US20050130193A1

US20050130193A1 - Methods for detecting, diagnosing and treating human renal cell carcinoma

Info

Publication number: US20050130193A1
Application number: US10/938,973
Authority: US
Inventors: Bruce Luxon; John Copland; Christopher Wood
Original assignee: Individual
Current assignee: Individual
Priority date: 2003-09-10
Filing date: 2004-09-10
Publication date: 2005-06-16
Also published as: WO2005024603A3; US20110294694A1; WO2005024603A2; US8361721B2; US20130203619A1

Abstract

Gene expression profiling and hierarchical clustering analysis readily identify differential gene expressions in normal renal epithelial cells and renal cell carcinomas. Genes identified by this analysis would be useful for diagnosis, prognosis and development of targeted therapy for the prevention and treatment of conventional renal cell carcinoma.

Description

CROSS-REFERENCE TO RELATED APPLICATION

This non-provisional patent application claims benefit of provisional patent application 60/502,038, filed Sep. 10, 2003, and 60/539,838, filed Jan. 28, 2004, now abandoned.

BACKGROUND OF THE INVENTION

1. Field of the Invention
The present invention relates generally to the field of cancer research. More specifically, the present invention relates to gene expression profiling for human renal cell carcinoma.
2. Description of the Related Art
Renal cell carcinoma (RCC) represents a major health issue. The American Cancer Society predicts 31,900 new cases will be diagnosed in the United States alone in the year 2003, with 11,900 people dying of the disease. When clinically localized or even locally advanced, renal cell carcinoma can be surgically resected for cure using a variety of approaches. With metastatic progression, however, renal cell carcinoma is incurable, and existing systemic therapies are largely ineffective in impacting disease response or patient survival. The lack of effective systemic therapy for metastatic renal cell carcinoma is, in part, due to a fundamental lack of understanding of the molecular events that result in cellular transformation, carcinogenesis, and progression in human kidney.
The advent of gene array technology has allowed classification of disease states at molecular level by examining changes in all mRNAs expressed in cells or tissues. Gene expression fingerprints representing large numbers of genes may allow precise and accurate grouping of renal cell carcinoma. Moreover, large scale gene expression analysis have the potential of identifying a number of differentially expressed genes in renal cell carcinoma compare to normal renal epithelial cells. These genes or markers may further be tested for clinical utility in the diagnosis and treatment of renal cell carcinoma.
Thus, the identification of novel renal cell carcinoma markers to be used for detection, diagnosis and development of effective therapy against the disease remains a high priority. The prior art is deficient in understanding the molecular differences between renal cell carcinoma and normal renal epithelium. The present invention fulfills this need in the art by providing gene expression profiling for these two types of tissues.

SUMMARY OF THE INVENTION

The present invention identifies genes with a differential pattern of expression between different subtypes of renal cell carcinomas (RCC) and normal renal epithelium. These genes and their products can be used to develop novel diagnostic and therapeutic markers for the treatment of renal cell carcinomas.
Genomic profiling of conventional renal cell carcinoma tissues and patient-matched normal kidney tissue samples was carried out using stringent statistical analyses (ANOVA with full Bonferroni corrections). Subtypes of renal cell carcinoma include stage I, II, III, and IV (reflecting differences in tumor size, lymph node and organ metastasis), stage I papillary renal cell carcinoma, and benign oncocytoma. Hierarchical clustering of the expression data readily distinguished normal tissue from renal cell carcinomas. The identified genes were verified by real-time PCR and immunohistochemical analyses.
Different subtypes of conventional renal cell carcinomas can be diagnosed either by drawing blood and identifying secreted gene products specific to renal cell carcinoma or by doing a biopsy of the tissue and then identify specific genes that are altered when renal cell carcinoma is present. An example of when this may be especially important is in distinguishing the deadly conventional renal cell carcinomas (account for 85% of all renal cell carcinomas) from renal oncocytoma (benign renal cell carcinoma) as well as identifying the histologic subtypes of papillary and sarcomatoid renal cell carcinoma. Identification of specific genes will also help in determining which patients will have a good prognosis verses that of a poor prognosis. In addition, subsets of genes identified in the present invention can be developed as targets for therapies that could cure, prevent, or stabilize the disease. Thus, results from the present invention could be used for diagnosis, prognosis, and development of therapies to treat or prevent renal cell carcinoma.
In one embodiment, there are provided methods of detecting conventional or clear cell renal cell carcinoma based on over-expression and/or down-regulation of a number of genes disclosed herein. In another embodiment, conventional or clear cell renal cell carcinoma is detected based on decreased expression of type III TGF-b receptor.
In yet another embodiment, there are provided methods of detecting stage I conventional or clear cell renal cell carcinoma based on over-expression and/or down-regulation of a number of genes disclosed herein. The present invention also provides methods of detecting stage II conventional or clear cell renal cell carcinoma based on over-expression and/or down-regulation of a number of genes disclosed herein.
The present invention also provides methods of detecting papillary renal cell carcinoma or benign oncocytoma based on over-expression and/or down-regulation of a number of genes disclosed herein.
In another embodiment, there is provided a method of targeting conventional or clear cell renal cell carcinoma cells based on generating antibodies or small molecules directed against a cell surface molecule over-expressed in conventional renal cell carcinoma cells.
In yet another embodiment, there is provided a method of treating conventional or clear cell renal cell carcinoma by replacing down-regulated tumor suppressor gene in conventional renal cell carcinoma.
Other and further aspects, features, and advantages of the present invention will be apparent from the following description of the presently preferred embodiments of the invention. These embodiments are given for the purpose of disclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A shows hierarchical clustering of genes expressed in normal renal cortex (12 patient tissue samples) verse stage I conventional renal cell carcinoma (6 patient tissue samples). Red indicates that a gene is highly expressed and green is indicative of low expression. Four hundred eighty eight genes were depicted in FIG. 1A. FIG. 1B shows hierarchical clustering of genes expressed in normal renal cortex (12 patient tissue samples) verse stage II conventional renal cell carcinoma (6 patient tissue samples). Red indicates that a gene is highly expressed and green is indicative of low expression. Six hundred twenty eight genes were depicted in FIG. 1B. FIG. 1C shows hierarchical clustering of genes selected from a Venn analysis in which the chosen genes were expressed in common in both stage I and II at a 99% confidence level. One hundred eighty eight genes were depicted in FIG. 1C. C, cancer cells; N, normal cells; S1, stage 1; S2, stage 2.
FIG. 2 shows TGF-b1 mRNA expression in stages I-IV renal cell carcinoma as measured by real time PCR. TGF-b1 mRNA levels were up-regulated in all stages of renal cell carcinoma as compared to normal tissue counterparts.
FIG. 3 shows TGF-a mRNA expression in stages I-IV renal cell carcinoma as measured by real time PCR. TGF-a mRNA levels were up-regulated in all stages of renal cell carcinoma as compared to normal tissue counterparts.
FIG. 4 shows adrenomedulin mRNA expression in stages I-IV renal cell carcinoma as measured by real time PCR. Adrenomedulin mRNA levels were up-regulated in all stages of renal cell carcinoma as compared to normal tissue counterparts.
FIG. 5 shows TGF-b2 mRNA expression in stages I-IV renal cell carcinoma as measured by real time PCR. TGF-b2 mRNA levels were not altered between normal and tumor matched samples.
FIG. 6 shows TGF-b3 mRNA expression in stages I-IV renal cell carcinoma as measured by real time PCR. TGF-b3 mRNA levels were not altered between normal and tumor matched samples.
FIG. 7 shows tumor suppressor gene Wilms Tumor 1 (WT1) mRNA expression in stages I-IV renal cell carcinoma as measured by real time PCR. WT1 mRNA levels were down-regulated in all stages of renal cell carcinoma as compared to normal tissue counterparts.
FIG. 8 shows von Hippel Lindau mRNA expression in stages I-IV renal cell carcinoma as measured by real time PCR. A small percentage of tumor tissues demonstrated attenuated von Hippel Lindau mRNA levels when compared to matched normal tissue.
FIG. 9 shows calbindin mRNA expression in stages I-IV renal cell carcinoma as measured by real time PCR. Calbindin mRNA was completely lost in all stage I renal cell carcinoma.
FIG. 10 shows MUC1 mRNA expression in stages I-IV renal cell carcinoma as measured by real time PCR. MUC1 mRNA levels were down-regulated in all tumor tissues as early as stage I.
FIGS. 11A-B show stepwise loss of type III TGF-b receptor (TBR3) and type II TGF-b receptor (TBR2) mRNA expression during renal cell carcinogenesis and progression in patient tissue samples. FIG. 11A shows gene array data from 10 patients—five diagnosed with localized renal cell carcinoma and five with metastatic disease. ‘+’ indicates statistical difference for TBR3 mRNA levels as compared to normal tissue and ‘*’ indicates statistical difference for TBR2 mRNA levels as compared to normal controls (P<0.05). Data are expressed as mean±s.e. FIG. 11B shows real-time RT-PCR verification of TBR1, TBR2, and TBR3 mRNA levels of tissue samples described in FIG. 11A. Data are expressed as mean±s.d.
FIG. 12 shows immunohistochemistry of patient tissue demonstrating loss of type III TGF-b receptor (TBR3) expression (top row) in all tumors, loss of type II TGF-b receptor (TBR2) expression (middle row) in patients diagnosed with metastatic tumors, and no change in type I TGF-b receptor (TBR1) protein expression (bottom row).
FIG. 13 demonstrates down-regulation of TGF-b-regulated genes in human tumor tissues by real-time PCR. Genes known to be up-regulated by TGF-b are suppressed in tumor tissues. Down-regulation of collagen IV type 6, fibulin 5, and connective tissue growth factor (CTGF) mRNA in tumor tissues were compared to matched normal tissue controls. Values were normalized to 18 s mRNA. Each matching tumor value was compared to its respective normal control. The mean±s.d. was calculated for each sample group with n values of 10-15 matched samples.
FIGS. 14A-B show tumor cell lines that lose type III TGF-b receptor (TBR3) and type II TGF-b receptor (TBR2) expression. FIG. 14A shows semi-quantitative RT-PCR measurements of mRNA levels of TBR1, TBR2, and TBR3 for UMRC3, UMRC6 and normal renal epithelial (NRE) cells. FIG. 14B shows immunohistochemistry of protein expression for TBR1, TBR2, and TBR3 (×40 magnification).
FIGS. 15A-B show loss of type III TGF-b receptor (TBR3) and type II TGF-b receptor (TBR2) expression in renal tumor cell lines correlate with loss of TGF-b-regulated growth inhibitory and transcriptional responses. FIG. 15A shows cell proliferation was inhibited as assessed by DNA content 3 days after TGF-b treatment. Percent of each respective untreated control was used for comparisons. Transient transfection using 3TP/lx along with a renilla luciferase control demonstrates loss of responsiveness to 2 ng/ml TGF-b1 with loss of TGF-b receptor expression (FIG. 15B). Firefly luciferase activity was normalized using the ratio of firefly luciferase/renilla luciferase. Data are expressed as mean±s.d.
FIG. 16A shows UMRC3 cells stably transfected with type II TGF-b receptor (UMRC3+TBR2) or type II and type III TGF-b receptor (UMRC3+TBR2+TBR3) demonstrated attenuated cell proliferation following the administration of exogenous TGF-b1 as compared to that of UMRC3 cells. The inset demonstrates RT-PCR derived mRNA expression of type III TGF-b receptor (TBR3), type II TGF-b receptor (TBR2), and type I TGF-b receptor (TBR1) in UMRC3 cells and cells stably transfected with TBR2 and TBR3. FIG. 16B shows UMRC3 cells, UMRC3+TBR2 cells, and UMRC3+TBR2+TBR3 stable cell lines transfected with 3TP/lux were treated with or without TGF-b and examined for luciferase activity. FIG. 16C shows real-time PCR measuring mRNA levels for collagen IV type 6 in UMRC3, UMRC3+TBR2 cells, and UMRC3+TBR2+TBR3 cells in the presence of 2 ng/ml TGF-b1 for 24 h. FIG. 16D shows colony formation assay demonstrates that UMRC3+TBR2+TBR3 cells have completely lost anchorage-independent growth, while attenuated growth in UMRC3+TBR2 cells occurs as compared to that of UMRC3 cells. The number of colonies were stained and counted after 45 days of growth. Data are expressed as mean±s.d.
FIG. 17A shows growth inhibition after re-expressing human type III TGF-b receptor (TBR3) in UMRC3 cells. UMRC3 cells were stably transfected with TBR3 or infected using an adenoviral vector expressing TBR3. Cells were plated in culture dishes at 20,000 cells/well. Cell number was determined at the indicated times using a Coulter cell counter. FIG. 17B shows RT-PCR data demonstrating the mRNA expression levels of type I, II, or III TGF-b receptors (TBR1, TBR2, TBR3) in UMRC3 cells in the presence or absence of the adenoviral vector expressing TBR3. Unmodified UMRC3 cells only express TBR1.
FIG. 18 shows re-expression of human type II or III TGF-b receptors (TBR2 or TBR3) inhibits tumor growth in nude mice. One million UMRC3 cells stably transfected with human type II or type III TGF-b receptors were implanted into nude mice ectopically and tumor growth was measured weekly. Tumor volume (mm³) was calculated by width×length×height×0.5236.
FIG. 19 shows hierarchical clustering of genes expressed in normal renal cortex verse stage I papillary renal cell carcinoma. Red indicates that a gene is highly expressed and green is indicative of low expression.
FIG. 20 shows hierarchical clustering of genes expressed in normal renal cortex verse benign oncocytoma. Red indicates that a gene is highly expressed and green is indicative of low expression.
FIG. 21 shows venn analysis of gene distribution among stage I renal cell carcinoma (RCC), oncocytoma and stage I papillary renal cell carcinoma.
FIG. 22 shows venn analysis of gene distribution among stage II renal cell carcinoma (RCC), oncocytoma and stage I papillary renal cell carcinoma.

DETAILED DESCRIPTION OF THE INVENTION

High-throughput technologies for assaying gene expression, such as high-density oligonucleotide and cDNA microarrays, offer the potential to identify clinically relevant genes differentially expressed between normal and tumor cells. The present invention discloses a genome-wide examination of differential gene expression between renal cell carcinomas (RCC) and normal renal epithelial cells.
Currently, there are no proven molecular markers useful clinically for the diagnosis, staging, or prognosis of sporadic renal cell carcinoma. The present invention detects genes that have differential expression between renal cell carcinomas and normal renal epithelial cells. The known function of some of these genes may provide insight into the biology of renal cell carcinomas while others may prove to be useful as diagnostic or therapeutic markers against renal cell carcinomas. Subtypes of renal cell carcinomas disclosed herein include stage I, II, III, and IV renal cell carcinomas (reflecting differences in tumor size, lymph node and organ metastasis), stage I papillary renal cell carcinoma, and benign oncocytoma.
The present invention provides methods of detecting conventional renal cell carcinoma based on determining the expression level of a number of genes that are found to have 2-fold or higher differential expression levels between tumor and normal tissue. In general, biological samples (e.g. tissue samples, serum samples, urine samples, saliva samples, blood samples or biopsy samples) are obtained from the individual to be tested and gene expression at RNA or protein level is compared to that in normal tissue. The normal tissue samples can be obtained from the same individual who is to be tested for renal cell carcinoma. It will be obvious to one of ordinary skill in the art that gene expression can be determined by DNA microarray and hierarchical cluster analysis, real-time PCR, RT-PCR, or northern analysis, whereas secreted gene products can be measured in blood samples by standard procedures.
In one embodiment, there is provided a method of detecting conventional or clear cell renal cell carcinoma based on differential expression of one or more of the following genes or proteins: TGF-b1, TGF-a, adrenomedulin, fibroblast growth factor 2 (FGF2), vascular epidermal growth factor (VEGF), osteonectin, follistatin like-3, inhibin beta A, spondin 2, chemokine X cytokine receptor 4 (CXCR4), fibronectin, neuropilin 1, frizzled homolog 1, insulin-like growth factor binding protein 3, laminin alpha 3, integrin beta 2, semaphorins 6A, semaphorins 5B, semaphorins 3B, caspase 1, sprouty 1, CDH16, PCDH9, compliment component 1-beta, compliment component 1-alpha, compliment component 1-gamma, CD53, CDW52, CD163, CD14, CD3Z, CD24, RAP1, angiopoietin 2, cytokine knot secreted protein, MAPKKKK4, 4-hydroxyphenylpyruvate dioxygenase, pyruvate carboxyknase 2, 11-beta-hydroxysteroid dehydrogenase 2, GAS1, CDKN1, nucleolar protein 3, interferon induced protein 44, NR3C1, vitamin D receptor, hypothetical protein FLJ14957 (Affy# 225817_at), metallothionein 2A, metallothionein-If gene, metallothionein 1H, secreted frizzled related protein 1, connective tissue growth factor, and epidermal growth factor.
In another embodiment, there is provided a method of detecting conventional renal cell carcinoma by examining the expression level of type III TGF-b receptor, wherein decreased expression of type III TGF-b receptor indicates the presence of renal cell carcinoma. In general, the expression level of type III TGF-b receptor can be determined at the mRNA or protein level.
The present invention also provides methods of detecting stage I conventional renal cell carcinoma, stage II conventional renal cell carcinoma, stage I papillary renal cell carcinoma, or benign oncocytoma based on over-expression or down-regulation of a number of genes identified in the present invention. The present invention discloses a number of genes that are up- or down-regulated specifically in these subtypes of renal cell carcinoma. Determining the expression levels of these genes would provide specific diagnosis for these different subtypes of renal cell carcinoma.
For example, stage I conventional renal cell carcinoma can be detected based on (i) over-expression of one or more genes listed in Table 1, (ii) down-regulation of one or more genes listed in Table 2, or (iii) over-expression of one or more genes listed in Table 1 and down-regulation of one or more genes listed in Table 2. Similarly, stage II conventional renal cell carcinoma can be detected based on (i) over-expression of one or more genes listed in Table 3, (ii) down-regulation of one or more genes listed in Table 4, or (iii) over-expression of one or more genes listed in Table 3 and down-regulation of one or more genes listed in Table 4.
The present invention also discloses a number of genes that are up- or down-regulated in both stage I and stage II conventional renal cell carcinoma (Tables 5 and 6 respectively). These genes would also provide diagnosis for stage I or stage II conventional renal cell carcinoma. Hence, stage I or stage II conventional renal cell carcinoma can be detected based on (i) over-expression of one or more genes listed in Table 5, or (ii) down-regulation of one or more genes listed in Table 6.
In another embodiment, stage I papillary renal cell carcinoma can be detected based on (i) over-expression of one or more genes listed in Table 8, (ii) down-regulation of one or more genes listed in Table 9, or (iii) over-expression of one or more genes listed in Table 8 and down-regulation of one or more genes listed in Table 9.
In yet another embodiment, benign oncocytoma can be detected based on (i) over-expression of one or more genes listed in Table 10, (ii) down-regulation of one or more genes listed in Table 11, or (iii) over-expression of one or more genes listed in Table 10 and down-regulation of one or more genes listed in Table 11.
In still yet another embodiment, there are provided methods of utilizing genes over-expressed on the cell surface of renal carcinoma tissue to develop antibodies or other small molecules for the purpose of specifically targeting the renal tumor cells. The present invention discloses a number of genes that are up-regulated in stage I renal cell carcinoma (RCC), stage II RCC tumor, stage I papillary RCC, and benign oncocytoma. Antibodies or small molecules directed against proteins encoded by these genes can be linked with a therapeutic drug to deliver drug to the tumor tissue, or be linked with dye, nanoparticle or other imaging agents for cancer imaging. Some of the novel genes identified herein for the first time include, but are not limited to, the following genes: calcitonin receptor-like (206331_at; 210815_s_at); receptor (calcitonin) activity modifying protein 2 (RAMP2; 205779_at); endothelin receptor type B (206701_x_at); beta 2 integrin (202803_s_at); alpha 5 integrin (201389_at); chemokine X cytokine receptor 4 (CXCR4); fibronectin; neuropilin 1 (212298_at; 210510_s_at); CD24; CD14; Cd163; CD53; Compliment Componenet 1-beta, 1-alpha, and 1-gamma; CDH4; integrin beta2; ADAM28; FK506 binding protein; collagen Valpha2; tumor necrosis factor receptor superfamily, member 6; tumor necrosis factor receptor superfamily, member 5; tumor necrosis factor (ligand) superfamily, member 13b; tumor necrosis factor receptor superfamily, member 12A; and the FGF receptor.
In another embodiment, there is provided a method of treating conventional or clear cell renal cell carcinoma. The method involves replacing tumor suppressor genes (e.g., via gene therapy) whose expression is down-regulated in tumor tissues or introducing a molecule that induces the down-regulated gene to be re-expressed in the tumor. The present invention discloses a number of genes that are down-regulated in stage I renal cell carcinoma (RCC), stage II RCC tumor, stage I papillary RCC, and benign oncocytoma. Some examples of down-regulated genes identified in stage I and/or II RCC tumors include, but are not limited to, CDKN1, secreted frizzled related protein 1, semaphoring 6D, semaphoring 3B, CDH16, TNF alpha, calbindin D28, defensin beta1, beta-catenin interacting protein 1, GAS1, vitamin D receptor, Kruppel-like factor 15. This method of treatment can be combined with other therapies to provide combinatorial therapy.
The genes that are found to have altered expression in stage I and stage II renal cell carcinoma would also be useful for determining patient prognosis. These genes or gene products (i.e., proteins) would have the unique characteristic of being altered in tumor verses normal samples in a subset of patients. For example, basic transcription element binding protein 1 is down-regulated in 7 out of 12 renal cell carcinoma tumors. Other examples include CD164, decreased 5/12; Map kinase kinase kinase 7, increased 6/12; Endoglin, increased 7/12; SERPIN A1, increased 6/12; Metalloprotease 11 (MMP11), increased 7/12; Integrin 3 alpha, increased 4/12; carbonic anhydrase II, decreased 7/12; protein tyrosine kinase 2, increased 4/12; fibroblast growth factor 11, increased 6/12; fibroblast growth factor 2, increased 7/12; VEGF B, increased 5/12.
Moreover, the levels of change may be a useful determinant of patient outcome and/or rationale for strategy of treatment course. An example of this is found for chemokine (C-X-C motif) ligand 14 (CXCL14, 222484_s_at). Six patients with stage I and six patients with stage II renal cell carcinoma were analyzed by genomic profiling. A patient with stage I renal cell carcinoma has CXCL14 mRNA expression levels of 19862 and 24.49 in his normal tissue and tumor tissue respectively. This patient would be predicted to have a poor prognosis or poor response to therapy based upon this result along with other gene predictors. On the other hand, a patient with stage II RCC has CXCL14 mRNA expression levels of 20435 and 18557 in his normal tissue and tumor tissue respectively. This patient would be predicted to have a good prognosis and good response to chemotherapy.
The following examples are given for illustrating various embodiments of the invention and are not meant to limit the present invention in any fashion. One skilled in the art will appreciate readily that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those objects, ends and advantages inherent herein. Changes therein and other uses which are encompassed within the spirit of the invention as defined by the scope of the claims will occur to those skilled in the art.

EXAMPLE 1

Tissue Banking
Renal tissue (normal and tumor) was transported to a sterile hood on ice and under sterile conditions. Tissue was dissected under the direction of a pathologist. The tissue was frozen in liquid nitrogen for isolation of RNA, DNA, and protein or processed to establish primary cell cultures. The tissue was fixed in formalin for immunohistochemistry and in situ hybridization and RNAlater (Ambion) for RNA isolation. Primary normal renal epithelial (NRE) cell cultures were established using standard collagenase/Dnase techniques to digest tissue and isolate single cells. NREs were easily isolated and grew well in culture for up to 10 passages. These cells were further analyzed for homogeneity with regard to epithelial population using appropriate immunohistochemical markers such as vimentin, cytokeratin, and megalin.

EXAMPLE 2

Genomic Gene Array and Microarray Data Analysis
Gene expression profiling was performed using Affymetrix HU95A oligonucleotide gene arrays (>12,600 genes) or HG-U133 A&B GeneChip® oligonucleotide microarrays (33,000+ probe sets). Total RNA (Trizol®, Ambion) was extracted from patient-matched normal renal cortex and tumor tissue from patients diagnosed with local disease confined to the kidney. Alternatively, the investigators analyzed metastatic disease defined by lesions in lymph nodes, adrenal, or other organs. Data were analyzed by a combination of two-dimensional ANOVA, Affymetrix MAS5.0®, and hierarchical cluster analysis using Spotfire®. Procedure that were used to identify altered expression of large sets of genes, as well as other issues concerning microarray analyses can be found in a recent review article by Copland et al. (2003).

EXAMPLE 3

Real-Time PCR
Applied Biosystems' assays-by-design or assays-on-demand 20X assay mix of primers and TaqMan® MGB probes (FAM® dye-labeled) for all target genes and predeveloped 18S rRNA (VIC® dye-labeled probe) TaqMan® assay reagent for internal control were used for real-time PCR measurements. These assays were designed to span exon-exon junctions so as not to detect genomic DNA and an primers and probes sequences were searched against the Celera database to confirm specificity. Validation experiments were performed to test the efficiency of the target amplification and the efficiency of the reference amplification. All absolute values of the slope of log input amount versus DC_Tis less than 0.1.
Separate tubes (singleplex) for one-step RT-PCR was performed with 50 ng RNA for both target genes and endogenous controls using TaqMan® one-step RT-PCR master mix reagent kit (Applied Biosystems). The cycling parameters for one-step RT-PCR were: reverse transcription 48° C. for 30 min, AmpliTaq® activation 95° C. for 10 min, denaturation 95° C. for 15 s, and annealing/extension 60° C. for 1 min (repeat 40 times) on ABI7000®. Duplicate C_Tvalues were analyzed with Microsoft Excel® using the comparative C_T(DDC_T) method as described by the manufacturer (Applied Biosystems). The amount of target (2^-DDCT) was obtained by normalizing to an endogenous reference (18smRNA) and relative to a calibrator (normal tissue).

EXAMPLE 4

Immunohistochemical Analyses of Protein Expression
For immunohistochemical analyses of type I TGF-b receptor (TBR1), type II TGF-b receptor (TBR2), and type III TGF-b receptor (TBR3) expression, patient-matched normal renal and tumor tissue samples were fixed in 10% neutral-buffered formalin and embedded in paraffin blocks. Consecutive sections were cut 5 um thick, deparaffinized, hydrated, and immunostained using antibodies recognizing human TBR1, TBR2, and TBR3 (1:100; Santa Cruz Biotechnology). Biotinylated secondary antibody (1:600; Santa Cruz Biotechnology) was detected using avidin-biotin-peroxidase detection according to the manufacturer's instructions (Vectastatin Elite ABC kit; Vector Lab). All slides were lightly counterstained with hematoxylin before dehydration and mounting.
For cell lines, cells were plated on glass coverslips in wells. Prior to the detection of TGF-b receptor expression as described above, cells were fixed onto the coverslips with 3% formalin.

EXAMPLE 5

Gene Expression Profiling of Renal Cell Carcinoma
Gene expression profiling was performed using Affymetrix oligonucleotide gene arrays. RNA was extracted from patient-matched normal renal cortical and tumor tissues from patients diagnosed with localized and metastatic renal cell carcinoma. Data were analyzed by a combination of two-dimensional ANOVA, Affymetrix MAS5.0®, and hierarchical cluster analysis using Spotfire® (reviewed in Copland et al., 2003).
A primary goal of microarray analysis is to discover hidden patterns of differential expression within a large data field. Normal renal cortical and primary tumor tissue with no metastasis were collected from patients diagnosed with local disease. Normal tissue, primary tumor, and metastatic tissue were also collected from patients diagnosed with metastatic disease. Comparison of patient-matched normal and tumor tissue allowed for the discovery of changes in mRNA levels between normal and tumor tissue, as well as local and metastatic disease.
Heatmaps with two-way dendograms depicting genes specifically altered in tumor tissue as compared to normal renal cortex are shown in FIG. 1. FIG. 1A shows hierarchical clustering of genes expressed in normal renal cortex verses stage I conventional renal cell carcinoma. FIG. 1B shows hierarchical clustering of genes expressed in normal renal cortex verses stage II renal cell carcinoma. FIG. 1C shows hierarchical clustering of genes selected from a Venn analysis in which the chosen genes were expressed in common in both stage I and II at a 99% confidence level.
TGF-b1, TGF-a and adrenomedulin mRNA levels were up-regulated in all stages of renal cell carcinoma as compared to normal tissue counterparts (FIGS. 2-4), whereas TGF-b2 and TGF-b3 mRNA levels were not altered between normal and tumor matched samples (FIGS. 5-6).
Tumor suppressor gene Wilms Tumor 1 (WT1) was down-regulated in all stages of renal cell carcinoma (FIG. 7). A small percentage of tumor tissues demonstrated attenuated von Hippel Lindau mRNA levels when compared to matched normal tissue (FIG. 8). Calbindin mRNA was completely lost (FIG. 9) while MUC1 was greatly attenuated in stage I renal cell carcinoma (FIG. 10).
The present analysis identifies 278 genes that were up-regulated in stage I renal cell carcinoma, whereas 380 genes were up-regulated in stage II renal cell carcinoma.
Among these genes, 82 were up-regulated in both stages I and II renal cell carcinoma. One hundred fifty nine genes were down-regulated in stage I renal cell carcinoma, whereas 195 genes were down-regulated in stage II RCC. Among these genes, 82 were down-regulated in both stage I and II renal cell carcinoma.

Genes over-expressed and down-regulated in stage I renal cell carcinoma are listed in Table 1 and Table 2 respectively. Genes over-expressed and down-regulated in stage II renal cell carcinoma are listed in Table 3 and Table 4 respectively. Genes over-expressed in both stage I and II renal cell carcinoma are listed in Table 5. Genes down-regulated in both stage I and II renal cell carcinoma are listed in Table 6.

TABLE 1


Genes With Up-Regulated Expression In stage I Renal Cell Carcinoma

	Genbank ID	Gene Symbol

	NM004356.1	CD81
	NM002293.2	LAMC1
	NM000980.1	RPL18A
	AK002091.1	MGEA5
	NM005721.2	ACTR3
	NM002668.1	PLP2
	NM021038.1	MBNL
	AF070656.1	YME1L1
	NM021029.1	RPL36A
	NM002945.1	RPA1
	NM002480.1	PPP1R12A
	NM001349.1	DARS
	NM005496.1	SMC4L1
	AW163148	MARCKS
	NM002356.4	MARCKS
	M68956.1	MARCKS
	AI589086	LAPTM5
	NM006762.1	LAPTM5
	NM014267.1	SMAP
	NM000235.1	LIPA
	NM000176.1	NR3C1
	NM005737.2	ARL7
	NM005737.2	ARL7
	BC001051.1	ARL7
	NM006169.1	NNMT
	NM005862.1	STAG1
	AI356412	LYN
	NM002350.1	LYN
	BG107456	TRIP-Br2
	NM021913.1	AXL
	NM002194.2	INPP1
	NM019058.1	RTP801
	NM004079.1	CTSS
	NM001784.1	CD97
	AF151853.1	PREI3
	NM000491.2	C1QB
	BC000125.1	TGFB1
	NM004520.1	KIF2
	NM000321.1	RB1
	NM012262.2	HS2ST1
	NM000560.1	CD53
	NM005502.1	ABCA1
	AF285167.1	ABCA1
	BG170541	MET
	NM021642.1	FCGR2A
	BE967532	KIAA0220
	NM006526.1	ZNF217
	NM000570.1	FCGR3B
	N26005	PPP1R3C
	NM006153.1	NCK1
	NM001549.1	IFIT4
	NM003141.1	SSA1
	NM014705.1	KIAA0716
	NM005197.1	CHES1
	NM002907.1	RECQL
	U43328.1	CRTL1
	NM017925.1	FLJ20686
	NM006773.2	DDX18
	U20350.1	CX3CR1
	NM005761.1	PLXNC1
	NM004834.1	MAP4K4
	NM021644.1	HNRPH3
	NM006640.1	MSF
	NM004180.1	TANK
	NM002110.1	HCK
	NM030755.1	TXNDC
	NM030984.1	TBXAS1
	NM014350.1	GG2-1
	BC001312.1	P5
	U14990.1	RPS3
	D83043.1	HLA-B
	AI888672	NAP1L1
	BC002387.1	NAP1L1
	M60334.1	HLA-DRA
	AF161522.1	C3orf4
	BG256677	IFI16
	M26880.1	UBC
	U17496.1	PSMB8
	AF141347.1	TUBA3
	L01639.1	CXCR4
	NM005445.1	CSPG6
	AB030655.1	EFEMP2
	AF165520.1	APOBEC3C
	AF009670.1	ABCC3
	AF020314.1	CMRF-35H
	BC001606.1	NCF2
	BC005352.1	GG2-1
	AF281030.1	HRIHFB2122
	BC001052.1	RECQL
	L32610.1	HNRPH3
	M23612.1	RASA1
	AF109683.1	LAIR1
	BC002841.1	HSA9761
	D29640.1	IQGAP1
	L25259.1	CD86
	M60333.1	HLA-DRA
	U13698.1	CASP1
	U90940.1	FCGR2C
	M90685.1	HLA-G
	M90684.1	HLA-G
	M90686.1	HLA-G
	L22453.1	RPL3
	U01351.1	NR3C1
	U62824.1	HLA-C
	L07950.1	HLA-B
	AF348491.1	CXCR4
	NM003079.1	SMARCE1
	BE646386	EXO70
	AI972475	N/A
	AA195999	MAPK1
	AL049397.1	N/A
	BE895685	KIAA0853
	M82882.1	ELF1
	AB020633.1	KIAA0826
	AL031781	N/A
	AW148801	NAP1L1
	AB011118.1	KIAA0546
	AU145005	SP3
	N80918	CG018
	BF439472	ATP11A
	BE968801	RPL35A
	AI985751	NAP1L1
	AI735692	LST1
	AA995910	ALOX5
	M12679.1	HUMMHCW1A
	AL133053.1	FLJ23861
	X03348.1	NR3C1
	AC005339	N/A
	AK024836.1	HLA-C
	AC003999	SCAP2
	AJ224869	CXCR4
	AL022067	PRDM1
	AL110158.1	KIAA1078
	S81916.1	N/A
	M80469	N/A
	NM002860.1	PYCS
	NM020198.1	GK001
	NM016304.1	C15orf15
	AA102574	BAZ1A
	NM024844.1	PCNT1
	NM015938.1	CGI-07
	NM018200.1	HMG20A
	NM025235.1	TNKS2
	NM015991.1	C1QA
	NM016090.1	RBM7
	NM024554.1	PGBD5
	NM017718.1	FLJ20220
	NM017923.1	FLJ20668
	NM030921.1	DC42
	BC004470.1	ASC
	AK021413.1	LARS
	BF444916	FAD104
	BC004819.1	PLDN
	AF247167.1	AD031
	U39402.1	N/A
	BC006112.1	DKFZP434B195
	BG388615	N/A
	AB033007.1	KIAA1181
	BG250721	N/A
	AK024221.1	C40
	BF477658	N/A
	BG251556	KIAA1949
	AB033091.1	KIAA1265
	AK024350.1	AMOTL1
	NM018440.1	PAG
	AW500180	N/A
	BF209337	MGC4677
	AI709406	N/A
	AI806905	N/A
	AI392933	FLJ36090
	AI142096	N/A
	AL137430.1	N/A
	AV724266	FLJ20093
	BF589359	N/A
	AW084125	CAPZA1
	N20927	RAP2B
	AI627666	LOC115548
	AV726322	N/A
	AI697657	LANPL
	BF002625	N/A
	BF439533	N/A
	AW026543	N/A
	AI092770	N/A
	NM020679.1	AD023
	AK024855.1	CTSS
	AK000119.1	N/A
	AW977527	PRDM1
	BE671060	N/A
	AL037450	N/A
	AI401535	N/A
	AV683852	N/A
	BF055144	N/A
	AA352113	N/A
	BF056209	N/A
	X60592	TNFRSF5

TABLE 2


Genes With Down-Regulated Expression
In stage I Renal Cell Carcinoma

	Genbank ID	Gene Symbol

	L38487	ESRRA
	NM004415.1	DSP
	NM005327.1	HADHSC
	NM003321.1	TUFM
	NM002084.2	GPX3
	AI983043	N/A
	NM006066.1	AKR1A1
	NM006384.2	CIB1
	NM001685.1	ATP5J
	NM014652.1	IMP13
	NM013410.1	AK3
	NM016725.1	FOLR1
	NM021151.1	CROT
	NM005951.1	MT1H
	NM005952.1	MT1X
	AL080102.1	N/A
	BC000931.2	ATP5C1
	BC005398.1	DKFZP566D193
	D87292.1	TST
	AU151428	IDH2
	BC000109.1	ILVBL
	AF333388.1	N/A
	NM005953.1	MT2A
	BF217861	N/A
	AA594937	COBL
	AW052179	COL4A5
	AI884867	LOC155066
	BF246115	N/A
	AW028110	KIAA0500
	AW242315	N/A
	AW080549	FUT3
	AW149846	GPX3
	AK024386.1	GRHPR
	AL109716.2	N/A
	AK026411.1	ALDOB
	M10943	N/A
	AW088547	N/A
	NM018049.1	GNRPX
	NM017900.1	AKIP
	NM006548.1	IMP-2
	NM025135.1	KIAA1695
	NM016458.2	LOC51236
	NM022128.1	RBSK
	NM015974.1	CRYL1
	NM013333.1	EPN1
	AA133341	C14orf87
	AF226732.1	NPD007
	AF265439.1	MRPS15
	AI743534	DKFZP564B1162
	AB042647.1	B29
	AL522667	ORF1-FL49
	BG255416	KIAA0114
	AF308301.1	MRPS26
	BE408081	N/A
	AL521634	FLJ32452
	BF203664	MGC14288
	BE645551	MGC39329
	AW193698	TGFBR3
	BF540829	N/A
	W72455	FLJ25476
	AI457453	N/A
	BF056892	N/A
	AI038402	N/A
	AI051046	MGC4614
	AI659456	N/A
	AW664964	N/A
	AI631895	SGK2
	AI263078	FLJ31168
	BF057634	HOXD8
	AA746038	GPR110
	AA442776	N/A
	AI913600	N/A
	AW771908	N/A
	AI807887	N/A
	AW102941	N/A
	AW024656	N/A
	AB002342	PRKWNK1

TABLE 3


Genes With Up-Regulated Expression In stage II Renal Cell Carcinoma

	Genbank ID	Gene Symbol

	NM006096.1	NDRG1
	NM006098.1	GNB2L1
	NM001780.1	CD63
	NM003118.1	SPARC
	NM000291.1	PGK1
	NM003870.1	IQGAP1
	AB032261.1	SCD
	NM002629.1	PGAM1
	NM003564.1	TAGLN2
	NM000310.1	PPT1
	NM003405.1	YWHAH
	U82164.1	MIC2
	NM002305.2	LGALS1
	NM001096.1	ACLY
	NM002121.1	HLA-DPB1
	NM021038.1	MBNL
	NM003651.1	CSDA
	AV685920	CAPZA2
	NM002654.1	PKM2
	NM001175.1	ARHGDIB
	BC000182.1	ANXA4
	NM001153.2	ANXA4
	NM001975.1	ENO2
	NM006435.1	IFITM2
	NM001387.1	DPYSL3
	BG398414	RPA1
	NM004039.1	ANXA2
	NM005534.1	IFNGR2
	AL136877.1	SMC4L1
	NM014876.1	KIAA0063
	NM024830.1	FLJ12443
	NM005505.1	SCARB1
	NM003025.1	SH3GL1
	NM013285.1	HUMAUANTIG
	NM005720.1	ARPC1B
	AW157070	EGFR
	NM002835.1	PTPN12
	NM004428.1	EFNA1
	AW006290	SUDD
	NM002053.1	GBP1
	NM000089.1	COL1A2
	NM021105.1	PLSCR1
	NM002467.1	MYC
	NM001284.1	AP3S1
	AI825926	PLSCR1
	NM014736.1	KIAA0101
	AF161461.1	LEPROTL1
	NM014873.1	KIAA0205
	AI005043	N/A
	NM000416.1	IFNGR1
	NM004172.1	SLC1A3
	NM004207.1	SLC16A3
	AI761561	HK2
	Y09216.1	N/A
	NM002922.1	RGS1
	NM005990.1	STK10
	NM014863.1	GALNAC4S-6ST
	NM014737.1	RASSF2
	NM000418.1	IL4R
	BC000658.1	STC2
	NM003751.1	EIF3S9
	NM002339.1	LSP1
	NM004604.1	STX4A
	NM006404.1	PROCR
	AF275945.1	EVA1
	NM004221.1	NK4
	NM004556.1	NFKBIE
	NM004688.1	NMI
	NM003332.1	TYROBP
	NM015136.1	STAB1
	NM006019.1	TCIRG1
	NM004877.1	GMFG
	NM002317.1	LOX
	NM025201.1	PP1628
	NM014800.1	ELMO1
	L41944.1	IFNAR2
	NM007268.1	Z39IG
	NM006994.2	BTN3A3
	NM014791.1	MELK
	NM014882.1	KIAA0053
	NM003864.1	SAP30
	NM001558.1	IL10RA
	NM003264.1	TLR2
	NM014221.1	MTCP1
	AV756141	CSF2RB
	AI123251	LCP2
	NM006433.2	GNLY
	NM000861.2	HRH1
	NM001870.1	CPA3
	NM003586.1	DOC2A
	NM004271.1	MD-1
	NM014932.1	NLGN1
	NM014947.1	KIAA1041
	NM000647.2	CCR2
	NM002562.1	P2RX7
	NM006058.1	TNIP1
	NM013447.1	EMR2
	NM013416.1	NCF4
	NM001776.1	ENTPD1
	NM020037.1	ABCC3
	NM006135.1	CAPZA1
	NM007036.2	ESM1
	AF034607.1	CLIC1
	BC000915.1	PDLIM1
	AL162068.1	NAP1L1
	NM006947.1	SRP72
	L12387.1	SRI
	AF141349.1	N/A
	AF263293.1	SH3GLB1
	BC000389.1	TM4SF7
	AF007162.1	CRYAB
	D38616.1	PHKA2
	AV717590	ENTPD1
	U87967.1	ENTPD1
	H23979	MOX2
	AF063591.1	MOX2
	BC005254.1	CLECSF2
	BC000893.1	H2BFT
	L22431.1	VLDLR
	AI741056	SELPLG
	AF084462.1	RIT1
	U62027.1	C3AR1
	M87507.1	CASP1
	J04132.1	CD3Z
	M31159.1	IGFBP3
	AF257318.1	SH3GLB1
	BC001388.1	ANXA2
	AF130095.1	FN1
	AF022375.1	VEGF
	AF091352.1	VEGF
	AB035482.1	ICB-1
	Z24727.1	TPM1
	M19267.1	TPM1
	U13700.1	CASP1
	M27281.1	VEGF
	BC005838.1	N/A
	BC005858.1	FN1
	BC005926.1	EVI2B
	BE513104	YARS
	AU147399	CAV1
	AK023154.1	HN1L
	AK021757.1	KIAA0648
	H95344	VEGF
	AB023231.1	FNBP4
	AL523076	N/A
	NM030666.1	SERPINB1
	AB018289.1	KIAA0746
	AW043713	SULF1
	BE880591	EP400
	AU158495	NOTCH2
	BE965029	N/A
	AL564683	CEBPB
	AA349595	RAB6IP1
	AI809341	PTPRC
	AW205215	KIAA0286
	BE349017	HA-1
	AF070592.1	HSKM-B
	AI769685	CARS
	AI935123	LOC113146
	BG255188	N/A
	AI088622	PRKCDBP
	BE222709	N/A
	AW007573	DKFZP586L151
	BG332462	N/A
	AI862658	FEM1C
	AI934469	KIAA0779
	AB018345.1	KIAA0802
	W87466	LOC92689
	BE908217	ANXA2
	NM005615.1	RNASE6
	BE300252	K-ALPHA-1
	BF740152	MYO1F
	AV711904	LYZ
	AW072388	N/A
	AW190316	SHMT2
	NM005412.1	SHMT2
	NM006417.1	IFI44
	AL008730	C6orf4
	L16895	LOC114990
	Z21533.1	HHEX
	AA807529	MCM5
	AK026737.1	FN1
	X14355.1	N/A
	AK025608.1	KIAA0930
	AF183421.1	RAB31
	NM002695.1	POLR2E
	AF288391.1	C1orf24
	NM003730.2	RNASE6PL
	NM016359.1	ANKT
	NM014164.2	FXYD5
	NM022736.1	FLJ14153
	NM021158.1	C20orf97
	NM017792.1	FLJ20373
	NM020142.1	LOC56901
	NM016448.1	RAMP
	NM005767.1	P2Y5
	NM020169.1	LXN
	NM022834.1	FLJ22215
	NM018460.1	BM046
	NM024629.1	FLJ23468
	NM018641.1	C4S-2
	NM018295.1	FLJ11000
	NM024576.1	FLJ21079
	NM016582.1	PHT2
	NM003116.1	SPAG4
	NM018454.1	ANKT
	NM018099.1	FLJ10462
	NM007072.1	HHLA2
	NM022445.1	TPK1
	AW173623	TDE1
	AB044088.1	BHLHB3
	AF043244.1	NOL3
	AF133207.1	H11
	AF313468.1	CLECSF12
	AA191576	NPM1
	AI765383	KIAA1466
	BC003654.1	SLC27A3
	W60806	N/A
	AI335263	NETO2
	AI378406	EGLN3
	BC005400.1	FKSG14
	AI761520	CENTA2
	BC000771.1	TPM3
	BC000190.1	HSPC216
	BC002776.1	SEMA5B
	AF132203.1	SCD
	BC006107.1	ARHGAP9
	AK024263.1	N/A
	AK024846.1	SET7
	BE878463	N/A
	AW304786	PTR4
	AK022955.1	DKFZp762L0311
	BF001267	N/A
	AL558987	N/A
	AA577672	LOC151636
	BE620734	ZAK
	AI937446	N/A
	H99792	N/A
	BE966748	N/A
	AI659418	MGC21854
	AI990891	DKFZp761K2222
	AA827892	N/A
	AL135264	N/A
	AI375753	N/A
	AA573502	TAP2
	BG387557	CASP2
	AA554833	MAP1B
	AK026764.1	N/A
	AU146532	PDK1
	BE348597	N/A
	AL577758	LOC133957
	AI133452	FGG
	AU157224	N/A
	AI742057	N/A
	BE500942	N/A
	N25631	RFXANK
	AU145366	N/A
	AW270037	KIAA0779
	BF526978	N/A
	AW182575	N/A
	BF339831	MGC13114
	AI056992	N/A
	BE222668	N/A
	BG165011	N/A
	AI188445	MGC14289
	BE551416	HAK
	AI972498	a1/3GTP
	AW662189	N/A
	AA142842	N/A
	BF939473	N/A
	AI681260	N/A
	AA551090	AP1S2
	AA045175	MS4A6A
	W05495	N/A
	AI093231	N/A
	AI565054	N/A
	AL553774	N/A
	AK023470.1	MGC15875
	AL157377	ENPP3
	AL139109	TEX11
	AK025631.1	POLH
	AI873425	N/A
	AI769269	N/A
	AI935334	N/A
	BF437747	SAMHD1
	AW300953	N/A
	H37811	N/A
	AA603344	SAMHD1
	AA742310	N/A
	AI248208	FLJ25804
	AI962367	ECGF1
	BF541967	N/A
	AI686890	N/A
	AI936034	ITGA4
	U88964	ISG20
	AJ243797	TREX1
	D29642	KIAA0053
	D87433	STAB1
	AI129310	FLJ21562

TABLE 4


Genes With Down-Regulated Expression
In stage II Renal Cell Carcinoma

	Genbank ID	Gene Symbol

	NM012248.1	SPS2
	NM002300.1	LDHB
	BC000306.1	HADHSC
	NM001640.2	APEH
	NM005875.1	GC20
	NM003365.1	UQCRC1
	BF031714	HYA22
	NM005808.1	HYA22
	AF113129.1	ATP6V1A1
	NM002402.1	MEST
	NM006844.1	ILVBL
	NM004636.1	SEMA3B
	NM002496.1	NDUFS8
	NM006556.1	PMVK
	NM004255.1	COX5A
	NM002225.2	IVD
	NM004524.1	LLGL2
	AI950380	BCL7A
	AB020707.1	WASF3
	NM000481.1	AMT
	NM012317.1	LDOC1
	NM006456.1	STHM
	NM006614.1	CHL1
	NM015393.1	DKFZP564O0823
	AV729634	DNAJC6
	NM002628.1	PFN2
	NM003500.1	ACOX2
	NM002655.1	PLAG1
	NM004393.1	DAG1
	NM003026.1	SH3GL2
	NM002010.1	FGF9
	NM014033.1	DKFZP586A0522
	NM004868.1	GPSN2
	BC000649.1	UQCRFS1
	S69189.1	ACOX1
	AF153330.1	SLC19A2
	AF094518.1	ESRRG
	M55575.1	BCKDHB
	AB019695.1	TXNRD2
	M61900.1	PTGDS
	BF967998	N/A
	BF967998	N/A
	AL526243	KIAA0446
	NM000532.1	PCCB
	BE042354	LDHB
	AI587323	ATP5A1
	AW195882	ATPW
	H71135	ADH6
	AV659180	ALDOB
	AK027006.1	TNRC9
	AV693216	PLXNB1
	BG398937	N/A
	NM002489.1	NDUFA4
	NM003849.1	SUCLG1
	NM014019.1	HSPC009
	NM024952.1	FLJ20950
	NM014185.1	MOG1
	NM018013.1	FLJ10159
	NM018373.1	SYNJ2BP
	NM014067.2	LRP16
	NM013261.1	PPARGC1
	NM021963.1	NAP1L2
	NM018658.1	KCNJ16
	NM014553.1	LBP-9
	AF112204.1	ATP6V1H
	AU145941	CDC14B
	AF061264.1	MGC4825
	BF941492	FLJ10496
	AI984229	HSPC121
	N71923	FLRT3
	BC005050.1	NICN1
	AF172327.1	N/A
	AF356515.1	HINT2
	BE620739	RHOBTB3
	BF435123	N/A
	AW149498	BTBD6
	BE044480	MGC32124
	BF382393	N/A
	AV751731	PNKP
	U55984	N/A
	BF059512	DNER
	AK025934.1	Evi1
	AL036088	SEMA6D
	BE964222	FLJ38482
	AW290940	N/A
	AL545998	N/A
	AW274874	N/A
	AI709389	N/A
	BF224092	MGC15854
	AU145805	N/A
	AW079843	MGC33338
	AW138815	N/A
	AW242286	N/A
	AW025023	N/A
	BE672659	N/A
	AW024437	LOC118491
	AW195353	N/A
	BE044193	N/A
	AI493303	FLJ31709
	AI636080	N/A
	BF509031	ATP6V1G3
	AW242920	N/A
	BF002046	ANGPTL1
	BF130943	N/A
	AW452631	N/A
	AI792937	N/A
	AI810572	N/A
	BG165743	LOC112817
	AW466989	N/A
	R48991	N/A
	BF029215	MSI2
	D21851	LARS2
	Z83838	ARHGAP8

TABLE 5


Genes With Up-Regulated Expression
In Both stage I And stage II Renal Cell Carcinoma

	Genbank ID	Gene Symbol

	NM005566.1	LDHA
	NM000291.1	PGK1
	NM001219.2	CALU
	NM002966.1	S100A10
	NM000034.1	ALDOA
	NM002627.1	PFKP
	NM006082.1	K-ALPHA-1
	AI922599	VIM
	NM020474.2	GALNT1
	NM006406.1	PRDX4
	NM015344.1	LEPROTL1
	NM014755.1	TRIP-Br2
	AI796269	NBS1
	NM005783.1	APACD
	BF197655	N/A
	NM001233.1	CAV2
	NM002845.1	PTPRM
	NM014302.1	SEC61G
	U47924	CD4
	NM004106.1	FCER1G
	NM015474.1	SAMHD1
	NM004915.2	ABCG1
	NM002432.1	MNDA
	NM005565.2	LCP2
	NM005531.1	IFI16
	NM005849.1	IGSF6
	NM002189.1	IL15RA
	NM004353.1	SERPINH1
	NM014812.1	KIAA0470
	AF208043.1	IFI16
	BC002654.1	TUBB-5
	BC006379.1	K-ALPHA-1
	BC006481.1	K-ALPHA-1
	AF000426.1	LST1
	AF000424.1	LST1
	BG500301	ITGB1
	AL516350	ARPC5
	M27487.1	HLA-DPA1
	M27487.1	HLA-DPA1
	AW517686	ATP2B4
	AL581768	K-ALPHA-1
	AA524505	TSGA
	Z78330	ACTR3
	Z78330	ACTR3
	BG532690	ITGA4
	AW005535	RAP2B
	NM007161.1	LST1
	AK026577.1	ALDOA
	AI091079	SHC1
	AV713720	LST1
	NM021103.1	TMSB10
	NM016337.1	RNB6
	NM013260.1	HCNGP
	NM021199.1	SQRDL
	NM018149.1	FLJ10587
	NM016951.2	CKLF1
	NM017760.1	FLJ20311
	NM022349.1	MS4A6A
	NM023003.1	TM6SF1
	NM016184.1	CLECSF6
	NM031284.1	DKFZP434B195
	BC002342.1	CORO1C
	AA775177	PTPRE
	AL162070.1	CORO1C
	AF253977.1	MS4A6A
	AF237908.1	MS4A6A
	W03103	DDEF1
	AK022888.1	FENS-1
	AI141784	N/A
	AB033038.1	FLJ10392
	AI184968	C1QG
	AL161725	FLJ00026
	NM018440.1	PAG
	AL553942	FLJ31951
	AI394438	N/A
	T64884	N/A
	T64884	N/A
	AW511319	N/A
	AI640834	RA-GEF-2
	AI655467	N/A
	AL161725	FLJ00026
	T92908	N/A

TABLE 6


Genes With Down-Regulated Expression
In Both stage I And stage II Renal Cell Carcinoma

	Genbank ID	Gene Symbol

	NM004092.2	ECHS1
	NM000270.1	NP
	NM002354.1	TACSTD1
	AF017987.1	SFRP1
	NM003012.2	SFRP1
	NM000666.1	ACY1
	NM000191.1	HMGCL
	NM015254.1	KIF13B
	NM000140.1	FECH
	U75667.1	ARG2
	NM000196.1	HSD11B2
	NM014636.1	RALGPS1A
	NM001441.1	FAAH
	NM005978.2	S100A2
	NM001678.1	ATP1B2
	NM001099.2	ACPP
	NM014731.1	ProSAPiP1
	BF343007	N/A
	NM000035.1	ALDOB
	NM005950.1	MT1G
	NM002371.2	MAL
	NM006984.1	CLDN10
	NM002567.1	PBP
	NM000019.1	ACAT1
	NM001692.1	ATP6V1B1
	X77737.1	N/A
	NM006226.1	PLCL1
	NM000893.1	KNG
	NM000412.2	HRG
	NM001963.2	EGF
	NM003361.1	UMOD
	NM000050.1	ASS
	NM001438.1	ESRRG
	BC002449.1	FLJ13612
	J02639.1	SERPINA5
	BC002571.1	DKFZP564O243
	U03884.1	KCNJ1
	AF173154.1	HYAL1
	AF130103.1	PBP
	AL117618.1	PDHB
	AF063606.1	N/A
	BC005314.1	N/A
	BF686267	PBP
	AI742553	PRKWNK1
	D83782.1	SCAP
	AB029031.1	TBC1D1
	AK025432.1	KIAA0564
	AL117643.1	N/A
	AW772192	N/A
	NM003944.1	SELENBP1
	AL049977.1	CLDN8
	AK023937.1	THEA
	AK025084.1	TNRC9
	X03363.1	ERBB2
	AK026411.1	ALDOB
	NM016026.1	RDH11
	NM016286.1	DCXR
	NM019027.1	FLJ20273
	BG338251	RAB7L1
	NM006113.2	VAV3
	NM018075.1	FLJ10375
	NM013271.1	PCSK1N
	NM017586.1	C9orf7
	NM016321.1	RHCG
	NM025247.1	MGC5601
	NM020632.1	ATP6V0A4
	AI632015	SLC12A1
	NM000701.1	ATP1A1
	NM031305.1	DKFZP564B1162
	AF130089.1	ALDH6A1
	AK025651.1	N/A
	W45551	MMP24
	W67995	FXC1
	AL136566.1	IBA2
	AF105366.1	SLC12A6
	AF284225.1	DMRT2
	AA191708	N/A
	AL355708.1	N/A
	BE783949	FLJ10101
	AL529672	N/A
	AL568674	MYBBP1A
	AU147564	CLMN
	AK000208.1	N/A
	AB051536.1	FLJ14957
	AI569747	TFDP2
	AK025562.1	N/A
	AI660243	TMPRSS2
	N50413	N/A
	AI347918	N/A
	AL536553	GRP58
	BC000282.1	LOC89894
	BF106962	FAM3B
	AI051248	FLJ32115
	AI928242	N/A
	BG236006	N/A
	AI653107	N/A
	AI824037	FLJ25461
	R61322	N/A
	AW071744	KCNJ10
	BF059276	N/A
	AI379517	N/A
	AA058832	MGC33926
	AW274034	N/A
	AI580268	NUDT6
	AI761947	DKFZP564B1162
	AI793201	N/A
	AK025898.1	N/A
	AB046810.1	C20orf23
	AK024204.1	N/A
	BF594722	N/A
	R88990	N/A
	N73742	N/A
	AI697028	FLJ90165
	BF590528	N/A
	AI733359	N/A
	H20179	N/A
	AA991551	MGC14839
	AI758950	SLC26A7
	AA911561	N/A
	AI769774	N/A
	AA669135	N/A
	AW136060	SLC13A2
	AI733593	N/A
	BF739841	N/A
	AA600175	N/A
	BF477980	N/A
	AI934557	N/A
	BE326951	KNG
	AI632567	N/A
	BE300882	N/A
	BE855713	N/A
	AA485440	DBP
	AA915989	FLJ10743
	AA085764	SIGIRR

EXAMPLE 6

Loss of TGF-b Receptor Expression Demonstrated by Gene Array and Real-Time PCR in Renal Cell Carcinoma
Expression of type I TGF-b receptor (TBR1), type II TGF-b receptor (TBR2), and type III TGF-b receptor (TBR3) mRNA were compared in normal renal tissue, primary renal cell carcinoma without metastasis, primary lesions of metastatic renal cell carcinoma, and metastatic lesions. A summary of gene array analysis was presented as average signal intensities in FIG. 11A (mean±standard error). The signal intensity for TBR1 (cross-hatched bars) was relatively low, although TBR1 was scored as ‘Present’ in all samples. No significant changes in TBR1 expression were observed. TBR2 (gray bars) was abundantly expressed in normal epithelium and in primary lesions of nonmetastatic renal cell carcinoma. TBR2 was significantly reduced in primary lesions with metastatic disease (P<0.028 by ANOVA). TBR2 was even more reduced in metastatic lesions. TBR3 expression was high in normal epithelium, but was significantly reduced in each of the five primary tumors with nonmetastatic disease (black bars). TBR3 expression was also reduced in primary tumors with metastatic lesions and in metastatic lesions themselves.
These expression patterns were confirmed by real-time PCR (Taqman®) in the 10 patients used for gene array analysis. Means and standard errors for individual samples are shown in FIG. 11B. All data were normalized to 18S rRNA and calibrated to target abundance in the paired normal tissues. TBR1 mRNA abundance did not change (cross-hatched bars), consistent with the gene chip data. TBR2 (gray bars) was not reduced in primary tumors without metastases, whereas TBR2 was significantly reduced in primary tumors with metastatic disease and in metastatic lesions. TBR3 was reduced in all tumors (black bars).
The investigators have subsequently completed real-time PCR analysis of TBR1, TBR2, and TBR3 expression in 16 primary tumors without metastases (plus paired normal epithelium) and nine samples of primary tumors with metastatic disease, paired metastatic lesions, and paired normal tissue. The data were consistent with those shown for the samples analyzed in FIG. 1A. TBR3 expression was significantly reduced in all tumors; whereas TBR2 expression was reduced in only 1/16 primary tumors without metastatic lesions, but was reduced in primary tumors with metastatic lesions (8/9). These data show that loss of TBR3 is an early event in renal cell carcinoma, strongly suggesting that TBR3 plays a critical role in renal cell carcinoma carcinogenesis.
The loss of TBR3 mRNA expression was also correlated with TNM scores (T, histological score; N, lymph node number; M, number of organ metastases) from patient samples (data not shown). TBR3 mRNA expression was suppressed in the earliest stage, stage I, and was found to be suppressed in all tumor stages (1-IV). In addition, loss of TBR2 in the primary tumor is significantly associated with acquisition of the metastatic phenotype and clinically manifests as metastatic progression.

EXAMPLE 7

Attenuation of TGF-b-Mediated Signal Transduction in Human Renal Cell Carcinoma
Decreased type III TGF-b receptor (TBR3) mRNA expression in all tumors was associated with failure to detect TBR3 protein by immunohistochemistry (FIG. 12). Type II TGF-b receptor (TBR2) protein was detected in localized tumor (primary, no mets), but was not detectable in primary tumors with metastatic disease or in corresponding metastatic lesions. Type I TGF-b receptor (TBR1) protein was detected in normal tissue and in all tumor samples.

The investigators hypothesized that these losses seen in TGF-b receptor expression would manifest as an attenuation of TGF-b-mediated signal transduction, and would significantly alter the expression of TGF-b-regulated genes. From the gene array data disclosed above, 13 known TGF-b/Smad-regulated genes were down-regulated in renal cell carcinoma (Table 7). Using mRNA from 35 patient-matched samples, the investigators verified loss of expression of three of these genes by comparing matched normal and tumor tissue. Real-time PCR was used to measure the expression of Collagen IV type 6, fibulin-5, and connective-tissue growth factor (CTGF). Collagen IV type 6 (gray bars) is an extracellular matrix protein that plays a critical role in the regulation of membrane integrity and cell signaling. Fibulin-5 is a recently discovered TGF-b-regulated gene, which has tumor suppressor activity. Fibulin-5 is an extracellular matrix protein that is believed to signal through interaction with integrins. CTGF is a secreted protein involved in angiogenesis, skeletogenesis, and wound healing. CTGF enhances TGF-b1 binding to TBR2, and CTGF and TGF-b collaborate to regulate the expression of extracellular matrix proteins during renal fibrosis. As summarized graphically in FIG. 13, all the evaluated TGF-b-regulated genes were down-regulated in early tumor stages, suggesting that renal cell carcinoma undergoes loss of TGF-b responsiveness at an early stage. These data indicate that this loss of TGF-b sensitivity is due, primarily, to loss of type III TGF-b receptor (TBR3) in early tumor development and further loss of sensitivity in metastatic disease is mediated through subsequent loss of type II TGF-b receptor (TBR2).

TABLE 7


Known TGF-b-Regulated Genes Found To Be Down-Regulated
In Localized Tumors By Gene Array Analysis

GenBank #	Gene name	Fold attenuation

S81439	TGFb-induced early growth factor	2.5
	(TIEG)
AF093118	Fibulin	5	4.0
U42408	Ladinin	1	15.4
U01244	Fibulin	1	4.8
J05257	Dipeptidase	1	7.7
D21337	Collagen, type IV, a6	3.6
X80031	Collagen, type IV, a3	2.4
M64108	Collagen, type XIV, a1	3.2
M98399	Collagen, type I receptor	4.2
L23808	Matrix metallo-proteinase 12	3.7
M35999	Integrin, b3	2.5
AI304854	p27^Kip1	2.1
J05581	Mucin	1	6.5

Data were analysed by a combination of two-dimensional ANOVA, Affymetrix MAS5.0, and hierarchical cluster analysis using Spotfire to identify genes that are down-regulated in local tumors versus that of normal renal cortex tissue.

EXAMPLE 8

TGF-b Receptor Expression in Renal Cell Carcinoma Cell Lines
Human renal cell carcinoma cell lines were identified that recapitulate the clinical observations of TGF-b receptor biology described above. UMRC6 cells were derived from a clinically localized human renal cell carcinoma (Grossman et al., 1985). As shown in FIG. 14A, UMRC6 cells express type II TGF-b receptor (TBR2) mRNA, but not type III TGF-b receptor (TBR3). Immunohistochemical analysis (FIG. 14B) confirms the presence of TBR2 protein and the absence of TBR3 expression. UMRC3 cells were derived from the primary tumor of a patient with metastatic renal cell carcinoma. This highly aggressive cell line lacks detectable TBR2 and TBR3 mRNA (FIG. 14A) and protein (FIG. 14B).
In addition to these relevant laboratory models, normal renal epithelial (NRE) tissue was harvested from nephrectomy specimens and established as primary cultures (Trifillis, 1999). As shown in FIGS. 14A and 14B, these primary cultures of NRE expressed TBR3, TBR2, and TBR1 mRNA and protein in vitro. NRE cells can be grown in culture for 10 passages and were easily isolated and characterized. NRE cells were characterized for cytokeratin expression and tubule-specific gene expression, for example, megalin (data not shown). Thus, there are relevant cell models in which TBR2 and TBR3 expression can be manipulated to examine the impact of TGF-b receptor biology on the carcinogenesis and progression of human renal cell carcinoma in vitro.

EXAMPLE 9

TGF-b Activity in Renal Cell Carcinoma Cell Lines
It is well known that TGF-b1 inhibits cell proliferation in epithelial cells. The present example demonstrates the effects of TGF-b on renal tumor cell proliferation.
DNA content of cells was used as a measure of cell proliferation. Cells were plated at 20,000 cells/well in 12-well plates. Cells were grown in 10% FBS:DMEM:penicillin:streptomycin. The following day, media were exchanged with appropriate treatment added to the media. On day 3 of treatment, cells were analyzed for DNA content using Hoechst reagent. DNA standard was used to correlate DNA content per well.
As shown in FIG. 15A (squares), TGF-b1 inhibited the proliferation of normal renal epithelial cells in culture. URMC3 cells expressed neither type II or type III TGF-b receptors and, not surprisingly, were resistant to the inhibitory effects of TGF-b on cell proliferation (triangles, FIG. 15A). UMRC6 cells expressed type II but not type III TGF-b receptors, and were partially resistant to TGF-b1 (circles, FIG. 15A).
TGF-b transcriptional activity was also measured in the above cell models using transient transfection of the 3TP/lux reporter, which contains an AP-1/Smad3 response element from the PAI-1 promoter. This luciferase reporter construct demonstrates increased transcriptional activity in response to exogenous TGF-b-mediated signal transduction. 3TP/lux was transiently transfected along with SV/renilla luciferase (Promega) into cells using fugene (Roche) as the transfection agent. Cells were treated with or without TGF-b1 24 h after transfection and luciferase activity (Promega Luciferase Assay system and Lumat luminometer) was determined 24 h after TGF-b treatment. Firefly luciferase activity was normalized using the ratio of firefly luciferase/renilla luciferase. As shown in FIG. 15B, normal renal epithelial cells were highly responsive to 2 ng/ml (80 pM) of TGF-b1. UMRC6 cells demonstrated significantly less luciferase activity in response to TGF-b1, and UMRC3 cells were entirely unresponsive.

EXAMPLE 10

Recapitulation of TGF-b Signaling Through Reintroduction of TGF-b Receptor Expression into Renal Cell Carcinoma
To test whether reintroduction of TGF-b receptor expression would result in re-establishment of TGF-b signal transduction and reacquisition of TGF-b cellular sensitivity, UMRC3 cells were engineered to express stably either type II TGF-b receptor (+TBR2) alone or type II plus type III TGF-b receptor (+TBR2+TBR3).
Plasmid construction and transfection were described as follows. The complete coding sequences for human type II TGF-b receptor (TBR2) was cloned into the EcoRI/XbaI site of pcDNA3/FLAG. The expression vector was stably transfected into UMRC3 cells using fugene as DNA carrier and genticin as selection antibiotic (Sigma, 1 mg/ml). Ten clones (UMRC3/TBR2) were selected and verified for TBR 2 mRNA and protein expression such as Western analysis using the FLAG antibody (data not shown). From these cell clones, one was to be selected that had equivalent protein expression of TBR2 to that of normal renal epithelial (NRE) and UMRC6 cells.
The type III TGF-b receptor (TBR3) coding sequence was PCR amplified from a plasmid expressing wild-type TBR3 in pSV7d (a gift from Dr C—H Heldin). TBR3 was then cloned into the EcoRI site of pcDNA4/TO/myc-His® (InVitrogen) in the sense and antisense (negative control) orientation. The orientation and sequence of TBR3 was verified. The antisense TBR3 (As TBR3) vector was used as a control. TBR3/pcDNA4/TO/myc-His and As TBR3/pcDNA4/TO/myc-His vectors were stably transfected into UMRC3/TBR2 cells. A clone was selected that demonstrated an equivalent expression of TBR3 mRNA to that of normal renal epithelial cells. As a control for UMRC3+TBR2 and UMRC3+TBR2+TBR3, wild-type UMRC3 were stably transfected with both pcDNA/FLAG and pcDNA4/TO/myc-His vectors.
As shown in FIG. 16A, stable transfection of type II TGF-b receptor (TBR2) alone or type II plus type III TGF-b receptor (TBR2+TBR3) resulted in detectable levels of mRNA for each receptor on RT-PCR analysis. On examining the in vitro growth kinetics of these re-engineered cells, it was noted that reintroduction of TBR2 resulted in a twofold reduction in cell proliferation and reintroduction of both TBR2 and TBR3 resulted in a fourfold reduction in cell proliferation with the addition of exogenous TGF-b 1.
The investigators then examined TGF-b-mediated transcriptional activity as a consequence of TGF-b receptor re-expression. As shown in FIG. 16B, reintroduction of TBR2 partially restored transcriptional responsiveness, as evidenced by a 5.6-fold increase in 3TP/lux activity after addition of TGF-b1. Reintroduction of both TBR2 and TBR3 into UMRC3 cells resulted in 17.5-fold increase in 3TP/lux activity after addition of TGF-b1.
To demonstrate reestablishment of TGF-b-regulated gene expression, collagen IV type 6 mRNA expression was examined by real-time PCR in these re-engineered cell lines in the presence of TGF-b1. As shown in FIG. 16C, reexpression of TBR2 in UMRC3 cells results in a sevenfold increase in collagen IV type 6 mRNA levels over that of UMRC3 controls, while reintroduction of both TBR2 and TBR3 enhanced collagen IV type 6 mRNA expression 11-fold. These data are consistent with a number of published reports that indicate expression of TBR3 is essential for full TGF-b responsiveness.
UMRC3 cells have been shown to be tumorigenic in athymic nude mice (Grossman et al., 1985). Anchorage independent growth in soft agar is a well-established in vitro correlate of in vivo tumorigenicity. Colonies formation in soft agar was determined as follows. UMRC3 (pcDNA/FLAG and pcDNA4/T0/myc-His empty vectors), UMRC3+TBR2, or UMRC3+TBR2+TBR3 cells were plated at 1000 cells/60 mm dish in an agarose/FBS/media sandwich in the presence of 2 ng/ml TGF-b. No selection antibodies were added to the agarose media mixture. The cells were incubated for 45 days to insure that no colony formation would occur. Cells were then stained with 0.005% Crystal Violet, photographed, and assessed for number and size of colonies.
As shown in FIG. 16D, UMRC3 cells demonstrated anchorage independent growth in soft agar. Reintroduction of TBR2 into UMRC3 cells significantly decreased the number and size of colonies that formed in soft agar. Reintroduction of both TBR2 and TBR3 completely abrogated the ability of UMRC3 cells to form colonies in soft agar, even after 45 days in culture. These data demonstrate that reintroduction of TBR2 resensitizes UMRC3 cells to the effects of exogenous TGF-b through reacquisition of TGF-b signal transduction. More interestingly, however, reintroduction of TBR3 in the presence of TBR2 into UMRC3 cells significantly enhanced TGF-b-regulated gene transcription, growth inhibition, and loss of anchorage-independent growth over that seen with reintroduction of TBR2 alone. These data clearly show that renal cell carcinoma cells are TGF-b resistant. Loss of TBR3 expression occurs early and appears to be associated with a relatively less aggressive state that is partially TGF-b responsive. Loss of TBR2 results in frank TGF-b resistance and is associated with acquisition of a more aggressive phenotype.
FIGS. 17-18 demonstrate that re-expression of type II or type III TGF-b receptor in the highly metastatic human renal cell carcinoma cell line UMRC3 inhibited cell proliferation in cell culture and tumor growth in a nude mouse model. The TGF-b receptors were either re-expressed in a stable vector system or as an adenoviral vector. For clinical purposes, it would be envisioned to treat patients with an adenovirus expressing one or both of the TGF-b receptors to block tumor growth or cause tumor regression.

EXAMPLE 11

Stepwise Sequential Loss of Type III And Type II TGF-b Receptor Expression in Renal Cell Carcinoma
With genomic profiling in human renal cell carcinoma, the data presented above demonstrated a stepwise sequential loss of type III and type II TGF-b receptor expression in association with renal cell carcinogenesis and progression. These findings were confirmed by both immunohistochemistry and real-time PCR in patient-matched tissue samples. This clinical observation was brought to the laboratory to identify relevant in vitro models. Using these models, it was demonstrated that loss of type III TGF-b receptor expression resulted in incremental desensitization to TGF-b and attenuation of TGF-b signaling. Subsequent loss of type II TGF-b receptor resulted in complete loss of TGF-b sensitivity. With in vitro modulation of TGF-b receptor expression, it was demonstrated that reconstitution of the TGF-b signaling pathway resulted in significant growth inhibition and loss of the aggressive phenotype.
These experiments are unique in that clinically relevant observations, which are derived from the evaluation of gene expression in normal renal cortical tissue, localized renal cell carcinoma and metastatic renal cell carcinoma, were brought to the laboratory for validation and experimental manipulation in relevant in vitro models. Other investigators have examined human renal cell carcinoma cell lines and identified alterations in the expression of TGF-b signaling pathway intermediaries, but those observations have not been validated in the clinical biology of renal cell carcinoma. To the investigators' knowledge, few studies have methodically examined the expression of all three TGF-b receptors in patient samples at the protein and mRNA level in an effort to correlate TGF-b receptor expression to disease-specific states of renal cell carcinoma (i.e. localized versus metastatic tumor). A major strength of the present study is that the investigators recognized distinct disease states in renal cell carcinoma, associated them with specific alterations in the TGF-b signaling pathway, and then validated and manipulated the clinical observations in the laboratory.
Although the mechanisms are not well understood, it is clear that TGF-b regulates a large number of diverse biological functions, including cell proliferation, differentiation, cell adhesion, apoptosis, extracellular matrix production, immune regulation, neuroprotection, and early embryonic development. In epithelial cells, the effect of TGF-b is generally to inhibit proliferation, promote cellular differentiation, and regulate interactions with the extracellular matrix. As a direct consequence, aberrations in TGF-b signaling can have a dramatic impact on cellular processes that are critically associated with neoplastic and malignant transformation. Given the well-documented observation that the end result of TGF-b signaling is largely growth inhibitory, it makes intuitive sense that cancer cell would develop mechanisms to escape TGF-b sensitivity. To date, these mechanisms have not been elucidated in human renal cell carcinoma.
Based on the data presented above, the investigators hypothesize that this escape from the growth-inhibitory effects of TGF-b is mediated through the stepwise sequential loss of type III and type II TGF-b receptor expression. To the investigators' knowledge, no one has linked sequential loss of these two types of receptors to carcinogenesis and metastatic progression in oncology. This is the first time that stepwise loss of a single transduction pathway has been associated with important biologic sequelae in a human cancer.
Results presented in the present invention demonstrate that loss of type III TGF-b receptor expression is an early event in renal cell carcinoma biology and that this loss has important sequelae with regard to renal cell carcinoma carcinogenesis and progression. All clinical samples of localized renal cell carcinoma demonstrated loss of type III TGF-b receptor, but had normal expression of type I and type II TGF-b receptors. Replication of this clinical observation in in vitro models demonstrated significant loss of TGF-b sensitivity, manifest as a significant reduction in the growth inhibitory effects of TGF-b1 and significantly reduced TGF-b-mediated transcription. Interestingly, cell lines derived from localized RCC retained type II TGF-b receptor expression and therefore, still demonstrated sensitivity, albeit reduced, to TGF-b. Only with metastatic progression and loss of type II TGF-b receptor expression does the cell become completely resistant to the effects of TGF-b. The investigators hypothesize that this retained, but attenuated, TGF-b signaling seen in local tumors must convey some as yet unrecognized biologic benefit for local tumors that is no longer required, and therefore discarded, with metastatic progression. In fact, this loss of type II TGF-b receptor expression may be an absolute integral component in the cascade of intracellular events that lead to the development of metastatic potential. In keeping with this hypothesis, it has been shown that loss of type II TGF-b receptor expression was one of 40 integral alterations of gene expression to predict for poor prognosis of patients diagnosed with renal cell carcinoma.
In summary, the above results demonstrate a clear link between loss of type III TGF-b receptor expression to a human disease state. Reduced type III TGF-b receptor (TBR3) expression has been reported in human breast tumor cell lines, suggesting that loss of TBR3 expression may be a more ubiquitous phenomena in carcinogenesis, rather than an isolated finding in human RCC biology. The fact that the investigators found down-regulation of TBR3 in every renal cell carcinoma specimen studied to date (35 patients) and that re-expression of TBR3 (in the presence of re-expressed TBR2) completely abolish growth on soft agar suggests an important role for TBR3 in normal renal epithelial homeostasis that must be abrogated for renal cell carcinogenesis and progression to occur. Little attention has been given to TBR3 in normal cell biology or the changes in expression that occur with carcinogenesis and progression. Observations from the present invention would suggest that TBR3 plays an important functional role in signaling and that loss of expression is an important event in the acquisition of the tumorigenic and metastatic phenotype.

EXAMPLE 12

Genomic Profiling for Stage I Papillary Renal Cell Carcinoma and Benign Oncocytoma

FIG. 19 shows hierarchical clustering of genes over-expressed or down-regulated (with at least 2 fold differences) in stage I papillary renal cell carcinoma verses normal renal cortex. Genes over-expressed and down-regulated in stage I papillary renal cell carcinoma are listed in Table 8 and Table 9 respectively.
FIG. 20 shows hierarchical clustering of genes over-expressed or down-regulated (with at least 2 fold differences) in benign oncocytoma verses normal renal cortex. Genes over-expressed and down-regulated in benign oncocytoma are listed in Table 10 and Table 11 respectively.
FIG. 21 shows venn analysis of gene distribution among stage I renal cell carcinoma (RCC), oncocytoma and stage I papillary renal cell carcinoma. Genes with at least 2-fold differences in expression were filtered at 95% confidence level (CL) in the following 3 t-tests: stage I RCC vs. normal; oncocytoma vs. normal; and stage I papillary renal cell carcinoma vs. normal. Six hundred twenty five genes were present only in stage I RCC (95% CL), 136 genes were present only in oncocytoma (95% CL), 344 genes were present only in stage I papillary renal cell carcinoma (95% CL), and 60 genes were common to stage I RCC, oncocytoma and stage I papillary renal cell carcinoma.

FIG. 22 shows venn analysis of gene distribution among stage II renal cell carcinoma (RCC), oncocytoma and stage I papillary renal cell carcinoma. Genes with at least 2-fold differences in expression were filtered at 95% confidence level (CL) in the following 3 t-tests: stage II RCC vs. normal; oncocytoma vs. normal; and stage I papillary renal cell carcinoma vs. normal. One thousand and five genes were present only in stage II RCC (95% CL), 152 genes were present only in oncocytoma (95% CL), 334 genes were present only in stage I papillary renal cell carcinoma (95% CL), and 43 genes were common to stage II RCC, oncocytoma and stage I papillary renal cell carcinoma.

TABLE 8


Genes With Up-Regulated Expression
In stage I Papillary Renal Cell Carcinoma

	Genbank ID	Gene Symbol

	NM_003505	FZD1
	AL035683	B4GALT5
	R56118	N/A
	NM_014575	SCHIP1
	AI694320	ZNF533
	BC031322	N/A
	BF346665	N/A
	BC004283	LOC283639
	AF302786	GNPTAG
	AU121975	PAICS
	NM_016315	GULP1
	AL541302	SERPINE2
	BG391217	C9orf80
	AC004382	DKFZP434K046
	NM_000248	MITF
	NM_022154	SLC39A8
	AI436813	N/A
	AF007162	CRYAB
	NM_015392	NPDC1
	AL136585	DKFZp761A132
	AB040120	SLC39A8
	NM_138473	SP1
	AU144387	182-FIP
	NM_022763	FAD104
	AI093231	APBB1IP
	NM_000235	LIPA
	NM_000700	ANXA1
	N30188	N/A
	NM_003651	CSDA
	AI830227	FLII
	U20350	CX3CR1
	NM_005692	ABCF2
	U34074	AKAP1
	AB056106	TARSH
	AU151483	CDH6
	BC026260	TTC3
	AL133001	SULF2
	NM_003358	UGCG
	NM_001282	AP2B1
	AF322067	RAB34
	NM_001540	HSPB1
	N58363	STATIP1
	AF072872	FZD1
	BF247552	SLC38A1
	X69397	CD24
	BC000251	GSK3B
	BF691447	B4GALT5
	AB046817	SYTL2
	AF255647	DKFZP566N034
	BF344237	N/A
	AW242720	LOC143381
	AA115485	MGC3222
	NM_006588	SULT1C2
	NM_000546	TP53
	N92494	JWA
	W74580	MGC3222
	AF131749	PSK-1
	AW026491	CCND2
	NM_012410	PSK-1
	NM_002800	PSMB9
	BF512748	JAK3
	AA404269	PRICKLE1
	M33376	AKR1C1
	AF035321	DNM1
	NM_002862	PYGB
	AF132000	DKFZP564K1964
	L07950	HLA-C
	AF114011	TNFSF13
	BF674052	VMP1
	AI922599	VIM
	AF044773	BANF1
	NM_015925	LISCH7
	NM_001684	ATP2B4
	AI123348	CHST11
	AI817079	EXOC7
	NM_004385	CSPG2
	NM_024801	TARSH
	BF218922	CSPG2
	BF590263	CSPG2
	NM_001233	CAV2
	AB020690	PNMA2
	AW188198	TNFAIP6
	NM_007115	TNFAIP6
	AI742838	DOCK11
	AW117264	N/A
	AF016266	TNFRSF10B
	NM_013952	PAX8
	AA771779	ZFP90
	W72333	FLJ21657
	H23979	MOX2
	BG542521	PPM2C
	AF063591	MOX2
	BF247383	BMPR2
	NM_005114	HS3ST1
	BE466145	N/A
	BC005352	TNFAIP8
	AC002045	LOC339047
	BC040558	D2LIC
	U13699	CASP1
	NM_002718	PPP2R3A
	BF476502	MPPE1
	BC034275	LOC253982
	AF279145	ANTXR1
	AV724216	NDRG4
	BG165613	N/A
	NM_018205	LRRC20
	NM_022083	C1orf24
	NM_006169	NNMT
	AF141347	TUBA3
	NM_000064	C3
	AV710838	BCDO2
	AI417917	EHD2
	AI681260	LILRB1
	NM_000389	CDKN1A
	AF288391	C1orf24
	NM_002627	PFKP
	NM_001975	ENO2
	NM_030786	SYNCOILIN
	NM_006169	NNMT
	AI417917	EHD2
	NM_006868	RAB31
	L03203	PMP22
	NM_001304	CPD
	NM_006762	LAPTM5
	NM_000211	ITGB2
	AA995910	ALOX5
	NM_018965	TREM2
	AL353715	STMN3
	BC019612	C20orf75
	AF086074	N/A
	NM_005045	RELN
	AI935123	C14orf78
	AL550875	C7orf28B
	L27624	TFPI2
	AL574096	TFPI2
	AA005141	MET
	D86983	D2S448
	AW439242	C6orf68
	AB000221	CCL18
	NM_002121	HLA-DPB1
	U17496	PSMB8
	U05598	AKR1C1
	BF342851	D2S448
	BF311866	PTGFRN
	NM_001449	FHL1
	AA954994	N/A
	Y13710	CCL18
	BG170541	MET
	AB037813	DKFZp762K222
	D28124	NBL1
	NM_021103	TMSB10
	AI949772	N/A
	AF199015	VIL2
	AI873273	SLC16A6
	NM_017821	RHBDL2
	BF740152	MYO1F
	AA954994	N/A
	AI458735	MGC26717
	NM_003254	TIMP1
	AI688631	N/A
	AK026037	N/A
	BG327863	CD24
	NM_016008	D2LIC
	AI394438	LOC253981
	AA947051	D2LIC
	AI819043	N/A
	AI378044	UGCG
	NM_024576	OGFRL1
	M76477	GM2A
	NM_002214	ITGB8
	AI879381	ADCK2
	NM_000152	GAA
	H15129	MEIS4
	L42024	HLA-C
	NM_002178	IGFBP6
	AI761561	HK2
	AA722799	DCBLD2
	NM_003255	TIMP2
	NM_000107	DDB2
	AV699565	CTSC
	NM_000861	HRH1

TABLE 9


Genes With Down-Regulated Expression
In stage I Papillary Renal Cell Carcinoma

	Genbank ID	Gene Symbol

	AF232217	N/A
	AI823572	MGC45438
	AU154994	SLC13A3
	AW979271	N/A
	AF064103	CDC14A
	AI524125	PCDH9
	AI733474	GPR155
	AI767756	HS6ST2
	NM_000412	HRG
	NM_021614	KCNN2
	M13149	HRG
	H17038	N/A
	NM_002010	FGF9
	NM_003877	SOCS2
	AI768894	CGN
	AW772192	N/A
	AF094518	ESRRG
	T40942	ANGPTL3
	NM_001146	ANGPT1
	AI242023	N/A
	BF970431	N/A
	NM_005670	EPM2A
	AW071744	KCNJ10
	AI928242	TFCP2L1
	AI769774	LOC155006
	AW274034	USP2
	AI635774	EMCN
	AW007532	IGFBP5
	NM_004070	CLCNKA
	NM_014621	HOXD4
	AI733593	N/A
	NM_020632	ATP6V0A4
	AI697028	FLJ90165
	AA897516	PTGER4
	NM_024307	MGC4171
	J02639	SERPINA5
	NM_000085	CLCNKB
	AA058832	MGC33926
	BF059276	N/A
	BC043647	LOC284578
	AL161958	THY1
	AL121845	KIAA1847
	AY079172	ATP6V0D2
	AA928708	CYP8B1
	H71135	ADH6
	NM_000102	CYP17A1
	Z92546	SUSD2
	AL558479	THY1
	BC005314	ALDOB
	NM_173591	FLJ90579
	BF510426	N/A
	AF331844	SOST
	X77737	SLC4A1
	NM_004392	DACH1
	BC001077	LOC87769
	AA218868	THY1
	BF478120	RECQL5
	BC041158	CYP4A11
	AI623321	MTP
	AI796189	PAH
	NM_021161	KCNK10
	NM_000163	GHR
	AL136880	ESPN
	NM_024426	WT1
	M61900	PTGDS
	AW963951	SIAT7C
	AW340588	MAN1C1
	AI263078	SLC23A3
	BF130943	PPAPDC1
	AI732596	N/A
	AA603467	ZNF503
	R41565	N/A
	AI951185	NR2F1
	NM_004633	IL1R2
	NM_003289	TPM2
	BF512388	C10orf58
	BC005830	ANXA9
	NM_000362	TIMP3
	NM_001438	ESRRG
	AU146204	ENPP6
	AA775681	FLJ23091
	AI393205	ACY-3
	AF017987	SFRP1
	NM_005951	MT1H
	NM_005950	MT1G
	NM_021805	SIGIRR
	AA557324	CYP4X1
	BF528646	DKFZP564I1171
	AW340112	LOC401022
	R73554	IGFBP5
	AI826437	N/A
	AV720650	KIAA0888
	AA780067	HS3ST3B1
	NM_000640	IL13RA2
	AI806338	TBX3
	NM_003155	STC1
	AA931562	N/A
	AI694325	N/A
	AF205940	EMCN
	NM_001290	LDB2
	NM_016242	EMCN
	AW014927	CALB1
	AI758950	SLC26A7
	AK024256	KIAA1573
	BF726212	ANK2
	AI985987	SCNN1G
	AW242408	UPP2
	NM_000860	HPGD
	BF447963	KIAA0962
	BF941499	GPR116
	AW242409	N/A
	BF509031	ATP6V1G3
	NM_000934	SERPINF2
	BF248364	AF15Q14
	AL534095	FLJ23091
	NM_004929	CALB1
	AI222435	N/A
	NM_005397	PODXL
	AI090268	N/A
	AI300520	STC1
	NM_002609	PDGFRB
	NM_006984	CLDN10
	BG413612	N/A
	D64137	CDKN1C
	AK026344	PEPP2
	AI670852	PTPRB
	AI693153	GABRB3
	NM_001393	ECM2
	N93191	PR1
	BC005090	AGMAT
	NM_000717	CA4
	D38300	PTGER3
	AI650260	N/A
	BC024226	IFRG15
	BC006294	DHRS10
	NM_003039	SLC2A5
	AI675836	SORCS1
	NM_005276	GPD1
	NM_014298	QPRT
	M10943	MT2A
	NM_005952	MT1X
	NM_002450	MT1X
	NM_002910	RENBP
	BF246115	MT1F
	AF078844	MT1F
	AF170911	SLC23A1
	AF333388	MT1H
	NM_003500	ACOX2
	AA995925	N/A
	NM_001218	CA12
	BF432333	FLJ31196
	NM_001385	DPYS
	NM_003052	SLC34A1
	NM_000778	CYP4A11
	AL136551	SESN2
	NM_000792	DIO1
	NM_016725	FOLR1
	NM_019101	APOM
	NM_014270	SLC7A9
	AF124373	SLC22A6
	NM_016327	UPB1
	NM_024734	CLMN
	NM_016527	HAO2
	NM_003645	SLC27A2
	AB051536	FLJ14957
	NM_025149	FLJ20920
	BC005939	PTGDS
	BC006236	MGC11324
	NM_024609	NES
	NM_002591	PCK1
	NM_005410	SEPP1
	AB020630	PPP1R16B
	AF022375	VEGF
	NM_016246	DHRS10
	AA873542	SLC6A19
	U95090	PRODH2
	D26054	FBP1
	AI732994	MGC13034
	NM_000151	G6PC
	AK025651	PNAS-4
	AF161441	N/A
	AF161454	APOM
	NM_022129	MAWBP
	AI733515	MGC52019
	NM_001443	FABP1
	AI433463	MME
	AL049313	N/A
	BF195998	ALDOB
	NM_022829	SLC13A3
	NM_000035	ALDOB
	NM_007287	MME
	NM_003399	XPNPEP2
	NM_000196	HSD11B2
	BF431313	N/A
	NM_004844	SH3BP5
	NM_003206	TCF21
	AI311917	DPYS
	AA843963	PRLR
	NM_017753	PRG-3
	NM_006633	IQGAP2
	NM_001133	AFM
	T90064	N/A
	BF696216	N/A
	NM_004413	DPEP1
	Z98443	FLJ38736
	NM_018456	EAF2
	AW771563	N/A
	NM_014495	ANGPTL3
	AI074145	KMO
	NM_000896	CYP4F3
	NM_001072	UGT1A6
	AI631993	N/A
	NM_000277	PAH
	M74220	PLG
	AL574184	HPGD
	NM_000161	GCH1
	H57166	N/A
	NM_000597	IGFBP2
	NM_000790	DDC
	NM_004668	MGAM
	NM_021027	UGT1A6
	AF348078	GPR91
	NM_016347	NAT8
	AF338650	PDZK3
	BE221817	CNTN3
	NM_004476	FOLH1
	NM_004615	TM4SF2
	NM_023940	RASL11B
	AI742872	SLC2A12
	BC001196	HS6ST1
	AW195353	TFCP2L1
	NM_003122	SPINK1
	NM_144707	PROM2
	AI653981	L1CAM
	AI796169	GATA3
	M96789	GJA4
	N74607	AQP3
	NM_014059	RGC32
	AI572079	SNAI2
	AI056877	N/A
	NM_006206	PDGFRA
	AW771314	MGC35434
	NM_016955	SLA/LP
	AI569804	LOC375295
	NM_001584	C11orf8
	BG261252	EVI1
	NM_006226	PLCL1
	NM_001172	ARG2
	AL050264	TU3A
	BC003070	GATA3
	AL120332	MGC20785
	NM_000459	TEK
	AW242836	LOC120224
	AI926697	Gup1
	NM_000486	AQP2
	AI870306	IRX1
	AW264204	CLDN11
	BF431989	THRB
	AI459140	N/A
	NM_001864	COX7A1
	AI471866	SLC7A13
	AI935789	UMOD
	NM_002472	MYH8
	BC020873	CLCNKA
	NM_000550	TYRP1
	AA806965	BTNL9
	NM_020163	LOC56920
	NM_004490	GRB14
	AA788946	COL12A1
	AW242315	N/A
	AI735586	LOC152573
	R88990	N/A
	NM_003278	TNA
	NM_007180	TREH
	AW173045	TBX2
	U28049	TBX2
	NM_001395	DUSP9
	NM_000336	SCNN1B
	U43604	N/A
	BC029135	N/A
	NM_005414	SKIL
	BQ894022	PDE1A
	NM_013335	GMPPA
	NM_003221	TFAP2B
	BF057634	HOXD8
	AA523172	N/A
	AF319520	ARG99
	NM_002885	RAP1GA1
	NM_003361	UMOD
	NM_000142	FGFR3
	NM_000893	KNG1
	BC029135	N/A
	NM_147174	HS6ST2
	NM_000218	KCNQ1
	U03884	KCNJ1
	X83858	PTGER3
	BF439270	N/A
	AA911235	MST1
	NM_000955	PTGER1
	NM_022844	MYH11
	BC042069	N/A
	NM_005518	HMGCS2
	NM_001963	EGF
	AI632015	SLC12A1
	AF339805	N/A
	BF106962	FAM3B
	NM_005019	PDE1A
	AU146305	PDE1A
	AI653107	NRK
	NM_004466	GPC5
	BF195936	KRT18L1
	NM_022454	SOX17
	AW299531	HOXD10
	AL137716	AQP6
	AI332407	SFRP1
	AL565812	PTN
	AI452457	LOC199920
	AI281593	DCN
	M21692	ADH1B
	AI660243	TMPRSS2
	AI754423	FLJ38507
	AA759244	FXYD4
	U75667	ARG2
	NM_000930	PLAT
	AF083105	SOX13
	NM_013231	FLRT2
	BI825302	PR1
	NM_003012	SFRP1
	AF138300	DCN
	AU155612	N/A
	BG435302	EBF
	NM_005978	S100A2
	NM_000900	MGP
	AK026748	DKFZP761M1511
	J03208	DBT
	NM_002345	LUM
	NM_006623	PHGDH
	AF063606	my048
	NM_001647	APOD
	AI935541	N/A
	NM_005558	LAD1
	AW138125	PRODH2
	NM_000663	ABAT
	AU119437	LOC144997
	BC036095	DRP2
	R49295	N/A
	AI623202	PRDM16
	AW452355	N/A
	AA563621	HSPB6
	X15217	SKIL
	AK095719	N/A
	AI056187	N/A
	AI668598	N/A
	AI700882	SLC13A3
	NM_000963	PTGS2
	AW051712	N/A
	AL832099	MGC33190
	AK057337	LOC145820
	AW300204	SLC30A8
	NM_005856	RAMP3
	AI458003	CYYR1
	AK026877	N/A
	AI632567	N/A
	U91903	FRZB
	AF352728	FLJ12541
	BM128432	IGFBP5
	NM_003102	SOD3
	BE676272	TACC1
	AI692180	PPFIBP2
	AL544576	LOC92162
	NM_017688	BSPRY
	AU146310	N/A
	AI912976	RASGRF2
	U83508	ANGPT1
	L47125	GPC3

TABLE 10


Genes With Up-Regulated Expression In Benign Oncocytoma

	Genbank ID	Gene Symbol

	NM_005114	HS3ST1
	AA650558	GNAS
	BF062244	LIN7A
	NM_030674	SLC38A1
	NM_014766	SCRN1
	BC002471	CPLX1
	AF183421	RAB31
	AK022100	KIAA0256
	BF508244	AKR1C2
	BG772511	N/A
	AB037848	SYT13
	AK055769	N/A
	T58048	N/A
	NM_012105	BACE2
	AA992805	LEF1
	AK026420	DMN
	NM_024812	BAALC
	AI057226	N/A
	AW138767	ELOVL7
	NM_013233	STK39
	AF178532	BACE2
	AI521166	LOC283104
	AA005023	NOD27
	AV725364	GPRC5B
	AW195581	GPSM2
	BG503479	B4GALT6
	BF031829	DSG2
	AW975728	SLC16A7
	NM_022495	C14orf135
	AA703159	N/A
	BF247552	SLC38A1
	NM_001673	ASNS
	NM_024622	FLJ21901
	AI565054	N/A
	AW058459	LOC134285
	NM_001233	CAV2
	BC036550	N/A
	BE464483	N/A
	NM_002512	NME2

TABLE 11


Genes With Down-Regulated Expression In Benign Oncocytoma

	Genbank ID	Gene Symbol

	BF593625	SYK
	AI310001	FLJ22789
	NM_006206	PDGFRA
	NM_003740	KCNK5
	AW138125	PRODH2
	NM_000336	SCNN1B
	BC005314	ALDOB
	AI796189	PAH
	NM_013363	PCOLCE2
	NM_004466	GPC5
	AI627531	N/A
	U28055	MSTP9
	NM_152759	MGC35140
	AW052159	N/A
	NM_017712	PGPEP1
	AI961231	TOX
	AI767962	BNC2
	AF350881	TRPM6
	AU146418	N/A
	BE875072	N/A
	AI653981	L1CAM
	AI634662	SLC13A3
	NM_000486	AQP2
	AW206292	AQP2
	AI572079	SNAI2
	AI694118	N/A
	NM_000142	FGFR3
	U78168	RAPGEF3
	AI913600	UNQ846
	W93847	MUC15
	NM_004616	TM4SF3
	AI935789	UMOD
	AW274034	USP2
	NM_147174	HS6ST2
	AA074145	PRODH
	AL049176	CHRDL1
	NM_020353	PLSCR4
	NM_024803	TUBAL3
	D16931	ALB
	NM_019076	UGT1A10
	AF138303	DCN
	D13705	CYP4A11
	NM_000587	C7
	R49295	N/A
	NM_000385	AQP1
	AI669229	RARRES1
	U36189	C5orf13
	AL110135	FLJ14753
	AW271605	N/A
	BF358386	N/A
	NM_016270	KLF2
	AA905508	LOC128153
	NM_021630	PDLIM2
	AA915989	TBC1D13
	AL565812	PTN
	AI990790	N/A
	BC041158	CYP4A11
	NM_138474	N/A
	NM_002899	RBP1
	AK024256	KIAA1573
	AW779672	SLC17A1
	NM_021161	KCNK10
	BF196891	TPMT
	AY028896	CARD10
	NM_007180	TREH
	AL110152	CD109
	AW051599	N/A
	AI796169	GATA3
	AF017987	SFRP1
	BE550027	DKFZp761N1114
	AA535065	KIAA1847
	NM_003361	UMOD
	AI263078	SLC23A3
	M13149	HRG
	AF278532	NTN4
	AI632015	SLC12A1
	NM_000412	HRG
	NM_000893	KNG1
	BG398937	KNG
	AL049977	CLDN8
	N74607	AQP3
	AW071744	KCNJ10
	AW015506	AQP2
	AI927000	SOSTDC1
	AI471866	SLC7A13
	NM_001099	ACPP
	NM_005074	SLC17A1
	AA995925	N/A
	AF352728	FLJ12541
	BF343007	TFAP2A
	NM_016929	CLIC5
	AA911235	MST1
	AA639753	N/A
	NM_004887	CXCL14
	AW771565	AIM1
	AI264671	N/A
	BF510426	N/A
	AV728958	TLN2
	T90064	N/A
	AA218868	THY1
	NM_003104	SORD
	AJ292204	AGXT2
	AI056359	MAPT
	AL568422	DZIP1
	AF339805	N/A
	NM_000163	GHR
	AI042017	NPL
	AW340457	N/A
	BF431199	DEHAL1
	BF432254	MGC15937
	AI368018	GPD1
	NM_018456	EAF2
	NM_017806	FLJ20406
	X59065	FGF1
	AI650353	DACH1
	AW771563	N/A
	BF431313	N/A
	NM_000896	CYP4F3
	BC005090	AGMAT
	U24267	ALDH4A1
	AI090268	N/A
	AW014927	CALB1
	AL023553	PIPPIN
	AL049313	N/A
	AK021539	NCAG1
	AI220117	MGST1
	NM_020300	MGST1
	NM_022568	ALDH8A1
	BE874872	FAM20C
	NM_004668	MGAM
	BF033242	CES2
	BC004542	PLXNB2
	NM_000204	IF
	NM_004525	LRP2
	AA442149	MAF
	NM_000049	ASPA
	AI830469	TFEC
	NM_003759	SLC4A4
	AF169017	FTCD
	AF170911	SLC23A1
	AA865601	LOC123876
	AA863031	MGC32871
	AW136060	SLC13A2
	NM_003041	SLC5A2
	NM_021924	MUCDHL
	AW299568	N/A
	AI927941	N/A
	AI433463	MME
	AL365347	SLC7A8
	AA502331	PRAP1
	NM_024709	FLJ14146
	AF289024	FTCD
	NM_017614	BHMT2
	NM_016347	NAT8
	NM_000277	PAH
	NM_000316	PTHR1
	NM_001091	ABP1
	NM_000790	DDC
	AF144103	CXCL14
	NM_016725	FOLR1
	NM_000050	ASS
	AA693817	N/A
	NM_004929	CALB1
	NM_000592	C4A
	AL574184	HPGD
	AA676742	DMGDH
	AI631993	N/A
	AI566130	AK3
	AW024233	GLYAT
	AA873542	SLC6A19
	AK026966	AK3
	NM_022829	SLC13A3
	NM_005950	MT1G
	AV700405	MGC52019
	AI733515	MGC52019
	NM_000860	HPGD
	U95090	PRODH2
	NM_001385	DPYS
	BG401568	SLC16A9
	NM_000846	GSTA1
	BF195998	ALDOB
	NM_004413	DPEP1
	NM_000151	G6PC
	NM_006744	RBP4
	NM_013410	AK3
	NM_000035	ALDOB
	AK026411	ALDOB
	AL135960	CYP4A11
	M74220	PLG
	NM_001713	BHMT
	AW614558	SLC39A5
	Z92546	SUSD2
	NM_000778	CYP4A11
	NM_000792	DIO1
	AI222435	N/A
	D26054	FBP1
	AW025165	SLC22A8
	NM_007287	MME
	BF217861	MT1E
	BF447963	KIAA0962
	NM_001081	CUBN
	NM_018484	SLC22A11
	AW192692	N/A
	BF000045	TINAG
	BC005830	ANXA9
	NM_025257	C6orf29
	NM_020973	GBA3
	NM_001977	ENPEP
	AI632692	N/A
	BI825302	PR1
	L12468	ENPEP
	AL571375	SCD4
	AL136858	ZMYND12
	NM_024027	COLEC11
	NM_014934	DZIP1
	BG496631	FBI4
	NM_018265	FLJ10901
	AI770035	UPB1
	AF177272	UGT2B28
	NM_004392	DACH1
	N95363	CDKN1C
	AF261715	FOLH1
	NM_000042	APOH
	NM_001393	ECM2
	R88990	N/A
	AA557324	CYP4X1
	AF116645	ALB
	BC015993	MGC27169
	AL558479	THY1
	NM_000785	CYP27B1
	AW051926	AMN
	AA928708	CYP8B1
	BE407830	KIFC3
	AI431643	RRAS2
	AF001434	EHD1
	BC005894	FMO2
	NM_006798	UGT2A1

The following references were cited herein:

Copland et al., Recent Prog. Horm. Res. 58:25-53 (2003).
Copland et al., Oncogene 22:8053-62 (2003).
Grossman et al., J. Surg. Oncol. 28:237-244 (1985).
Trifillis, Exp. Nephrol. 7:353-359 (1999).

Claims

1. A method of detecting conventional or clear cell renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining gene expression level of one or more gene encoding one or more protein selected from the group consisting of TGF-b1, TGF-a, adrenomedulin, fibroblast growth factor 2 (FGF2), vascular epidermal growth factor (VEGF), osteonectin, follistatin like-3, inhibin beta A, spondin 2, chemokine X cytokine receptor 4 (CXCR4), fibronectin, neuropilin 1, frizzled homolog 1, insulin-like growth factor binding protein 3, laminin alpha 3, integrin beta 2, semaphorins 6A, semaphorins 5B, semaphorins 3B, caspase 1, sprouty 1, CDH16, PCDH9, compliment component 1-beta, compliment component 1-alpha, compliment component 1-gamma, CD53, CDW52, CD163, CD14, CD3Z, CD24, RAP1, angiopoietin 2, cytokine knot secreted protein, MAPKKKK4, 4-hydroxyphenylpyruvate dioxygenase, pyruvate carboxyknase 2, 11-beta-hydroxysteroid dehydrogenase 2, GAS1, CDKN1, nucleolar protein 3, interferon induced protein 44, NR3C1, vitamin D receptor, hypothetical protein FLJ14957 (Affy# 225817_at), metallothionein 2A, metallothionein-If gene, metallothionein 1H, secreted frizzled related protein 1, connective tissue growth factor, and epidermal growth factor; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal biological samples, wherein statistically different gene expression levels would indicate said individual has conventional or clear cell renal cell carcinoma.

2. The method of claim 1, wherein said normal biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

3. The method of claim 1, wherein said biological samples are obtained from said individual.

4. The method of claim 1, wherein said gene expression is determined by a method selected from the group consisting of DNA microarray, real-time PCR, RT-PCR, and northern analysis.

5. The method of claim 1, wherein said statistical analysis is selected from the group consisting of hierarchical cluster analysis, Bonferoni Analysis and Students t test.

6. The method of claim 2, wherein gene expression in the blood samples are based on the amount of protein detected in the blood samples.

7. A method of detecting conventional or clear cell renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining in said samples the expression level of type III TGF-b receptor; and

comparing said expression level to that present in normal tissue, wherein decreased level of said TGF-b receptor indicates that said individual has conventional or clear cell renal cell carcinoma.

8. The method of claim 7, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

9. The method of claim 7, wherein said biological samples are obtained from said individual.

10. The method of claim 7, wherein type III TGF-b receptor expression level is determined at RNA or protein level.

11. A method of detecting stage I conventional or clear cell renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining in the biological samples expression level of one or more gene having a GenBank accession number selected from the group consisting of NM004356.1, NM002293.2, NM000980.1, AK002091.1, NM005721.2, NM002668.1, NM021038.1, AF070656.1, NM021029.1, NM002945.1, NM002480.1, NM001349.1, NM005496.1, AW163148, NM002356.4, M68956.1, AI589086, NM006762.1, NM014267.1, NM000235.1, NM000176.1, NM005737.2, NM005737.2, BC001051.1, NM006169.1, NM005862.1, AI356412, NM002350.1, BG107456, NM021913.1, NM002194.2, NM019058.1, NM004079.1, NM001784.1, AF151853.1, NM000491.2, BC000125.1, NM004520.1, NM000321.1, NM012262.2, NM000560.1, NM005502.1, AF285167.1, BG170541, NM021642.1, BE967532, NM006526.1, NM000570.1, N26005, NM006153.1, NM001549.1, NM003141.1, NM014705.1, NM005197.1, NM002907.1, U43328.1, NM017925.1, NM006773.2, U20350.1, NM005761.1, NM004834.1, NM021644.1, NM006640.1, NM004180.1, NM002110.1, NM030755.1, NM030984.1, NM014350.1, BC001312.1, U14990.1, D83043.1, AI888672, BC002387.1, M60334.1, AF161522.1, BG256677, M26880.1, U17496.1, AF141347.1, L01639.1, NM005445.1, AB030655.1, AF165520.1, AF009670.1, AF020314.1, BC001606.1, BC005352.1, AF281030.1, BC001052.1, L32610.1, M23612.1, AF109683.1, BC002841.1, D29640.1, L25259.1, M60333.1, U13698.1, U90940.1, M90685.1, M90684.1, M90686.1, L22453.1, U01351.1, U62824.1, L07950.1, AF348491.1, NM003079.1, BE646386, AI972475, AA95999, AL049397.1, BE895685, M82882.1, AB020633.1, AL031781, AW148801, AB011118.1, AU145005, N80918, BF439472, BE968801, AI985751, AI735692, AA995910, M12679.1, AL133053.1, X03348.1, AC005339, AK024836.1, AC003999, AJ224869, AL022067, AL110158.1, S81916.1, M80469, NM002860.1, NM020198.1, NM016304.1, AA02574, NM024844.1, NM015938.1, NM018200.1, NM025235.1, NM015991.1, NM016090.1, NM024554.1, NM017718.1, NM017923.1, NM030921.1, BC004470.1, AK021413.1, BF444916, BC004819.1, AF247167.1, U39402.1, BC006112.1, BG388615, AB033007.1, BG250721, AK024221.1, BF477658, BG251556, AB033091.1, AK024350.1, NM018440.1, AW500180, BF209337, AI709406, AI806905, AI392933, AI142096, AL137430.1, AV724266, BF589359, AW084125, N20927, AI627666, AV726322, AI697657, BF002625, BF439533, AW026543, AI092770, NM020679.1, AK024855.1, AK000119.1, AW977527, BE671060, AL037450, AI401535, AV683852, BF055144, AA352113, BF056209, and X60592; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein over-expression of said gene indicates that said individual has stage I conventional or clear cell renal cell carcinoma.

12. The method of claim 11, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

13. The method of claim 11, wherein said normal tissue samples are obtained from said individual.

14. The method of claim 11, wherein gene expression level is determined at RNA or protein level.

15. The method of claim 11, wherein said gene is over-expressed at least 2 fold as compared to that expressed in normal tissue.

16. A method of detecting stage I conventional or clear cell renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining in the biological samples expression level of one or more gene having a GenBank accession number selected from the group consisting of L38487, NM004415.1, NM005327.1, NM003321.1, NM002084.2, AI983043, NM006066.1, NM006384.2, NM001685.1, NM014652.1, NM013410.1, NM016725.1, NM021151.1, NM005951.1, NM005952.1, AL080102.1, BC000931.2, BC005398.1, D87292.1, AU151428, BC000109.1, AF333388.1, NM005953.1, BF217861, AA594937, AW052179, AI884867, BF246115, AW028110, AW242315, AW080549, AW149846, AK024386.1, AL109716.2, AK026411.1, M10943, AW088547, NM018049.1, NM017900.1, NM006548.1, NM025135.1, NM016458.2, NM022128.1, NM015974.1, NM013333.1, AA33341, AF226732.1, AF265439.1, AI743534, AB042647.1, AL522667, BG255416, AF308301.1, BE408081, AL521634, BF203664, BE645551, AW193698, BF540829, W72455, AI457453, BF056892, AI038402, AI051046, AI659456, AW664964, AI631895, AI263078, BF057634, AA746038, AA442776, AI913600, AW771908, AI807887, AW102941, AW024656, and AB002342; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein down-regulation of said gene indicates that said individual has stage I conventional or clear cell renal cell carcinoma.

17. The method of claim 16, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

18. The method of claim 16, wherein said normal tissue samples are obtained from said individual.

19. The method of claim 16, wherein gene expression level is determined at RNA or protein level.

20. The method of claim 16, wherein said gene is down-regulated at least 2 fold as compared to that expressed in normal tissue.

21. A method of detecting stage I conventional or clear cell renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining expression level of one or more gene in a first gene group comprising genes with GenBank accession numbers NM004356.1, NM002293.2, NM000980.1, AK002091.1, NM005721.2, NM002668.1, NM021038.1, AF070656.1, NM021029.1, NM002945.1, NM002480.1, NM001349.1, NM005496.1, AW163148, NM002356.4, M68956.1, AI589086, NM006762.1, NM014267.1, NM000235.1, NM000176.1, NM005737.2, NM005737.2, BC001051.1, NM006169.1, NM005862.1, AI356412, NM002350.1, BG107456, NM021913.1, NM002194.2, NM019058.1, NM004079.1, NM001784.1, AF151853.1, NM000491.2, BC000125.1, NM004520.1, NM000321.1, NM012262.2, NM000560.1, NM005502.1, AF285167.1, BG170541, NM021642.1, BE967532, NM006526.1, NM000570.1, N26005, NM006153.1, NM001549.1, NM003141.1, NM014705.1, NM005197.1, NM002907.1, U43328.1, NM017925.1, NM006773.2, U20350.1, NM005761.1, NM004834.1, NM021644.1, NM006640.1, NM004180.1, NM002110.1, NM030755.1, NM030984.1, NM014350.1, BC001312.1, U14990.1, D83043.1, AI888672, BC002387.1, M60334.1, AF161522.1, BG256677, M26880.1, U17496.1, AF141347.1, L01639.1, NM005445.1, AB030655.1, AF165520.1, AF009670.1, AF020314.1, BC001606.1, BC005352.1, AF281030.1, BC001052.1, L32610.1, M23612.1, AF109683.1, BC002841.1, D29640.1, L25259.1, M60333.1, U13698.1, U90940.1, M90685.1, M90684.1, M90686.1, L22453.1, U01351.1, U62824.1, L07950.1, AF348491.1, NM003079.1, BE646386, AI972475, AA195999, AL049397.1, BE895685, M82882.1, AB020633.1, AL031781, AW148801, AB011118.1, AU145005, N80918, BF439472, BE968801, AI985751, AI735692, AA995910, M12679.1, AL133053.1, X03348.1, AC005339, AK024836.1, AC003999, AJ224869, AL022067, AL110158.1, S81916.1, M80469, NM002860.1, NM020198.1, NM016304.1, AA102574, NM024844.1, NM015938.1, NM018200.1, NM025235.1, NM015991.1, NM016090.1, NM024554.1, NM017718.1, NM017923.1, NM030921.1, BC004470.1, AK021413.1, BF444916, BC004819.1, AF247167.1, U39402.1, BC006112.1, BG388615, AB033007.1, BG250721, AK024221.1, BF477658, BG251556, AB033091.1, AK024350.1, NM018440.1, AW500180, BF209337, AI709406, AI806905, AI392933, AI142096, AL137430.1, AV724266, BF589359, AW084125, N20927, AI627666, AV726322, AI697657, BF002625, BF439533, AW026543, AI092770, NM020679.1, AK024855.1, AK000119.1, AW977527, BE671060, AL037450, AI401535, AV683852, BF055144, AA352113, BF056209, and X60592;

determining expression level of one or more gene in a second gene group comprising genes with GenBank accession numbers L38487, NM004415.1, NM005327.1, NM003321.1, NM002084.2, AI983043, NM006066.1, NM006384.2, NM001685.1, NM014652.1, NM013410.1, NM016725.1, NM021151.1, NM005951.1, NM005952.1, AL080102.1, BC000931.2, BC005398.1, D87292.1, AU151428, BC000109.1, AF333388.1, NM005953.1, BF217861, AA594937, AW052179, AI884867, BF246115, AW028110, AW242315, AW080549, AW149846, AK024386.1, AL109716.2, AK026411.1, M10943, AW088547, NM018049.1, NM017900.1, NM006548.1, NM025135.1, NM016458.2, NM022128.1, NM015974.1, NM013333.1, AA133341, AF226732.1, AF265439.1, AI743534, AB042647.1, AL522667, BG255416, AF308301.1, BE408081, AL521634, BF203664, BE645551, AW193698, BF540829, W72455, AI457453, BF056892, AI038402, AI051046, AI659456, AW664964, AI631895, AI263078, BF057634, AA746038, AA442776, AI913600, AW771908, AI807887, AW102941, AW024656, and AB002342; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein over-expression of one or more gene belonging to said first gene group and down-regulation of one or more gene belonging to said second gene group indicates that said individual has stage I conventional or clear cell renal cell carcinoma.

22. The method of claim 21, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

23. The method of claim 21, wherein said normal tissue samples are obtained from said individual.

24. The method of claim 21, wherein gene expression level is determined at RNA or protein level.

25. The method of claim 21, wherein said down-regulation or over-expression is at least 2 fold as compared to that expressed in normal tissue.

26. A method of detecting stage II conventional or clear cell renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining in said samples expression level of a gene having a GenBank accession number selected from the group consisting of NM006096.1, NM006098.1, NM001780.1, NM003118.1, NM000291.1, NM003870.1, AB032261.1, NM002629.1, NM003564.1, NM000310.1, NM003405.1, U82164.1, NM002305.2, NM001096.1, NM002121.1, NM021038.1, NM003651.1, AV685920, NM002654.1, NM001175.1, BC000182.1, NM001153.2, NM001975.1, NM006435.1, NM001387.1, BG398414, NM004039.1, NM005534.1, AL136877.1, NM014876.1, NM024830.1, NM005505.1, NM003025.1, NM013285.1, NM005720.1, AW157070, NM002835.1, NM004428.1, AW006290, NM002053.1, NM000089.1, NM021105.1, NM002467.1, NM001284.1, AI825926, NM014736.1, AF161461.1, NM014873.1, AI005043, NM000416.1, NM004172.1, NM004207.1, AI761561, Y09216.1, NM002922.1, NM005990.1, NM014863.1, NM014737.1, NM000418.1, BC000658.1, NM003751.1, NM002339.1, NM004604.1, NM006404.1, AF275945.1, NM004221.1, NM004556.1, NM004688.1, NM003332.1, NM015136.1, NM006019.1, NM004877.1, NM002317.1, NM025201.1, NM014800.1, L41944.1, NM007268.1, NM006994.2, NM014791.1, NM014882.1, NM003864.1, NM001558.1, NM003264.1, NM014221.1, AV756141, AI123251, NM006433.2, NM000861.2, NM001870.1, NM003586.1, NM004271.1, NM014932.1, NM014947.1, NM000647.2, NM002562.1, NM006058.1, NM013447.1, NM013416.1, NM001776.1, NM020037.1, NM006135.1, NM007036.2, AF034607.1, BC000915.1, AL162068.1, NM006947.1, L12387.1, AF141349.1, AF263293.1, BC000389.1, AF007162.1, D38616.1, AV717590, U87967.1, H23979, AF063591.1, BC005254.1, BC000893.1, L22431.1, AI741056, AF084462.1, U62027.1, M87507.1, J04132.1, M31159.1, AF257318.1, BC001388.1, AF130095.1, AF022375.1, AF091352.1, AB035482.1, Z24727.1, M19267.1, U13700.1, M27281.1, BC005838.1, BC005858.1, BC005926.1, BE513104, AU147399, AK023154.1, AK021757.1, H95344, AB023231.1, AL523076, NM030666.1, AB018289.1, AW043713, BE880591, AU158495, BE965029, AL564683, AA349595, AI809341, AW205215, BE349017, AF070592.1, AI769685, AI935123, BG255188, AI088622, BE222709, AW007573, BG332462, AI862658, AI934469, AB018345.1, W87466, BE908217, NM005615.1, BE300252, BF740152, AV711904, AW072388, AW190316, NM005412.1, NM006417.1, AL008730, L16895, Z21533.1, AA807529, AK026737.1, X14355.1, AK025608.1, AF183421.1, NM002695.1, AF288391.1, NM003730.2, NM016359.1, NM014164.2, NM022736.1, NM021158.1, NM017792.1, NM020142.1, NM016448.1, NM005767.1, NM020169.1, NM022834.1, NM018460.1, NM024629.1, NM018641.1, NM018295.1, NM024576.1, NM016582.1, NM003116.1, NM018454.1, NM018099.1, NM007072.1, NM022445.1, AW173623, AB044088.1, AF043244.1, AF133207.1, AF313468.1, AA191576, AI765383, BC003654.1, W60806, AI335263, AI378406, BC005400.1, AI761520, BC000771.1, BC000190.1, BC002776.1, AF132203.1, BC006107.1, AK024263.1, AK024846.1, BE878463, AW304786, AK022955.1, BF001267, AL558987, AA577672, BE620734, AI937446, H99792, BE966748, AI659418, AI990891, AA827892, AL135264, AI375753, AA573502, BG387557, AA554833, AK026764.1, AU146532, BE348597, AL577758, AI133452, AU157224, AI742057, BE500942, N25631, AU145366, AW270037, BF526978, AW182575, BF339831, AI056992, BE222668, BG165011, AI188445, BE551416, AI972498, AW662189, AA142842, BF939473, AI681260, AA551090, AA045175, WO5495, AI093231, AI565054, AL553774, AK023470.1, AL157377, AL139109, AK025631.1, AI873425, AI769269, AI935334, BF437747, AW300953, H37811, AA603344, AA742310, AI248208, AI962367, BF541967, AI686890, AI936034, U88964, AJ243797, D29642, D87433, and AI129310; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein over-expression of said gene indicates that said individual has stage II conventional or clear cell renal cell carcinoma.

27. The method of claim 26, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

28. The method of claim 26, wherein said normal tissue samples are obtained from said individual.

29. The method of claim 26, wherein gene expression level is determined at RNA or protein level.

30. The method of claim 26, wherein said gene is over-expressed at least 2 fold as compared to that expressed in normal tissue.

31. A method of detecting stage II conventional or clear cell renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining in said samples expression level of a gene having a GenBank accession number selected from the group consisting of NM012248.1, NM002300.1, BC000306.1, NM001640.2, NM005875.1, NM003365.1, BF031714, NM005808.1, AF113129.1, NM002402.1, NM006844.1, NM004636.1, NM002496.1, NM006556.1, NM004255.1, NM002225.2, NM004524.1, AI950380, AB020707.1, NM000481.1, NM012317.1, NM006456.1, NM006614.1, NM015393.1, AV729634, NM002628.1, NM003500.1, NM002655.1, NM004393.1, NM003026.1, NM002010.1, NM014033.1, NM004868.1, BC000649.1, S69189.1, AF153330.1, AF094518.1, M55575.1, AB019695.1, M61900.1, BF967998, BF967998, AL526243, NM000532.1, BE042354, AI587323, AW195882, H71135, AV659180, AK027006.1, AV693216, BG398937, NM002489.1, NM003849.1, NM014019.1, NM024952.1, NM014185.1, NM018013.1, NM018373.1, NM014067.2, NM013261.1, NM021963.1, NM018658.1, NM014553.1, AF112204.1, AU145941, AF061264.1, BF941492, AI984229, N71923, BC005050.1, AF172327.1, AF356515.1, BE620739, BF435123, AW149498, BE044480, BF382393, AV751731, U55984, BF059512, AK025934.1, AL036088, BE964222, AW290940, AL545998, AW274874, AI709389, BF224092, AU145805, AW079843, AW138815, AW242286, AW025023, BE672659, AW024437, AW195353, BE044193, AI493303, AI636080, BF509031, AW242920, BF002046, BF130943, AW452631, AI1792937, AI810572, BG165743, AW466989, R48991, BF029215, D21851, and Z83838; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein down-regulation of said gene indicates that said individual has stage II conventional or clear cell renal cell carcinoma.

32. The method of claim 31, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

33. The method of claim 31, wherein said normal tissue samples are obtained from said individual.

34. The method of claim 31, wherein gene expression level is determined at RNA or protein level.

35. The method of claim 31, wherein said gene is down-regulated at least 2 fold as compared to that expressed in normal tissue.

36. A method of detecting stage II conventional or clear cell renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining expression level of one or more gene in a first gene group comprising genes with GenBank accession numbers NM006096.1, NM006098.1, NM001780.1, NM003118.1, NM000291.1, NM003870.1, AB032261.1, NM002629.1, NM003564.1, NM000310.1, NM003405.1, U82164.1, NM002305.2, NM001096.1, NM002121.1, NM021038.1, NM003651.1, AV685920, NM002654.1, NM001175.1, BC000182.1, NM001153.2, NM001975.1, NM006435.1, NM001387.1, BG398414, NM004039.1, NM005534.1, AL136877.1, NM014876.1, NM024830.1, NM005505.1, NM003025.1, NM013285.1, NM005720.1, AW157070, NM002835.1, NM004428.1, AW006290, NM002053.1, NM000089.1, NM021105.1, NM002467.1, NM001284.1, AI825926, NM014736.1, AF161461.1, NM014873.1, AI005043, NM000416.1, NM004172.1, NM004207.1, AI761561, Y09216.1, NM002922.1, NM005990.1, NM014863.1, NM014737.1, NM000418.1, BC000658.1, NM003751.1, NM002339.1, NM004604.1, NM006404.1, AF275945.1, NM004221.1, NM004556.1, NM004688.1, NM003332.1, NM015136.1, NM006019.1, NM004877.1, NM002317.1, NM025201.1, NM014800.1, L41944.1, NM007268.1, NM006994.2, NM014791.1, NM014882.1, NM003864.1, NM001558.1, NM003264.1, NM014221.1, AV756141, AI123251, NM006433.2, NM000861.2, NM001870.1, NM003586.1, NM004271.1, NM014932.1, NM014947.1, NM000647.2, NM002562.1, NM006058.1, NM013447.1, NM013416.1, NM001776.1, NM020037.1, NM006135.1, NM007036.2, AF034607.1, BC000915.1, AL162068.1, NM006947.1, L12387.1, AF141349.1, AF263293.1, BC000389.1, AF007162.1, D38616.1, AV717590, U87967.1, H23979, AF063591.1, BC005254.1, BC000893.1, L22431.1, AI741056, AF084462.1, U62027.1, M87507.1, J04132.1, M31159.1, AF257318.1, BC001388.1, AF130095.1, AF022375.1, AF091352.1, AB035482.1, Z24727.1, M19267.1, U13700.1, M27281.1, BC005838.1, BC005858.1, BC005926.1, BE513104, AU147399, AK023154.1, AK021757.1, H95344, AB023231.1, AL523076, NM030666.1, AB018289.1, AW043713, BE880591, AU158495, BE965029, AL564683, AA349595, AI809341, AW205215, BE349017, AF070592.1, AI769685, AI935123, BG255188, AI088622, BE222709, AW007573, BG332462, AI862658, AI934469, AB018345.1, W87466, BE908217, NM005615.1, BE300252, BF740152, AV711904, AW072388, AW190316, NM005412.1, NM006417.1, AL008730, L16895, Z21533.1, AA807529, AK026737.1, X14355.1, AK025608.1, AF183421.1, NM002695.1, AF288391.1, NM003730.2, NM016359.1, NM014164.2, NM022736.1, NM021158.1, NM017792.1, NM020142.1, NM016448.1, NM005767.1, NM020169.1, NM022834.1, NM018460.1, NM024629.1, NM018641.1, NM018295.1, NM024576.1, NM016582.1, NM003116.1, NM018454.1, NM018099.1, NM007072.1, NM022445.1, AW173623, AB044088.1, AF043244.1, AF133207.1, AF313468.1, AA191576, AI765383, BC003654.1, W60806, AI335263, AI378406, BC005400.1, AI761520, BC000771.1, BC000190.1, BC002776.1, AF132203.1, BC006107.1, AK024263.1, AK024846.1, BE878463, AW304786, AK022955.1, BF001267, AL558987, AA577672, BE620734, AI937446, H99792, BE966748, AI659418, AI990891, AA827892, AL135264, AI375753, AA573502, BG387557, AA554833, AK026764.1, AU146532, BE348597, AL577758, AI133452, AU157224, AI742057, BE500942, N25631, AU145366, AW270037, BF526978, AW182575, BF339831, AI056992, BE222668, BG165011, AI188445, BE551416, AI972498, AW662189, AA142842, BF939473, AI681260, AA551090, AA045175, WO5495, AI093231, AI565054, AL553774, AK023470.1, AL157377, AL139109, AK025631.1, AI873425, AI769269, AI935334, BF437747, AW300953, H37811, AA603344, AA742310, AI248208, AI962367, BF541967, AI686890, AI936034, U88964, AJ243797, D29642, D87433, and AI129310;

determining expression level of one or more gene in a second gene group comprising genes with GenBank accession numbers NM012248.1, NM002300.1, BC000306.1, NM001640.2, NM005875.1, NM003365.1, BF031714, NM005808.1, AF113129.1, NM002402.1, NM006844.1, NM004636.1, NM002496.1, NM006556.1, NM004255.1, NM002225.2, NM004524.1, AI950380, AB020707.1, NM000481.1, NM012317.1, NM006456.1, NM006614.1, NM015393.1, AV729634, NM002628.1, NM003500.1, NM002655.1, NM004393.1, NM003026.1, NM002010.1, NM014033.1, NM004868.1, BC000649.1, S69189.1, AF153330.1, AF094518.1, M55575.1, AB019695.1, M61900.1, BF967998, BF967998, AL526243, NM000532.1, BE042354, AI587323, AW195882, H71135, AV659180, AK027006.1, AV693216, BG398937, NM002489.1, NM003849.1, NM014019.1, NM024952.1, NM014185.1, NM018013.1, NM018373.1, NM014067.2, NM013261.1, NM021963.1, NM018658.1, NM014553.1, AF112204.1, AU145941, AF061264.1, BF941492, AI984229, N71923, BC005050.1, AF172327.1, AF356515.1, BE620739, BF435123, AW149498, BE044480, BF382393, AV751731, U55984, BF059512, AK025934.1, AL036088, BE964222, AW290940, AL545998, AW274874, AI709389, BF224092, AU145805, AW079843, AW138815, AW242286, AW025023, BE672659, AW024437, AW195353, BE044193, AI493303, AI636080, BF509031, AW242920, BF002046, BF130943, AW452631, AI792937, AI810572, BG165743, AW466989, R48991, BF029215, D21851, and Z83838; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein over-expression of one or more gene belonging to said first gene group and down-regulation of one or more gene belonging to said second gene group indicates that said individual has stage II conventional or clear cell renal cell carcinoma.

37. The method of claim 36, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

38. The method of claim 36, wherein said normal tissue samples are obtained from said individual.

39. The method of claim 36, wherein gene expression level is determined at RNA or protein level.

40. The method of claim 36, wherein said down-regulation or over-expression is at least 2 fold as compared to that expressed in normal tissue.

41. A method of detecting stage I or stage II conventional or clear cell renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining in said samples the expression level of one or more gene having a GenBank accession number selected from the group consisting of NM005566.1, NM000291.1, NM001219.2, NM002966.1, NM000034.1, NM002627.1, NM006082.1, AI922599, NM020474.2, NM006406.1, NM015344.1, NM014755.1, AI796269, NM005783.1, BF197655, NM001233.1, NM002845.1, NM014302.1, U47924, NM004106.1, NM015474.1, NM004915.2, NM002432.1, NM005565.2, NM005531.1, NM005849.1, NM002189.1, NM004353.1, NM014812.1, AF208043.1, BC002654.1, BC006379.1, BC006481.1, AF000426.1, AF000424.1, BG500301, AL516350, M27487.1, M27487.1, AW517686, AL581768, AA524505, Z78330, Z78330, BG532690, AW005535, NM007161.1, AK026577.1, AI091079, AV713720, NM021103.1, NM016337.1, NM013260.1, NM021199.1, NM018149.1, NM016951.2, NM017760.1, NM022349.1, NM023003.1, NM016184.1, NM031284.1, BC002342.1, AA775177, AL162070.1, AF253977.1, AF237908.1, WO3103, AK022888.1, AI141784, AB033038.1, AI184968, AL161725, NM018440.1, AL553942, AI394438, T64884, T64884, AW511319, AI640834, AI655467, AL161725, and T92908; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein up-regulation of said gene indicates that said individual has stage I or stage II conventional or clear cell renal cell carcinoma.

42. The method of claim 41, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

43. The method of claim 41, wherein said normal tissue samples are obtained from said individual.

44. The method of claim 41, wherein gene expression level is determined at RNA or protein level.

45. The method of claim 41, wherein said gene is up-regulated at least 2 fold as compared to that expressed in normal tissue.

46. A method of detecting stage I or stage II conventional or clear cell renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining in said samples the expression level of one or more gene having a GenBank accession number selected from the group consisting of NM004092.2, NM000270.1, NM002354.1, AF017987.1, NM003012.2, NM000666.1, NM000191.1, NM015254.1, NM000140.1, U75667.1, NM000196.1, NM014636.1, NM001441.1, NM005978.2, NM001678.1, NM001099.2, NM014731.1, BF343007, NM000035.1, NM005950.1, NM002371.2, NM006984.1, NM002567.1, NM000019.1, NM001692.1, X77737.1, NM006226.1, NM000893.1, NM000412.2, NM001963.2, NM003361.1, NM000050.1, NM001438.1, BC002449.1, J02639.1, BC002571.1, U03884.1, AF173154.1, AF130103.1, AL117618.1, AF063606.1, BC005314.1, BF686267, AI742553, D83782.1, AB029031.1, AK025432.1, AL117643.1, AW772192, NM003944.1, AL049977.1, AK023937.1, AK025084.1, X03363.1, AK026411.1, NM016026.1, NM016286.1, NM019027.1, BG338251, NM006113.2, NM018075.1, NM013271.1, NM017586.1, NM016321.1, NM025247.1, NM020632.1, AI632015, NM000701.1, NM031305.1, AF130089.1, AK025651.1, W45551, W67995, AL136566.1, AF105366.1, AF284225.1, AA191708, AL355708.1, BE783949, AL529672, AL568674, AU147564, AK000208.1, AB051536.1, AI569747, AK025562.1, AI660243, N50413, AI347918, AL536553, BC000282.1, BF106962, AI051248, AI928242, BG236006, AI653107, AI824037, R61322, AW071744, BF059276, AI379517, AA058832, AW274034, AI580268, AI761947, AI793201, AK025898.1, AB046810.1, AK024204.1, BF594722, R88990, N73742, AI697028, BF590528, AI733359, H20179, AA991551, AI758950, AA911561, AI769774, AA669135, AW136060, AI733593, BF739841, AA600175, BF477980, AI934557, BE326951, AI632567, BE300882, BE855713, AA485440, AA915989, and AA085764; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein down-regulation of said gene indicates that said individual has stage I or stage II conventional or clear cell renal cell carcinoma.

47. The method of claim 46, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

48. The method of claim 46, wherein said normal tissue samples are obtained from said individual.

49. The method of claim 46, wherein gene expression level is determined at RNA or protein level.

50. The method of claim 46, wherein said gene is down-regulated at least 2 fold as compared to that expressed in normal tissue.

51. A method of targeting conventional or clear cell renal cell carcinoma cells, comprising the step of generating antibodies or small molecules directed against a cell surface molecule encoded by a gene over-expressed in conventional renal cell carcinoma cells.

52. The method of claim 51, wherein said antibodies or small molecules are linked with a therapeutic drug or an imaging agent.

53. The method of claim 51, wherein said over-expressed gene encodes a protein selected from the group consisting of calcitonin receptor-like (206331_at; 210815_s_at), receptor (calcitonin) activity modifying protein 2 (RAMP2; 205779_at), endothelin receptor type B (206701_x_at), beta 2 integrin (202803_s_at), alpha 5 integrin (201389_at), chemokine X cytokine receptor 4 (CXCR4), fibronectin, neuropilin 1 (212298_at; 210510_s_at), CD24, CD14, Cd163, CD53, Compliment Component 1-beta, Compliment Component 1-alpha, Compliment Component 1-gamma, CDH4, integrin beta2, ADAM28, FK506 binding protein, collagen Valpha2, tumor necrosis factor receptor superfamily member 6, tumor necrosis factor receptor superfamily member 5, tumor necrosis factor (ligand) superfamily member 13b, tumor necrosis factor receptor superfamily member 12A, and the FGF receptor.

54. A method of treating conventional or clear cell renal cell carcinoma, comprising the step of replacing in said carcinoma tumor suppressor gene whose expression is down-regulated in conventional renal cell carcinoma, or inducing the expression of said tumor suppressor gene in said carcinoma.

55. The method of claim 54, wherein said down-regulated gene encodes a protein selected from the group consisting of CDKN1, secreted frizzled related protein 1, semaphoring 6D, semaphoring 3B, CDH16, TNF alpha, calbindin D28, defensin beta1, beta-catenin interacting protein 1, GAS 1, vitamin D receptor, and Kruppel-like factor 15.

56. A method of detecting stage I papillary renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining in the biological samples expression level of one or more gene having a GenBank accession number selected from the group consisting of NM_—003505, AL035683, R56118, NM_—014575, AI694320, BC031322, BF346665, BC004283, AF302786, AU121975, NM_—016315, AL541302, BG391217, AC004382, NM_—000248, NM_—022154, AI436813, AF007162, NM_—015392, AL136585, AB040120, NM_—138473, AU144387, NM_—022763, AI093231, NM_—000235, NM_—000700, N30188, NM_—003651, AI830227, U20350, NM_—005692, U34074, AB056106, AU151483, BC026260, AL133001, NM_—003358, NM_—001282, AF322067, NM_—001540, N58363, AF072872, BF247552, X69397, BC000251, BF691447, AB046817, AF255647, BF344237, AW242720, AA115485, NM_—006588, NM_—000546, N92494, W74580, AF131749, AW026491, NM_—012410, NM_—002800, BF512748, AA404269, M33376, AF035321, NM_—002862, AF132000, L07950, AF114011, BF674052, AI922599, AF044773, NM 015925, NM_—001684, AI123348, AI817079, NM_—004385, NM_—024801, BF218922, BF590263, NM_—001233, AB020690, AW188198, NM_—007115, AI742838, AW117264, AF016266, NM_—013952, AA771779, W72333, H23979, BG542521, AF063591, BF247383, NM_—005114, BE466145, BC005352, AC002045, BC040558, U13699, NM_—002718, BF476502, BC034275, AF279145, AV724216, BG165613, NM_—018205, NM_—022083, NM_—006169, AF141347, NM_—000064, AV710838, AI417917, AI681260, NM_—000389, AF288391, NM_—002627, NM_—001975, NM_—030786, NM_—006169, AI417917, NM_—006868, L03203, NM_—001304, NM_—006762, NM_—000211, AA995910, NM_—018965, AL353715, BC019612, AF086074, NM_—005045, AI935123, AL550875, L27624, AL574096, AA005141, D86983, AW439242, AB000221, NM_—002121, U17496, U05598, BF342851, BF311866, NM_—001449, AA954994, Y13710, BG170541, AB037813, D28124, NM_—021103, AI949772, AF199015, AI873273, NM_—017821, BF740152, AA954994, AI458735, NM_—003254, AI688631, AK026037, BG327863, NM_—016008, AI394438, AA947051, AI819043, AI378044, NM_—024576, M76477, NM_—002214, AI879381, NM_—000152, H15129, L42024, NM_—002178, AI761561, AA722799, NM_—003255, NM_—000107, AV699565, and NM_—000861; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein over-expression of said gene indicates that said individual has stage I papillary renal cell carcinoma.

57. The method of claim 56, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

58. The method of claim 56, wherein said normal tissue samples are obtained from said individual.

59. The method of claim 56, wherein gene expression level is determined at RNA or protein level.

60. The method of claim 56, wherein said gene is over-expressed at least 2 fold as compared to that expressed in normal tissue.

61. A method of detecting stage I papillary renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining in the biological samples expression level of one or more gene having a GenBank accession number selected from the group consisting of AF232217, AI823572, AU154994, AW979271, AF064103, AI524125, AI733474, AI767756, NM_—000412, NM_—021614, M13149, H17038, NM_—002010, NM_—003877, AI768894, AW772192, AF094518, T40942, NM_—001146, AI242023, BF970431, NM_—005670, AW071744, AI928242, AI769774, AW274034, AI635774, AW007532, NM_—004070, NM_—014621, AI733593, NM_—020632, AI697028, AA897516, NM_—024307, J02639, NM_—000085, AA058832, BF059276, BC043647, AL161958, AL121845, AY079172, AA928708, H71135, NM_—000102, Z92546, AL558479, BC005314, NM_—173591, BF510426, AF331844, X77737, NM_—004392, BC001077, AA218868, BF478120, BC041158, AI623321, AI796189, NM_—021161, NM_—000163, AL136880, NM_—024426, M61900, AW963951, AW340588, AI263078, BF130943, AI732596, AA603467, R41565, AI951185, NM_—004633, NM_—003289, BF512388, BC005830, NM_—000362, NM_—001438, AU146204, AA775681, AI393205, AF017987, NM 005951, NM_—005950, NM_—021805, AA557324, BF528646, AW340112, R73554, AI826437, AV720650, AA780067, NM_—000640, AI806338, NM_—003155, AA931562, AI694325, AF205940, NM_—001290, NM_—016242, AW014927, AI758950, AK024256, BF726212, AI985987, AW242408, NM_—000860, BF447963, BF941499, AW242409, BF509031, NM_—000934, BF248364, AL534095, NM_—004929, AI222435, NM_—005397, AI090268, AI300520, NM_—002609, NM_—006984, BG413612, D64137, AK026344, AI670852, AI693153, NM_—001393, N93191, BC005090, NM_—000717, D38300, AI650260, BC024226, BC006294, NM_—003039, AI675836, NM_—005276, NM_—014298, M10943, NM_—005952, NM_—002450, NM_—002910, BF246115, AF078844, AF170911, AF333388, NM_—003500, AA995925, NM_—001218, BF432333, NM_—001385, NM_—003052, NM_—000778, AL136551, NM_—000792, NM_—016725, NM_—019101, NM_—014270, AF124373, NM_—016327, NM_—024734, NM_—016527, NM_—003645, AB051536, NM_—025149, BC005939, BC006236, NM_—024609, NM_—002591, NM_—005410, AB020630, AF022375, NM_—016246, AA873542, U95090, D26054, AI732994, NM_—000151, AK025651, AF161441, AF161454, NM_—022129, AI733515, NM_—001443, AI433463, AL049313, BF195998, NM_—022829, NM_—000035, NM_—007287, NM_—003399, NM_—000196, BF431313, NM_—004844, NM_—003206, AI311917, AA843963, NM_—017753, NM_—006633, NM_—001133, T90064, BF696216, NM_—004413, Z98443, NM_—018456, AW771563, NM_—014495, AI074145, NM_—000896, NM_—001072, AI631993, NM_—000277, M74220, AL574184, NM_—000161, H57166, NM_—000597, NM_—000790, NM_—004668, NM_—021027, AF348078, NM_—016347, AF338650, BE221817, NM_—004476, NM_—004615, NM_—023940, AI742872, BC001196, AW195353, NM_—003122, NM_—144707, AI653981, AI796169, M96789, N74607, NM_—014059, AI572079, AI056877, NM_—006206, AW771314, NM_—016955, AI569804, NM_—001584, BG261252, NM_—006226, NM_—001172, AL050264, BC003070, AL120332, NM_—000459, AW242836, AI926697, NM_—000486, AI870306, AW264204, BF431989, AI459140, NM_—001864, AI471866, AI935789, NM_—002472, BC020873, NM_—000550, AA806965, NM_—020163, NM_—004490, AA788946, AW242315, AI735586, R88990, NM_—003278, NM_—007180, AW173045, U28049, NM_—001395, NM_—000336, U43604, BC029135, NM_—005414, BQ894022, NM_—013335, NM_—003221, BF057634, AA523172, AF319520, NM_—002885, NM_—003361, NM_—000142, NM_—000893, BC029135, NM_—147174, NM_—000218, U03884, X83858, BF439270, AA911235, NM 000955, NM_—022844, BC042069, NM_—005518, NM_—001963, AI632015, AF339805, BF106962, NM_—005019, AU146305, AI653107, NM_—004466, BF195936, NM_—022454, AW299531, AL137716, AI332407, AL565812, AI452457, AI281593, M21692, AI660243, AI754423, AA759244, U75667, NM_—000930, AF083105, NM_—013231, B1825302, NM_—003012, AF138300, AU155612, BG435302, NM_—005978, NM_—000900, AK026748, J03208, NM_—002345, NM_—006623, AF063606, NM_—001647, AI935541, NM_—005558, AW138125, NM_—000663, AU119437, BC036095, R49295, AI623202, AW452355, AA563621, X15217, AK095719, AI056187, AI668598, AI700882, NM_—000963, AW051712, AL832099, AK057337, AW300204, NM_—005856, AI458003, AK026877, AI632567, U91903, AF352728, BM128432, NM_—003102, BE676272, AI692180, AL544576, NM_—017688, AU146310, AI912976, U83508, L47125; and

62. The method of claim 61, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

63. The method of claim 61, wherein said normal tissue samples are obtained from said individual.

64. The method of claim 61, wherein gene expression level is determined at RNA or protein level.

65. The method of claim 61, wherein said gene is down-regulated at least 2 fold as compared to that expressed in normal tissue.

66. A method of detecting stage I papillary renal cell carcinoma, comprising the steps of:

obtaining biological samples from an individual;

determining expression level of one or more gene in a first gene group comprising genes with GenBank accession numbers NM_—003505, AL035683, R56118, NM_—014575, AI694320, BC031322, BF346665, BC004283, AF302786, AU121975, NM_—016315, AL541302, BG391217, AC004382, NM_—000248, NM_—022154, AI436813, AF007162, NM_—015392, AL136585, AB040120, NM_—138473, AU144387, NM_—022763, AI093231, NM_—000235, NM_—000700, N30188, NM_—003651, AI830227, U20350, NM_—005692, U34074, AB056106, AU151483, BC026260, AL133001, NM_—003358, NM_—001282, AF322067, NM_—001540, N58363, AF072872, BF247552, X69397, BC000251, BF691447, AB046817, AF255647, BF344237, AW242720, AA115485, NM_—006588, NM_—000546, N92494, W74580, AF131749, AW026491, NM_—012410, NM_—002800, BF512748, AA404269, M33376, AF035321, NM_—002862, AF132000, L07950, AF114011, BF674052, AI922599, AF044773, NM_—015925, NM_—001684, AI123348, AI817079, NM_—004385, NM_—024801, BF218922, BF590263, NM_—001233, AB020690, AW188198, NM_—007115, AI742838, AW117264, AF016266, NM_—013952, AA771779, W72333, H23979, BG542521, AF063591, BF247383, NM_—005114, BE466145, BC005352, AC002045, BC040558, U13699, NM_—002718, BF476502, BC034275, AF279145, AV724216, BG165613, NM 018205, NM_—022083, NM_—006169, AF141347, NM_—000064, AV710838, AI417917, AI681260, NM_—000389, AF288391, NM_—002627, NM_—001975, NM_—030786, NM_—006169, AI417917, NM_—006868, L03203, NM_—001304, NM_—006762, NM_—000211, AA995910, NM_—018965, AL353715, BC019612, AF086074, NM_—005045, AI935123, AL550875, L27624, AL574096, AA005141, D86983, AW439242, AB000221, NM_—002121, U17496, U05598, BF342851, BF311866, NM_—001449, AA954994, Y13710, BG170541, AB037813, D28124, NM_—021103, AI949772, AF199015, AI873273, NM_—017821, BF740152, AA954994, AI458735, NM_—003254, AI688631, AK026037, BG327863, NM_—016008, AI394438, AA947051, AI819043, AI378044, NM_—024576, M76477, NM_—002214, AI879381, NM_—000152, H15129, L42024, NM_—002178, AI761561, AA722799, NM_—003255, NM_—000107, AV699565, and NM_—000861;

determining expression level of one or more gene in a second gene group comprising genes with GenBank accession numbers AF232217, AI823572, AU154994, AW979271, AF064103, AI524125, AI733474, AI767756, NM_—000412, NM_—021614, M13149, H17038, NM_—002010, NM_—003877, AI768894, AW772192, AF094518, T40942, NM_—001146, AI242023, BF970431, NM_—005670, AW071744, AI928242, AI769774, AW274034, AI635774, AW007532, NM_—004070, NM_—014621, AI733593, NM_—020632, AI697028, AA897516, NM_—024307, J02639, NM_—000085, AA058832, BF059276, BC043647, AL161958, AL121845, AY079172, AA928708, H71135, NM_—000102, Z92546, AL558479, BC005314, NM_—173591, BF510426, AF331844, X77737, NM_—004392, BC001077, AA218868, BF478120, BC041158, AI623321, AI796189, NM_—021161, NM_—000163, AL136880, NM_—024426, M61900, AW963951, AW340588, AI263078, BF130943, AI732596, AA603467, R41565, AI951185, NM_—004633, NM_—003289, BF512388, BC005830, NM_—000362, NM_—001438, AU146204, AA775681, AI393205, AF017987, NM_—005951, NM_—005950, NM_—021805, AA557324, BF528646, AW340112, R73554, AI826437, AV720650, AA780067, NM_—000640, AI806338, NM_—003155, AA931562, AI694325, AF205940, NM_—001290, NM_—016242, AW014927, AI758950, AK024256, BF726212, AI985987, AW242408, NM_—000860, BF447963, BF941499, AW242409, BF509031, NM_—000934, BF248364, AL534095, NM_—004929, AI222435, NM_—005397, AI090268, AI300520, NM_—002609, NM_—006984, BG413612, D64137, AK026344, AI670852, AI693153, NM_—001393, N93191, BC005090, NM_—000717, D38300, AI650260, BC024226, BC006294, NM_—003039, AI675836, NM_—005276, NM_—014298, M10943, NM_—005952, NM_—002450, NM_—002910, BF246115, AF078844, AF170911, AF333388, NM_—003500, AA995925, NM_—001218, BF432333, NM_—001385, NM_—003052, NM_—000778, AL136551, NM_—000792, NM_—016725, NM_—019101, NM_—014270, AF124373, NM_—016327, NM_—024734, NM_—016527, NM_—003645, AB051536, NM_—025149, BC005939, BC006236, NM_—024609, NM_—002591, NM_—005410, AB020630, AF022375, NM_—016246, AA873542, U95090, D26054, AI732994, NM_—000151, AK025651, AF161441, AF161454, NM_—022129, AI733515, NM_—001443, AI433463, AL049313, BF195998, NM_—022829, NM_—000035, NM_—007287, NM_—003399, NM_—000196, BF431313, NM_—004844, NM_—003206, AI311917, AA843963, NM_—017753, NM_—006633, NM_—001133, T90064, BF696216, NM_—004413, Z98443, NM_—018456, AW771563, NM_—014495, AI074145, NM_—000896, NM_—001072, AI631993, NM_—000277, M74220, AL574184, NM_—000161, H57166, NM_—000597, NM_—000790, NM_—004668, NM_—021027, AF348078, NM_—016347, AF338650, BE221817, NM_—004476, NM_—004615, NM_—023940, AI742872, BC001196, AW195353, NM_—003122, NM_—144707, AI653981, AI796169, M96789, N74607, NM_—014059, AI572079, AI056877, NM_—006206, AW771314, NM_—016955, AI569804, NM_—001584, BG261252, NM_—006226, NM_—001172, AL050264, BC003070, AL120332, NM_—000459, AW242836, AI926697, NM_—000486, AI870306, AW264204, BF431989, AI459140, NM_—001864, AI471866, AI935789, NM_—002472, BC020873, NM_—000550, AA806965, NM_—020163, NM_—004490, AA788946, AW242315, AI735586, R88990, NM_—003278, NM_—007180, AW173045, U28049, NM_—001395, NM_—000336, U43604, BC029135, NM_—005414, BQ894022, NM_—013335, NM_—003221, BF057634, AA523172, AF319520, NM_—002885, NM_—003361, NM_—000142, NM_—000893, BC029135, NM_—147174, NM_—000218, U03884, X83858, BF439270, AA911235, NM_—000955, NM_—022844, BC042069, NM_—005518, NM 001963, AI632015, AF339805, BF106962, NM_—005019, AU146305, AI653107, NM_—004466, BF195936, NM_—022454, AW299531, AL137716, AI332407, AL565812, AI452457, AI281593, M21692, AI660243, AI754423, AA759244, U75667, NM_—000930, AF083105, NM_—013231, B1825302, NM_—003012, AF138300, AU155612, BG435302, NM_—005978, NM_—000900, AK026748, J03208, NM_—002345, NM_—006623, AF063606, NM_—001647, AI935541, NM_—005558, AW138125, NM_—000663, AU119437, BC036095, R49295, AI623202, AW452355, AA563621, X15217, AK095719, AI056187, AI668598, AI700882, NM_—000963, AW051712, AL832099, AK057337, AW300204, NM 005856, AI458003, AK026877, AI632567, U91903, AF352728, BM128432, NM_—003102, BE676272, AI692180, AL544576, NM_—017688, AU146310, AI912976, U83508, L47125; and

67. The method of claim 66, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

68. The method of claim 66, wherein said normal tissue samples are obtained from said individual.

69. The method of claim 66, wherein gene expression level is determined at RNA or protein level.

70. The method of claim 66, wherein said down-regulation or over-expression is at least 2 fold as compared to that expressed in normal tissue.

71. A method of detecting benign oncocytoma, comprising the steps of:

obtaining biological samples from an individual;

determining in the biological samples expression level of one or more gene having a GenBank accession number selected from the group consisting of NM_—005114, AA650558, BF062244, NM_—030674, NM_—014766, BC002471, AF183421, AK022100, BF508244, BG772511, AB037848, AK055769, T58048, NM_—012105, AA992805, AK026420, NM_—024812, AI057226, AW138767, NM_—013233, AF178532, AI521166, AA005023, AV725364, AW195581, BG503479, BF031829, AW975728, NM_—022495, AA703159, BF247552, NM_—001673, NM_—024622, AI565054, AW058459, NM_—001233, BC036550, BE464483, NM_—002512; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein over-expression of said gene indicates that said individual has benign oncocytoma.

72. The method of claim 71, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

73. The method of claim 71, wherein said normal tissue samples are obtained from said individual.

74. The method of claim 71, wherein gene expression level is determined at RNA or protein level.

75. The method of claim 71, wherein said gene is over-expressed at least 2 fold as compared to that expressed in normal tissue.

76. A method of detecting benign oncocytoma, comprising the steps of:

obtaining biological samples from an individual;

determining in the biological samples expression level of one or more gene having a GenBank accession number selected from the group consisting of BF593625, AI310001, NM_—006206, NM_—003740, AW138125, NM_—000336, BC005314, AI796189, NM_—013363, NM_—004466, AI627531, U28055, NM_—152759, AW052159, NM_—017712, AI961231, AI767962, AF350881, AU146418, BE875072, AI653981, AI634662, NM_—000486, AW206292, AI572079, AI694118, NM_—000142, U78168, AI913600, W93847, NM_—004616, AI935789, AW274034, NM_—147174, AA074145, AL049176, NM_—020353, NM_—024803, D16931, NM_—019076, AF138303, D13705, NM_—000587, R49295, NM_—000385, AI669229, U36189, AL110135, AW271605, BF358386, NM_—016270, AA905508, NM_—021630, AA915989, AL565812, AI990790, BC041158, NM_—138474, NM_—002899, AK024256, AW779672, NM_—021161, BF196891, AY028896, NM_—007180, AL110152, AW051599, AI796169, AF017987, BE550027, AA535065, NM_—003361, AI263078, M13149, AF278532, AI632015, NM_—000412, NM_—000893, BG398937, AL049977, N74607, AW071744, AW015506, AI927000, AI471866, NM_—001099, NM_—005074, AA995925, AF352728, BF343007, NM_—016929, AA911235, AA639753, NM_—004887, AW771565, AI264671, BF510426, AV728958, T90064, AA218868, NM_—003104, AJ292204, AI056359, AL568422, AF339805, NM_—000163, AI042017, AW340457, BF431199, BF432254, AI368018, NM_—018456, NM_—017806, X59065, AI650353, AW771563, BF431313, NM_—000896, BC005090, U24267, AI090268, AW014927, AL023553, AL049313, AK021539, AI220117, NM_—020300, NM_—022568, BE874872, NM_—004668, BF033242, BC004542, NM_—000204, NM_—004525, AA442149, NM_—000049, AI830469, NM_—003759, AF169017, AF170911, AA865601, AA863031, AW136060, NM_—003041, NM_—021924, AW299568, AI927941, AI433463, AL365347, AA502331, NM_—024709, AF289024, NM_—017614, NM_—016347, NM_—000277, NM_—000316, NM_—001091, NM_—000790, AF144103, NM_—016725, NM_—000050, AA693817, NM_—004929, NM_—000592, AL574184, AA676742, AI631993, AI566130, AW024233, AA873542, AK026966, NM_—022829, NM_—005950, AV700405, AI733515, NM_—000860, U95090, NM_—001385, BG401568, NM_—000846, BF195998, NM_—004413, NM_—000151, NM_—006744, NM_—013410, NM_—000035, AK026411, AL135960, M74220, NM_—001713, AW614558, Z92546, NM_—000778, NM_—000792, AI222435, D26054, AW025165, NM_—007287, BF217861, BF447963, NM_—001081, NM_—018484, AW192692, BF000045, BC005830, NM_—025257, NM_—020973, NM_—001977, AI632692, BI825302, L12468, AL571375, AL136858, NM_—024027, NM_—014934, BG496631, NM_—018265, AI770035, AF177272, NM_—004392, N95363, AF261715, NM_—000042, NM_—001393, R88990, AA557324, AF116645, BC015993, AL558479, NM_—000785, AW051926, AA928708, BE407830, AI431643, AF001434, BC005894, NM_—006798; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein down-regulation of said gene indicates that said individual has benign oncocytoma.

77. The method of claim 76, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

78. The method of claim 76, wherein said normal tissue samples are obtained from said individual.

79. The method of claim 76, wherein gene expression level is determined at RNA or protein level.

80. The method of claim 76, wherein said gene is down-regulated at least 2 fold as compared to that expressed in normal tissue.

81. A method of detecting benign oncocytoma, comprising the steps of:

obtaining biological samples from an individual;

determining expression level of one or more gene in a first gene group comprising genes with GenBank accession numbers NM_—005114, AA650558, BF062244, NM_—030674, NM_—014766, BC002471, AF183421, AK022100, BF508244, BG772511, AB037848, AK055769, T58048, NM_—012105, AA992805, AK026420, NM_—024812, AI057226, AW138767, NM_—013233, AF178532, AI521166, AA005023, AV725364, AW195581, BG503479, BF031829, AW975728, NM_—022495, AA703159, BF247552, NM_—001673, NM_—024622, AI565054, AW058459, NM_—001233, BC036550, BE464483, NM_—002512;

determining expression level of one or more gene in a second gene group comprising genes with GenBank accession numbers BF593625, AI310001, NM_—006206, NM_—003740, AW138125, NM_—000336, BC005314, AI796189, NM_—013363, NM_—004466, AI627531, U28055, NM_—152759, AW052159, NM_—017712, AI961231, AI767962, AF350881, AU146418, BE875072, AI653981, AI634662, NM_—000486, AW206292, AI572079, AI694118, NM_—000142, U78168, AI913600, W93847, NM_—004616, AI935789, AW274034, NM_—147174, AA074145, AL049176, NM_—020353, NM_—024803, D16931, NM_—019076, AF138303, D13705, NM_—000587, R49295, NM_—000385, AI669229, U36189, AL110135, AW271605, BF358386, NM_—016270, AA905508, NM_—021630, AA915989, AL565812, AI990790, BC041158, NM_—138474, NM_—002899, AK024256, AW779672, NM_—021161, BF196891, AY028896, NM_—007180, AL110152, AW051599, AI796169, AF017987, BE550027, AA535065, NM_—003361, AI263078, M13149, AF278532, AI632015, NM_—000412, NM_—000893, BG398937, AL049977, N74607, AW071744, AW015506, AI927000, AI471866, NM_—001099, NM_—005074, AA995925, AF352728, BF343007, NM_—016929, AA911235, AA639753, NM_—004887, AW771565, AI264671, BF510426, AV728958, T90064, AA218868, NM_—003104, AJ292204, AI056359, AL568422, AF339805, NM_—000163, AI042017, AW340457, BF431199, BF432254, AI368018, NM_—018456, NM_—017806, X59065, AI650353, AW771563, BF431313, NM_—000896, BC005090, U24267, AI090268, AW014927, AL023553, AL049313, AK021539, AI220117, NM_—020300, NM_—022568, BE874872, NM_—004668, BF033242, BC004542, NM 000204, NM_—004525, AA442149, NM_—000049, AI830469, NM_—003759, AF169017, AF170911, AA865601, AA863031, AW136060, NM_—003041, NM_—021924, AW299568, AI927941, AI433463, AL365347, AA502331, NM_—024709, AF289024, NM_—017614, NM_—016347, NM_—000277, NM_—000316, NM_—001091, NM_—000790, AF144103, NM_—016725, NM_—000050, AA693817, NM_—004929, NM_—000592, AL574184, AA676742, AI631993, AI566130, AW024233, AA873542, AK026966, NM_—022829, NM_—005950, AV700405, AI733515, NM_—000860, U95090, NM_—001385, BG401568, NM_—000846, BF195998, NM_—004413, NM_—000151, NM_—006744, NM_—013410, NM_—000035, AK026411, AL135960, M74220, NM_—001713, AW614558, Z92546, NM_—000778, NM_—000792, AI222435, D26054, AW025165, NM_—007287, BF217861, BF447963, NM_—001081, NM_—018484, AW192692, BF000045, BC005830, NM_—025257, NM_—020973, NM_—001977, AI632692, BI825302, L12468, AL571375, AL136858, NM_—024027, NM_—014934, BG496631, NM_—018265, AI770035, AF177272, NM_—004392, N95363, AF261715, NM_—000042, NM_—001393, R88990, AA557324, AF116645, BC015993, AL558479, NM_—000785, AW051926, AA928708, BE407830, AI431643, AF001434, BC005894, NM_—006798; and

performing statistical analysis on the expression level of said gene as compared to that expressed in normal tissue samples, wherein over-expression of one or more gene belonging to said first gene group and down-regulation of one or more gene belonging to said second gene group indicates that said individual has benign oncocytoma.

82. The method of claim 81, wherein said biological samples are selected from the group consisting of tissue samples, serum samples, urine samples, saliva samples, blood samples and biopsy samples.

83. The method of claim 81, wherein said normal tissue samples are obtained from said individual.

84. The method of claim 81, wherein gene expression level is determined at RNA or protein level.

85. The method of claim 81, wherein said down-regulation or over-expression is at least 2 fold as compared to that expressed in normal tissue.