MtDNA mutation pattern in tumors and human evolution are shaped by similar selective constraints

Genome Research

Volumn 19, Issue 4, 2009, Pages 576-580

  Zhidkov, Ilia ^a   Livneh, Erez A ^a   Rubin, Eitan ^a   Mishmar, Dan ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

ARTICLE; GENE MUTATION; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; MOLECULAR EVOLUTION; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION GENETIC PARAMETERS; PRIORITY JOURNAL; TUMOR GENE;

DNA, MITOCHONDRIAL; DNA, NEOPLASM; EVOLUTION; HAPLOTYPES; HUMANS; MUTATION; NEOPLASMS; SELECTION (GENETICS);

EID: 63849153962     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.086462.108     Document Type: Article

References (32)

1. Anderson, A.R., Weaver, A.M., Cummings, P.T., and Quaranta, V. 2006. Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment. Cell 127: 905-915.
2. Bamshad, M. and Wooding, S.P. 2003. Signatures of natural selection in the human genome. Nat. Rev. Genet. 4: 99-111.
3. Beerenwinkel, N., Antal, T., Dingli, D., Traulsen, A., Kinzler, K.W., Velculescu, V.E., Vogelstein, B., and Nowak, M.A. 2007. Genetic progression and the waiting time to cancer. PLoS Comput. Biol. 3: e225. doi: 10.1371/journal.pcbi.0030225.
4. Brandon, M., Baldi, P., and Wallace, D.C. 2006. Mitochondrial mutations in cancer. Oncogene 25: 4647-4662.
5. Brandon, M.C., Ruiz-Pesini, E., Mishmar, D., Procaccio, V., Lott, M.T., Nguyen, K.C., Spolim, S., Patil, U., Baldi, P., and Wallace, D.C. 2009. MITOMASTER: A bioinformatics tool for the analysis of mitochondrial DNA sequences. Hum. Mutat. 30: 1-6.
6. Canter, J.A., Kallianpur, A.R., Parl, F.F., and Millikan, R.C. 2005. Mitochondrial DNA G10398A polymorphism and invasive breast cancer in African-American women. Cancer Res. 65: 8028-8033.
7. Chamary, J.V., Parmley, J.L., and Hurst, L.D. 2006. Hearing silence: Non-neutral evolution at synonymous sites in mammals. Nat. Rev. Genet. 7:98-108.
8. Chimpanzee Sequencing and Analysis Consortium, C.S.a.A.2005. Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
9. Coller, H.A., Khrapko, K., Bodyak, N.D., Nekhaeva, E., Herrero-Jimenez, P., and Thilly, W.G. 2001. High frequency of homoplasmic mitochondrial DNA mutations in human tumors can be explained without selection. Nat. Genet. 28: 147-150.
10. Darvishi, K., Sharma, S., Bhat, A.K., Rai, E., and Bamezai, R.N. 2007. Mitochondrial DNA G10398A polymorphism imparts maternal Haplogroup N a risk for breast and esophageal cancer. Cancer Lett. 249:249-255.
11. Feder, J., Blech, I., Ovadia, O., Amar, S., Wainstein, J., Raz, I., Dadon, S., Arking, D.E., Glaser, B., and Mishmar, D. 2008. Differences in mtDNA haplogroup distribution among 3 Jewish populations alter susceptibility to T2DM complications. BMC Genomics 9: 198. doi:10.1186/1471-2164-9-198.
12. International HapMap Consortium 2005. A haplotype map of the human genome. Nature 437: 1299-1320.
13. Kassauei, K., Habbe, N., Mullendore, M.E., Karikari, C.A., Maitra, A., and Feldmann, G. 2006. Mitochondrial DNA mutations in pancreatic cancer. Int. J. Gastrointest. Cancer 37: 57-64.
14. Knudson Jr., A.G. 1971. Mutation and cancer: statistical study of retinoblastoma. Proc. Natl. Acad. Sci. 68: 820-823.
15. Meiklejohn, C.D., Montooth, K.L., and Rand, D.M. 2007. Positive and negative selection on the mitochondrial genome. Trends Genet. 23:259-263.
16. Mishmar, D., Ruiz-Pesini, E., Golik, P., Macaulay, V., Clark, A.G., Hosseini, S., Brandon, M., Easley, K., Chen, E., Brown, M.D., et al. 2003. Natural selection shaped regional mtDNA variation in humans. Proc. Natl. Acad. Sci. 100: 171-176.
17. Mithani, S.K., Taube, J.M., Zhou, S., Smith, I.M., Koch, W.M., Westra, W.H., and Califano, J.A. 2007. Mitochondrial mutations are a late event in the progression of head and neck squamous cell cancer. Clin. Cancer Res. 13: 4331-4335.
18. Montiel-Sosa, F., Ruiz-Pesini, E., Enriquez, J.A., Marcuello, A., Diez-Sanchez, C., Montoya, J., Wallace, D.C., and Lopez-Perez, M.J. 2006. Differences of sperm motility in mitochondrial DNA haplogroup U sublineages. Gene 368: 21-27.
19. Nielsen, R., Bustamante, C., Clark, A.G., Glanowski, S., Sackton, T.B., Hubisz, M.J., Fledel-Alon, A., Tanenbaum, D.M., Civello, D., White, T.J., et al. 2005. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3: e170. doi: 10.1371/journal.pbio. 0030170.
20. Ohta, S. 2006. Contribution of somatic mutations in the mitochondrial genome to the development of cancer and tolerance against anticancer drugs. Oncogene 25: 4768-4776.
21. Ruiz-Pesini, E. and Wallace, D.C. 2006. Evidence for adaptive selection acting on the tRNA and rRNA genes of human mitochondrial DNA. Hum. Mutat. 27: 1072-1081.
22. Ruiz-Pesini, E., Lapena, A.C., Diez-Sanchez, C., Perez-Martos, A., Montoya, J., Alvarez, E., Diaz, M., Urries, A., Montoro, L., Lopez-Perez, M.J., et al. 2000. Human mtDNA haplogroups associated with high or reduced spermatozoa motility. Am. J. Hum. Genet. 67: 682-696.
23. Ruiz-Pesini, E., Mishmar, D., Brandon, M., Procaccio, V., and Wallace, D.C. 2004. Effects of purifying and adaptive selection on regional variation in human mtDNA. Science 303: 223-226.
24. Ruiz-Pesini, E., Lott, M.T., Procaccio, V., Poole, J.C., Brandon, M.C., Mishmar, D., Yi, C., Kreuziger, J., Baldi, P., and Wallace, D.C. 2007. An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res. 35: D823-D828.
25. Sabeti, P.C., Schaffner, S.F., Fry, B., Lohmueller, J., Varilly, P., Shamovsky, O., Palma, A., Mikkelsen, T.S., Altshuler, D., and Lander, E.S. 2006. Positive natural selection in the human lineage. Science 312: 1614-1620.
26. Setiawan, V.W., Chu, L.H., John, E.M., Ding, Y.C., Ingles, S.A., Bernstein, L., Press, M.F., Ursin, G., Haiman, C.A., and Neuhausen, S.L. 2008. Mitochondrial DNA G10398A variant is not associated with breast cancer in African-American women. Cancer Genet. Cytogenet. 181:16-19.
27. Sjoblom, T., Jones, S., Wood, L.D., Parsons, D.W., Lin, J., Barber, T.D., Mandelker, D., Leary, R.J., Ptak, J., Silliman, N., et al. 2006. The consensus coding sequences of human breast and colorectal cancers. Science 314: 268-274.
28. Verma, M. and Kumar, D. 2007. Application of mitochondrial genome information in cancer epidemiology. Clin. Chim. Acta 383: 41-50.
29. Wang, E.T., Kodama, G., Baldi, P., and Moyzis, R.K. 2006. Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc. Natl. Acad. Sci. 103: 135-140.
30. Weir, B.A., Woo, M.S., Getz, G., Perner, S., Ding, L., Beroukhim, R., Lin, W.M., Province, M.A., Kraja, A., Johnson, L.A., et al. 2007. Characterizing the cancer genome in lung adenocarcinoma. Nature 450: 893-898.
31. Wood, L.D., Parsons, D.W., Jones, S., Lin, J., Sjoblom, T., Leary, R.J., Shen, D., Boca, S.M., Barber, T., Ptak, J., et al. 2007. The genomic landscapes of human breast and colorectal cancers. Science 318: 1108-1113.
32. Zhou, S., Kachhap, S., Sun, W., Wu, G., Chuang, A., Poeta, L., Grumbine, L., Mithani, S.K., Chatterjee, A., Koch, W., et al. 2007. Frequency and phenotypic implications of mitochondrial DNA mutations in human squamous cell cancers of the head and neck. Proc. Natl. Acad. Sci. 104:7540- 7545.