Mutation-profile-based Methods for Understanding Selection Forces in Cancer Somatic Mutations: a Comparative Analysis

Overview

Journal Oncotarget

Specialty Oncology

Date 2017 Sep 24

PMID 28938601

Citations 6

Authors

Zhan Zhou

Yangyun Zou

Gangbiao Liu

Jingqi Zhou

Jingcheng Wu

Shimin Zhao

Zhixi Su

Xun Gu

Affiliations

Soon will be listed here.

Abstract

Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes ( / ) and normal populations ( / ). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels. Both the relaxation of purifying selection on passenger mutations and the positive selection of driver mutations may contribute to the increased / values of human genes in cancer genomes compared with the / values in human populations. The / values also contribute to the improved classification of cancer genes and a better understanding of the onco-functionalization of cancer genes during oncogenesis. The use of our computational pipeline to identify cancer-specific positively and negatively selected genes may provide useful information for understanding the evolution of cancers and identifying possible targets for therapeutic intervention.

Citing Articles

Neutral evolution of rare cancer mutations in the computer and the clinic.

Beckman R NPJ Syst Biol Appl. 2024; 10(1):110.

PMID: 39358357 PMC: 11447017. DOI: 10.1038/s41540-024-00436-3.

Evolutionary dependency of cancer mutations in gene pairs inferred by nonsynonymous-synonymous mutation ratios.

Han D, Kim S, Lee S, Moon Y, Kang S, Yoo J Genome Med. 2024; 16(1):103.

PMID: 39160568 PMC: 11331682. DOI: 10.1186/s13073-024-01376-7.

Unraveling the Drivers of Tumorigenesis in the Context of Evolution: Theoretical Models and Bioinformatics Tools.

Zhu X, Zhao W, Zhou Z, Gu X J Mol Evol. 2023; 91(4):405-423.

PMID: 37246992 DOI: 10.1007/s00239-023-10117-0.

Use of Publication Dynamics to Distinguish Cancer Genes and Bystander Genes.

Banyai L, Trexler M, Patthy L Genes (Basel). 2022; 13(7).

PMID: 35885888 PMC: 9315931. DOI: 10.3390/genes13071105.

Use of signals of positive and negative selection to distinguish cancer genes and passenger genes.

Banyai L, Trexler M, Kerekes K, Csuka O, Patthy L Elife. 2021; 10.

PMID: 33427197 PMC: 7877913. DOI: 10.7554/eLife.59629.

References

Kim J, Yu J, Cho Y, Jung C, Ahn S, Gong G . Expression of SPRR3 is associated with tumor cell proliferation in less advanced stages of breast cancer. Breast Cancer Res Treat. 2011; 133(3):909-16. DOI: 10.1007/s10549-011-1868-5. View

Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S . Tumor evolution. High burden and pervasive positive selection of somatic mutations in normal human skin. Science. 2015; 348(6237):880-6. PMC: 4471149. DOI: 10.1126/science.aaa6806. View

Beckman R, Loeb L . Negative clonal selection in tumor evolution. Genetics. 2005; 171(4):2123-31. PMC: 1456124. DOI: 10.1534/genetics.105.040840. View

Merlo L, Pepper J, Reid B, Maley C . Cancer as an evolutionary and ecological process. Nat Rev Cancer. 2006; 6(12):924-35. DOI: 10.1038/nrc2013. View

Stratton M, Campbell P, Futreal P . The cancer genome. Nature. 2009; 458(7239):719-24. PMC: 2821689. DOI: 10.1038/nature07943. View

Cairns J . Mutation selection and the natural history of cancer. Nature. 1975; 255(5505):197-200. DOI: 10.1038/255197a0. View

Podlaha O, Riester M, De S, Michor F . Evolution of the cancer genome. Trends Genet. 2012; 28(4):155-63. PMC: 3711268. DOI: 10.1016/j.tig.2012.01.003. View

Ostrow S, 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(3):e1004239. PMC: 3945297. DOI: 10.1371/journal.pgen.1004239. View

Perez-Mancera P, Rust A, van der Weyden L, Kristiansen G, Li A, Sarver A . The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma. Nature. 2012; 486(7402):266-70. PMC: 3376394. DOI: 10.1038/nature11114. View

10.

Kandoth C, McLellan M, Vandin F, Ye K, Niu B, Lu C . Mutational landscape and significance across 12 major cancer types. Nature. 2013; 502(7471):333-339. PMC: 3927368. DOI: 10.1038/nature12634. View

11.

Chen H, Xing K, He X . The dJ/dS Ratio Test Reveals Hundreds of Novel Putative Cancer Drivers. Mol Biol Evol. 2015; 32(8):2181-5. PMC: 4833070. DOI: 10.1093/molbev/msv083. View

12.

Yang , Bielawski . Statistical methods for detecting molecular adaptation. Trends Ecol Evol. 2000; 15(12):496-503. PMC: 7134603. DOI: 10.1016/s0169-5347(00)01994-7. View

13.

Rhodes D, Kalyana-Sundaram S, Mahavisno V, Varambally R, Yu J, Briggs B . Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia. 2007; 9(2):166-80. PMC: 1813932. DOI: 10.1593/neo.07112. View

14.

Samocha K, Robinson E, Sanders S, Stevens C, Sabo A, McGrath L . A framework for the interpretation of de novo mutation in human disease. Nat Genet. 2014; 46(9):944-50. PMC: 4222185. DOI: 10.1038/ng.3050. View

15.

Meyer C, Hofmann J, Burmeister T, Groger D, Park T, Emerenciano M . The MLL recombinome of acute leukemias in 2013. Leukemia. 2013; 27(11):2165-76. PMC: 3826032. DOI: 10.1038/leu.2013.135. View

16.

Luo H, Lin Y, Gao F, Zhang C, Zhang R . DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements. Nucleic Acids Res. 2013; 42(Database issue):D574-80. PMC: 3965060. DOI: 10.1093/nar/gkt1131. View

17.

Greaves M, Maley C . Clonal evolution in cancer. Nature. 2012; 481(7381):306-13. PMC: 3367003. DOI: 10.1038/nature10762. View

18.

Endo T, Ikeo K, Gojobori T . Large-scale search for genes on which positive selection may operate. Mol Biol Evol. 1996; 13(5):685-90. DOI: 10.1093/oxfordjournals.molbev.a025629. View

19.

Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, Shmoish M . GeneCards Version 3: the human gene integrator. Database (Oxford). 2010; 2010:baq020. PMC: 2938269. DOI: 10.1093/database/baq020. View

20.

Lawrence M, Stojanov P, Mermel C, Robinson J, Garraway L, Golub T . Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014; 505(7484):495-501. PMC: 4048962. DOI: 10.1038/nature12912. View