Identification of BAP1 mutation as a common mutation correlated with tumor mutation burden and immune infiltration in kidney renal clear cell carcinoma

References

• Balasubramani A, Larjo A, Bassein JA, Chang X, Hastie RB, Togher SM, et al. 2015. Cancer-associated ASXL1 mutations may act as gain-of-function mutations of the ASXL1-BAP1 complex. Nat Commun. 6:7307. https://pubmed.ncbi.nlm.nih.gov/26095772/.
   PubMed Web of Science ®Google Scholar
• Barata PC, Rini BI. 2017. Treatment of renal cell carcinoma: current status and future directions. CA Cancer J Clin 67(6):507–524. https://pubmed.ncbi.nlm.nih.gov/28961310/.
   PubMed Web of Science ®Google Scholar
• Carbone M, Harbour JW, Brugarolas J, Bononi A, Pagano I, Dey A, et al. 2020. Biological mechanisms and clinical significance of BAP1 mutations in human Cancer. Cancer Discov. 10:1103–1120. https://pubmed.ncbi.nlm.nih.gov/32690542/.
   PubMed Web of Science ®Google Scholar
• Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO, Aksoy BA, et al. 2012 May. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2(5):401–404.
   PubMed Web of Science ®Google Scholar
• Chalmers ZR, Connelly CF, Fabrizio D, Gay L, Ali SM, Ennis R, et al. 2017. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med. 9(1):34. https://pubmed.ncbi.nlm.nih.gov/28420421/.
   PubMed Web of Science ®Google Scholar
• Chau C, van Doorn R, van Poppelen NM, van der Stoep N, Mensenkamp AR, Sijmons RH, et al. 2019. Families with BAP1-tumor predisposition syndrome in the Netherlands: path to identification and a proposal for genetic screening guidelines. Cancers. 11(8):1114. https://pubmed.ncbi.nlm.nih.gov/31382694/.
   PubMed Web of Science ®Google Scholar
• Correa JK, Brown TA. 2019. Expression of generalized anxiety disorder across the lifespan. J Psychopathol Behav Assess. 41(1):53–59. https://pubmed.ncbi.nlm.nih.gov/31938010/.
   PubMed Web of Science ®Google Scholar
• Dudeck A, Köberle M, Goldmann O, Meyer N, Dudeck J, Lemmens S, et al. 2019. Mast cells as protectors of health. J Allergy Clin Immunol. 144(4):S4–18. https://pubmed.ncbi.nlm.nih.gov/30468774/.
   PubMed Web of Science ®Google Scholar
• Gallan AJ, Parilla M, Segal J, Ritterhouse L, Antic T. 2021. BAP1-mutated clear cell renal cell carcinoma. Am J Clin Pathol. 155(5):718–728.
   PubMed Web of Science ®Google Scholar
• Greco F, Mallio CA. 2021. Relationship between visceral adipose tissue and genetic mutations (VHL and KDM5C) in clear cell renal cell carcinoma. Radiol Med. 126(5):645–651. doi:10.1007/s11547-020-01310-y.
   PubMed Web of Science ®Google Scholar
• Greco F, Quarta LG, Grasso RF, Beomonte Zobel B, Mallio CA. 2020. Increased visceral adipose tissue in clear cell renal cell carcinoma with and without peritumoral collateral vessels. Br J Radiol. 93(1112):20200334. doi:10.1259/bjr.20200334.
   PubMed Web of Science ®Google Scholar
• Jensen DE, Proctor M, Marquis ST, Gardner HP, Ha SI, Chodosh LA, et al. 1998. BAP1: a novel ubiquitin hydrolase which binds to the BRCA1 RING finger and enhances BRCA1-mediated cell growth suppression. Oncogene. 16(9):1097–1112. https://pubmed.ncbi.nlm.nih.gov/9528852/.
   PubMed Web of Science ®Google Scholar
• Kowalewski A, Zdrenka M, Grzanka D, Szylberg Ł. 2020. Targeting the deterministic evolutionary trajectories of clear cell renal cell carcinoma. Cancers MDPI AG. 12:1–13. https://pubmed.ncbi.nlm.nih.gov/33182233/.
   Web of Science ®Google Scholar
• Landskron G, De La Fuente M, Thuwajit P, Thuwajit C, Hermoso MA. 2014. Chronic inflammation and cytokines in the tumor microenvironment. J. Immunol. Res. 2014:149185. https://pubmed.ncbi.nlm.nih.gov/24901008/.
   PubMed Web of Science ®Google Scholar
• Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. 2018. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 28(11):1747–1756. https://pubmed.ncbi.nlm.nih.gov/30341162/.
   PubMed Web of Science ®Google Scholar
• Méjean A, Ravaud A, Thezenas S, Colas S, Beauval J-B, Bensalah K, et al. 2018. Sunitinib alone or after nephrectomy in metastatic renal-cell carcinoma. N Engl J Med. 379(5):417–427. https://pubmed.ncbi.nlm.nih.gov/29860937/.
   PubMed Web of Science ®Google Scholar
• Merluzzi S, Betto E, Ceccaroni AA, Magris R, Giunta M, Mion F. 2015. Mast cells, basophils and B cell connection network. Mol. Immunol. 63:94–103. https://pubmed.ncbi.nlm.nih.gov/24671125/.
   PubMed Web of Science ®Google Scholar
• Moore AL, Batavia AA, Kuipers J, Singer J, Burcklen E, Schraml P, et al. 2021. Spatial distribution of private gene mutations in clear cell renal cell carcinoma. Cancers. 13(9):2163. https://pubmed.ncbi.nlm.nih.gov/33946379.
   PubMed Web of Science ®Google Scholar
• Motzer RJ, Bukowski RM, Figlin RA, Hutson TE, Michaelson MD, Kim ST, et al. 2008. Prognostic nomogram for sunitinib in patients with metastatic renal cell carcinoma. Cancer. 113(7):1552–1558. https://pubmed.ncbi.nlm.nih.gov/18720362/.
   PubMed Web of Science ®Google Scholar
• Motzer RJ, Jonasch E, Agarwal N, Bhayani S, Bro WP, Chang SS, et al. 2017. Kidney cancer, version 2.2017: clinical practice guidelines in oncology. J Natl Compr Cancer Netw. 15:804–834. https://pubmed.ncbi.nlm.nih.gov/28596261/.
   PubMed Web of Science ®Google Scholar
• Motzer RJ, Penkov K, Haanen J, Rini B, Albiges L, Campbell MT, et al. 2019. Avelumab plus axitinib versus sunitinib for advanced renal-cell carcinoma. N Engl J Med. 380(12):1103–1115. https://pubmed.ncbi.nlm.nih.gov/30779531/.
   PubMed Web of Science ®Google Scholar
• Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, et al. 2015. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 12(5):453–457. https://pubmed.ncbi.nlm.nih.gov/25822800/.
   PubMed Web of Science ®Google Scholar
• Pinato DJ, Urus H, Newsom-Davis T, Du Parcq P, Belessiotis K, Mapara L, et al. 2020. Applicability of routine targeted next-generation sequencing to estimate tumor mutational burden (TMB) in patients treated with immune checkpoint inhibitor therapy. J Immunother. 43(2):53–56. https://pubmed.ncbi.nlm.nih.gov/31567705/.
   PubMed Web of Science ®Google Scholar
• Purwar R, Schlapbach C, Xiao S, Kang HS, Elyaman W, Jiang X, et al. 2012. Robust tumor immunity to melanoma mediated by interleukin-9-producing T cells. Nat Med. 18(8):1248–1253. https://pubmed.ncbi.nlm.nih.gov/22772464/.
   PubMed Web of Science ®Google Scholar
• Rajandram R, Bennett NC, Morais C, Johnson DW, Gobe GC. 2012. Renal cell carcinoma: resistance to therapy, role of apoptosis, and the prognostic and therapeutic target potential of TRAF proteins. Med Hypotheses. 78(2):330–336. https://pubmed.ncbi.nlm.nih.gov/22153576/.
   PubMed Web of Science ®Google Scholar
• Ricciuti B, Kravets S, Dahlberg SE, Umeton R, Albayrak A, Subegdjo SJ, et al. 2019. Use of targeted next generation sequencing to characterize tumor mutational burden and efficacy of immune checkpoint inhibition in small cell lung cancer. J Immunother Cancer. 7(1):87. https://pubmed.ncbi.nlm.nih.gov/30922388/.
   PubMedGoogle Scholar
• Salk JJ, Schmitt MW, Loeb LA. 2018. Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations. Nat Rev Genet. 19:269–285. https://pubmed.ncbi.nlm.nih.gov/29576615/.
   PubMed Web of Science ®Google Scholar
• Shrestha R, Nabavi N, Lin YY, Mo F, Anderson S, Volik S, et al. 2019. BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma. Genome Med. 11(1):8. https://pubmed.ncbi.nlm.nih.gov/30777124/.
   PubMedGoogle Scholar
• Siegel RL, Miller KD, Jemal A. 2019. Cancer statistics, 2019. CA Cancer J Clin. 69(1):7–34. https://pubmed.ncbi.nlm.nih.gov/30620402/.
   PubMed Web of Science ®Google Scholar
• Tan G, Xuan Z, Li Z, Huang S, Chen G, Wu Y, et al. 2020. The critical role of BAP1 mutation in the prognosis and treatment selection of kidney renal clear cell carcinoma. Transl Androl Urol. 9(4):1725–1734. http://tau.amegroups.com/article/view/49617/html.
   PubMed Web of Science ®Google Scholar
• Varricchi G, De Paulis A, Marone G, Galli SJ. 2019. Future needs in mast cell biology. Int J Mol Sci. 20:4397. https://pubmed.ncbi.nlm.nih.gov/31500217/.
   PubMed Web of Science ®Google Scholar
• Vugrin D. 1987. Systemic therapy of metastatic renal cell carcinoma. Vol. 7, seminars in nephrology. N Engl J Med. 7(2):152–162. https://pubmed.ncbi.nlm.nih.gov/28121507/.
   Google Scholar
• Weinstein JN, Collisson EA, Mills GB, Shaw KRM, Ozenberger BA, Ellrott K, et al. 2013. The cancer genome atlas pan-cancer analysis project. Nat Genet. 45(10):1113–1120.
   PubMed Web of Science ®Google Scholar
• Zhang J, Baran J, Cros A, Guberman JM, Haider S, Hsu J, et al. 2011. International cancer genome consortium data portal – a one-stop shop for cancer genomics data. Database. 2011:bar026. doi:10.1093/database/bar026 
   PubMedGoogle Scholar
• Zhao W, Steinfeld JB, Liang F, Chen X, Maranon DG, Jian Ma C, et al. 2017. BRCA1-BARD1 promotes RAD51-mediated homologous DNA pairing. Nature. 550(7676):360–365. https://pubmed.ncbi.nlm.nih.gov/28976962/.
   PubMed Web of Science ®Google Scholar