Corrected on Jun 19, 2018.
Source: the publisher, via Crossref · checked Oct 16, 2026 · Read the notice
- Corrected on Apr 23, 2024. Source: the publisher, via Crossref · Read the notice
The Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
Christopher J. Ricketts, Aguirre A. De Cubas, Huihui Fan and 97 more
Cell Reports · 2018 · CC BY
doi:10.1016/j.celrep.2018.03.075
Abstract
Renal cell carcinoma (RCC) is not a single disease, but several histologically defined cancers with different genetic drivers, clinical courses, and therapeutic responses. The current study evaluated 843 RCC from the three major histologic subtypes, including 488 clear cell RCC, 274 papillary RCC, and 81 chromophobe RCC. Comprehensive genomic and phenotypic analysis of the RCC subtypes reveals distinctive features of each subtype that provide the foundation for the development of subtype-specific therapeutic and management strategies for patients affected with these cancers. Somatic alteration of BAP1, PBRM1, and PTEN and altered metabolic pathways correlated with subtype-specific decreased survival, while CDKN2A alteration, increased DNA hypermethylation, and increases in the immune-related Th2 gene expression signature correlated with decreased survival within all major histologic subtypes. CIMP-RCC demonstrated an increased immune signature, and a uniform and distinct metabolic expression pattern identified a subset of metabolically divergent (MD) ChRCC that associated with extremely poor survival.
References 62
- 1.
Aine M, Eriksson P, Liedberg F, Sjödahl G, Höglund M. Biological determinants of bladder cancer gene expression subtypes. Sci Rep. 2015;5:10957.
Not in our library10.1038/srep10957
- 2.
Beck AH, Espinosa I, Edris B, Li R, Montgomery K, Zhu S, Varma S, Marinelli RJ, van de Rijn M, West RB. The macrophage colony-stimulating factor 1 response signature in breast carcinoma. Clin Cancer Res. 2009;15:778-787.
Not in our library10.1158/1078-0432.ccr-08-1283
- 3.
Bindea G, Mlecnik B, Tosolini M, Kirilovsky A, Waldner M, Obenauf AC, Angell H, Fredriksen T, Lafontaine L, Berger A, et al. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. Immunity. 2013;39:782-795.
Not in our library10.1016/j.immuni.2013.10.003
- 4.
Bolotin DA, Shugay M, Mamedov IZ, Putintseva EV, Turchaninova MA, Zvyagin IV, Britanova OV, Chudakov DM. MiTCR: software for T-cell receptor sequencing data analysis. Nat Methods. 2013;10:813-814.
Not in our library10.1038/nmeth.2555
- 5.
Calabrese C, Simone D, Diroma MA, Santorsola M, Guttà C, Gasparre G, Picardi E, Pesole G, Attimonelli M. MToolBox: a highly automated pipeline for heteroplasmy annotation and prioritization analysis of human mitochondrial variants in high-throughput sequencing. Bioinformatics. 2014;30:3115-3117.
Not in our library10.1093/bioinformatics/btu483
- 6.
Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature. 2013;499:43-49.
Not in our library10.1038/nature12222
- 7.
Cancer Genome Atlas Research Network, Linehan WM, Spellman PT, Ricketts CJ, Creighton CJ, Fei SS, Davis C, Wheeler DA, Murray BA, Schmidt L, Vocke CD, et al. Comprehensive molecular characterization of papillary renal-cell carcinoma. N Engl J Med. 2016;374:135-145.
Not in our library10.1056/nejmoa1505917
- 8.
Casuscelli J, Weinhold N, Gundem G, Wang L, Zabor EC, Drill E, Wang PI, Nanjangud GJ, Redzematovic A, Nargund AM, et al. Genomic landscape and evolution of metastatic chromophobe renal cell carcinoma. JCI Insight. 2017;2:2.
Not in our library10.1172/jci.insight.92688
- 9.
Chen F, Zhang Y, Şenbabaoglu Y, Ciriello G, Yang L, Reznik E, Shuch B, Micevic G, De Velasco G, Shinbrot E, et al. Multilevel genomics-based taxonomy of renal cell carcinoma. Cell Rep. 2016;14:2476-2489.
Not in our library10.1016/j.celrep.2016.02.024
- 10.
Chu A, Robertson G, Brooks D, Mungall AJ, Birol I, Coope R, Ma Y, Jones S, Marra MA. Large-scale profiling of microRNAs for The Cancer Genome Atlas. Nucleic Acids Res. 2016;44:e3.
Not in our library10.1093/nar/gkv808
- 11.
Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31:213-219.
Not in our library10.1038/nbt.2514
- 12.
Davis CF, Ricketts CJ, Wang M, Yang L, Cherniack AD, Shen H, Buhay C, Kang H, Kim SC, Fahey CC, The Cancer Genome Atlas Research Network, et al. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell. 2014;26:319-330.
Not in our library10.1016/j.ccr.2014.07.014
- 13.
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29:15-21.
Not in our library10.1093/bioinformatics/bts635
- 14.
- 15.
- 16.
- 17.
Geissler K, Fornara P, Lautenschlager C, Holzhausen HJ, Seliger B, Riemann D. Immune signature of tumor infiltrating immune cells in renal cancer. OncoImmunology. 2015;4:e985082.
Not in our library10.4161/2162402x.2014.985082
- 18.
Hakimi AA, Ostrovnaya I, Reva B, Schultz N, Chen YB, Gonen M, Liu H, Takeda S, Voss MH, Tickoo SK, ccRCC Cancer Genome Atlas (KIRC TCGA) Research Network investigators, 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;19:3259-3267.
Not in our library10.1158/1078-0432.ccr-12-3886
- 19.
Hamilton E, Infante JR. Targeting CDK4/6 in patients with cancer. Cancer Treat Rev. 2016;45:129-138.
Not in our library10.1016/j.ctrv.2016.03.002
- 20.
Hirata H, Hinoda Y, Nakajima K, Kawamoto K, Kikuno N, Ueno K, Yamamura S, Zaman MS, Khatri G, Chen Y, et al. Wnt antagonist DKK1 acts as a tumor suppressor gene that induces apoptosis and inhibits proliferation in human renal cell carcinoma. Int J Cancer. 2011;128:1793-1803.
Not in our library10.1002/ijc.25507
- 21.
Hsieh JJ, Purdue MP, Signoretti S, Swanton C, Albiges L, Schmidinger M, Heng DY, Larkin J, Ficarra V. Renal cell carcinoma. Nat Rev Dis Primers. 2017;3:17009.
Not in our library10.1038/nrdp.2017.9
- 22.
Iglesia MD, Vincent BG, Parker JS, Hoadley KA, Carey LA, Perou CM, Serody JS. Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer. Clin Cancer Res. 2014;20:3818-3829.
Not in our library10.1158/1078-0432.ccr-13-3368
- 23.
Kapur P, Peña-Llopis S, Christie A, Zhrebker L, Pavía-Jiménez A, Rathmell WK, Xie XJ, Brugarolas J. Effects on survival of BAP1 and PBRM1 mutations in sporadic clear-cell renal-cell carcinoma: a retrospective analysis with independent validation. Lancet Oncol. 2013;14:159-167.
Not in our library10.1016/s1470-2045(12)70584-3
- 24.
Kardos J, Chai S, Mose LE, Selitsky SR, Krishnan B, Saito R, Iglesia MD, Milowsky MI, Parker JS, Kim WY, Vincent BG. Claudin-low bladder tumors are immune infiltrated and actively immune suppressed. JCI Insight. 2016;1:e85902.
Not in our library10.1172/jci.insight.85902
- 25.
Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22:568-576.
Not in our library10.1101/gr.129684.111
- 26.
- 27.
Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics. 2012;28:311-317.
Not in our library10.1093/bioinformatics/btr665
- 28.
Lee CH, Motzer RJ. Immune checkpoint therapy in renal cell carcinoma. Cancer J. 2016;22:92-95.
Not in our library10.1097/ppo.0000000000000177
- 29.
Li J, Tibshirani R. Finding consistent patterns: a nonparametric approach for identifying differential expression in RNA-Seq data. Stat Methods Med Res. 2013;22:519-536.
Not in our library10.1177/0962280211428386
- 30.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25:2078-2079.
Not in our library10.1093/bioinformatics/btp352
- 31.
Linehan WM. Genetic basis of kidney cancer: role of genomics for the development of disease-based therapeutics. Genome Res. 2012;22:2089-2100.
Not in our library10.1101/gr.131110.111
- 32.
Linehan WM, Coleman JA, Walther MM, Zbar B, Vogelzang NJ, Scardino PT, Shipley WU, DeBruyne FMJ, Linehan WM. Genetic basis of kidney cancer. Comprehensive Textbook of Genitourinary Oncology. 2006;701-709.
Not in our library
- 33.
Linehan WM, Srinivasan R, Schmidt LS. The genetic basis of kidney cancer: a metabolic disease. Nat Rev Urol. 2010;7:277-285.
Not in our library10.1038/nrurol.2010.47
- 34.
- 35.
McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet. 2008;40:1166-1174.
Not in our library10.1038/ng.238
- 36.
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297-1303.
Not in our library10.1101/gr.107524.110
- 37.
Moch H, Cubilla AL, Humphrey PA, Reuter VE, Ulbright TM. The 2016 WHO classification of tumours of the urinary system and male genital organs-part A: renal, penile, and testicular tumours. Eur Urol. 2016;70:93-105.
Not in our library10.1016/j.eururo.2016.02.029
- 38.
Monti S, Tamayo P, Mesirov J, Golub T. Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Mach Learn. 2003;52:91-118.
Not in our library
- 39.
Motzer RJ, Escudier B, McDermott DF, George S, Hammers HJ, Srinivas S, Tykodi SS, Sosman JA, Procopio G, Plimack ER, CheckMate 025 Investigators, et al. Nivolumab versus everolimus in advanced renal-cell carcinoma. N Engl J Med. 2015;373:1803-1813.
Not in our library10.1056/nejmoa1510665
- 40.
Ooi A, Wong JC, Petillo D, Roossien D, Perrier-Trudova V, Whitten D, Min BWH, Tan MH, Zhang Z, Yang XJ, et al. An antioxidant response phenotype shared between hereditary and sporadic type 2 papillary renal cell carcinoma. Cancer Cell. 2011;20:511-523.
Not in our library10.1016/j.ccr.2011.08.024
- 41.
- 42.
Patra KC, Hay N. The pentose phosphate pathway and cancer. Trends Biochem Sci. 2014;39:347-354.
Not in our library10.1016/j.tibs.2014.06.005
- 43.
Radenbaugh AJ, Ma S, Ewing A, Stuart JM, Collisson EA, Zhu J, Haussler D. RADIA: RNA and DNA integrated analysis for somatic mutation detection. PLoS ONE. 2014;9:e111516.
Not in our library10.1371/journal.pone.0111516
- 44.
Rahman M, Jackson LK, Johnson WE, Li DY, Bild AH, Piccolo SR. Alternative preprocessing of RNA-sequencing data in The Cancer Genome Atlas leads to improved analysis results. Bioinformatics. 2015;31:3666-3672.
Not in our library10.1093/bioinformatics/btv377
- 45.
- 46.
- 47.
Ricketts CJ, Hill VK, Linehan WM. Tumor-specific hypermethylation of epigenetic biomarkers, including SFRP1, predicts for poorer survival in patients from the TCGA Kidney Renal Clear Cell Carcinoma (KIRC) project. PLoS ONE. 2014;9:e85621.
Not in our library10.1371/journal.pone.0085621
- 48.
- 49.
- 50.
Ronan T, Qi Z, Naegle KM. Avoiding common pitfalls when clustering biological data. Sci Signal. 2016;9:re6.
Not in our library10.1126/scisignal.aad1932
- 51.
Schmidt M, Böhm D, von Törne C, Steiner E, Puhl A, Pilch H, Lehr HA, Hengstler JG, Kölbl H, Gehrmann M. The humoral immune system has a key prognostic impact in node-negative breast cancer. Cancer Res. 2008;68:5405-5413.
Not in our library10.1158/0008-5472.can-07-5206
- 52.
- 53.
Sourbier C, Ricketts CJ, Matsumoto S, Crooks DR, Liao PJ, Mannes PZ, Yang Y, Wei MH, Srivastava G, Ghosh S, et al. Targeting ABL1-mediated oxidative stress adaptation in fumarate hydratase-deficient cancer. Cancer Cell. 2014;26:840-850.
Not in our library10.1016/j.ccell.2014.10.005
- 54.
- 55.
Tiedemann RL, Hlady RA, Hanavan PD, Lake DF, Tibes R, Lee JH, Choi JH, Ho TH, Robertson KD. Dynamic reprogramming of DNA methylation in SETD2-deregulated renal cell carcinoma. Oncotarget. 2016;7:1927-1946.
Not in our library10.18632/oncotarget.6481
- 56.
Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013;31:46-53.
Not in our library10.1038/nbt.2450
- 57.
Urakami S, Shiina H, Enokida H, Hirata H, Kawamoto K, Kawakami T, Kikuno N, Tanaka Y, Majid S, Nakagawa M, et al. Wnt antagonist family genes as biomarkers for diagnosis, staging, and prognosis of renal cell carcinoma using tumor and serum DNA. Clin Cancer Res. 2006;12:6989-6997.
Not in our library10.1158/1078-0432.ccr-06-1194
- 58.
Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, et al. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci USA. 2010;107:16910-16915.
Not in our library10.1073/pnas.1009843107
- 59.
Wilkerson MD, Hayes DN. ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics. 2010;26:1572-1573.
Not in our library10.1093/bioinformatics/btq170
- 60.
Wu TD, Watanabe CK. GMAP: a genomic mapping and alignment program for mRNA and EST sequences. Bioinformatics. 2005;21:1859-1875.
Not in our library10.1093/bioinformatics/bti310
- 61.
Yang Y, Vocke CD, Ricketts CJ, Wei D, Padilla-Nash HM, Lang M, Sourbier C, Killian JK, Boyle SL, Worrell R, et al. Genomic and metabolic characterization of a chromophobe renal cell carcinoma cell line model (UOK276). Genes Chromosomes Cancer. 2017;56:719-729.
Not in our library10.1002/gcc.22476
- 62.
Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25:2865-2871.
Not in our library10.1093/bioinformatics/btp394
Cited by papers we hold 15
- Mitochondrial complex I promotes kidney cancer metastasis · 2024No notice
- Fumarate induces vesicular release of mtDNA to drive innate immunity · 2023No notice
- Clinical validation of a 90-gene expression test for tumor tissue of origin diagnosis: a large-scale multicenter study of 1417 patients · 2022Not checked
- Comprehensive Analysis of Pyroptosis-Related Genes and Tumor Microenvironment Infiltration Characterization in Papillary Renal Cell Carcinoma · 2022Not checked
- A proteogenomic analysis of clear cell renal cell carcinoma in a Chinese population · 2022No notice
- Single cell derived mRNA signals across human kidney tumors · 2021Not checked
- ERK activation via A1542/3 limonoids attenuates erythroleukemia through transcriptional stimulation of cholesterol biosynthesis genes · 2021Not checked
- Subgroup-Independent Mapping of Renal Cell Carcinoma—Machine Learning Reveals Prognostic Mitochondrial Gene Signature Beyond Histopathologic Boundaries · 2021Not checked
- Integrated exome and RNA sequencing of TFE3-translocation renal cell carcinoma · 2021No notice
- Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma · 2021No notice
- Predictive genomic markers of response to VEGF targeted therapy in metastatic renal cell carcinoma. · 2019Not checked
- Pan-Renal Cell Carcinoma classification and survival prediction from histopathology images using deep learning · 2019No notice
- Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma · 2019Corrected
- Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer · 2019No notice
- SCINA: A Semi-Supervised Subtyping Algorithm of Single Cells and Bulk Samples · 2019No notice
Reads
Read by people on this page
None yet.
Checked or read by AI through naulon
None yet.
A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.
Are you an author?
Is this your paper?
Claim it to add your note and be paid when agents cite it. Free.