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BAP1, PBRM1 and SETD2 in clear-cell renal cell carcinoma: molecular diagnostics and possible targets for personalized therapies

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References

  • Escudier B, Pluzanska A, Koralewski P, et al. Bevacizumab plus interferon alfa-2a for treatment of metastatic renal cell carcinoma: a randomised, double-blind phase III trial. Lancet 2007;370:2103-11
  • Rini BI, Halabi S, Rosenberg JE, et al. Bevacizumab plus interferon alfa compared with interferon alfa monotherapy in patients with metastatic renal cell carcinoma: CALGB 90206. J Clin Oncol 2008;26:5422-8
  • Escudier B, Eisen T, Stadler WM, et al. Sorafenib in advanced clear-cell renal-cell carcinoma. N Engl J Med 2007;356:125-34
  • Motzer RJ, Hutson TE, Tomczak P, et al. Sunitinib versus interferon alfa in metastatic renal-cell carcinoma. N Engl J Med 2007;356:115-24
  • Sternberg CN, Davis ID, Mardiak J, et al. Pazopanib in locally advanced or metastatic renal cell carcinoma: results of a randomized phase III trial. J Clin Oncol 2010;28:1061-8
  • Rini BI, Escudier B, Tomczak P, et al. Comparative effectiveness of axitinib versus sorafenib in advanced renal cell carcinoma (AXIS): a randomised phase 3 trial. Lancet 2011;378:1931-9
  • Hudes G, Carducci M, Tomczak P, et al. Temsirolimus, interferon alfa, or both for advanced renal-cell carcinoma. N Engl J Med 2007;356:2271-81
  • Motzer RJ, Escudier B, Oudard S, et al. Efficacy of everolimus in advanced renal cell carcinoma: a double-blind, randomised, placebo-controlled phase III trial. Lancet 2008;372:449-56
  • Iacovelli R, Alesini D, Palazzo A, et al. Targeted therapies and complete responses in first line treatment of metastatic renal cell carcinoma. A meta-analysis of published trials. Cancer Treat Rev 2014;40:271-5
  • Brugarolas J. Molecular genetics of clear-cell renal cell carcinoma. J Clin Oncol 2014;32:1968-76
  • Young AP, Schlisio S, Minamishima YA, et al. VHL loss actuates a HIF-independent senescence programme mediated by Rb and p400. Nat Cell Biol 2008;10:361-9
  • Pena-Llopis S, Vega-Rubin-de-Celis S, Liao A, et al. BAP1 loss defines a new class of renal cell carcinoma. Nat Genet 2012;44:751-9
  • Hakimi AA, Ostrovnaya I, Reva B, et al. 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. Clin Cancer Res 2013;19:3259-67
  • Kapur P, Pena-Llopis S, Christie A, et al. Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: a retrospective analysis with independent validation. Lancet Oncol 2013;14:159-67
  • Nishikawa H, Wu W, Koike A, et al. BRCA1-associated protein 1 interferes with BRCA1/BARD1 RING heterodimer activity. Cancer Res 2009;69:111-19
  • Mallery DL, Vandenberg CJ, Hiom K. Activation of the E3 ligase function of the BRCA1/BARD1 complex by polyubiquitin chains. EMBO J 2002;21:6755-62
  • Wang SS, Gu YF, Wolff N, et al. Bap1 is essential for kidney function and cooperates with Vhl in renal tumorigenesis. Proc Natl Acad Sci USA 2014;111:16538-43
  • Harbour JW, Onken MD, Roberson ED, et al. Frequent mutation of BAP1 in metastasizing uveal melanomas. Science 2010;330:1410-13
  • Landreville S, Agapova OA, Matatall KA, et al. Histone deacetylase inhibitors induce growth arrest and differentiation in uveal melanoma. Clin Cancer Res 2012;18:408-16
  • Pan H, Jia R, Zhang L, et al. BAP1 regulates cell cycle progression through E2F1 target genes and mediates transcriptional silencing via H2A monoubiquitination in uveal melanoma cells. Int J Biochem Cell Biol 2015;60:176-84
  • Kumar R, Taylor M, Miao B, et al. BAP1 Has a Survival Role in Cutaneous Melanoma. J Invest Dermatol 2015;135:1089-97
  • Bott M, Brevet M, Taylor BS, et al. The nuclear deubiquitinase BAP1 is commonly inactivated by somatic mutations and 3p21.1 losses in malignant pleural mesothelioma. Nat Genet 2011;43:668-72
  • Su D, Singer EA, Srinivasan R. Molecular pathways in renal cell carcinoma: recent advances in genetics and molecular biology. Curr Opin Oncol 2015;27:217-23
  • Xia W, Nagase S, Montia AG, et al. BAF180 is a critical regulator of p21 induction and a tumor suppressor mutated in breast cancer. Cancer Res 2008;68:1667-74
  • Burrows AE, Smogorzewska A, Elledge SJ. Polybromo-associated BRG1-associated factor components BRD7 and BAF180 are critical regulators of p53 required for induction of replicative senescence. Proc Natl Acad Sci USA 2010;107:14280-5
  • Kakarougkas A, Ismail A, Chambers AL, et al. Requirement for PBAF in transcriptional repression and repair at DNA breaks in actively transcribed regions of chromatin. Mol Cell 2014;55:723-32
  • Brownlee PM, Chambers AL, Cloney R, et al. BAF180 promotes cohesion and prevents genome instability and aneuploidy. Cell Rep 2014;6:973-81
  • Varela I, Tarpey P, Raine K, et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 2011;469:539-42
  • Shain AH, Giacomini CP, Matsukuma K, et al. Convergent structural alterations define SWItch/Sucrose NonFermentable (SWI/SNF) chromatin remodeler as a central tumor suppressive complex in pancreatic cancer. Proc Natl Acad Sci USA 2012;109:E252-9
  • Al Sarakbi W, Sasi W, Jiang WG, et al. The mRNA expression of SETD2 in human breast cancer: correlation with clinico-pathological parameters. BMC Cancer 2009;9:290
  • Zhang J, Ding L, Holmfeldt L, et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature 2012;481:157-63
  • Creighton CJ, Morgan M, Gunaratne PH, et al. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 2013;499:43-9
  • Simon JM, Hacker KE, Singh D, et al. Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Res 2014;24:241-50
  • Li F, Mao G, Tong D, et al. The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutSalpha. Cell 2013;153:590-600
  • Carvalho S, Vitor AC, Sridhara SC, et al. SETD2 is required for DNA double-strand break repair and activation of the p53-mediated checkpoint. Elife 2014;3:e02482
  • Pfister SX, Ahrabi S, Zalmas LP, et al. SETD2-dependent histone H3K36 trimethylation is required for homologous recombination repair and genome stability. Cell Rep 2014;7:2006-18
  • Raponi M, Douglas AG, Tammaro C, et al. Evolutionary constraint helps unmask a splicing regulatory region in BRCA1 exon 11. PLoS One 2012;7:e37255
  • Piva F, Giulietti M, Burini AB, Principato G. SpliceAid 2: a database of human splicing factors expression data and RNA target motifs. Hum Mutat 2012;33:81-5
  • Hakimi AA, Chen YB, Wren J, et al. Clinical and pathologic impact of select chromatin-modulating tumor suppressors in clear cell renal cell carcinoma. Eur Urol 2013;63:848-54
  • Pawlowski R, Muhl SM, Sulser T, et al. Loss of PBRM1 expression is associated with renal cell carcinoma progression. Int J Cancer 2013;132:E11-17
  • Ho TH, Kapur P, Joseph RW, et al. Loss of PBRM1 and BAP1 expression is less common in non-clear cell renal cell carcinoma than in clear cell renal cell carcinoma. Urol Oncol 2015;33:23 e9-14
  • Durinck S, Stawiski EW, Pavia-Jimenez A, et al. Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes. Nat Genet 2015;47:13-21
  • Gerlinger M, Horswell S, Larkin J, et al. Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat Genet 2014;46:225-33
  • Pena-Llopis S, Christie A, Xie XJ, Brugarolas J. Cooperation and antagonism among cancer genes: the renal cancer paradigm. Cancer Res 2013;73:4173-9
  • Kandoth C, McLellan MD, Vandin F, et al. Mutational landscape and significance across 12 major cancer types. Nature 2013;502:333-9
  • Popova T, Hebert L, Jacquemin V, et al. Germline BAP1 mutations predispose to renal cell carcinomas. Am J Hum Genet 2013;92:974-80
  • Farley MN, Schmidt LS, Mester JL, et al. A novel germline mutation in BAP1 predisposes to familial clear-cell renal cell carcinoma. Mol Cancer Res 2013;11:1061-71
  • Abdel-Rahman MH, Pilarski R, Cebulla CM, et al. Germline BAP1 mutation predisposes to uveal melanoma, lung adenocarcinoma, meningioma, and other cancers. J Med Genet 2011;48:856-9
  • Testa JR, Cheung M, Pei J, et al. Germline BAP1 mutations predispose to malignant mesothelioma. Nat Genet 2011;43:1022-5
  • Njauw CN, Kim I, Piris A, et al. Germline BAP1 inactivation is preferentially associated with metastatic ocular melanoma and cutaneous-ocular melanoma families. PLoS ONE 2012;7:e35295
  • Aoude LG, Vajdic CM, Kricker A, et al. Prevalence of germline BAP1 mutation in a population-based sample of uveal melanoma cases. Pigment Cell Melanoma Res 2013;26:278-9
  • de la Fouchardiere A, Cabaret O, Savin L, et al. Germline BAP1 mutations predispose also to multiple basal cell carcinomas. Clin Genet 2014
  • Betti M, Casalone E, Ferrante D, et al. Inference on germline BAP1 mutations and asbestos exposure from the analysis of familial and sporadic mesothelioma in a high-risk area. Genes Chromosomes Cancer 2015;54:51-62
  • Jiayin W CL, Mingchao X, et al. Integrated analysis of germline and somatic variants in renal clear cell carcinoma. AACR Annual Meeting 2014; Cancer Res, San Diego, CA, 2014
  • Ibragimova I, Maradeo ME, Dulaimi E, Cairns P. Aberrant promoter hypermethylation of PBRM1, BAP1, SETD2, KDM6A and other chromatin-modifying genes is absent or rare in clear cell RCC. Epigenetics 2013;8:486-93
  • Buck MJ, Raaijmakers LM, Ramakrishnan S, et al. Alterations in chromatin accessibility and DNA methylation in clear cell renal cell carcinoma. Oncogene 2014;33:4961-5
  • Joseph RW, Kapur P, Serie DJ, et al. Loss of BAP1 protein expression is an independent marker of poor prognosis in patients with low-risk clear cell renal cell carcinoma. Cancer 2014;120:1059-67
  • Karlo CA, Di Paolo PL, Chaim J, et al. Radiogenomics of clear cell renal cell carcinoma: associations between CT imaging features and mutations. Radiology 2014;270:464-71
  • Eletr ZM, Yin L, Wilkinson KD. BAP1 is phosphorylated at serine 592 in S-phase following DNA damage. FEBS Lett 2013;587:3906-11
  • Yu H, Pak H, Hammond-Martel I, et al. Tumor suppressor and deubiquitinase BAP1 promotes DNA double-strand break repair. Proc Natl Acad Sci USA 2014;111:285-90
  • Hainsworth JD, Infante JR, Spigel DR, et al. A phase II trial of panobinostat, a histone deacetylase inhibitor, in the treatment of patients with refractory metastatic renal cell carcinoma. Cancer Invest 2011;29:451-5
  • Stadler WM, Margolin K, Ferber S, et al. A phase II study of depsipeptide in refractory metastatic renal cell cancer. Clin Genitourin Cancer 2006;5:57-60
  • Clinical trials.gov, A service of the U.S. National Institutes of Health, Vorinostat in Treating Patients With Kidney Cancer. Available from: https://clinicaltrials.gov/ct2/show/NCT00278395
  • Clinical trials.gov, A service of the U.S. National Institutes of Health, MS-275 in Treating Patients With Advanced Solid Tumors or Lymphoma. Available from: https://clinicaltrials.gov/ct2/show/NCT00020579
  • Clinical trials.gov, A service of the U.S. National Institutes of Health, Study of Oral PXD101 in Patients With Advanced Solid Tumors or Lymphoma. Available from: https://clinicaltrials.gov/ct2/show/NCT00413075
  • Clinical trials.gov, A service of the U.S. National Institutes of Health, Entinostat in Combination With Aldesleukin in Treating Patients With Metastatic Kidney Cancer. Available from: https://clinicaltrials.gov/ct2/show/NCT01038778
  • Clinical trials.gov, A service of the U.S. National Institutes of Health, Trial of Olaparib in Combination With AZD5363 (ComPAKT). Available from: https://clinicaltrials.gov/ct2/show/NCT02338622
  • Guo G, Gui Y, Gao S, et al. Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma. Nat Genet 2012;44:17-19
  • Sato Y, Yoshizato T, Shiraishi Y, et al. Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet 2013;45:860-7

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