Association of DNA sequence variation in mitochondrial DNA polymerase with mitochondrial DNA synthesis and risk of oral cancer

Gene

Volumn 575, Issue 2, 2016, Pages 650-654

  Datta, Sayantan ^a   Ray, Anindita ^a   Roy, Roshni ^a   Roy, Bidyut ^a  

^a INDIAN STATISTICAL INSTITUTE   (India)

Author keywords

Association; DNA polymerase 2; DNA sequence variation; Mitochondrial DNA content; Oral precancer and cancer

Indexed keywords

DNA DIRECTED DNA POLYMERASE GAMMA; DNA DIRECTED RNA POLYMERASE; DNA POLYMERASE GAMMA 2; GENOMIC DNA; MITOCHONDRIAL DNA; MITOCHONDRIAL TRANSCRIPTION FACTOR A; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR B1; TRANSCRIPTION FACTOR B2; TUMOR MARKER; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; DNA DIRECTED DNA POLYMERASE; MITOCHONDRIAL PROTEIN; POLGBETA PROTEIN, HUMAN; POLRMT PROTEIN, HUMAN; TFAM PROTEIN, HUMAN;

ADULT; AGED; ALLELE; ARTICLE; CANCER PATIENT; CANCER RISK; CANCER TISSUE; CARCINOGENESIS; COMPUTER MODEL; CONTROLLED STUDY; DNA CONTENT; DNA SEQUENCE; DNA SYNTHESIS; DNA TRANSCRIPTION; FEMALE; GENETIC ASSOCIATION; GENETIC VARIATION; GENOTYPE; GENOTYPE ENVIRONMENT INTERACTION; HETEROZYGOTE; HISTOPATHOLOGY; HUMAN; HUMAN CELL; HUMAN TISSUE; LEUKOPLAKIA; MAJOR CLINICAL STUDY; MALE; MASTICATION; MOUTH CANCER; PRIORITY JOURNAL; RNA TRANSCRIPTION; SINGLE NUCLEOTIDE POLYMORPHISM; SMOKING; ADVERSE EFFECTS; GENETIC PREDISPOSITION; GENETICS; METABOLISM; MIDDLE AGED; MITOCHONDRION; MOUTH TUMOR; RISK FACTOR; VERY ELDERLY; YOUNG ADULT;

ADULT; AGED; AGED, 80 AND OVER; DNA, MITOCHONDRIAL; DNA-BINDING PROTEINS; DNA-DIRECTED DNA POLYMERASE; DNA-DIRECTED RNA POLYMERASES; FEMALE; GENE-ENVIRONMENT INTERACTION; GENETIC PREDISPOSITION TO DISEASE; HUMANS; LEUKOPLAKIA, ORAL; MALE; MIDDLE AGED; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; MOUTH NEOPLASMS; POLYMORPHISM, SINGLE NUCLEOTIDE; RISK FACTORS; SMOKING; TRANSCRIPTION FACTORS; YOUNG ADULT;

EID: 84964697610     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2015.09.039     Document Type: Article

References (26)

1. The International HapMap Project, Nature 426 (2003), 789–796.
2. Abecasis, G.R., Auton, A., Brooks, L.D., DePristo, M.A., Durbin, R.M., Handsaker, R.E., Kang, H.M., Marth, G.T., McVean, G.A., An integrated map of genetic variation from 1092 human genomes. Nature 491 (2012), 56–65.
3. Dasgupta, S., Soudry, E., Mukhopadhyay, N., Shao, C., Yee, J., Lam, S., Lam, W., Zhang, W., Gazdar, A.F., Fisher, P.B., Sidransky, D., Mitochondrial DNA mutations in respiratory complex-I in never-smoker lung cancer patients contribute to lung cancer progression and associated with EGFR gene mutation. J. Cell. Physiol. 227 (2012), 2451–2460.
4. Datta, S., Chattopadhyay, E., Ray, J.G., Majumder, M., Roy, P.D., Roy, B., D-loop somatic mutations and approximately 5 kb “common” deletion in mitochondrial DNA: important molecular markers to distinguish oral precancer and cancer. Tumour Biol., 2014.
5. Datta, S., Majumder, M., Biswas, N.K., Sikdar, N., Roy, B., Increased risk of oral cancer in relation to common Indian mitochondrial polymorphisms and autosomal GSTP1 locus. Cancer 110 (2007), 1991–1999.
6. Di Re, M., Sembongi, H., He, J., Reyes, A., Yasukawa, T., Martinsson, P., Bailey, L.J., Goffart, S., Boyd-Kirkup, J.D., Wong, T.S., Fersht, A.R., Spelbrink, J.N., Holt, I.J., The accessory subunit of mitochondrial DNA polymerase gamma determines the DNA content of mitochondrial nucleoids in human cultured cells. Nucleic Acids Res. 37 (2009), 5701–5713.
7. Ferlay, J., Shin, H.-R., Bray, F., Forman, D., Mathers, C., Parkin, D.M., Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int. J. Cancer 127 (2010), 2893–2917.
8. Garrido, N., Griparic, L., Jokitalo, E., Wartiovaara, J., van der Bliek, A.M., Spelbrink, J.N., Composition and dynamics of human mitochondrial nucleoids. Mol. Biol. Cell 14 (2003), 1583–1596.
9. Guo, J., Zheng, L., Liu, W., Wang, X., Wang, Z., French, A.J., Kang, D., Chen, L., Thibodeau, S.N., Frequent truncating mutation of TFAM induces mitochondrial DNA depletion and apoptotic resistance in microsatellite-unstable colorectal cancer. Cancer Res. 71 (2011), 2978–2987.
10. Gupta, P.C., Bhonsle, R.B., Murti, P.R., Daftary, D.K., Mehta, F.S., Pindborg, J.J., An epidemiologic assessment of cancer risk in oral precancerous lesions in India with special reference to nodular leukoplakia. Cancer 63 (1989), 2247–2252.
11. Hahn, L.W., Ritchie, M.D., Moore, J.H., Multifactor dimensionality reduction software for detecting gene–gene and gene–environment interactions. Bioinformatics 19 (2003), 376–382.
12. Hochberg, Y.B.a.Y., Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B Methodol. 57 (1995), 289–300.
13. Jiang, W.W., Masayesva, B., Zahurak, M., Carvalho, A.L., Rosenbaum, E., Mambo, E., Zhou, S., Minhas, K., Benoit, N., Westra, W.H., Alberg, A., Sidransky, D., Koch, W., Califano, J., Increased mitochondrial DNA content in saliva associated with head and neck cancer. Clin. Cancer Res. 11 (2005), 2486–2491.
14. Lacko, M., Braakhuis, B.J., Sturgis, E.M., Boedeker, C.C., Suarez, C., Rinaldo, A., Ferlito, A., Takes, R.P., Genetic susceptibility to head and neck squamous cell carcinoma. Int. J. Radiat. Oncol. Biol. Phys. 89 (2014), 38–48.
15. Lappalainen, T., Sammeth, M., Friedlander, M.R., t Hoen, P.A., Monlong, J., Rivas, M.A., Gonzalez-Porta, M., Kurbatova, N., Griebel, T., Ferreira, P.G., Barann, M., Wieland, T., Greger, L., van Iterson, M., Almlof, J., Ribeca, P., Pulyakhina, I., Esser, D., Giger, T., Tikhonov, A., Sultan, M., Bertier, G., MacArthur, D.G., Lek, M., Lizano, E., Buermans, H.P., Padioleau, I., Schwarzmayr, T., Karlberg, O., Ongen, H., Kilpinen, H., Beltran, S., Gut, M., Kahlem, K., Amstislavskiy, V., Stegle, O., Pirinen, M., Montgomery, S.B., Donnelly, P., McCarthy, M.I., Flicek, P., Strom, T.M., Lehrach, H., Schreiber, S., Sudbrak, R., Carracedo, A., Antonarakis, S.E., Hasler, R., Syvanen, A.C., van Ommen, G.J., Brazma, A., Meitinger, T., Rosenstiel, P., Guigo, R., Gut, I.G., Estivill, X., Dermitzakis, E.T., Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501 (2013), 506–511.
16. Michiels, S., Danoy, P., Dessen, P., Bera, A., Boulet, T., Bouchardy, C., Lathrop, M., Sarasin, A., Benhamou, S., Polymorphism discovery in 62 DNA repair genes and haplotype associations with risks for lung and head and neck cancers. Carcinogenesis 28 (2007), 1731–1739.
17. Moore, J.H., Epistasis Blog. http://compgen.blogspot.in/2006/12/mdr-101-part-4-results.html, 2006.
18. Motsinger-Reif, A.A., The effect of alternative permutation testing strategies on the performance of multifactor dimensionality reduction. BMC Res Notes, 1, 2008, 139.
19. Popanda, O., Seibold, P., Nikolov, I., Oakes, C.C., Burwinkel, B., Hausmann, S., Flesch-Janys, D., Plass, C., Chang-Claude, J., Schmezer, P., Germline variants of base excision repair genes and breast cancer: a polymorphism in DNA polymerase gamma modifies gene expression and breast cancer risk. Int. J. Cancer 132 (2013), 55–62.
20. Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A., Bender, D., Maller, J., Sklar, P., de Bakker, P.I., Daly, M.J., Sham, P.C., PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81 (2007), 559–575.
21. Ratanajaraya, C., Nishiyama, H., Takahashi, M., Kawaguchi, T., Saito, R., Mikami, Y., Suyama, M., Lathrop, M., Yamada, R., Ogawa, O. and Matsuda, F., 2011. A polymorphism of the POLG2 gene is genetically associated with the invasiveness of urinary bladder cancer in Japanese males. J. Hum. Genet. 56, 572–6.
22. Reibel, J., Prognosis of oral pre-malignant lesions: significance of clinical, histopathological, and molecular biological characteristics. Crit. Rev. Oral Biol. Med. 14 (2003), 47–62.
23. Ritchie, M.D., Hahn, L.W., Roodi, N., Bailey, L.R., Dupont, W.D., Parl, F.F., Moore, J.H., Multifactor-dimensionality reduction reveals high-order interactions among estrogen-metabolism genes in sporadic breast cancer. Am. J. Hum. Genet. 69 (2001), 138–147.
24. Salem, A.F., Whitaker-Menezes, D., Howell, A., Sotgia, F., Lisanti, M.P., Mitochondrial biogenesis in epithelial cancer cells promotes breast cancer tumor growth and confers autophagy resistance. Cell Cycle 11 (2012), 4174–4180.
25. Sotgia, F., Whitaker-Menezes, D., Martinez-Outschoorn, U.E., Salem, A.F., Tsirigos, A., Lamb, R., Sneddon, S., Hulit, J., Howell, A., Lisanti, M.P., Mitochondria “fuel” breast cancer metabolism: fifteen markers of mitochondrial biogenesis label epithelial cancer cells, but are excluded from adjacent stromal cells. Cell Cycle 11 (2012), 4390–4401.
26. Stranger, B.E., Forrest, M.S., Dunning, M., Ingle, C.E., Beazley, C., Thorne, N., Redon, R., Bird, C.P., de Grassi, A., Lee, C., Tyler-Smith, C., Carter, N., Scherer, S.W., Tavare, S., Deloukas, P., Hurles, M.E., Dermitzakis, E.T., Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315 (2007), 848–853.