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MP71-10 CLINICAL FEATURES OF RECURRENT SOMATIC MUTATIONS IN CLEAR CELL RENAL CELL CARCINOMA: A LARGE COHORT
THE JOURNAL OF UROLOGYâ
Vol. 195, No. 4S, Supplement, Monday, May 9, 2016
MP71-09 MUTUAL EXCLUSIVITY OF CHROMOSOME 9P AND 3P LOSS PROVIDES NOVEL THERAPEUTIC TARGET
e919
CONCLUSIONS: Our analysis found enrichment of several gene mutations related to ccRCC in the setting of larger tumors and those with advanced disease.
Chenghen Feng*, Hui Wen, Shanghai, China, People’s Republic of INTRODUCTION AND OBJECTIVES: To study the mutual exclusivity of arm-level chromosomal (Chr) alterations in clear cell renal cell carcinoma (ccRCC) and its therapeutic potential. METHODS: We conducted an in silico analysis using the Cancer Genome Atlas (TCGA) and COSMIC databases to identify chromosomal changes (Copy number variance, CNV, and mutation) in ccRCC samples and cell lines. In vitro genetic silencing assays were performed to compare proliferation, cell cycle, and apoptosis in a series of ccRCC cells. RESULTS: Querying hallmark genes on Chr 9p (CDKN2A and CDKN2B) and Chr 3p (VHL, PBRM1, SETD2, and BAP1) on TCGA, we found no cases with simultaneous homogenous deletion of 9p and 3p. Genetic alteration (CNV/mutation) of CDKN2A/CDKN2B was significantly mutually exclusive to those of SETD2 and PBRM1. Worsened prognosis of 9p was neutralized when queried with alteration of either 3p or 9p genes. In ccRCC cell lines however, loss of >¼ 2 3p genes other than VHL were associated with CN neutral CDKN2A/CDKN2B. Silencing both PBRM1 and BAP1 exhibited strongest synthetic lethality in CDKN2A/CDKN2B loss ccRCC cells, followed by PBRM1 and SETD2, and BAP1 and SETD2. Addition of VHL silencing in VHL wildtype cell lines did not show additive effect. Silencing of any two major 3p genes (PBRM1/BAP1/SETD2) in combination with loss of either major 9p genes (CDKN2A/CDKN2B) induced potent apoptosis but not cell cycle arrest. CONCLUSIONS: Mutual exclusivity and synthetic lethality assays revealed novel approaches against ccRCC with specific genotypes. Source of Funding: This study was supported in part by the Science and Technology Commission Shanghai Municipality (Grant No. 15411965000), and National Natural Science Foundation of China (Grant No. 81502189)
Source of Funding: Ruth L. Kirschstein National Research Service Award T32CA082088, NIH/NCI Cancer Center Support Grant P30 CA008748, The Thompson Foundation, The German Research Foundation
MP71-11 MP71-10 CLINICAL FEATURES OF RECURRENT SOMATIC MUTATIONS IN CLEAR CELL RENAL CELL CARCINOMA: A LARGE COHORT Brandon J Manley*, Jozefina Casuscelli, Daniel M Tennenbaum, Maria F Becerra, Almedina Redzematovic, Maria E Arcila, Martin H. Voss, Darren R. Feldman, Jonathan A. Coleman, Paul Russo, Robert J. Motzer, James J Hsieh, A. Ari Hakimi, New York, NY INTRODUCTION AND OBJECTIVES: There have been several large scale efforts by groups including The Cancer Genome Atlas (TCGA), The International Cancer Genome Consortium (ICGC) and the University of Tokyo (Sato) to characterize the mutational frequencies of clear cell renal cell carcinoma (ccRCC). Sequencing efforts have revealed recurrent somatic mutations in a number of genes. In our study we pooled patients from available public cohorts and our institution for analysis of the clinical implications of these mutations. METHODS: We assessed 867 ccRCC patients with available genomic and clinical data. 645 patients came from published cohorts including TCGA, ICGC and Sato. 212 patients were from our institutional database. We analyzed the maximum size of the primary tumor with respect to mutation status in 14 recurrently mutated genes in ccRCC using a two-tailed Mann-Whitney U test. We also analyzed the frequency of these gene mutations between patients with American Joint Committee on Cancer stage I-III and those with stage IV disease using two-tailed z-test for proportions. RESULTS: The overall median maximum primary tumor dimension in our cohort was 6 cm. Figure 1 displays the sizes of six genes based on their mutation status and includes the four genes found to have a significant difference in size. The comparison of stage I-III patients to those with stage IV found seven genes to be significantly more common in stage IV patients, Table 1.
GENOMIC LANSCAPE OF CLEAR CELL RENAL CELL CARCINOMA METASTASIS Maria F. Becerra*, Brandon J. Manley, Jozefina Casuscelli, Almedina Redzematovic, Daniel M. Tennenbaum, Robert J. Motzer, Darren R. Feldman, Martin H. Voss, Maria Arcila, Paul Russo, Jonathan A. Coleman, James J. Hsieh, A. Ari Hakimi, New York, NY INTRODUCTION AND OBJECTIVES: The landscape of genomic alterations from primary sites of clear cell renal cell carcinoma (ccRCC) have been well characterized and adequately reported. However, the mutation status of metastatic tumors has not been well explored. Our study aims to better characterize the mutational landscape of metastatic ccRCC, including mutation status according to metastatic site. METHODS: From a prospectively collected, intuitional genomic database, we identified patients with ccRCC whose metastases had been sequenced. All tumors underwent next-generation sequencing using MSK-IMPACT, a panel of genes commonly mutated in human malignancies performed in a CLIA environment. Samples were subdivided into groups based on metastatic site (lung, lymph node, bone, adrenal gland, brain, liver, or other). The frequency of several genes found to be recurrently mutated in ccRCC was examined, grouped by metastatic site, and compared using chi-square analysis. RESULTS: Sixty patients were included in our study. Previously identified high-frequency somatic mutations (including VHL, PBRM1, SETD2, KDM5C, PTEN) were found to be present in metastatic tissue but were not preferentially expressed at a particular site. Mutations in NF2 were found to be more common in bone metastasis than in any other site (p¼0.0035). Also, MTOR mutations were more frequently present at atypical sites of metastasis than in any other
Vol. 195, No. 4S, Supplement, Monday, May 9, 2016
MP71-09 MUTUAL EXCLUSIVITY OF CHROMOSOME 9P AND 3P LOSS PROVIDES NOVEL THERAPEUTIC TARGET
e919
CONCLUSIONS: Our analysis found enrichment of several gene mutations related to ccRCC in the setting of larger tumors and those with advanced disease.
Chenghen Feng*, Hui Wen, Shanghai, China, People’s Republic of INTRODUCTION AND OBJECTIVES: To study the mutual exclusivity of arm-level chromosomal (Chr) alterations in clear cell renal cell carcinoma (ccRCC) and its therapeutic potential. METHODS: We conducted an in silico analysis using the Cancer Genome Atlas (TCGA) and COSMIC databases to identify chromosomal changes (Copy number variance, CNV, and mutation) in ccRCC samples and cell lines. In vitro genetic silencing assays were performed to compare proliferation, cell cycle, and apoptosis in a series of ccRCC cells. RESULTS: Querying hallmark genes on Chr 9p (CDKN2A and CDKN2B) and Chr 3p (VHL, PBRM1, SETD2, and BAP1) on TCGA, we found no cases with simultaneous homogenous deletion of 9p and 3p. Genetic alteration (CNV/mutation) of CDKN2A/CDKN2B was significantly mutually exclusive to those of SETD2 and PBRM1. Worsened prognosis of 9p was neutralized when queried with alteration of either 3p or 9p genes. In ccRCC cell lines however, loss of >¼ 2 3p genes other than VHL were associated with CN neutral CDKN2A/CDKN2B. Silencing both PBRM1 and BAP1 exhibited strongest synthetic lethality in CDKN2A/CDKN2B loss ccRCC cells, followed by PBRM1 and SETD2, and BAP1 and SETD2. Addition of VHL silencing in VHL wildtype cell lines did not show additive effect. Silencing of any two major 3p genes (PBRM1/BAP1/SETD2) in combination with loss of either major 9p genes (CDKN2A/CDKN2B) induced potent apoptosis but not cell cycle arrest. CONCLUSIONS: Mutual exclusivity and synthetic lethality assays revealed novel approaches against ccRCC with specific genotypes. Source of Funding: This study was supported in part by the Science and Technology Commission Shanghai Municipality (Grant No. 15411965000), and National Natural Science Foundation of China (Grant No. 81502189)
Source of Funding: Ruth L. Kirschstein National Research Service Award T32CA082088, NIH/NCI Cancer Center Support Grant P30 CA008748, The Thompson Foundation, The German Research Foundation
MP71-11 MP71-10 CLINICAL FEATURES OF RECURRENT SOMATIC MUTATIONS IN CLEAR CELL RENAL CELL CARCINOMA: A LARGE COHORT Brandon J Manley*, Jozefina Casuscelli, Daniel M Tennenbaum, Maria F Becerra, Almedina Redzematovic, Maria E Arcila, Martin H. Voss, Darren R. Feldman, Jonathan A. Coleman, Paul Russo, Robert J. Motzer, James J Hsieh, A. Ari Hakimi, New York, NY INTRODUCTION AND OBJECTIVES: There have been several large scale efforts by groups including The Cancer Genome Atlas (TCGA), The International Cancer Genome Consortium (ICGC) and the University of Tokyo (Sato) to characterize the mutational frequencies of clear cell renal cell carcinoma (ccRCC). Sequencing efforts have revealed recurrent somatic mutations in a number of genes. In our study we pooled patients from available public cohorts and our institution for analysis of the clinical implications of these mutations. METHODS: We assessed 867 ccRCC patients with available genomic and clinical data. 645 patients came from published cohorts including TCGA, ICGC and Sato. 212 patients were from our institutional database. We analyzed the maximum size of the primary tumor with respect to mutation status in 14 recurrently mutated genes in ccRCC using a two-tailed Mann-Whitney U test. We also analyzed the frequency of these gene mutations between patients with American Joint Committee on Cancer stage I-III and those with stage IV disease using two-tailed z-test for proportions. RESULTS: The overall median maximum primary tumor dimension in our cohort was 6 cm. Figure 1 displays the sizes of six genes based on their mutation status and includes the four genes found to have a significant difference in size. The comparison of stage I-III patients to those with stage IV found seven genes to be significantly more common in stage IV patients, Table 1.
GENOMIC LANSCAPE OF CLEAR CELL RENAL CELL CARCINOMA METASTASIS Maria F. Becerra*, Brandon J. Manley, Jozefina Casuscelli, Almedina Redzematovic, Daniel M. Tennenbaum, Robert J. Motzer, Darren R. Feldman, Martin H. Voss, Maria Arcila, Paul Russo, Jonathan A. Coleman, James J. Hsieh, A. Ari Hakimi, New York, NY INTRODUCTION AND OBJECTIVES: The landscape of genomic alterations from primary sites of clear cell renal cell carcinoma (ccRCC) have been well characterized and adequately reported. However, the mutation status of metastatic tumors has not been well explored. Our study aims to better characterize the mutational landscape of metastatic ccRCC, including mutation status according to metastatic site. METHODS: From a prospectively collected, intuitional genomic database, we identified patients with ccRCC whose metastases had been sequenced. All tumors underwent next-generation sequencing using MSK-IMPACT, a panel of genes commonly mutated in human malignancies performed in a CLIA environment. Samples were subdivided into groups based on metastatic site (lung, lymph node, bone, adrenal gland, brain, liver, or other). The frequency of several genes found to be recurrently mutated in ccRCC was examined, grouped by metastatic site, and compared using chi-square analysis. RESULTS: Sixty patients were included in our study. Previously identified high-frequency somatic mutations (including VHL, PBRM1, SETD2, KDM5C, PTEN) were found to be present in metastatic tissue but were not preferentially expressed at a particular site. Mutations in NF2 were found to be more common in bone metastasis than in any other site (p¼0.0035). Also, MTOR mutations were more frequently present at atypical sites of metastasis than in any other