title: Adverse outcomes in clear cell renal cell carcinoma with mutations of 3p21 epigenetic regulators BAP1 and SETD2: a report by MSKCC and the KIRC TCGA research network.
abstract: OBJECTIVE
  To investigate the impact of newly identified chromosome 3p21 epigenetic tumor suppressors PBRM1, SETD2, and BAP1 on cancer-specific survival (CSS) of 609 patients with clear cell renal cell carcinoma (ccRCC) from 2 distinct cohorts.
  
  
  METHODS
  Select sequencing on 3p tumor suppressors of 188 patients who underwent resection of primary ccRCC at the Memorial Sloan-Kettering Cancer Center (MSKCC) was conducted to interrogate the genotype-phenotype associations. These findings were compared with analyses of the genomic and clinical dataset from our nonoverlapping The Cancer Genome Atlas (TCGA) cohort of 421 patients with primary ccRCC.
  
  
  RESULTS
  3p21 tumor suppressors are frequently mutated in both the MSKCC (PBRM1, 30.3%; SETD2, 7.4%; BAP1, 6.4%) and the TCGA (PBRM1, 33.5%; SETD2, 11.6%; BAP1, 9.7%) cohorts. BAP1 mutations are associated with worse CSS in both cohorts [MSKCC, P = 0.002; HR 7.71; 95% confidence interval (CI)2.08-28.6; TCGA, P = 0.002; HR 2.21; 95% CI 1.35-3.63]. SETD2 are associated with worse CSS in the TCGA cohort (P = 0.036; HR 1.68; 95% CI 1.04-2.73). On the contrary, PBRM1 mutations, the second most common gene mutations of ccRCC, have no impact on CSS.
  
  
  CONCLUSIONS
  The chromosome 3p21 locus harbors 3 frequently mutated ccRCC tumor suppressor genes. BAP1 and SETD2 mutations (6%-12%) are associated with worse CSS, suggesting their roles in disease progression. PBRM1 mutations (30%-34%) do not impact CSS, implicating its principal role in the tumor initiation. Future efforts should focus on therapeutic interventions and further clinical, pathologic, and molecular interrogation of this novel class of tumor suppressors.
authors.affiliation: Urology Service, Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
authors.forename: A Ari
authors.initials: AA
authors.lastname: Hakimi
authors.forename: Irina
authors.initials: I
authors.lastname: Ostrovnaya
authors.forename: Boris
authors.initials: B
authors.lastname: Reva
authors.forename: Nikolaus
authors.initials: N
authors.lastname: Schultz
authors.forename: Ying-Bei
authors.initials: YB
authors.lastname: Chen
authors.forename: Mithat
authors.initials: M
authors.lastname: Gonen
authors.forename: Han
authors.initials: H
authors.lastname: Liu
authors.forename: Shugaku
authors.initials: S
authors.lastname: Takeda
authors.forename: Martin H
authors.initials: MH
authors.lastname: Voss
authors.forename: Satish K
authors.initials: SK
authors.lastname: Tickoo
authors.forename: Victor E
authors.initials: VE
authors.lastname: Reuter
authors.forename: Paul
authors.initials: P
authors.lastname: Russo
authors.forename: Emily H
authors.initials: EH
authors.lastname: Cheng
authors.forename: Chris
authors.initials: C
authors.lastname: Sander
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Motzer
authors.forename: James J
authors.initials: JJ
authors.lastname: Hsieh
mesh_terms: D000368:Aged; D002292:Carcinoma, Renal Cell / Q000378:metabolism* / Q000473:pathology / Q000601:surgery; D002471:Cell Transformation, Neoplastic; D002893:Chromosomes, Human, Pair 3; D002986:Clinical Trials as Topic; D004268:DNA-Binding Proteins; D018572:Disease-Free Survival; D044127:Epigenesis, Genetic / Q000235:genetics; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D011495:Histone-Lysine N-Methyltransferase / Q000096:biosynthesis* / Q000235:genetics; D006801:Humans; D007680:Kidney Neoplasms / Q000235:genetics / Q000378:metabolism* / Q000473:pathology; D008297:Male; D008875:Middle Aged; D009154:Mutation; D009367:Neoplasm Staging; D009687:Nuclear Proteins / Q000096:biosynthesis / Q000235:genetics; D014157:Transcription Factors / Q000096:biosynthesis / Q000235:genetics; D025521:Tumor Suppressor Proteins / Q000096:biosynthesis* / Q000235:genetics; D043222:Ubiquitin Thiolesterase / Q000096:biosynthesis* / Q000235:genetics
chemical_list: C400134:BAP1 protein, human; D004268:DNA-Binding Proteins; D009687:Nuclear Proteins; C102195:PBRM1 protein, human; D014157:Transcription Factors; D025521:Tumor Suppressor Proteins; D011495:Histone-Lysine N-Methyltransferase; C521636:SETD2 protein, human; D043222:Ubiquitin Thiolesterase