Cancer Evolution Is Associated with Pervasive Positive Selection on Globally Expressed Genes

PLoS Genetics

Volumn 10, Issue 3, 2014, Pages

  Ostrow, Sheli L ^a   Barshir, Ruth ^b   DeGregori, James ^c   Yeger Lotem, Esti ^b   Hershberg, Ruth ^a  

^a TECHNION ISRAEL INSTITUTE OF TECHNOLOGY   (Israel)

^b BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^c UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BREAST CANCER; CANCER EVOLUTION; CANCER GROWTH; CARCINOGENESIS; CELL FUNCTION; EVOLUTIONARY ADAPTATION; EVOLUTIONARY RATE; FITNESS; GENE EXPRESSION; GENE FUNCTION; GENETIC ASSOCIATION; GENETIC SELECTION; GENETIC VARIABILITY; HOUSEKEEPING GENE; MOLECULAR EVOLUTION; MUTATION; POSITIVE SELECTION; PURIFYING SELECTION; SOMATIC MUTATION; TUMOR GENE; BREAST TUMOR; FEMALE; GENE EXPRESSION REGULATION; GENETICS; HUMAN; PATHOLOGY;

BREAST NEOPLASMS; CARCINOGENESIS; EVOLUTION, MOLECULAR; FEMALE; GENE EXPRESSION REGULATION, NEOPLASTIC; HUMANS; MUTATION; SELECTION, GENETIC;

EID: 84897448471     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004239     Document Type: Article

References (51)

1. Frank SA, Nowak MA, (2004) Problems of somatic mutation and cancer. Bioessays 26: 291-299.
2. Merlo LM, Pepper JW, Reid BJ, Maley CC, (2006) Cancer as an evolutionary and ecological process. Nat Rev Cancer 6: 924-935.
3. Podlaha O, Riester M, De S, Michor F, (2012) Evolution of the cancer genome. Trends Genet 28: 155-163.
4. Greaves M, Maley CC, (2012) Clonal evolution in cancer. Nature 481: 306-313.
5. DeGregori J, (2011) Evolved tumor suppression: why are we so good at not getting cancer? Cancer Res 71: 3739-3744.
6. Keightley PD, (1998) Inference of genome-wide mutation rates and distributions of mutation effects for fitness traits: a simulation study. Genetics 150: 1283-1293.
7. Orr HA, (2000) Adaptation and the cost of complexity. Evolution 54: 13-20.
8. Orr HA, (2005) The genetic theory of adaptation: a brief history. Nat Rev Genet 6: 119-127.
9. Eyre-Walker A, Keightley PD, (2007) The distribution of fitness effects of new mutations. Nat Rev Genet 8: 610-618.
10. Hershberg R, Tang H, Petrov DA, (2007) Reduced selection leads to accelerated gene loss in Shigella. Genome Biol 8: R164.
11. Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 56-65.
12. Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, et al. (2008) High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol 6: e311.
13. Daubin V, Moran NA (2004) Comment on "The origins of genome complexity". Science 306: 978; author reply 978.
14. Fay JC, Wu CI, (2003) Sequence divergence, functional constraint, and selection in protein evolution. Annu Rev Genomics Hum Genet 4: 213-235.
15. Nei M, Gojobori T, (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426.
16. Hershberg R, Petrov DA, (2010) Evidence that mutation is universally biased towards AT in bacteria. PLoS Genet 6: e1001115 doi:10.1371/journal.pgen.1001115.
17. Woo YH, Li WH, (2012) DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes. Nat Commun 3: 1004.
18. Kuo CH, Moran NA, Ochman H, (2009) The consequences of genetic drift for bacterial genome complexity. Genome Res 19: 1450-1454.
19. Markova-Raina P, Petrov D, (2011) High sensitivity to aligner and high rate of false positives in the estimates of positive selection in the 12 Drosophila genomes. Genome Res 21: 863-874.
20. Naugler CT, (2010) Population genetics of cancer cell clones: possible implications of cancer stem cells. Theor Biol Med Model 7: 42.
21. Kumar P, Henikoff S, Ng PC, (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc 4: 1073-1081.
22. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, et al. (2010) A method and server for predicting damaging missense mutations. Nat Methods 7: 248-249.
23. Jordan IK, Rogozin IB, Wolf YI, Koonin EV, (2002) Microevolutionary genomics of bacteria. Theor Popul Biol 61: 435-447.
24. Lawrie DS, Messer PW, Hershberg R, Petrov DA, (2013) Strong purifying selection at synonymous sites in D. melanogaster. PLoS Genet 9: e1003527.
25. Sella GC, Lopes Pereira Neto AR, Maziero Volpato CA, de Vasconcellos DK, Pekkan G, et al. (2013) Influence of different maintenance times of torque application on the removal torque values to loosen the prosthetic abutment screws of external hexagon implants. Implant Dent 22: 534-539.
26. Ovens K, Naugler C, (2012) Preliminary evidence of different selection pressures on cancer cells as compared to normal tissues. Theor Biol Med Model 9: 44.
27. Endo T, Ikeo K, Gojobori T, (1996) Large-scale search for genes on which positive selection may operate. Mol Biol Evol 13: 685-690.
28. Arbiza L, Dopazo J, Dopazo H, (2006) Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome. PLoS Comput Biol 2: e38.
29. Messier W, Stewart CB, (1997) Episodic adaptive evolution of primate lysozymes. Nature 385: 151-154.
30. Jordan IK, Rogozin IB, Wolf YI, Koonin EV, (2002) Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res 12: 962-968.
31. Network TCGA, (2012) Comprehensive molecular portraits of human breast tumours. Nature 490: 61-70.
32. McFarland CD, Korolev KS, Kryukov GV, Sunyaev SR, Mirny LA, (2013) Impact of deleterious passenger mutations on cancer progression. Proc Natl Acad Sci U S A 110: 2910-2915.
33. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, et al. (2011) COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res 39: D945-950.
34. Barshir R, Shwartz O, Smoly IY, Yeger-Lotem E (2014) Differential analysis of human tissues reveals major factors leading to the tissue-specific manifestation of hereditary diseases. [Submitted.].
35. Georgi B, Voight BF, Bucan M, (2013) From mouse to human: evolutionary genomics analysis of human orthologs of essential genes. PLoS Genet 9: e1003484.
36. Duret L, Mouchiroud D, (2000) Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol 17: 68-74.
37. Bissell MJ, Hines WC, (2011) Why don't we get more cancer? A proposed role of the microenvironment in restraining cancer progression. Nat Med 17: 320-329.
38. Gatenby RA, Gillies RJ, (2008) A microenvironmental model of carcinogenesis. Nat Rev Cancer 8: 56-61.
39. Gatenby RA, Gillies RJ, (2004) Why do cancers have high aerobic glycolysis? Nat Rev Cancer 4: 891-899.
40. de Visser KE, Eichten A, Coussens LM, (2006) Paradoxical roles of the immune system during cancer development. Nat Rev Cancer 6: 24-37.
41. Elena SF, Lenski RE, (2003) Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 4: 457-469.
42. Li L, Zhang K, Lee J, Cordes S, Davis DP, et al. (2009) Discovering cancer genes by integrating network and functional properties. BMC Med Genomics 2: 61.
43. Cingolani P, Platts A, Wangle L, Coon M, Nguyen T, et al. (2012) A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin) 6: 80-92.
44. Barshir R, Basha O, Eluk A, Smoly IY, Lan A, et al. (2013) The TissueNet database of human tissue protein-protein interactions. Nucleic Acids Res 41: D841-844.
45. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A 101: 6062-6067.
46. Bradley RK, Merkin J, Lambert NJ, Burge CB, (2012) Alternative splicing of RNA triplets is often regulated and accelerates proteome evolution. PLoS Biol 10: e1001229.
47. Yanai I, Benjamin H, Shmoish M, Chalifa-Caspi V, Shklar M, et al. (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21: 650-659.
48. Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, et al. (2013) Ensembl 2013. Nucleic Acids Res 41: D48-55.
49. Gray KA, Daugherty LC, Gordon SM, Seal RL, Wright MW, et al. (2013) Genenames.org: the HGNC resources in 2013. Nucleic Acids Res 41: D545-552.
50. Safran M, Dalah I, Alexander J, Rosen N, Iny Stein T, et al. (2010) GeneCards Version 3: the human gene integrator. Database (Oxford) 2010: baq020.
51. Messer PW, (2009) Measuring the rates of spontaneous mutation from deep and large-scale polymorphism data. Genetics 182: 1219-1232.