CD31, EDNRB and TSPAN7 are promising prognostic markers in clear-cell renal cell carcinoma revealed by genome-wide expression analyses of primary tumors and metastases.

Currently used clinicopathological parameters are insufficient for a reliable prediction of metastatic risk and disease-free survival (DFS) of patients with clear-cell renal cell carcinoma (ccRCC). To identify prognostic genes, the expression profiles of primary ccRCC obtained from patients with different DFS--eight synchronously, nine metachronously and seven not metastasized tumors--were determined by genome-wide expression analyses. Synchronously and metachronously metastasized primary ccRCC differed in the expression of 167 genes. Thirty-six of these genes were also differentially expressed in synchronously vs. metachronously developed pulmonary metastases analyzed in a previous study. Because of their DFS-associated deregulation that is concordant in metastases and primary ccRCC, these genes are potentially functionally involved in metastatic tumor growth and are also prognostically useful. A prognostic impact was confirmed for the genes CD31, EDNRB and TSPAN7 at the mRNA level (n=86), and for TSPAN7 at the protein level (n=106). Patients with a higher gene expression of EDNRB or TSPAN7, or with TSPAN7-positive vessels in both cores investigated on tissue microarrays had a significantly longer DFS and tumor-specific survival (TSS). Patients with a higher CD31 gene expression showed a significantly longer TSS. EDNRB was an independent prognostic marker for the DFS. CD31, EDNRB and TSPAN7 had an independent impact on the TSS. In summary, comparative analysis of primary tumors and metastases is appropriate to identify independent prognostic markers in ccRCC. Gene expression of CD31 and EDNRB, and endothelial TSPAN7 protein level are potentially useful to improve outcome prediction because of their independent prognostic impact.

Identification of genomic alterations associated with metastasis and cancer specific survival in clear cell renal cell carcinoma.

PURPOSE: We identified regions of DNA copy number changes that are significantly associated with metastasis and clinical outcome in patients with clear cell renal cell carcinoma. MATERIALS AND METHODS: We analyzed 53 primary clear cell renal cell carcinomas, including 31 metastasized and 22 nonmetastasized tumors, by array comparative genomic hybridization with a median resolution of 1 to 1.5 Mbp. To validate copy number aberrations with potential prognostic value we performed fluorescence in situ hybridization analysis using commercially available fluorescent probes. RESULTS: We identified 5 recurrent chromosomal aberrations that were significantly associated with metastasis, including gains of 1q21.3, 12q13.12, 12q13.3q14.1 and 20q11.21q13.2, and loss of 9p21.3p24.1. The most prominent of them with the highest OR for metastatic risk were loss of 9p21.3p24.1, and gains of 1q21.3 and 20q11.21q13.32. Eight alterations involving chromosomes 7, 9, 12, 16 and 20 significantly correlated with shortened cancer specific survival. The lowest p values on Kaplan-Meier analysis showed losses of 9p21.3p24.1 and 9q32q33.1, and gains of 7q36.3 and 20q11.21q13.32. Fluorescence in situ hybridization done in the same cohort for the 4 select regions 1q21.3, 7q36.3, 9p21.3p24.1 and 20q11.21q13.32 clearly confirmed the results of array comparative genomic hybridization. CONCLUSIONS: Data suggest that specific chromosomal alterations in clear cell renal cell carcinoma can be used to predict metastasis and cancer specific survival in patients with clear cell renal cell carcinoma. It seems possible to design a combined fluorescence in situ hybridization assay based on these genetic targets for outcome prediction, which can be used for routine diagnostics.

A specific gene expression signature characterizes metastatic potential in clear cell renal cell carcinoma.

PURPOSE: The discovery of metastasis markers in clear cell renal cell carcinoma is of critical importance to define individual metastatic risk and select patients for new targeted therapies. We identified potential biomarkers for metastatic clear cell renal cell carcinoma by gene expression analysis. MATERIALS AND METHODS: We performed transcriptional profiling of 16 primary metastatic and 18 nonmetastatic clear cell renal cell carcinomas with PIQOR™ microarrays. Differentially expressed genes were validated by quantitative real-time polymerase chain reaction. RESULTS: Genes discriminating between metastatic and nonmetastatic tumors were identified at q <0.001 by significance analysis of microarrays. The metastatic signature contained 127 transcripts. In metastatic samples a greater than 4-fold decrease in expression was detected for the genes CD151 and IKBA (t/F statistic p <0.0001) while the genes MMP16, B7-H1, BCL2L2 and FRA2 showed greater than 4-fold increase of expression in metastatic primary tumors (p <0.0001). Quantitative real-time polymerase chain reaction revealed significant differences in expression among all metastatic tumors, including synchronously and metachronously metastasized tumors, and nonmetastatic tumors for FRA2 (p = 0.032) and CD151 (p = 0.005). In addition, the genes B7-H1 (p = 0.040), FRA2 (p = 0.035), CD151 (p = 0.004) and BCL2L2 (p = 0.035) showed significantly higher expression in early metastasized than in nonmetastatic tumor samples. Different B7-H1 (p = 0.002) and BCL2L2 (p = 0.007) expression levels were found in samples with late metastasis compared to those in synchronously metastasized tumors. CONCLUSIONS: We determined a metastatic signature of clear cell renal cell carcinoma by microarray analysis. Our data provide the possibility of defining the metastatic potential of primary clear cell renal cell carcinoma based on a select number of genes even in a localized situation.

Specific miRNA signatures are associated with metastasis and poor prognosis in clear cell renal cell carcinoma.

PURPOSE: MicroRNAs (miRNAs) play an important role as regulators of gene expression in tumourigenesis by controlling many biological processes in growth, development, differentiation and apoptosis. Previous studies have shown an altered expression of specific miRNAs in clear cell renal cell carcinoma (ccRCC). But the function in cancerogenesis and metastasis in this tumour type is almost unknown. We aimed at identifying specific miRNA expression patterns that are associated with metastasis and prognosis in ccRCC patients. METHODS: MiRNA of 30 human ccRCC including ten non-metastatic tumours, four tumours with metastasis after 3 years or later and four tumours with primary metastasis was isolated. We analysed the miRNA expression by using microarrays and qRT-PCR. RESULTS: We detected a miRNA signature that distinguishes between metastatic and non-metastatic ccRCC, including miR-451, miR-221, miR-30a, miR-10b and miR-29a. Furthermore, we identified a group of 12 miRNAs, such as let-7 family, miR-30c, miR-26a, which are decreased in highly aggressive primary metastatic tumours. We found also correlations between expression levels of specific miRNAs with progression-free survival and overall survival. CONCLUSION: Our findings suggest that specific miRNAs are involved in metastasis and have an impact on the progression of the ccRCC. Furthermore, we identified specific miRNAs characterising very aggressive tumours with early metastasis. In addition, we determined candidate markers associated with survival of the patients. Thus, it seems possible to use miRNAs for prediction of progression to distant metastasis and prognosis analysing the primary tumour.

Multi-colour FISH on preoperative renal tumour biopsies to confirm the diagnosis of uncertain renal masses.

PURPOSE: In some cases with uncertain renal tumour lesions, it would be helpful to perform biopsies for the preoperative differential diagnosis. In our study, we evaluated the benefit of multi-colour interphase fluorescence in situ hybridization (M-FISH) on fine-needle core biopsies in uncertain renal masses. METHODS: We prospectively performed three ultrasound-guided percutaneous biopsies in 25 patients with indeterminate renal masses preoperatively. Histopathology was performed on two remaining cores samples. M-FISH was performed on one core for chromosomes 1, 2, 6, 9, 7, 17, the loci 3p24pter, and 3p13p14. After interphase FISH evaluation, we classified tumours and compared the results with histopathological findings. RESULTS: 16 were classified as renal malignancies: 14 (56%) clear cell renal cell carcinomas (RCCs), 1 papillary RCCs (4%), and 1 "adenocarcinoma" (4%). Seven patients (28%) had a benign tumour, i.e. 6 (24%) were oncocytomas and 1 was classified as leiomyoma (4%). In two cases (8%), no renal neoplasms were found. In 19 out of 21 cases (90.5%), the preoperative diagnostic fine-needle biopsy matched the final histological findings. The combination of histopathological examination and M-FISH leads to a higher (95.5 vs. 90.5%) diagnostic fidelity as histology alone. CONCLUSIONS: Ultrasound-guided percutaneous renal tumour biopsy is an accurate and safety method for the histopathologic evaluation of uncertain renal masses. The M-FISH represents a new highly sensitive and specific method to confirm histopathological classification in less than 24 h which can be used in routine laboratory diagnosis.

Comparative transcriptional and functional profiling of clear cell and papillary renal cell carcinoma.

Renal cell carcinoma (RCC) is known to effectively prevent immune recognition. However, little is known about the mechanisms that underlie this phenomenon. Thus, the identification of immunogenic molecules associated with RCC and the elucidation of the corresponding signaling pathways are crucial to the development of effective treatments. We performed transcriptional and functional profiling with cDNA microarrays (1070 cDNA probes) on a total of 17 RCCs, 11 clear cell and 6 papillary, and on corresponding normal tissue. Samples were clustered based on their expression profiles. We found a total of 45 genes to be regulated equally by both tumor types compared to the normal tissue. A set of 13 differentially expressed genes was identified between the examined tumor subtypes. Functional analysis was performed for both gene sets and showed a significant enrichment of cell surface genes regulated in both tumor subtypes. Within these we found five surface marker genes to be upregulated (TNFRSF10B, CD70, TNFR1, PDGFRB, and BAFF) which are involved in immune responses via the regulation of lymphocytes and can also induce apoptosis. Their overexpression in both tumor subtypes suggests a possible involvement in the immune escape strategies of RCC. The combination of transcriptional and functional profiling revealed potential target molecules for novel therapy strategies that must be studied in more detail.

Comparative study of renal cell carcinoma by CGH, multicolor-FISH and conventional cytogenic banding analysis.

Using different cytogenetic techniques in combination is crucial to studying the high complexity of genetic rearrangements in tumor cells. The 8 clear cell (cc) and 5 papillary (p) renal cell carcinomas (RCC) were analyzed using multicolor fluorescence in situ hybridization (multicolor-FISH), conventional Giemsa banding (G-banding) and comparative genomic hybridization (CGH) analysis. CGH analysis was carried out with DNA from frozen tissue sections and short-term cultures of primary tumors. Using CGH analysis, both tissue sections and cell cultures of ccRCC showed the typical chromosomal changes such as the loss of 3p, 4q, 6q, 8p, 9q, 14 and a gain of 5q and 7. Most imbalances detected by CGH in cell culture could be deciphered by multicolor-FISH and G-banding analysis as unbalanced trans-locations t(3;6)(p11.1;p11.1), t(8;14)(p11.1;q11.1), t(3;5) (p14;q21-22), t(1;15)(p11;q11.1), t(3;15)(p11;q11.1)t(8;17) (p11.1;q11.1), t(8;17)(q22;p11.1). Only one balanced trans-location t(9;18)(q34;q11.1) was shown in ccRCC. CGH of papillary RCC displayed mostly gains of whole chromosomes 7, 12, 16 and 17 and a loss of chromosome Y. There was 1 papillary RCC that displayed a partial gain of chromosome 7, showing an unbalanced translocation t(7;11)(q11.1;q25). The balanced translocations t(2;9)(q11.1;q34) and t(7;15) (q22 approximately 31;q21-22) were registered in pRCC. The combined analysis of RCC by different methods allowed a more accurate characterization of the complex karyotypes of tumor tissue, and offered a comprehensive description of given tumors.

Identification of tumor entities of renal cell carcinoma using interphase fluorescence in situ hybridization.

PURPOSE: We developed a rapid interphase fluorescence in situ hybridization (FISH) test to differentiate renal cell carcinoma (RCC) based on known genetic alterations and verified the suitability of this test for practical use. MATERIALS AND METHODS: We composed 2 FISH test sets using 6 centromere specific and 2 region specific DNA probes of human chromosomes. Test set 1 contained centromeric probes for chromosomes 1, 2, 6 and 9, as labeled by 4 fluorescence dyes. For test set 2 we chose 3p24pter and 3p13p14 regions, and centromeric probes of chromosomes 7 and 17. Interphase nuclei of tumor specimens were prepared from 50 mum frozen tissue sections and fixed on slides. The 2 sets were hybridized simultaneously side by side on the same slide. RESULTS: Seven clear cell carcinomas, 8 papillary carcinomas, 7 chromophobe RCCs and 3 oncocytomas were analyzed by interphase FISH. Results were compared with comparative genomic hybridization findings and pathological reports. Genetic alterations were detected in 22 of 25 analyzed tumors by FISH. FISH findings absolutely correlated with comparative genomic hybridization results. Of the analyzed carcinomas 22 could be identified correctly. In 3 tumors the histological subtypes were revised. CONCLUSIONS: The results of this study demonstrate that the performed test set allows the accurate identification of RCC in 1 hybridization step. Therefore, FISH represents an effective method for the rapid classification of RCC.