Merlo LM, Pepper JW, Reid BJ, Maley CC. Cancer as an evolutionary and ecological process. Nat Rev Cancer. 2006;6:924–35.
Article
PubMed
CAS
Google Scholar
Greaves M, Maley CC. Clonal evolution in cancer. Nature. 2012;481:306–13.
Article
PubMed
PubMed Central
CAS
Google Scholar
Nowell PC. The clonal evolution of tumor cell populations. Science. 1976;194:23–8.
Article
PubMed
CAS
Google Scholar
Yates LR, Campbell PJ. Evolution of the cancer genome. Nat Rev Genet. 2012;13:795–806.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144:646–74.
Article
PubMed
CAS
Google Scholar
Zapata L, Susak H, Drechsel O, Friedländer MR, Estivill X, Ossowski S. Signatures of positive selection reveal a universal role of chromatin modifiers as cancer driver genes. Sci Rep. 2017;7:13124.
Article
PubMed
PubMed Central
Google Scholar
Tamborero D, Gonzalez-Perez A, Lopez-Bigas N. OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics. 2013;29:2238–44.
Article
PubMed
CAS
Google Scholar
Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008;455:1061–8.
Article
Google Scholar
Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487:330–7.
Article
Google Scholar
Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012;489:519–25.
Article
Google Scholar
Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61–70.
Article
Google Scholar
Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature. 2009;458:719–24.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502:333–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Xie M, Lu C, Wang J, McLellan MD, Johnson KJ, Wendl MC, et al. Age-related mutations associated with clonal hematopoietic expansion and malignancies. Nat Med. 2014;20:1472–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Beckman RA, Loeb LA. Negative clonal selection in tumor evolution. Genetics. 2005;171:2123–31.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ovens K, Naugler C. Preliminary evidence of different selection pressures on cancer cells as compared to normal tissues. Theor Biol Med Model. 2012;9:44.
Article
PubMed
PubMed Central
Google Scholar
Weghorn D, Sunyaev S. Bayesian inference of negative and positive selection in human cancers. Nat Genet. 2017;49:1785–8.
Article
PubMed
CAS
Google Scholar
Martincorena I, Raine KM, Gerstung M, Dawson KJ, Haase K, Van Loo P, et al. Universal Patterns of Selection in Cancer and Somatic Tissues. Cell. 2017;171:1029–41. e21
Article
PubMed
PubMed Central
CAS
Google Scholar
Miller TE, Liau BB, Wallace LC, Morton AR, Xie Q, Dixit D, et al. Transcription elongation factors represent in vivo cancer dependencies in glioblastoma. Nature. 2017;547:355–9.
Article
PubMed
PubMed Central
CAS
Google Scholar
Vorontsov IE, Khimulya G, Lukianova EN, Nikolaeva DD, Eliseeva IA, Kulakovskiy IV, Makeev VJ. Negative selection maintains transcription factor binding motifs in human cancer. BMC Genomics. 2016;17(Suppl 2):395.
Article
PubMed
PubMed Central
Google Scholar
Pyatnitskiy M, Karpov D, Poverennaya E, Lisitsa A, Moshkovskii S. Bringing Down Cancer Aircraft: Searching for Essential Hypomutated Proteins in Skin Melanoma. PLoS One. 2015;10:e0142819.
Article
PubMed
PubMed Central
Google Scholar
Lindeboom RG, Supek F, Lehner B. The rules and impact of nonsense-mediated mRNA decay in human cancers. Nat Genet. 2016;48:1112–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hurst LD, Batada NN. Depletion of somatic mutations in splicing-associated sequences in cancer genomes. Genome Biol. 2017;18:213.
Article
PubMed
PubMed Central
Google Scholar
Van den Eynden J, Basu S, Larsson E. Somatic Mutation Patterns in Hemizygous Genomic Regions Unveil Purifying Selection during Tumor Evolution. PLoS Genet 2016;12:e1006506.
Bakhoum SF, Landau DA. Cancer Evolution: No Room for Negative Selection. Cell. 2017;171:987–9.
Article
PubMed
CAS
Google Scholar
Ezawa K, Landan G, Graur D. Detecting negative selection on recurrent mutations using gene genealogy. BMC Genet. 2013;14:37.
Article
PubMed
PubMed Central
Google Scholar
Van den Eynden J, Larsson E. Mutational Signatures Are Critical for Proper Estimation of Purifying Selection Pressures in Cancer Somatic Mutation Data When Using the dN/dS Metric. Front Genet. 2017;8:74.
Article
PubMed
PubMed Central
Google Scholar
Yang Z, Bielawski JP. Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 2000;15:496–503.
Article
PubMed
CAS
Google Scholar
Greenman C, Wooster R, Futreal PA, Stratton MR, Easton DF. Statistical analysis of pathogenicity of somatic mutations in cancer. Genetics. 2006;173:2187–98.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lawrence MS, Stojanov P, Mermel CH, Robinson JT, Garraway LA, Golub TR, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014;505:495–501.
Article
PubMed
PubMed Central
CAS
Google Scholar
Wu CI, Wang HY, Ling S, Lu X. The Ecology and Evolution of Cancer: The Ultra-Microevolutionary Process. Annu Rev Genet. 2016;50:347–69.
Article
PubMed
CAS
Google Scholar
Gonzalez-Perez A, Lopez-Bigas N. Functional impact bias reveals cancer drivers. Nucleic Acids Res. 2012;40:e169.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gu Z, Steinmetz LM, Gu X, Scharfe C, Davis RW, Li WH. Role of duplicate genes in genetic robustness against null mutations. Nature. 2003;421:63–6.
Article
PubMed
CAS
Google Scholar
Wang T, Birsoy K, Hughes NW, Krupczak KM, Post Y, Wei JJ, et al. Identification and characterization of essential genes in the human genome. Science. 2015;350:1096–101.
Article
PubMed
PubMed Central
CAS
Google Scholar
Ohno S. Evolution by gene duplication. 1970.
Book
Google Scholar
Kondrashov FA, Rogozin IB, Wolf YI, Koonin EV. Selection in the evolution of gene duplications. Genome Biol. 2002;3:8–1.
Article
Google Scholar
Toufighi K, Yang JS, Luis NM, Aznar Benitah S, Lehner B, Serrano L, Kiel C. Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses. PLoS Comput Biol. 2015;11:e1004256.
Article
PubMed
PubMed Central
Google Scholar
Strong MA, Vidal-Cardenas SL, Karim B, Yu H, Guo N, Greider CW. Phenotypes in mTERT+/− and mTERT−/− mice are due to short telomeres, not telomere-independent functions of telomerase reverse transcriptase. Mol Cell Biol. 2011;31:2369–79.
Article
PubMed
PubMed Central
CAS
Google Scholar
Artandi SE, Alson S, Tietze MK, Sharpless NE, Ye S, Greenberg RA, et al. Constitutive telomerase expression promotes mammary carcinomas in aging mice. Proc Natl Acad Sci U S A. 2002;99:8191–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Horn S, Figl A, Rachakonda PS, Fischer C, Sucker A, Gast A, et al. TERT promoter mutations in familial and sporadic melanoma. Science. 2013;339:959–61.
Article
PubMed
CAS
Google Scholar
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102:15545–50.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schaefer MH, Serrano L. Cell type-specific properties and environment shape tissue specificity of cancer genes. Sci Rep. 2016;6:20707.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, et al. The Reactome pathway Knowledgebase. Nucleic Acids Res. 2016;44:D481–7.
Article
PubMed
CAS
Google Scholar
Ferrandiz-Pulido C, Masferrer E, Toll A, Hernandez-Losa J, Mojal S, Pujol RM, et al. mTOR signaling pathway in penile squamous cell carcinoma: pmTOR and peIF4E over expression correlate with aggressive tumor behavior. J Urol. 2013;190:2288–95.
Article
PubMed
CAS
Google Scholar
Warburg O, Wind F, Negelein E. The metabolism of tumors in the body. J Gen Physiol. 1927;8:519–30.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pavlova NN, Thompson CB. The Emerging Hallmarks of Cancer Metabolism. Cell Metab. 2016;23:27–47.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lopez-Serra P, Marcilla M, Villanueva A, Ramos-Fernandez A, Palau A, Leal L, et al. A DERL3-associated defect in the degradation of SLC2A1 mediates the Warburg effect. Nat Commun. 2014;5:3608.
Article
PubMed
PubMed Central
Google Scholar
Zhang TB, Zhao Y, Tong ZX, Guan YF. Inhibition of glucose-transporter 1 (GLUT-1) expression reversed Warburg effect in gastric cancer cell MKN45. Int J Clin Exp Med. 2015;8:2423–8.
PubMed
PubMed Central
CAS
Google Scholar
Wang YD, Li SJ, Liao JX. Inhibition of glucose transporter 1 (GLUT1) chemosensitized head and neck cancer cells to cisplatin. Technol Cancer Res Treat. 2013;12:525–35.
Article
PubMed
Google Scholar
Li S, Yang X, Wang P, Ran X. The effects of GLUT1 on the survival of head and neck squamous cell carcinoma. Cell Physiol Biochem. 2013;32:624–34.
Article
PubMed
Google Scholar
Haber RS, Rathan A, Weiser KR, Pritsker A, Itzkowitz SH, Bodian C, et al. GLUT1 glucose transporter expression in colorectal carcinoma: a marker for poor prognosis. Cancer. 1998;83:34–40.
Article
PubMed
CAS
Google Scholar
Younes M, Brown RW, Stephenson M, Gondo M, Cagle PT. Overexpression of Glut1 and Glut3 in stage I nonsmall cell lung carcinoma is associated with poor survival. Cancer. 1997;80:1046–51.
Article
PubMed
CAS
Google Scholar
Kharitonenkov A, Shiyanova TL, Koester A, Ford AM, Micanovic R, Galbreath EJ, et al. FGF-21 as a novel metabolic regulator. J Clin Invest. 2005;115:1627–35.
Article
PubMed
PubMed Central
CAS
Google Scholar
Gerlinger M, Santos CR, Spencer-Dene B, Martinez P, Endesfelder D, Burrell RA, et al. Genome-wide RNA interference analysis of renal carcinoma survival regulators identifies MCT4 as a Warburg effect metabolic target. J Pathol. 2012;227:146–56.
Article
PubMed
PubMed Central
CAS
Google Scholar
Fisel P, Kruck S, Winter S, Bedke J, Hennenlotter J, Nies AT, et al. DNA methylation of the SLC16A3 promoter regulates expression of the human lactate transporter MCT4 in renal cancer with consequences for clinical outcome. Clin Cancer Res. 2013;19:5170–81.
Article
PubMed
CAS
Google Scholar
Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, et al. CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res. 2008;36:D646–50.
Article
PubMed
CAS
Google Scholar
Kim M, Jiang L-H, Wilson HL, North RA, Surprenant A. Proteomic and functional evidence for a P2X7 receptor signalling complex. EMBO J. 2001;20:6347–58.
Article
PubMed
PubMed Central
CAS
Google Scholar
Amoroso F, Falzoni S, Adinolfi E, Ferrari D, Di Virgilio F. The P2X7 receptor is a key modulator of aerobic glycolysis. Cell Death Dis. 2012;3:e370.
Article
PubMed
PubMed Central
CAS
Google Scholar
Adinolfi E, Melchiorri L, Falzoni S, Chiozzi P, Morelli A, Tieghi A, et al. P2X7 receptor expression in evolutive and indolent forms of chronic B lymphocytic leukemia. Blood. 2002;99:706–8.
Article
PubMed
CAS
Google Scholar
Salaro E, Rambaldi A, Falzoni S, Amoroso FS, Franceschini A, Sarti AC, et al. Involvement of the P2X7-NLRP3 axis in leukemic cell proliferation and death. Sci Rep. 2016;6:26280.
Article
PubMed
PubMed Central
CAS
Google Scholar
Roger S, Pelegrin P. P2X7 receptor antagonism in the treatment of cancers. Expert Opin Investig Drugs. 2011;20:875–80.
Article
PubMed
CAS
Google Scholar
Blomen VA, Májek P, Jae LT, Bigenzahn JW, Nieuwenhuis J, Staring J, et al. Gene essentiality and synthetic lethality in haploid human cells. Science. 2015;350:1092–6.
Article
PubMed
CAS
Google Scholar
Schumacher TN, Schreiber RD. Neoantigens in cancer immunotherapy. Science. 2015;348:69–74.
Article
PubMed
CAS
Google Scholar
Jarmalavicius S, Welte Y, Walden P. High immunogenicity of the human leukocyte antigen peptidomes of melanoma tumor cells. J Biol Chem. 2012;287:33401–11.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rooney MS, Shukla SA, Wu CJ, Getz G, Hacohen N. Molecular and genetic properties of tumors associated with local immune cytolytic activity. Cell. 2015;160:48–61.
Article
PubMed
PubMed Central
CAS
Google Scholar
zur Hausen H. Papillomavirus infections--a major cause of human cancers. Biochim Biophys Acta. 1996;1288:F55–78.
PubMed
Google Scholar
Alfonso C, Liljedahl M, Winqvist O, Surh CD, Peterson PA, Fung-Leung WP, Karlsson L. The role of H2-O and HLA-DO in major histocompatibility complex class II-restricted antigen processing and presentation. Immunol Rev. 1999;172:255–66.
Article
PubMed
CAS
Google Scholar
Fallas JL, Tobin HM, Lou O, Guo D, Sant'Angelo DB, Denzin LK. Ectopic expression of HLA-DO in mouse dendritic cells diminishes MHC class II antigen presentation. J Immunol. 2004;173:1549–60.
Article
PubMed
CAS
Google Scholar
Yi W, Seth NP, Martillotti T, Wucherpfennig KW, Sant'Angelo DB, Denzin LK. Targeted regulation of self-peptide presentation prevents type I diabetes in mice without disrupting general immunocompetence. J Clin Invest. 2010;120:1324–36.
Article
PubMed
PubMed Central
CAS
Google Scholar
Kreiter S, Vormehr M, van de Roemer N, Diken M, Löwer M, Diekmann J, et al. Mutant MHC class II epitopes drive therapeutic immune responses to cancer. Nature. 2015;520:692–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Hofmann MW, Höning S, Rodionov D, Dobberstein B, von Figura K, Bakke O. The leucine-based sorting motifs in the cytoplasmic domain of the invariant chain are recognized by the clathrin adaptors AP1 and AP2 and their medium chains. J Biol Chem. 1999;274:36153–8.
Article
PubMed
CAS
Google Scholar
McCormick PJ, Martina JA, Bonifacino JS. Involvement of clathrin and AP-2 in the trafficking of MHC class II molecules to antigen-processing compartments. Proc Natl Acad Sci U S A. 2005;102:7910–5.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lubben NB, Sahlender DA, Motley AM, Lehner PJ, Benaroch P, Robinson MS. HIV-1 Nef-induced down-regulation of MHC class I requires AP-1 and clathrin but not PACS-1 and is impeded by AP-2. Mol Biol Cell. 2007;18:3351–65.
Article
PubMed
PubMed Central
CAS
Google Scholar
Roeth JF, Williams M, Kasper MR, Filzen TM, Collins KL. HIV-1 Nef disrupts MHC-I trafficking by recruiting AP-1 to the MHC-I cytoplasmic tail. J Cell Biol. 2004;167:903–13.
Article
PubMed
PubMed Central
CAS
Google Scholar
Marty R, Kaabinejadian S, Rossell D, Slifker MJ, de Haar JV, Engin HB, et al. MHC-I Genotype Restricts the Oncogenic Mutational Landscape. Cell. 2017;171:1272–83. e15
Article
PubMed
CAS
Google Scholar
Ostrow SL, Barshir R, DeGregori J, Yeger-Lotem E, Hershberg R. Cancer evolution is associated with pervasive positive selection on globally expressed genes. PLoS Genet. 2014;10:e1004239.
Article
PubMed
PubMed Central
Google Scholar
Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, et al. High burden and pervasive positive selection of somatic mutations in normal human skin. Science. 2015;348:880–6.
Article
PubMed
PubMed Central
CAS
Google Scholar
Williams MJ, Werner B, Barnes CP, Graham TA, Sottoriva A. Identification of neutral tumor evolution across cancer types. Nat Genet. 2016;48:238–44.
Article
PubMed
PubMed Central
CAS
Google Scholar
Zhou Z, Zou Y, Liu G, Zhou J, Wu J, Zhao S, et al. Mutation-profile-based methods for understanding selection forces in cancer somatic mutations: a comparative analysis. Oncotarget. 2017;8:58835–46.
PubMed
PubMed Central
Google Scholar
Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348:124–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Puente XS, Beà S, Valdés-Mas R, Villamor N, Gutiérrez-Abril J, Martín-Subero JI, et al. Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature. 2015;526:519–24.
Article
PubMed
CAS
Google Scholar
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17:1.
Article
Google Scholar
Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, et al. Ensembl 2016. Nucleic Acids Res. 2016;44:D710–6.
Article
PubMed
CAS
Google Scholar
GTEx Consortium. Human genomics. The Genotype-Tissue Expression (GTEx) pilot analysis: multitissue gene regulation in humans. Science. 2015;348:648–60.
Article
PubMed Central
Google Scholar
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, et al. InterPro in 2017—beyond protein family and domain annotations. Nucleic Acids Res. 2016;45:D190–9.
Article
PubMed
PubMed Central
Google Scholar
Schaefer MH, Yang JS, Serrano L, Kiel C. Protein conservation and variation suggest mechanisms of cell type-specific modulation of signaling pathways. PLoS Comput Biol. 2014;10:e1003659.
Article
PubMed
PubMed Central
Google Scholar
Kamburov A, Stelzl U, Lehrach H, Herwig R. The ConsensusPathDB interaction database: 2013 update. Nucleic Acids Res. 2013;41:D793–800.
Article
PubMed
CAS
Google Scholar
The UniProt Consortium. UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017;45:D158–69.
Article
Google Scholar
Wilhelm M, Schlegl J, Hahne H, Gholami AM, Lieberenz M, Savitski MM, et al. Mass-spectrometry-based draft of the human proteome. Nature. 2014;509:582–7.
Article
PubMed
CAS
Google Scholar
Gray KA, Yates B, Seal RL, Wright MW, Bruford EA. Genenames.org: the HGNC resources in 2015. Nucleic Acids Res. 2015;43:D1079–85.
Article
PubMed
CAS
Google Scholar
Vita R, Overton JA, Greenbaum JA, Ponomarenko J, Clark JD, Cantrell JR, et al. The immune epitope database (IEDB) 3.0. Nucleic Acids Res. 2015;43:D405–12.
Article
PubMed
CAS
Google Scholar
Nielsen M, Lund O. NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. BMC Bioinformatics. 2009;10:296.
Article
PubMed
PubMed Central
Google Scholar
Andreatta M, Nielsen M. Gapped sequence alignment using artificial neural networks: application to the MHC class I system. Bioinformatics. 2016;32:511–7.
Article
PubMed
CAS
Google Scholar
Quinlan AR. BEDTools: the Swiss-army tool for genome feature analysis. Curr Protoc Bioinformatics. 2014;47:11.12.1–11.12.34.
Article
Google Scholar
Shukla SA, Rooney MS, Rajasagi M, Tiao G, Dixon PM, Lawrence MS, et al. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat Biotechnol. 2015;33:1152–8.
Article
PubMed
PubMed Central
CAS
Google Scholar
Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, et al. Pan-cancer Immunogenomic Analyses Reveal Genotype-Immunophenotype Relationships and Predictors of Response to Checkpoint Blockade. Cell Rep. 2017;18:248–62.
Article
PubMed
CAS
Google Scholar
Naruse TK, Kawata H, Anzai T, Takashige N, Kagiya M, Nose Y, et al. Limited polymorphism in the HLA-DOA gene. Tissue Antigens. 1999;53:359–65.
Article
PubMed
CAS
Google Scholar