; immediate early response
3; cadherin 5, type 2, VE-cadherin (vascular epithelium); RGC32
protein; guanylate cyclase 1, soluble, beta 3; major
histocompatibility complex, class I, B; ribonuclease, RNase A
family, 1 (pancreatic); collagen, type XVIII, alpha 1; v-jun
sarcoma virus 17 oncogene homolog (avian); Homo sapiens mRNA; cDNA
DKFZp686G1610 (from clone DKFZp686G1610); nucleolin; lectin,
galactoside-binding, soluble, 3 binding protein;
Lysosomal-associated multispanning membrane protein-5; ribosomal
protein S16; guanine nucleotide binding protein (G protein), gamma
12; serine (or cysteine) proteinase inhibitor, Glade E (nexin,
plasminogen activator inhibitor type 1), member 1; biglycan; DnaJ
(Hsp40) homolog, subfamily B, member 1; tumor rejection antigen
(gp96) 1; interferon, alpha-inducible protein (clone IFI-15K);
solute carrier family 21 (prostaglandin transporter), member 2;
CD74 antigen (invariant polypeptide of major histocompatibility
complex, class II antigen-associated); serum/glucocorticoid
regulated kinase; mitogen-activated protein kinase; receptor
(calcitonin) activity modifying protein 3; sema domain,
immunoglobulin domain (Ig); benzodiazapine receptor
(peripheral)--mitochondrial; C1 domain-containing phosphatase &
tensin-like; and Notch homolog 3 (Drosophila), whereby an immune
response to the protein is induced.
37. The method of claim 36 wherein a protein is administered.
38. The method of claim 36 wherein a nucleic acid is
administered.
39. The method of claim 38 wherein the nucleic acid is administered
intramuscularly.
40. The method of claim 36 further comprising administering an
immune adjuvant to the mammal.
41. The method of claim 36 wherein the mammal has a breast
tumor.
42. The method of claim 36 wherein the mammal has had a breast
tumor surgically removed.
Description
TECHNICAL FIELD OF THE INVENTION
[0001] This invention is related to the area of angiogenesis and
anti-angiogenesis. In particular, it relates to genes which are
characteristically expressed in breast tumor endothelial cells.
BACKGROUND OF THE INVENTION
[0002] To date, global gene expression profiles from endothelial
cell-specific populations is limited to normal and tumorigenic
colon tissue [St Croix, 2000]. There is a need in the art for
analysis of endothelial cells from other tissue, so that diagnostic
and therapeutic agents for non-colonic tumors can be developed.
SUMMARY OF THE INVENTION
[0003] According to one embodiment of the invention a method is
provided to aid in diagnosing breast tumors. An expression product
(protein or RNA) of at least one gene in a first breast tissue
sample suspected of being neoplastic is detected. The at least one
gene is selected from the group consisting of hypothetical protein
DKFZp434G171; heat shock 70kDa protein 1A; jagged 1 (Alagille
syndrome); cyclin-dependent kinase 3; 6-phosphogluconolactonase;
likely homolog of rat and mouse retinoid-inducible serine
carboxypeptidase; plasmalemma vesicle associated protein;
NADH:ubiquinone oxidoreductase MLRQ subunit homolog; HIF-1
responsive RTP801; ribosomal protein L27; secreted protein, acidic,
cysteine-rich (osteonectin); hexokinase 1; ribosomal protein L13a;
collagen, type IV, alpha 1; insulin-like growth factor binding
protein 7; collagen, type III, alpha 1 (Ehlers-Danlos syndrome type
IV, autosomal dominant); heat shock 10kDa protein 1 (chaperonin
10); calcium channel, voltage-dependent, alpha 1H subunit; CD9
antigen (p24); TEM17; TEM13, Thy-1 cell surface antigen; Tax
interaction protein 1; dysferlin, limb girdle muscular dystrophy 2B
(autosomal recessive); hypothetical protein MGC34648; putative
translation initiation factor; insulin-like growth factor binding
protein 4; matrix metalloproteinase 9 (gelatinase B, 92kDa
gelatinase, 92kDa type IV collagenase); heterogeneous nuclear
ribonucleoprotein R; bHLH factor Hes4; collagen, type VI, alpha 2;
T-box 2; glyceraldehyde-3-phosphate dehydrogenase; G
protein-coupled receptor 4; collagen, type I, alpha 1; ras-related
C3 botulinum toxin substrate 1 (rho family, small GTP binding
protein Rac1); ribosomal protein, large, P1; TEM10, COL1A2 involved
in tissue remodeling; heat shock 70kDa protein 8; KIAA0152 gene
product; Ca2+-promoted Ras inactivator; serine/arginine repetitive
matrix 2; hypoxia-inducible factor 1, alpha subunit (basic
helix-loop-helix transcription factor); benzodiazapine receptor
(peripheral); ectonucleoside triphosphate diphosphohydrolase 1;
heparan sulfate proteoglycan 2 (perlecan); fibromodulin;
hairy/enhancer-of-split related with YRPW motif 1; collagen, type
V, alpha 3; hairy/enhancer-of-split related with YRPW motif-like;
hypothetical protein MGC2731; amino-terminal enhancer of split;
mitogen-activated protein kinase 9; regulator of G-protein
signalling 5; prothymosin, alpha (gene sequence 28); tubulin, beta,
2; protease, serine, 23; hypothetical protein FLJ20898; calpain 1,
(mu/I) large subunit; interferon, alpha-inducible protein (clone
IFI-6-16); ESTs, Weakly similar to T25031 hypothetical protein
T20D3.3--Caenorhabditis elegans [C. elegans]; major
histocompatibility complex, class I, C; hypoxia up-regulated 1;
complement component 4B; prefoldin 2; cytoskeleton-associated
protein 1; Rho GTPase activating protein 4; Homo sapiens clone
FLC1492 PRO3121 mRNA, complete cds; transducin-like enhancer of
split 2 (E(sp1) homolog, Drosophila); ribosomal protein L37;
hypothetical protein MGC4677; ESTs, Highly similar to MT1A_HUMAN
METALLOTHIONEIN-IA (MT-1A) [H. sapiens]; TEM11, nidogen (enactin);
guanine nucleotide binding protein (G protein), gamma 5; matrix Gla
protein; heat shock 105kD; GNAS complex locus; Homo sapiens cDNA
FLJ11658 fis, clone HEMBA1004577; H19, imprinted maternally
expressed untranslated mR NA; protein tyrosine phosphatase type
IVA, member 3; snail homolog 1 (Drosophila); integrin-binding
sialoprotein (bone sialoprotein, bone sialoprotein II); tissue
inhibitor of metalloproteinase 1 (erythroid potentiating activity,
collagenase inhibitor); peptidylprolyl isomerase B (cyclophilin B);
MARCKS-like protein; FAST kinase; protease, serine, 11 (IGF
binding); beta-2-microglobulin; delta sleep inducing peptide,
immunoreactor; collagen, type IV, alpha 2; immediate early response
3; cadherin 5, type 2, VE-cadherin (vascular epithelium); RGC32
protein; guanylate cyclase 1, soluble, beta 3; major
histocompatibility complex, class I, B; ribonuclease, RNase A
family, 1 (pancreatic); collagen, type XVIII, alpha 1; v-jun
sarcoma virus 17 oncogene homolog (avian); Homo sapiens mRNA; cDNA
DKFZp686G1610 (from clone DKFZp686G1610); nucleolin; lectin,
galactoside-binding, soluble, 3 binding protein;
Lysosomal-associated multispanning membrane protein-5; ribosomal
protein S16; guanine nucleotide binding protein (G protein), gamma
12; serine (or cysteine) proteinase inhibitor, Glade E (nexin,
plasminogen activator inhibitor type 1), member 1; biglycan; DnaJ
(Hsp40) homolog, subfamily B, member 1; tumor rejection antigen
(gp96) 1; interferon, alpha-inducible protein (clone IFI-15K);
solute carrier family 21 (prostaglandin transporter), member 2;
CD74 antigen (invariant polypeptide of major histocompatibility
complex, class II antigen-associated); serum/glucocorticoid
regulated kinase; mitogen-activated protein kinase; receptor
(calcitonin) activity modifying protein 3; sema domain,
immunoglobulin domain (Ig); benzodiazapine receptor
(peripheral)--mitochondrial; C1 domain-containing phosphatase &
tensin-like; and Notch homolog 3 (Drosophila). Expression of the at
least one gene in the first breast tissue sample is compared to
expression of the at least one gene in a second breast tissue
sample which is normal. Increased expression of the at least one
gene in the first breast endothelial tissue sample relative to the
second tissue sample identifies the first breast tissue sample as
likely to be neoplastic.
[0004] According to another embodiment of the invention a method is
provided of treating a breast tumor. Cells of the breast tumor are
contacted with an antibody. The antibody specifically binds to an
extracellular epitope of a protein selected from the group
consisting of benzodiazapine receptor (peripheral); cadherin 5,
type 2, VE-cadherin (vascular epithelium); calcium channel,
voltage-dependent, alpha 1H subunit; CD74 antigen (invariant
polypeptide of major histocompatibility complex, class II
antigen-associated); CD9 antigen (p24); dysferlin, limb girdle
muscular dystrophy 2B (autosomal recessive); ectonucleoside
triphosphate diphosphohydrolase 1; G protein-coupled receptor 4;
hypothetical protein FLJ20898; hypoxia up-regulated 1; immediate
early response 3; interferon, alpha-inducible protein (clone
IFI-6-16); jagged 1 (Alagille syndrome); KIAA0152 gene product;
Lysosomal-associated multispanning membrane protein-5; major
histocompatibility complex, class I, B; major histocompatibility
complex, class I, C; NADH:ubiquinone oxidoreductase MLRQ subunit
homolog; Notch homolog 3 (Drosophila); plasmalemma vesicle
associated protein; solute carrier family 21 (prostaglandin
transporter), member 2; TEM13, Thy-1 cell surface antigen; receptor
(calcitonin) activity modifying protein 3; sema domain,
immunoglobulin domain (Ig); benzodiazapine receptor
(peripheral)--mitochondrial; and TEM17. Immune destruction of cells
of the breast tumor is thereby triggered.
[0005] According to still another embodiment of the invention a
method is provided for identifying a test compound as a potential
anti-cancer or anti-breast tumor drug. A test compound is contacted
with a cell which expresses at least one gene selected from the
group consisting of: hypothetical protein DKFZp434G171; heat shock
70kDa protein 1A; jagged 1 (Alagille syndrome); cyclin-dependent
kinase 3; 6-phosphogluconolactonase; likely homolog of rat and
mouse retinoid-inducible serine carboxypeptidase; plasmalemma
vesicle associated protein; NADH:ubiquinone oxidoreductase MLRQ
subunit homolog; HIF-1 responsive RTP801; ribosomal protein L27;
secreted protein, acidic, cysteine-rich (osteonectin); hexokinase
1; ribosomal protein L13a; collagen, type IV, alpha 1; insulin-like
growth factor binding protein 7; collagen, type III, alpha 1
(Ehlers-Danlos syndrome type IV, autosomal dominant); heat shock
10kDa protein 1 (chaperonin 10); calcium channel,
voltage-dependent, alpha 1H subunit; CD9 antigen (p24); TEM17;
TEM13, Thy-1 cell surface antigen; Tax interaction protein 1;
dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive);
hypothetical protein MGC34648; putative translation initiation
factor; insulin-like growth factor binding protein 4; matrix
metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV
collagenase); heterogeneous nuclear ribonucleoprotein R; bHLH
factor Hes4; collagen, type VI, alpha 2; T-box 2;
glyceraldehyde-3-phosphate dehydrogenase; G protein-coupled
receptor 4; collagen, type I, alpha 1; ras-related C3 botulinum
toxin substrate 1 (rho family, small GTP binding protein Rac1);
ribosomal protein, large, P1; TEM10, COL1A2 involved in tissue
remodeling; heat shock 70kDa protein 8; KIAA0152 gene product;
Ca2+-promoted Ras inactivator; serine/arginine repetitive matrix 2;
hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix
transcription factor); benzodiazapine receptor (peripheral);
ectonucleoside triphosphate diphosphohydrolase 1; heparan sulfate
proteoglycan 2 (perlecan); fibromodulin; hairy/enhancer-of-split
related with YRPW motif 1; collagen, type V, alpha 3;
hairy/enhancer-of-split related with YRPW motif-like; hypothetical
protein MGC2731; amino-terminal enhancer of split;
mitogen-activated protein kinase 9; regulator of G-protein
signalling 5; prothymosin, alpha (gene sequence 28); tubulin, beta,
2; protease, serine, 23; hypothetical protein FLJ20898; calpain 1,
(mu/I) large subunit; interferon, alpha-inducible protein (clone
IFI-6-16); ESTs, Weakly similar to T25031 hypothetical protein
T20D3.3--Caenorhabditis elegans [C. elegans]; major
histocompatibility complex, class I, C; hypoxia up-regulated 1;
complement component 4B; prefoldin 2; cytoskeleton-associated
protein 1; Rho GTPase activating protein 4; Homo sapiens clone
FLC1492 PRO3121 mRNA, complete cds; transducin-like enhancer of
split 2 (E(sp1) homolog, Drosophila); ribosomal protein L37;
hypothetical protein MGC4677; ESTs, Highly similar to MT1A_HUMAN
METALLOTHIONEIN-IA (MT-1A) [H. sapiens]; TEM11, nidogen (enactin);
guanine nucleotide binding protein (G protein), gamma 5; matrix Gla
protein; heat shock 105kD; GNAS complex locus; Homo sapiens cDNA
FLJ11658 fis, clone HEMBA1004577; H19, imprinted maternally
expressed untranslated mR NA; protein tyrosine phosphatase type
IVA, member 3; snail homolog 1 (Drosophila); integrin-binding
sialoprotein (bone sialoprotein, bone sialoprotein II); tissue
inhibitor of metalloproteinase 1 (erythroid potentiating activity,
collagenase inhibitor); peptidylprolyl isomerase B (cyclophilin B);
MARCKS-like protein; FAST kinase; protease, serine, 11 (IGF
binding); beta-2-microglobulin; delta sleep inducing peptide,
immunoreactor; collagen, type IV, alpha 2; immediate early response
3; cadherin 5, type 2, VE-cadherin (vascular epithelium); RGC32
protein; guanylate cyclase 1, soluble, beta 3; major
histocompatibility complex, class I, B; ribonuclease, RNase A
family, 1 (pancreatic); collagen, type XVIII, alpha 1; v-jun
sarcoma virus 17 oncogene homolog (avian); Homo sapiens mRNA; cDNA
DKFZp686G1610 (from clone DKFZp686G1610); nucleolin; lectin,
galactoside-binding, soluble, 3 binding protein;
Lysosomal-associated multispanning membrane protein-5; ribosomal
protein S16; guanine nucleotide binding protein (G protein), gamma
12; serine (or cysteine) proteinase inhibitor, Glade E (nexin,
plasminogen activator inhibitor type 1), member 1; biglycan; DnaJ
(Hsp40) homolog, subfamily B, member 1; tumor rejection antigen
(gp96) 1; interferon, alpha-inducible protein (clone IFI-15K);
solute carrier family 21 (prostaglandin transporter), member 2;
CD74 antigen (invariant polypeptide of major histocompatibility
complex, class II antigen-associated); serum/glucocorticoid
regulated kinase; mitogen-activated protein kinase; receptor
(calcitonin) activity modifying protein 3; sema domain,
immunoglobulin domain (Ig); benzodiazapine receptor
(peripheral)--mitochondrial; C1 domain-containing phosphatase &
tensin-like; and Notch homolog 3 (Drosophila). An expression
product of the at least one gene is monitored. The test compound is
identified as a potential anti-cancer drug if it decreases the
expression of the at least one gene.
[0006] Still another embodiment of the invention is a method to
induce an immune response to a breast tumor. A protein or nucleic
acid encoding a protein is administered to a mammal, preferably a
human. The protein is selected from the group consisting of:
hypothetical protein DKFZp434G171; heat shock 70kDa protein 1A;
jagged 1 (Alagille syndrome); cyclin-dependent kinase 3;
6-phosphogluconolactonase; likely homolog of rat and mouse
retinoid-inducible serine carboxypeptidase; plasmalemma vesicle
associated protein; NADH:ubiquinone oxidoreductase MLRQ subunit
homolog; HIF-1 responsive RTP801; ribosomal protein L27; secreted
protein, acidic, cysteine-rich (osteonectin); hexokinase 1;
ribosomal protein L13a; collagen, type IV, alpha 1; insulin-like
growth factor binding protein 7; collagen, type III, alpha 1
(Ehlers-Danlos syndrome type IV, autosomal dominant); heat shock
10kDa protein 1 (chaperonin 10); calcium channel,
voltage-dependent, alpha 1H subunit; CD9 antigen (p24); TEM17;
TEM13, Thy-1 cell surface antigen; Tax interaction protein 1;
dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive);
hypothetical protein MGC34648; putative translation initiation
factor; insulin-like growth factor binding protein 4; matrix
metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV
collagenase); heterogeneous nuclear ribonucleoprotein R; bHLH
factor Hes4; collagen, type VI, alpha 2; T-box 2;
glyceraldehyde-3-phosphate dehydrogenase; G protein-coupled
receptor 4; collagen, type I, alpha 1; ras-related C3 botulinum
toxin substrate 1 (rho family, small GTP binding protein Rac1);
ribosomal protein, large, P1; TEM10, COL1A2 involved in tissue
remodeling; heat shock 70kDa protein 8; KIAA0152 gene product;
Ca2+-promoted Ras inactivator; serine/arginine repetitive matrix 2;
hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix
transcription factor); benzodiazapine receptor (peripheral);
ectonucleoside triphosphate diphosphohydrolase 1; heparan sulfate
proteoglycan 2 (perlecan); fibromodulin; hairy/enhancer-of-split
related with YRPW motif 1; collagen, type V, alpha 3;
hairy/enhancer-of-split related with YRPW motif-like; hypothetical
protein MGC2731; amino-terminal enhancer of split;
mitogen-activated protein kinase 9; regulator of G-protein
signalling 5; prothymosin, alpha (gene sequence 28); tubulin, beta,
2; protease, serine, 23; hypothetical protein FLJ20898; calpain 1,
(mu/I) large subunit; interferon, alpha-inducible protein (clone
IFI-6-16); ESTs, Weakly similar to T25031 hypothetical protein
T20D3.3--Caenorhabditis elegans [C. elegans]; major
histocompatibility complex, class I, C; hypoxia up-regulated 1;
complement component 4B; prefoldin 2; cytoskeleton-associated
protein 1; Rho GTPase activating protein 4; Homo sapiens clone
FLC1492 PRO3121 mRNA, complete cds; transducin-like enhancer of
split 2 (E(sp1) homolog, Drosophila); ribosomal protein L37;
hypothetical protein MGC4677; ESTs, Highly similar to MT1A_HUMAN
METALLOTHIONEIN-IA (MT-1A) [H. sapiens]; TEM11, nidogen (enactin);
guanine nucleotide binding protein (G protein), gamma 5; matrix Gla
protein; heat shock 105kD; GNAS complex locus; Homo sapiens cDNA
FLJ11658 fis, clone HEMBA1004577; H19, imprinted maternally
expressed untranslated mR NA; protein tyrosine phosphatase type
IVA, member 3; snail homolog 1 (Drosophila); integrin-binding
sialoprotein (bone sialoprotein, bone sialoprotein II); tissue
inhibitor of metalloproteinase 1 (erythroid potentiating activity,
collagenase inhibitor); peptidylprolyl isomerase B (cyclophilin B);
MARCKS-like protein; FAST kinase; protease, serine, 11 (IGF
binding); beta-2-microglobulin; delta sleep inducing peptide,
immunoreactor; collagen, type IV, alpha 2; immediate early response
3; cadherin 5, type 2, VE-cadherin (vascular epithelium); RGC32
protein; guanylate cyclase 1, soluble, beta 3; major
histocompatibility complex, class I, B; ribonuclease, RNase A
family, 1 (pancreatic); collagen, type XVIII, alpha 1; v-jun
sarcoma virus 17 oncogene homolog (avian); Homo sapiens mRNA; cDNA
DKFZp686G1610 (from clone DKFZp686G1610); nucleolin; lectin,
galactoside-binding, soluble, 3 binding protein;
Lysosomal-associated multispanning membrane protein-5; ribosomal
protein S16; guanine nucleotide binding protein (G protein), gamma
12; serine (or cysteine) proteinase inhibitor, Glade E (nexin,
plasminogen activator inhibitor type 1), member 1; biglycan; DnaJ
(Hsp40) homolog, subfamily B, member 1; tumor rejection antigen
(gp96) 1; interferon, alpha-inducible protein (clone IFI-15K);
solute carrier family 21 (prostaglandin transporter), member 2;
CD74 antigen (invariant polypeptide of major histocompatibility
complex, class II antigen-associated); serum/glucocorticoid
regulated kinase; mitogen-activated protein kinase; receptor
(calcitonin) activity modifying protein 3; sema domain,
immunoglobulin domain (Ig); benzodiazapine receptor
(peripheral)--mitochondrial; C1 domain-containing phosphatase &
tensin-like; and Notch homolog 3 (Drosophila). An immune response
to the protein is thereby induced.
[0007] The present invention thus provides the art with methods of
diagnosing and treating breast tumors.
DETAILED DESCRIPTION OF THE INVENTION
[0008] Using SAGE (Serial Analysis of Gene Expression) profiling,
the present inventors were able to identify previously
unrecognized, angiogenesis-specific markers that discriminate
between non-proliferative and pathologic endothelial cells. In
addition, a set of previously identified angiogenesis-specific
markers from other tumor types (colon and/or brain) were found to
be expressed in breast tumor endothelium as well. We identified 111
human genes that were expressed at significantly higher levels in
breast tumor endothelium than in normal breast endothelium. See
Table 1. Additional such genes which can be used similarly to the
11 human genes are shown in Table 2. We have named these markers
BEMs (breast tumor endothelial markers). BEMs that are expressed in
both colon and breast tumor epithelium are identified in Table 3.
BEMs that are expressed in both brain and breast tumor epithelium
are identified in Table 4. BEMs that are expressed in each of
brain, colon, and breast tumor epithelium are identified in Table
5.
TABLE-US-00001 TABLE 1 111 Breast Markers Unigene ID Function
OMIMID Protein Hs.8728 hypothetical protein DKFZp434G171 CAB61365
Hs.8997 heat shock 70 kDa protein 1A 140550 NP_005336 Hs.91143
jagged 1 (Alagille syndrome) 601920 NP_000205 Hs.100009
cyclin-dependent kinase 3 123828 Hs.100071
6-phosphogluconolactonase 604951 NP_036220 Hs.106747 likely homolog
of rat and mouse retinoid-inducible NP_067639 serine
carboxypeptidase Hs.107125 plasmalemma vesicle associated protein
NP_112600 Hs.110024 NADH:ubiquinone oxidoreductase MLRQ subunit
NP_064527 homolog Hs.111244 HIF-1 responsive RTP801 NP_061931
Hs.111611 ribosomal protein L27 607526 NP_000979 Hs.111779 secreted
protein, acidic, cysteine-rich (osteonectin) 182120 NP_003109
Hs.118625 hexokinase 1 142600 NP_277035 Hs.119122 ribosomal protein
L13a Hs.119129 collagen, type IV, alpha 1 120130 NP_001836
Hs.119206 insulin-like growth factor binding protein 7 602867
NP_001544 Hs.119571 collagen, type III, alpha 1 (Ehlers-Danlos
syndrome 120180 NP_000081 type IV, autosomal dominant) Hs.1197 heat
shock 10 kDa protein 1 (chaperonin 10) 600141 NP_002148 Hs.122359
calcium channel, voltage-dependent, alpha 1H NP_066921 subunit
Hs.1244 CD9 antigen (p24) 143030 NP_001760 Hs.125036 TEM17 606826
NP_065138 Hs.125359 TEM13, Thy-1 cell surface antigen 188230
NP_006279 Hs.12956 Tax interaction protein 1 NP_055419 Hs.143897
dysferlin, limb girdle muscular dystrophy 2B 603009 NP_003485
(autosomal recessive) Hs.146360 hypothetical protein MGC34648
NP_689873 Hs.150580 putative translation initiation factor
NP_005792 Hs.1516 insulin-like growth factor binding protein 4
146733 NP_001543 Hs.151738 matrix metalloproteinase 9 (gelatinase
B, 92 kDa 120361 NP_004985 gelatinase, 92 kDa type IV collagenase)
Hs.15265 heterogeneous nuclear ribonucleoprotein R 607201 NP_005817
Hs.154029 bHLH factor Hes4 NP_066993 Hs.159263 collagen, type VI,
alpha 2 120240 NP_001840 Hs.168357 T-box 2 600747 NP_005985
Hs.169476 glyceraldehyde-3-phosphate dehydrogenase 138400 NP_002037
Hs.17170 G protein-coupled receptor 4 600551 NP_005273 Hs.172928
collagen, type I, alpha 1 120150 NP_000079 Hs.173737 ras-related C3
botulinum toxin substrate 1 (rho family, 602048 small GTP binding
protein Rac1) Hs.177592 ribosomal protein, large, P1 180520
Hs.179573 TEM10, COL1A2 involved in tissue remodeling 120160
NP_000080 Hs.180414 heat shock 70 kDa protein 8 600816 NP_006588
Hs.181418 KIAA0152 gene product NP_055545 Hs.184367 Ca2+-promoted
Ras inactivator BAA25464 Hs.197114 serine/arginine repetitive
matrix 2 606032 NP_057417 Hs.197540 hypoxia-inducible factor 1,
alpha subunit (basic helix- 603348 NP_001521 loop-helix
transcription factor) Hs.202 benzodiazapine receptor (peripheral)
109610 NP_000705 Hs.205353 ectonucleoside triphosphate
diphosphohydrolase 1 601752 NP_001767 Hs.211573 heparan sulfate
proteoglycan 2 (perlecan) 142461 NP_005520 Hs.230 Fibromodulin
600245 NP_002014 Hs.234434 hairy/enhancer-of-split related with
YRPW motif 1 602953 NP_036390 Hs.235368 collagen, type V, alpha 3
120216 NP_056534 Hs.23823 hairy/enhancer-of-split related with YRPW
motif-like NP_055386 Hs.240170 hypothetical protein MGC2731
NP_076973 Hs.244 amino-terminal enhancer of split 600188 Hs.246857
mitogen-activated protein kinase 9 602896 NP_620708 Hs.24950
regulator of G-protein signalling 5 603276 NP_003608 Hs.250655
prothymosin, alpha (gene sequence 28) 188390 NP_002814 Hs.251653
tubulin, beta, 2 602660 NP_006079 Hs.25338 protease, serine, 23
Hs.25549 hypothetical protein FLJ20898 NP_078876 Hs.2575 calpain 1,
(mu/l) large subunit 114220 NP_005177 Hs.265827 interferon,
alpha-inducible protein (clone IFI-6-16) 147572 NP_075011 Hs.267200
ESTs, Weakly similar to T25031 hypothetical protein T20D3.3 -
Caenorhabditis elegans [C. elegans] Hs.277477 major
histocompatibility complex, class I, C 142840 NP_002108 Hs.277704
hypoxia up-regulated 1 601746 NP_006380 Hs.278625 complement
component 4B 120820 NP_000583 Hs.298229 prefoldin 2 NP_036526
Hs.31053 cytoskeleton-associated protein 1 601303 NP_001272 Hs.3109
Rho GTPase activating protein 4 300023 NP_001657 Hs.327412 Homo
sapiens clone FLC1492 PRO3121 mRNA, complete cds Hs.332173
transducin-like enhancer of split 2 (E(sp1) homolog, 601041
NP_003251 Drosophila) Hs.337445 ribosomal protein L37 604181
NP_000988 Hs.337986 hypothetical protein MGC4677 NP_443103
Hs.353882 ESTs, Highly similar to MT1A_HUMAN METALLOTHIONEIN-IA
(MT-1A) [H. sapiens] Hs.356624 TEM11, nidogen (enactin) 131390
NP_002499 Hs.356668 guanine nucleotide binding protein (G protein),
600874 NP_005265 gamma 5 Hs.365706 matrix Gla protein 154870
NP_000891 Hs.36927 heat shock 105 Kd NP_006635 Hs.374523 GNAS
complex locus 139320 NP_536350 Hs.380824 Homo sapiens cDNA FLJ11658
fis, clone HEMBA1004577 Hs.406410 H19, imprinted maternally
expressed untranslated 103280 BAB71280 mRNA Hs.43666 protein
tyrosine phosphatase type IVA, member 3 606449 NP_116000 Hs.48029
snail homolog 1 (Drosophila) 604238 NP_005976 Hs.49215
integrin-binding sialoprotein (bone sialoprotein, bone 147563
NP_004958 sialoprotein II) Hs.5831 tissue inhibitor of
metalloproteinase 1 (erythroid 305370 NP_003245 potentiating
activity, collagenase inhibitor) Hs.699 peptidylprolyl isomerase B
(cyclophilin B) 123841 NP_000933 Hs.75061 MARCKS-like protein
602940 NP_075385 Hs.75087 FAST kinase 606965 NP_079372 Hs.75111
protease, serine, 11 (IGF binding) 602194 NP_002766 Hs.75415
beta-2-microglobulin 109700 NP_004039 Hs.75450 delta sleep inducing
peptide, immunoreactor 602960 Hs.75617 collagen, type IV, alpha 2
120090 NP_001837 Hs.76095 immediate early response 3 602996
NP_434702 Hs.76206 cadherin 5, type 2, VE-cadherin (vascular
epithelium) 601120 NP_001786 Hs.76640 RGC32 protein Hs.77890
guanylate cyclase 1, soluble, beta 3 139397 NP_000848 Hs.77961
major histocompatibility complex, class I, B 142830 NP_005505
Hs.78224 ribonuclease, RNase A family, 1 (pancreatic) 180440
AAH05324 Hs.78409 collagen, type XVIII, alpha 1 120328 NP_085059
Hs.78465 v-jun sarcoma virus 17 oncogene homolog (avian) 165160
NP_002219 Hs.7869 Homo sapiens mRNA; cDNA DKFZp686G1610 (from clone
DKFZp686G1610) Hs.79110 Nucleolin 164035 NP_005372 Hs.79339 lectin,
galactoside-binding, soluble, 3 binding protein 600626 NP_005558
Hs.79356 Lysosomal-associated multispanning membrane 601476
NP_006753 protein-5 Hs.80617 ribosomal protein S16 603675 Hs.8107
guanine nucleotide binding protein (G protein), gamma 12 Hs.82085
serine (or cysteine) proteinase inhibitor, clade E 173360 NP_000593
(nexin, plasminogen activator inhibitor type 1), member 1 Hs.821
Biglycan 301870 NP_001702 Hs.82646 DnaJ (Hsp40) homolog, subfamily
B, member 1 604572 NP_006136 Hs.82689 tumor rejection antigen
(gp96) 1 191175 NP_003290 Hs.833 interferon, alpha-inducible
protein (clone IFI-15K) 147571 NP_005092 Hs.83974 solute carrier
family 21 (prostaglandin transporter), 601460 NP_005621 member 2
Hs.84298 CD74 antigen (invariant polypeptide of major 142790
NP_004346 histocompatibility complex, class II antigen- associated)
Hs.8546 Notch homolog 3 (Drosophila) 600276 NP_000426
TABLE-US-00002 TABLE 2 Additional Tumor Endothelial Markers in
Breast Unigene ID Function OMIMID Protein Hs.296323
serum/glucocorticoid regulated 602958 NP_005618 kinase Hs.246857
mitogen-activated protein kinase 602896 NP_620708 Hs.25691 receptor
(calcitonin) activity 605155 NP_005847 modifying protein 3 Hs.9598
sema domain, immunoglobulin -- BAB21836 domain (Ig) Hs.202
benzodiazapine receptor 109610 NP_000715 (peripheral) -
mitochondrial Hs.6147 C1 domain-containing -- NP_056134 phosphatase
& tensin-like
TABLE-US-00003 TABLE 3 Markers in Colon and Breast Tumor Epithelium
Unigene ID Function OMIMID Protein Hs.8997 heat shock 70 kDa
protein 1A 140550 NP_005336 Hs.110024 NADH:ubiquinone
oxidoreductase MLRQ subunit homolog NP_064527 Hs.111779 secreted
protein, acidic, cysteine-rich (osteonectin) 182120 NP_003109
Hs.119129 collagen, type IV, alpha 1 120130 NP_001836 Hs.119206
insulin-like growth factor binding protein 7 602867 NP_001544
Hs.119571 collagen, type III, alpha 1 (Ehlers-Danlos syndrome type
120180 NP_000081 IV, autosomal dominant) Hs.1197 heat shock 10 kDa
protein 1 (chaperonin 10) 600141 NP_002148 Hs.125036 TEM17 606826
NP_065138 Hs.125359 TEM13, Thy-1 cell surface antigen 188230
NP_006279 Hs.151738 matrix metalloproteinase 9 (gelatinase B, 92
kDa 120361 NP_004985 gelatinase, 92 kDa type IV collagenase)
Hs.159263 collagen, type VI, alpha 2 120240 NP_001840 Hs.168357
T-box 2 600747 NP_005985 Hs.172928 collagen, type I, alpha 1 120150
NP_000079 Hs.179573 TEM10, COL1A2 involved in tissue remodeling
120160 NP_000080 Hs.230 Fibromodulin 600245 NP_002014 Hs.23823
hairy/enhancer-of-split related with YRPW motif-like NP_055386
Hs.24950 regulator of G-protein signalling 5 603276 NP_003608
Hs.265827 interferon, alpha-inducible protein (clone IFI-6-16)
147572 NP_075011 Hs.327412 Homo sapiens clone FLC1492 PRO3121 mRNA,
complete cds Hs.337986 hypothetical protein MGC4677 NP_443103
Hs.356624 TEM11, nidogen (enactin) 131390 NP_002499 Hs.36927 heat
shock 105 kD NP_006635 Hs.43666 protein tyrosine phosphatase type
IVA, member 3 606449 NP_116000 Hs.5831 tissue inhibitor of
metalloproteinase 1 (erythroid 305370 NP_003245 potentiating
activity, collagenase inhibitor) Hs.699 peptidylprolyl isomerase B
(cyclophilin B) 123841 NP_000933 Hs.75617 collagen, type IV, alpha
2 120090 NP_001837 Hs.77890 guanylate cyclase 1, soluble, beta 3
139397 NP_000848 Hs.78409 collagen, type XVIII, alpha 1 120328
NP_085059 Hs.78465 v-jun sarcoma virus 17 oncogene homolog (avian)
165160 NP_002219 Hs.821 Biglycan 301870 NP_001702 Hs.82646 DnaJ
(Hsp40) homolog, subfamily B, member 1 604572 NP_006136 Hs.8546
Notch homolog 3 (Drosophila) 600276 NP_000426
TABLE-US-00004 TABLE 4 Markers in Brain and Breast Tumor Epithelium
Unigene ID Function OMIMID Protein Hs.107125 plasmalemma vesicle
associated protein NP_112600 Hs.111611 ribosomal protein L27 607526
NP_000979 Hs.111779 Secreted protein, acidic, cysteine-rich 182120
NP_003109 (osteonectin) Hs.119129 Collagen, type IV, alpha 1 120130
NP_001836 Hs.119571 Collagen, type III, alpha 1 (Ehlers- 120180
NP_000081 Danlos syndrome type IV, autosomal dominant) Hs.125359
TEM13, Thy-1 cell surface antigen 188230 NP_006279 Hs.143897
Dysferlin, limb girdle muscular dystrophy 603009 NP_003485 2B
(autosomal recessive) Hs.151738 matrix metalloproteinase 9
(gelatinase 120361 NP_004985 B, 92 kDa gelatinase, 92 kDa type IV
collagenase) Hs.159263 Collagen, type VI, alpha 2 120240 NP_001840
Hs.172928 Collagen, type I, alpha 1 120150 NP_000079 Hs.179573
TEM10, COL1A2 involved in tissue remodeling 120160 NP_000080
Hs.211573 Heparan sulfate proteoglycan 2 142461 NP_005520
(perlecan) Hs.277477 major histocompatibility complex, class I, C
142840 NP_002108 Hs.327412 Homo sapiens clone FLC1492 PRO3121 mRNA,
complete cds Hs.332173 transducin-like enhancer of split 2 601041
NP_003251 (E(sp1) homolog, Drosophila) Hs.337986 hypothetical
protein MGC4677 NP_443103 Hs.365706 matrix Gla protein 154870
NP_000891 Hs.75061 MARCKS-like protein 602940 NP_075385 Hs.75111
Protease, serine, 11 (IGF binding) 602194 NP_002766 Hs.75617
collagen, type IV, alpha 2 120090 NP_001837 Hs.77961 major
histocompatibility complex, class I, B 142830 NP_005505 Hs.79356
Lysosomal-associated multispanning 601476 NP_006753 membrane
protein-5 Hs.82085 serine (or cysteine) proteinase inhibitor,
173360 NP_000593 clade E (nexin, plasminogen activator inhibitor
type 1), member 1 Hs.821 Biglycan 301870 NP_001702
TABLE-US-00005 TABLE 5 Breast, Brain, and Colon Tumor Endothelial
Markers Unigene ID Function OMIMID Protein Hs.111779 secreted
protein, acidic, 182120 NP_003109 cysteine-rich (osteonectin)
Hs.119129 collagen, type IV, alpha 1 120130 NP_001836 Hs.119571
collagen, type III, alpha 1 120180 NP_000081 (Ehlers-Danlos
syndrome type IV, autosomal dominant) Hs.125359 TEM13, Thy-1 cell
surface 188230 NP_006279 antigen Hs.151738 matrix metalloproteinase
9 120361 NP_004985 (gelatinase B, 92 kDa gelatinase, 92 kDa type IV
collagenase) Hs.159263 collagen, type VI, alpha 2 120240 NP_001840
Hs.172928 collagen, type I, alpha 1 120150 NP_000079 Hs.179573
TEM10, COL1A2 involved 120160 NP_000080 in tissue remodeling
Hs.327412 Homo sapiens clone FLC1492 PRO3121 mRNA, complete cds
Hs.337986 hypothetical protein NP_443103 MGC4677 Hs.75617 collagen,
type IV, alpha 2 120090 NP_001837 Hs.821 biglycan 301870
NP_001702
[0009] Endothelial cells (ECs) represent only a minor fraction of
the total cells within normal or tumor tissues, and only those EC
transcripts expressed at the highest levels would be expected to be
represented in libraries constructed from unfractionated tissues.
The genes described in the current study should therefore provide a
valuable resource for basic and clinical studies of human breast
angiogenesis in the future.
[0010] Isolated and purified nucleic acids, according to the
present invention are those which are not linked to those genes to
which they are linked in the human genome. Moreover, they are not
present in a mixture such as a library containing a multitude of
distinct sequences from distinct genes. They may be, however,
linked to other genes such as vector sequences or sequences of
other genes to which they are not naturally adjacent.
[0011] The nucleic acids may represent either the sense or the
anti-sense strand. Nucleic acids and proteins although disclosed
herein with sequence particularity, may be derived from a single
individual. Allelic variants which occur in the population of
humans are included within the scope of such nucleic acids and
proteins. Those of skill in the art are well able to identify
allelic variants as being the same gene or protein. Given a nucleic
acid, one of ordinary skill in the art can readily determine an
open reading frame present, and consequently the sequence of a
polypeptide encoded by the open reading frame and, using techniques
well known in the art, express such protein in a suitable host.
Proteins comprising such polypeptides can be the naturally
occurring proteins, fusion proteins comprising exogenous sequences
from other genes from humans or other species, epitope tagged
polypeptides, etc. Isolated and purified proteins are not in a
cell, and are separated from the normal cellular constituents, such
as nucleic acids, lipids, etc. Typically the protein is purified to
such an extent that it comprises the predominant species of protein
in the composition, such as greater than 50, 60 70, 80, 90, or even
95% of the proteins present.
[0012] Using the proteins according to the invention, one of
ordinary skill in the art can readily generate antibodies which
specifically bind to the proteins. Such antibodies can be
monoclonal or polyclonal. They can be chimeric, humanized, or
totally human. Any functional fragment or derivative of an antibody
can be used including Fab, Fab', Fab2, Fab'2, and single chain
variable regions. So long as the fragment or derivative retains
specificity of binding for the endothelial marker protein it can be
used. Antibodies can be tested for specificity of binding by
comparing binding to appropriate antigen to binding to irrelevant
antigen or antigen mixture under a given set of conditions. If the
antibody binds to the appropriate antigen at least 2, 5, 7, and
preferably 10 times more than to irrelevant antigen or antigen
mixture then it is considered to be specific.
[0013] Techniques for making such partially to fully human
antibodies are known in the art and any such techniques can be
used. According to one particularly preferred embodiment, fully
human antibody sequences are made in a transgenic mouse which has
been engineered to express human heavy and light chain antibody
genes. Multiple strains of such transgenic mice have been made
which can produce different classes of antibodies. B cells from
transgenic mice which are producing a desirable antibody can be
fused to make hybridoma cell lines for continuous production of the
desired antibody. See for example, Nina D. Russel, Jose R. F.
Corvalan, Michael L. Gallo, C. Geoffrey Davis, Liise-Anne Pirofski.
Production of Protective Human Antipneumococcal Antibodies by
Transgenic Mice with Human Immunoglobulin Loci Infection and
Immunity April 2000, p. 1820-1826; Michael L. Gallo, Vladimir E.
Ivanov, Aya Jakobovits, and C. Geoffrey Davis. The human
immunoglobulin loci introduced into mice: V (D) and J gene segment
usage similar to that of adult humans European Journal of
Immunology 30: 534-540, 2000; Larry L. Green. Antibody engineering
via genetic engineering of the mouse: XenoMouse strains are a
vehicle for the facile generation of therapeutic human monoclonal
antibodies Journal of Immunological Methods 231 11-23, 1999; Yang
X-D, Corvalan J R F, Wang P, Roy C M-N and Davis C G. Fully Human
Anti-interleukin-8 Monoclonal Antibodies: Potential Therapeutics
for the Treatment of Inflammatory Disease States. Journal of
Leukocyte Biology Vol. 66, pp 401-410 (1999); Yang X-D, Jia X-C,
Corvalan J R F, Wang P, C G Davis and Jakobovits A. Eradication of
Established Tumors by a Fully Human Monoclonal Antibody to the
Epidermal Growth Factor Receptor without Concomitant Chemotherapy.
Cancer Research Vol. 59, Number 6, pp 1236-1243 (1999); Jakobovits
A. Production and selection of antigen-specific fully human
monoclonal antibodies from mice engineered with human Ig loci.
Advanced Drug Delivery Reviews Vol. 31, pp: 33-42 (1998); Green L
and Jakobovits A. Regulation of B cell development by variable gene
complexity in mice reconstituted with human immunoglobulin yeast
artificial chromosomes. J. Exp. Med. Vol. 188, Number 3, pp:
483-495 (1998); Jakobovits A. The long-awaited magic bullets:
therapeutic human monoclonal antibodies from transgenic mice. Exp.
Opin. Invest. Drugs Vol. 7(4), pp: 607-614 (1998); Tsuda H,
Maynard-Currie K, Reid L, Yoshida T, Edamura K, Maeda N, Smithies
O, Jakobovits A. Inactivation of Mouse HPRT locus by a 203-bp
retrotransposon insertion and a 55-kb gene-targeted deletion:
establishment of new HPRT-Deficient mouse embryonic sBEM cell
lines. Genomics Vol. 42, pp: 413-421 (1997); Sherman-Gold, R.
Monoclonal Antibodies: The Evolution from '80s Magic Bullets To
Mature, Mainstream Applications as Clinical Therapeutics. Genetic
Engineering News Vol. 17, Number 14 (August 1997); Mendez M, Green
L, Corvalan J, Jia X-C, Maynard-Currie C, Yang X-d, Gallo M, Louie
D, Lee D, Erickson K, Luna J, Roy C, Abderrahim H, Kirschenbaum F,
Noguchi M, Smith D, Fukushima A, Hales J, Finer M, Davis C, Zsebo
K, Jakobovits A. Functional transplant of megabase human
immunoglobulin loci recapitulates human antibody response in mice.
Nature Genetics Vol. 15, pp: 146-156 (1997); Jakobovits A. Mice
engineered with human immunoglobulin YACs: A new technology for
production of fully human antibodies for autoimmunity therapy.
Weir's Handbook of Experimental Immunology, The Integrated Immune
System Vol. IV, pp: 194.1-194.7 (1996); Jakobovits A. Production of
fully human antibodies by transgenic mice. Current Opinion in
Biotechnology Vol. 6, No. 5, pp: 561-566 (1995); Mendez M,
Abderrahim H, Noguchi M, David N, Hardy M, Green L, Tsuda H, Yoast
S, Maynard-Currie C, Garza D, BEMmill R, Jakobovits A, Klapholz S.
Analysis of the structural integrity of YACs comprising human
immunoglobulin genes in yeast and in embryonic sBEM cells. Genomics
Vol. 26, pp: 294-307 (1995); Jakobovits A. YAC Vectors: Humanizing
the mouse genome. Current Biology Vol. 4, No. 8, pp: 761-763
(1994); Arbones M, Ord D, Ley K, Ratech H, Maynard-Curry K, Otten
G, Capon D, Tedder T. Lymphocyte homing and leukocyte rolling and
migration are impaired in L-selectin-deficient mice. Immunity Vol.
1, No. 4, pp: 247-260 (1994); Green L, Hardy M, Maynard-Curry K,
Tsuda H, Louie D, Mendez M, Abderrahim H, Noguchi M, Smith D, Zeng
Y, et. al. Antigen-specific human monoclonal antibodies from mice
engineered with human Ig heavy and light chain YACs. Nature
Genetics Vol. 7, No. 1, pp: 13-21 (1994); Jakobovits A, Moore A,
Green L, Vergara G, Maynard-Curry K, Austin H, Klapholz S.
Germ-line transmission and expression of a human-derived yeast
artificial chromosome. Nature Vol. 362, No. 6417, pp: 255-258
(1993); Jakobovits A, Vergara G, Kennedy J, Hales J, McGuinness R,
Casentini-Borocz D, Brenner D, Otten G. Analysis of homozygous
mutant chimeric mice: deletion of the immunoglobulin heavy-chain
joining region blocks B-cell development and antibody production.
Proceedings of the National Academy of Sciences USA Vol. 90, No. 6,
pp: 2551-2555 (1993); Kucherlapati et al., U.S. Pat. No.
6,1075,181.
[0014] Antibodies can also be made using phage display techniques.
Such techniques can be used to isolate an initial antibody or to
generate variants with altered specificity or avidity
characteristics. Single chain Fv can also be used as is convenient.
They can be made from vaccinated transgenic mice, if desired.
Antibodies can be produced in cell culture, in phage, or in various
animals, including but not limited to cows, rabbits, goats, mice,
rats, hamsters, guinea pigs, sheep, dogs, cats, monkeys,
chimpanzees, apes.
[0015] Antibodies can be labeled with a detectable moiety such as a
radioactive atom, a chromophore, a fluorophore, or the like. Such
labeled antibodies can be used for diagnostic techniques, either in
vivo, or in an isolated test sample. Antibodies can also be
conjugated, for example, to a pharmaceutical agent, such as
chemotherapeutic drug or a toxin. They can be linked to a cytokine,
to a ligand, to another antibody. Suitable agents for coupling to
antibodies to achieve an anti-tumor effect include cytokines, such
as interleukin 2 (IL-2) and Tumor Necrosis Factor (TNF);
photosensitizers, for use in photodynamic therapy, including
aluminum (III) phthalocyanine tetrasulfonate, hematoporphyrin, and
phthalocyanine; radionuclides, such as iodine-131 (.sup.131I),
yttrium-90 (.sup.90Y), bismuth-212 (.sup.212Bi), bismuth-213
(.sup.213Bi), technetium-99m (.sup.99mTc), rhenium-186
(.sup.186Re), and rhenium-188 (.sup.188Re); antibiotics, such as
doxorubicin, adriamycin, daunorubicin, methotrexate, daunomycin,
neocarzinostatin, and carboplatin; bacterial, plant, and other
toxins, such as diphtheria toxin, pseudomonas exotoxin A,
staphylococcal enterotoxin A, abrin-A toxin, ricin A
(deglycosylated ricin A and native ricin A), TGF-alpha toxin,
cytotoxin from chinese cobra (naja naja atra), and gelonin (a plant
toxin); ribosome inactivating proteins from plants, bacteria and
fungi, such as restrictocin (a ribosome inactivating protein
produced by Aspergillus restrictus), saporin (a ribosome
inactivating protein from Saponaria officinalis), and RNase;
tyrosine kinase inhibitors; ly207702 (a difluorinated purine
nucleoside); liposomes containing antitumor agents (e.g., antisense
oligonucleotides, plasmids which encode for toxins, methotrexate,
etc.); and other antibodies or antibody fragments, such as
F(ab).
[0016] Those of skill in the art will readily understand and be
able to make such antibody derivatives, as they are well known in
the art. The antibodies may be cytotoxic on their own, or they may
be used to deliver cytotoxic agents to particular locations in the
body. The antibodies can be administered to individuals in need
thereof as a form of passive immunization.
[0017] Characterization of extracellular regions for the cell
surface and secreted proteins from the protein sequence is based on
the prediction of signal sequence, transmembrane domains and
functional domains. Antibodies are preferably specifically
immunoreactive with membrane associated proteins, particularly to
extracellular domains of such proteins or to secreted proteins.
Such targets are readily accessible to antibodies, which typically
do not have access to the interior of cells or nuclei. However, in
some applications, antibodies directed to intracellular proteins
may be useful as well. Moreover, for diagnostic purposes, an
intracellular protein may be an equally good target since cell
lysates may be used rather than a whole cell assay.
[0018] Computer programs can be used to identify extracellular
domains of proteins whose sequences are known. Such programs
include SMART software (Schultz et al., Proc. Natl. Acad. Sci. USA
95: 5857-5864, 1998) and Pfam software (BaBEMan et al., Nucleic
acids Res. 28: 263-266, 2000) as well as PSORTII. Typically such
programs identify transmembrane domains; the extracellular domains
are identified as immediately adjacent to the transmembrane
domains. Prediction of extracellular regions and the signal
cleavage sites are only approximate. It may have a margin of error+
or -5 residues. Signal sequence can be predicted using three
different methods (Nielsen et al, Protein Engineering 10: 1-6,
1997, Jagla et. al, Bioinformatics 16: 245-250 , 2000, Nakai, K and
Horton, P. Trends in Biochem. Sci. 24:34-35, 1999) for greater
accuracy. Similarly transmembrane (TM) domains can be identified by
multiple prediction methods. (Pasquier, et. al, Protein Eng.
12:381-385, 1999, Sonnhammer et al., In Proc. of Sixth Int. Conf.
on Intelligent Systems for Molecular Biology, p. 175-182, Ed J.
Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C.
Sensen Menlo Park, Calif.: AAAI Press, 1998, Klein, et. al,
Biochim. Biophys. Acta, 815:468, 1985, Nakai and Kanehisa Genomics,
14: 897-911, 1992). In ambiguous cases, locations of functional
domains in well characterized proteins are used as a guide to
assign a cellular localization.
[0019] Putative functions or functional domains of novel proteins
can be inferred from homologous regions in the database identified
by BLAST searches (Altschul et. al. Nucleic Acid Res. 25:
3389-3402, 1997) and/or from a conserved domain database such as
Pfam (BaBEMan et. al, Nucleic Acids Res. 27:260-262 1999) BLOCKS
(Henikoff, et. al, Nucl. Acids Res. 28:228-230, 2000) and SMART
(Ponting, et. al, Nucleic Acid Res. 27,229-232, 1999).
Extracellular domains include regions adjacent to a transmembrane
domain in a single transmembrane domain protein (out-in or type I
class). For multiple transmembrane domains proteins, the
extracellular domain also includes those regions between two
adjacent transmembrane domains (in-out and out-in). For type II
transmembrane domain proteins, for which the N-terminal region is
cytoplasmic, regions following the transmembrane domain is
generally extracellular. Secreted proteins on the other hand do not
have a transmembrane domain and hence the whole protein is
considered as extracellular.
[0020] Membrane associated proteins can be engineered to delete the
transmembrane domains, thus leaving the extracellular portions
which can bind to ligands. Such soluble forms of transmembrane
receptor proteins can be used to compete with natural forms for
binding to ligand. Thus such soluble forms act as inhibitors and
can be used therapeutically as anti-angiogenic agents, as
diagnostic tools for the quantification of natural ligands, and in
assays for the identification of small molecules which modulate or
mimic the activity of a BEM:ligand complex.
[0021] Alternatively, the endothelial markers themselves can be
used as vaccines to raise an immune response in the vaccinated
animal or human. For such uses, a protein, or immunogenic fragment
of such protein, corresponding to the intracellular, extracellular
or secreted BEM of interest is administered to a subject. The
immogenic agent may be provided as a purified preparation or in an
appropriately expressing cell. The administration may be direct, by
the delivery of the immunogenic agent to the subject, or indirect,
through the delivery of a nucleic acid encoding the immunogenic
agent under conditions resulting in the expression of the
immunogenic agent of interest in the subject. The BEM of interest
may be delivered in an expressing cell, such as a purified
population of breast tumor endothelial cells or a population of
fused breast tumor endothelial and dendritic cells. Nucleic acids
encoding the BEM of interest may be delivered in a viral or
non-viral delivery vector or vehicle. Non-human sequences encoding
the human BEM of interest or other mammalian homolog can be used to
induce the desired immunologic response in a human subject. For
several of the BEMs of the present invention, mouse, rat or other
ortholog sequences can be obtained from the literature or using
techniques well within the skill of the art.
[0022] Endothelial cells can be identified using the markers which
are disclosed herein as being endothelial cell specific. Antibodies
specific for such markers can be used to identify such cells, by
contacting the antibodies with a population of cells containing
some endothelial cells. The presence of cross-reactive material
with the antibodies identifies particular cells as endothelial.
Similarly, lysates of cells can be tested for the presence of
cross-reactive material. Any known format or technique for
detecting cross-reactive material can be used including,
immunoblots, radioimmunoassay, ELISA, immunoprecipitation, and
immunohistochemistry. In addition, nucleic acid probes for these
markers can also be used to identify endothelial cells. Any
hybridization technique known in the art including Northern
blotting, RT-PCR, microarray hybridization, and in situ
hybridization can be used.
[0023] One can identify breast tumor endothelial cells for
diagnostic purposes, testing cells suspected of containing one or
more BEMs. One can test both tissues and bodily fluids of a
subject. For example, one can test a patient's blood for evidence
of intracellular and membrane associated BEMs, as well as for
secreted BEMs. Of particular interest in this context is the
testing of breast duct fluid. Intracellular and/or membrane
associated BEMs may be present in bodily fluids as the result of
high levels of expression of these factors and/or through lysis of
cells expressing the BEMs.
[0024] Populations of various types of endothelial cells can also
be made using the antibodies to endothelial markers of the
invention. The antibodies can be used to purify cell populations
according to any technique known in the art, including but not
limited to fluorescence activated cell sorting. Such techniques
permit the isolation of populations which are at least 50, 60, 70,
80, 90, 92, 94, 95, 96, 97, 98, and even 99% the type of
endothelial cell desired, whether normal, tumor, or
pan-endothelial. Antibodies can be used to both positively select
and negatively select such populations. Preferably at least 1, 5,
10, 15, 20, or 25 of the appropriate markers are expressed by the
endothelial cell population.
[0025] Populations of endothelial cells made as described herein,
can be used for screening drugs to identify those suitable for
inhibiting the growth of tumors by virtue of inhibiting the growth
of the tumor vasculature.
[0026] Populations of endothelial cells made as described herein,
can be used for screening candidate drugs to identify those
suitable for modulating angiogenesis, such as for inhibiting the
growth of tumors by virtue of inhibiting the growth of endothelial
cells, such as inhibiting the growth of the tumor or other
undesired vasculature, or alternatively, to promote the growth of
endothelial cells and thus stimulate the growth of new or
additional large vessel or microvasculature.
[0027] Inhibiting the growth of endothelial cells means either
regression of vasculature which is already present, or the slowing
or the absence of the development of new vascularization in a
treated system as compared with a control system. By stimulating
the growth of endothelial cells, one can influence development of
new (neovascularization) or additional vasculature development
(revascularization). A variety of model screening systems are
available in which to test the angiogenic and/or anti-angiogenic
properties of a given candidate drug. Typical tests involve assays
measuring the endothelial cell response, such as proliferation,
migration, differentiation and/or intracellular interaction with a
given candidate drug. By such tests, one can study the signals and
effects of the test stimuli. Some common screens involve
measurement of the inhibition of heparanase, endothelial tube
formation on Matrigel, scratch induced motility of endothelial
cells, platelet-derived growth factor driven proliferation of
vascular smooth muscle cells, and the rat aortic ring assay (which
provides an advantage of capillary formation rather than just one
cell type).
[0028] Drugs can be screened for the ability to mimic or modulate,
inhibit or stimulate, growth of tumor endothelium cells and/or
normal endothelial cells. Drugs can be screened for the ability to
inhibit tumor endothelium growth but not normal endothelium growth
or survival. Similarly, human cell populations, such as normal
endothelium populations or breast tumor endothelial cell
populations, can be contacted with test substances and the
expression of breast tumor endothelial markers and/or normal
endothelial markers determined. Test substances that decrease the
expression of breast tumor endothelial markers (BEMs) are
candidates for inhibiting angiogenesis and the growth of tumors. In
cases where the activity of a BEM is known, agents can be screened
for their ability to decrease or increase the activity.
[0029] For those breast tumor endothelial markers identified as
containing transmembrane regions, it is desirable to identify drug
candidates capable of binding to the BEM receptors found at the
cell surface. For some applications, the identification of drug
candidates capable of blocking the BEM receptor from its native
ligand will be desired. For some applications, the identification
of a drug candidate capable of binding to the BEM receptor may be
used as a means to deliver a therapeutic or diagnostic agent. For
other applications, the identification of drug candidates capable
of mimicking the activity of the native ligand will be desired.
Thus, by manipulating the binding of a transmembrane BEM
receptor:ligand complex, one may be able to promote or inhibit
further development of endothelial cells and hence,
vascularization.
[0030] For those breast tumor endothelial markers identified as
being secreted proteins, i.e., extracellular, it is desirable to
identify drug candidates capable of binding to the secreted BEM
protein. For some applications, the identification of drug
candidates capable of interfering with the binding of the secreted
BEM it is native receptor. For other applications, the
identification of drug candidates capable of mimicking the activity
of the native receptor will be desired. Thus, by manipulating the
binding of the secreted BEM:receptor complex, one may be able to
promote or inhibit further development of endothelial cells, and
hence, vascularization.
[0031] Expression can be monitored according to any convenient
method. Protein or mRNA can be monitored. Any technique known in
the art for monitoring specific genes' expression can be used,
including but not limited to ELISAs, SAGE, microarray
hybridization, Western blots. Changes in expression of a single
marker may be used as a criterion for significant effect as a
potential pro-angiogenic, anti-angiogenic or anti-tumor agent.
However, it also may be desirable to screen for test substances
that are able to modulate the expression of at least 5, 10, 15, or
20 of the relevant markers, such as the tumor or normal endothelial
markers Inhibition of BEM protein activity can also be used as a
drug screen.
[0032] Test substances for screening can come from any source. They
can be libraries of natural products, combinatorial chemical
libraries, biological products made by recombinant libraries, etc.
The source of the test substances is not critical to the invention.
The present invention provides means for screening compounds and
compositions that may previously have been overlooked in other
screening schemes. Nucleic acids and the corresponding encoded
proteins of the markers of the present invention can be used
therapeutically in a variety of modes. BEMs can be used to
stimulate the growth of vasculature, such as for wound healing or
to circumvent a blocked vessel. The nucleic acids and encoded
proteins can be administered by any means known in the art. Such
methods include, using liposomes, nanospheres, viral vectors,
non-viral vectors comprising polycations, etc. Suitable viral
vectors include adenovirus, retroviruses, and sindbis virus.
Administration modes can be any known in the art, including
parenteral, intravenous, intramuscular, intraperitoneal, topical,
intranasal, intrarectal, intrabronchial, etc.
[0033] Specific biological antagonists of BEMs can also be used to
therapeutic benefit. For example, antibodies, T cells specific for
a BEM, antisense to a BEM, interferance RNA to a BEM, and ribozymes
specific for a BEM can be used to restrict, inhibit, reduce, and/or
diminish tumor or other abnormal or undesirable vasculature growth.
Such antagonists can be administered as is known in the art for
these classes of antagonists generally. Anti-angiogenic drugs and
agents can be used to inhibit tumor growth, as well as to treat
diabetic retinopathy, rheumatoid arthritis, psoriasis, polycystic
kidney disease (PKD), and other diseases requiring angiogenesis for
their pathologies.
[0034] Mouse counterparts to human BEMs can be used in mouse cancer
models or in cell lines or in vitro to evaluate potential
anti-angiogenic or anti-tumor compounds or therapies. Their
expression can be monitored as an indication of effect. Mouse BEMs
can be used as antigens for raising antibodies which can be tested
in mouse tumor models. Mouse BEMs with transmembrane domains are
particularly preferred for this purpose. Mouse BEMs can also be
used as vaccines to raise an immunological response in a human to
the human ortholog.
[0035] The above disclosure generally describes the present
invention. All references disclosed herein are expressly
incorporated by reference in their entireties. A more complete
understanding can be obtained by reference to the following
specific examples which are provided herein for purposes of
illustration only, and are not intended to limit the scope of the
invention.
Example 1
[0036] Function of BEM proteins was determined using bioinformatics
tools. BEMs that are putative functional receptors with short
cytoplasmic tails make particularly interesting targets.
TABLE-US-00006 Breast Tumor Endothelial Putative Functional
Receptors with Short Cytoplasmic Tails Unigene ID Function OMIMID
Protein Hs.181418 KIAA0152 gene product -- 055545 Hs.25691 receptor
(calcitonin) activity 605155 005847 modifying protein 3 Hs.9598
sema domain -- BAB212835
Example 2
[0037] Protein kinases were identified among the BEMs. These are
particularly good druggable targets, especially for small
molecules.
TABLE-US-00007 Protein Kinases Unigene ID Function OMIMID Protein
Hs.100009 cyclin-dependent 123828 kinase 3 Hs.143897 dysferlin,
limb girdle 603009 NP_003485 muscular dystrophy 2B (autosomal
recessive) Hs.184367 Ca2+-promoted Ras BAA25464 inactivator
Hs.246857 mitogen-activated 602896 NP_620708 protein kinase 9
Hs.75087 FAST kinase 606965 NP-079372 Hs.296323
serum/glucocorticoid 602958 NP_005618 regulated kinase Hs.246857
mitogen-activated 602986 NP_620708 protein kinase
Example 3
[0038] Kinases with non-protein substrates were also identified.
These similarly are believed to be exceedingly good druggable
targets.
TABLE-US-00008 Kinases with non-protein substrates Unigene ID
Function OMIMID Protein Hs.118625 hexokinase 1 142600 NP_277035
Hs.82689 tumor rejection antigen (gp96) 1 191175 NP_003290
Example 4
[0039] Growth factors were identified among the BEMs:
TABLE-US-00009 Growth factors Unigene ID Function OMIMID Protein
Hs.91143 jagged 1 (Alagille syndrome) 601920 NP_000205 Hs.119206
insulin-like growth factor 602867 NP_001544 binding protein 7
Hs.1516 insulin-like growth factor 146733 NP_001543 binding protein
4 Hs.211573 heparan sulfate proteoglycan 2 142461 NP_005520
(perlecan) Hs.75111 protease, serine, 11 (IGF 602194 NP_002766
binding) Hs.8546 Notch homolog 3 (Drosophila) 600276 NP_000426
Example 5
[0040] Phosphatases, like kinases, are readily amenable to
screening for inhibitors, especially small molecule inhibitors:
TABLE-US-00010 Phosphatases Unigene ID Function OMIMID Protein
Hs.8997 heat shock 70 kDa 140550 NP_005336 protein 1A/1B [Homo
sapiens Hs.205353 ectonucleoside 601752 NP_001767 triphosphate
diphosphohydrolase 1 isoform 1 [Homo sapiens] Hs.43666 protein
tyrosine 606449 NP_116000 phosphatase type IVA 3 isoform 1 [Homo
sapiens] Hs.6147 tensin-like C1 domain- -- NP_056134 containing
phosphatase isoform 1 [Homo sapiens]
Example 6
[0041] GPCRs were identified among the BEMs:
TABLE-US-00011 GPCRs Unigene ID Function OMIMID Protein Hs.17170 G
protein-coupled receptor 4 600551 NP_005273
Example 7
[0042] The cellular location of the BEMs was determined to be
either cytoplasmic, extracellular, membrane, or nuclear, as shown
below.
TABLE-US-00012 Extracellular Proteins Unigene ID Function OMIMID
Protein Hs.75415 Beta-2-microglobulin 109700 NP_004039 Hs.821
Biglycan 301870 NP_001702 Hs.172928 collagen, type I, alpha 1
120150 NP_000079 Hs.119571 collagen, type III, alpha 1
(Ehlers-Danlos syndrome 120180 NP_000081 type IV, autosomal
dominant) Hs.119129 collagen, type IV, alpha 1 120130 NP_001836
Hs.75617 collagen, type IV, alpha 2 120090 NP_001837 Hs.235368
collagen, type V, alpha 3 120216 NP_056534 Hs.159263 collagen, type
VI, alpha 2 120240 NP_001840 Hs.78409 collagen, type XVIII, alpha 1
120328 NP_085059 Hs.278625 complement component 4B 120820 NP_000583
Hs.230 Fibromodulin 600245 NP_002014 Hs.211573 heparan sulfate
proteoglycan 2 (perlecan) 142461 NP_005520 Hs.1516 insulin-like
growth factor binding protein 4 146733 NP_001543 Hs.119206
insulin-like growth factor binding protein 7 602867 NP_001544
Hs.49215 integrin-binding sialoprotein (bone sialoprotein, bone
147563 NP_004958 sialoprotein II) Hs.79339 lectin,
galactoside-binding, soluble, 3 binding protein 600626 NP_005558
Hs.106747 likely homolog of rat and mouse retinoid-inducible
NP_067639 serine carboxypeptidase Hs.365706 matrix Gla protein
154870 NP_000891 Hs.151738 matrix metalloproteinase 9 (gelatinase
B, 92 kDa 120361 NP_004985 gelatinase, 92 kDa type IV collagenase)
Hs.699 peptidylprolyl isomerase B (cyclophilin B) 123841 NP_000933
Hs.75111 protease, serine, 11 (IGF binding) 602194 NP_002766
Hs.25338 protease, serine, 23 Hs.78224 ribonuclease, RNase A
family, 1 (pancreatic) 180440 AAH05324 Hs.111779 secreted protein,
acidic, cysteine-rich (osteonectin) 182120 NP_003109 Hs.82085
serine (or cysteine) proteinase inhibitor, clade E 173360 NP_000593
(nexin, plasminogen activator inhibitor type 1), member 1 Hs.179573
TEM10, COL1A2 involved in tissue remodeling 120160 NP_000080
Hs.356624 TEM11, nidogen (enactin) 131390 NP_002499 Hs.5831 tissue
inhibitor of metalloproteinase 1 (erythroid 305370 NP_003245
potentiating activity, collagenase inhibitor) Hs.82689 tumor
rejection antigen (gp96) 1 191175 NP_003290
TABLE-US-00013 Membrane Proteins Orientation TM of N- Unigene ID
Function Protein Domains TM Location terminus Hs.202 benzodiazapine
receptor (peripheral) NP_000705 3 107-129, 78-100, OUT 133-155
Hs.76206 cadherin 5, type 2, VE-cadherin (vascular epithelium)
NP_001786 1 598-620 Unsure Hs.122359 calcium channel,
voltage-dependent, alpha 1H subunit NP_066921 19 1370-1392, IN
1614-1636, 1533-1555, 141-163, 915-937, 396-418, 1651-1673,
1745-1767, 990-1012, 234-256, 1430-1452, 1333-1355, 1680-1702,
855-877, 1295-1316, 826-848, 100-122, 1840-1862, 364-386 Hs.84298
CD74 antigen (invariant polypeptide of major NP_004346 1 49-71 IN
histocompatibility complex, class II antigen- associated) Hs.1244
CD9 antigen (p24) NP_001760 4 59-81, 88-110, IN 12-34, 194-216
Hs.143897 dysferlin, limb girdle muscular dystrophy 2B NP_003485 1
2045-2067 Unsure (autosomal recessive) Hs.205353 ectonucleoside
triphosphate diphosphohydrolase 1 NP_001767 1 477-499 IN Hs.17170 G
protein-coupled receptor 4 NP_005273 5 55-77, 92-113, OUT 20-42,
225-244, 183-205 Hs.25549 hypothetical protein FLJ20898 NP_078876 3
102-124, 139-161, Unsure 168-190 Hs.277704 hypoxia up-regulated 1
NP_006380 1 13-35 IN Hs.76095 Immediate early response 3 NP_434702
1 123-145 Unsure Hs.265827 interferon, alpha-inducible protein
(clone IFI-6-16) NP_075011 2 5-24, 44-66 IN Hs.91143 jagged 1
(Alagille syndrome) NP_000205 1 1069-1091 Unsure Hs.181418 KIAA0152
gene product NP_055545 1 271-290 OUT Hs.79356 Lysosomal-associated
multispanning membrane NP_006753 5 63-85, 100-121, Unsure protein-5
142-164, 15-37, 184-206 Hs.77961 major histocompatibility complex,
class I, B NP_005505 1 308-330 OUT Hs.277477 major
histocompatibility complex, class I, C NP_002108 1 308-330 OUT
Hs.110024 NADH:ubiquinone oxidoreductase MLRQ subunit NP_064527 1
20-42 Unsure homolog Hs.8546 Notch homolog 3 (Drosophila) NP_000426
3 1641-1663, Unsure 1496-1518, 20-42 Hs.107125 plasmalemma vesicle
associated protein NP_112600 1 42-64 IN Hs.83974 solute carrier
family 21 (prostaglandin transporter), NP_005621 12 256-278,
363-385, Unsure member 2 397-419, 100-122, 208-230, 326-348,
173-195, 514-536, 71-93, 557-576, 606-628, 25-47 Hs.125359 TEM13,
Thy-1 cell surface antigen NP_006279 1 140-161 Unsure Hs.125036
TEM17 NP_065138 1 425-447 OUT Hs.9598 sema domain, immunoglobulin
domain (Ig) BAB21836 1 727-794 OUT Hs.202 Benzodiazapine receptor
(peripheral)-mitochondrial NP_00715 3 107-129, 78-100, OUT
133-155
TABLE-US-00014 Nuclear Proteins Unigene ID Function OMIMID Protein
Hs.244 amino-terminal enhancer of split 600188 Hs.154029 bHLH
factor Hes4 NP_066993 Hs.75450 delta sleep inducing peptide,
immunoreactor 602960 Hs.75087 FAST kinase 606965 NP_079372
Hs.356668 guanine nucleotide binding protein (G protein), gamma 5
600874 NP_005265 Hs.406410 H19, imprinted maternally expressed
untranslated mRNA 103280 BAB71280 Hs.234434 hairy/enhancer-of-split
related with YRPW motif 1 602953 NP_036390 Hs.23823
hairy/enhancer-of-split related with YRPW motif-like NP_055386
Hs.15265 heterogeneous nuclear ribonucleoprotein R 607201 NP_005817
Hs.8728 hypothetical protein DKFZp434G171 CAB61365 Hs.240170
hypothetical protein MGC2731 NP_076973 Hs.146360 hypothetical
protein MGC34648 NP_689873 Hs.337986 hypothetical protein MGC4677
NP_443103 Hs.197540 hypoxia-inducible factor 1, alpha subunit
(basic helix- 603348 NP_001521 loop-helix transcription factor)
Hs.75061 MARCKS-like protein 602940 NP_075385 Hs.246857
mitogen-activated protein kinase 9 602896 NP_620708 Hs.79110
Nucleolin 164035 NP_005372 Hs.298229 prefoldin 2 NP_036526
Hs.250655 prothymosin, alpha (gene sequence 28) 188390 NP_002814
Hs.24950 regulator of G-protein signalling 5 603276 NP_003608
Hs.76640 RGC32 protein Hs.3109 Rho GTPase activating protein 4
300023 NP_001657 Hs.337445 ribosomal protein L37 604181 NP_000988
Hs.197114 serine/arginine repetitive matrix 2 606032 NP_057417
Hs.48029 snail homolog 1 (Drosophila) 604238 NP_005976 Hs.168357
T-box 2 600747 NP_005985 Hs.332173 transducin-like enhancer of
split 2 (E(sp1) homolog, 601041 NP_003251 Drosophila) Hs.78465
v-jun sarcoma virus 17 oncogene homolog (avian) 165160
NP_002219
TABLE-US-00015 Cytoplasmic proteins Unigene ID Function OMIMID
Protein Hs.184367 Ca2+-promoted Ras inactivator BAA25464 Hs.2575
calpain 1, (mu/l) large subunit 114220 NP_005177 Hs.100009
cyclin-dependent kinase 3 123828 Hs.31053 cytoskeleton-associated
protein 1 601303 NP_001272 Hs.82646 DnaJ (Hsp40) homolog, subfamily
B, member 1 604572 NP_006136 Hs.169476 glyceraldehyde-3-phosphate
dehydrogenase 138400 NP_002037 Hs.77890 guanylate cyclase 1,
soluble, beta 3 139397 NP_000848 Hs.36927 heat shock 105 Kd
NP_006635 Hs.1197 heat shock 10 kDa protein 1 (chaperonin 10)
600141 NP_002148 Hs.8997 heat shock 70 kDa protein 1A 140550
NP_005336 Hs.180414 heat shock 70 kDa protein 8 600816 NP_006588
Hs.118625 hexokinase 1 142600 NP_277035 Hs.327412 Homo sapiens
clone FLC1492 PRO3121 mRNA, complete cds Hs.833 interferon,
alpha-inducible protein (clone IFI-15K) 147571 NP_005092 Hs.150580
putative translation initiation factor NP_005792 Hs.173737
ras-related C3 botulinum toxin substrate 1 (rho 602048 family,
small GTP binding protein Rac1) Hs.119122 ribosomal protein L13a
Hs.111611 ribosomal protein L27 607526 NP_000979 Hs.177592
ribosomal protein, large, P1 180520 Hs.12956 Tax interaction
protein 1 NP_055419 Hs.251653 tubulin, beta, 2 602660 NP_006079
REFERENCES
[0043] Abounader, R., Lal, B., Luddy, C., Koe, G., Davidson, B.,
Rosen, E. M., and Laterra, J. (2002). In vivo targeting of SF/HGF
and c-met expression via U1snRNA/ribozymes inhibits breast tumor
growth and angiogenesis and promotes apoptosis. Faseb J 16, 108-10.
[0044] Bart, J., Groen, H. J., Hendrikse, N. H., van der Graaf, W.
T., Vaalburg, W., and de Vries, E. G. (2000). The blood-brain
barrier and oncology: new insights into function and modulation.
Cancer Treat Rev 26, 449-62. [0045] Bernsen, H. J., Rijken, P. F.,
Oostendorp, T., and van der Kogel, A. J. (1995). Vascularity and
perfusion of human breast tumors xenografted in the athymic nude
mouse. Br J Cancer 71, 721-6. [0046] Bowers, D. C., Fan, S.,
Walter, K. A., Abounader, R., Williams, J. A., Rosen, E. M., and
Laterra, J. (2000). Scatter factor/hepatocyte growth factor
protects against cytotoxic death in human glioblastoma via
phosphatidylinositol 3-kinase- and AKT-dependent pathways. Cancer
Res 60, 4277-83. [0047] Chen, H., Centola, M., Altschul, S. F., and
Metzger, H. (1998). Characterization of gene expression in resting
and activated mast cells. J Exp Med 188, 1657-68. [0048] Guerin,
C., Wolff, J. E., Laterra, J., Drewes, L. R., Brem, H., and
Goldstein, G. W. (1992). Vascular differentiation and glucose
transporter expression in rat breast tumors: effects of steroids.
Ann Neurol 31, 481-7. [0049] Hobbs, S. K., Monsky, W. L., Yuan, F.,
Roberts, W. G., Griffith, L., Torchilin, V. P., and Jain, R. K.
(1998). Regulation of transport pathways in tumor vessels: role of
tumor type and microenvironment. Proc Natl Acad Sci USA 95,
4607-12. [0050] Holash, J., Maisonpierre, P. C., Compton, D.,
Boland, P., Alexander, C. R., Zagzag, D., Yancopoulos, G. D., and
Wiegand, S. J. (1999). Vessel cooption, regression, and growth in
tumors mediated by angiopoietins and VEGF. Science 284, 1994-8.
[0051] Huminiecki, L., and Bicknell, R. (2000). In silico cloning
of novel endothelial-specific genes. Genome Res 10, 1796-806.
[0052] Lamszus, K., Laterra, J., Westphal, M., and Rosen, E. M.
(1999). Scatter factor/hepatocyte growth factor (SF/HGF) content
and function in human breast tumors. Int J Dev Neurosci 17, 517-30.
[0053] Marx, J. (2001). Caveolae: a once-elusive structure gets
some respect. Science 294, 1862-5. [0054] Roberts, W. G., and
Palade, G. E. (1997). Neovasculature induced by vascular
endothelial growth factor is fenestrated. Cancer Res 57, 765-72.
[0055] Shinoura, N., Shamraj, O. I., Hugenholz, H., Zhu, J. G.,
McBlack, P., Warrick, R., Tew, J. J., Wani, M. A., and Menon, A. G.
(1995). Identification and partial sequence of a cDNA that is
differentially expressed in human brain tumors. Cancer Lett 89,
215-21. [0056] Smith, R. M., Jarret, L. (1988). Lab. Invest. 58,
613-629. [0057] St Croix, B., Rago, C., Velculescu, V., Traverso,
G., Romans, K. E., Montgomery, E., Lal, A., Riggins, G. J.,
Lengauer, C., Vogelstein, B., and Kinzler, K. W. (2000). Genes
expressed in human tumor endothelium. Science 289, 1197-202. [0058]
Stan, R. V., Arden, K. C., and Palade, G. E. (2001). cDNA and
protein sequence, genomic organization, and analysis of cis
regulatory elements of mouse and human PLVAP genes. Genomics 72,
304-13. [0059] Tamagnone, L., Artigiani, S., Chen, H., He, Z.,
Ming, G. I., Song, H., Chedotal, A., Winberg, M. L., Goodman, C.
S., Poo, M., Tessier-Lavigne, M., and Comoglio, P. M. (1999).
Plexins are a large family of receptors for transmembrane,
secreted, and GPI-anchored semaphorins in vertebrates. Cell 99,
71-80. [0060] Vajkoczy, P., and Menger, M. D. (2000). Vascular
microenvironment in breast tumors. J Neurooncol 50, 99-108. [0061]
Vajkoczy, P., Schilling, L., Ullrich, A., Schmiedek, P., and
Menger, M. D. (1998). Characterization of angiogenesis and
microcirculation of high-grade breast tumor: an intravital
multifluorescence microscopic approach in the athymic nude mouse. J
Cereb Blood Flow Metab 18, 510-20. [0062] Vick, N. A., and Bigner,
D. D. (1972). Microvascular abnormalities in virally-induced canine
BREAST tumors. Structural bases for altered blood-brain barrier
function. J Neurol Sci 17, 29-39.
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