Mitochondrial DNA variation analysis in cervical cancer

Mitochondrion

Volumn 16, Issue , 2014, Pages 73-82

  Kabekkodu, Shama Prasada ^a   Bhat, Samatha ^a   Mascarenhas, Roshan ^a   Mallya, Sandeep ^a   Bhat, Manoj ^a   Pandey, Deeksha ^b   Kushtagi, Pralhad ^b   Thangaraj, Kumarasamy ^c   Gopinath, P M ^a   Satyamoorthy, Kapaettu ^a  

^a MANIPAL UNIVERSITY   (India)

^b KASTURBA MEDICAL COLLEGE   (India)

^c CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

Cervical cancer; Copy number; D loop and coding region; Haplogroup; HPV; MtDNA

Indexed keywords

MITOCHONDRIAL DNA; RIBOSOME RNA; TRANSFER RNA;

ADULT; ARTICLE; BIOINFORMATICS; CANCER TISSUE; CARCINOGENESIS; COMPUTER MODEL; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA DAMAGE; FEMALE; GENETIC VARIABILITY; HUMAN; HUMAN TISSUE; PAPILLOMAVIRUS INFECTION; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROTEIN STABILITY; RNA GENE; STRUCTURE ANALYSIS; UTERINE CERVIX CANCER; WART VIRUS; AGED; BIOLOGY; BIOSTATISTICS; DNA SEQUENCE; GENETICS; MIDDLE AGED; MUTATION; UTERINE CERVIX TUMOR;

HUMAN PAPILLOMAVIRUS;

AGED; BIOSTATISTICS; COMPUTATIONAL BIOLOGY; DNA, MITOCHONDRIAL; FEMALE; HUMANS; MIDDLE AGED; MUTATION; SEQUENCE ANALYSIS, DNA; UTERINE CERVICAL NEOPLASMS;

EID: 84900544744     PISSN: 15677249     EISSN: 18728278     Source Type: Journal    
DOI: 10.1016/j.mito.2013.07.001     Document Type: Article

References (58)

1. Allalunis-Turner J., Ma I., Hanson J., Pearcey R.G. mtDNA mutations in invasive cervix tumors: a retrospective analysis. Cancer Lett. 2006, 243:193-201.
2. Asmann Y.W., Stump C.S., Short K.R., Coenen-Schimke J.M., Guo Z., Bigelow M.L., Nair K.S. Skeletal muscle mitochondrial functions, mitochondrial DNA copy numbers, and gene transcript profiles in type 2 diabetic and nondiabetic subjects at equal levels of low or high insulin and euglycemia. Diabetes 2006, 55:3309-3319.
3. Bai R.K., Leal S.M., Covarrubias D., Liu A., Wong L.J. Mitochondrial genetic background modifies breast cancer risk. Cancer Res. 2007, 67:4687-4694.
4. Benn M., Schwartz M., Nordestgaard B.G., Tybjaerg-Hansen A. Mitochondrial haplogroups: ischemic cardiovascular disease, other diseases, mortality, and longevity in the general population. Circulation 2008, 117:2492-2501.
5. Booker L.M., Habermacher G.M., Jessie B.C., Sun Q.C., Baumann A.K., Amin M., Lim S.D., Fernandez-Golarz C., Lyles R.H., Brown M.D., Marshall F.F., Petros J.A. North American white mitochondrial haplogroups in prostate and renal cancer. J. Urol. 2006, 175:468-472. (discussion 472-463).
6. Bravard A., Vacher M., Moritz E., Vaslin L., Hall J., Epe B., Radicella J.P. Oxidation status of human OGG1-S326C polymorphic variant determines cellular DNA repair capacity. Cancer Res. 2009, 69:3642-3649.
7. Chatterjee A., Mambo E., Sidransky D. Mitochondrial DNA mutations in human cancer. Oncogene 2006, 25:4663-4674.
8. Chen D., Zhan H. Study on the mutations in the D-loop region of mitochondrial DNA in cervical carcinoma. J. Cancer Res. Clin. Oncol. 2009, 135:291-295.
9. Chen D., Yu Z., Zhu Z., Lopez C.D. The p53 pathway promotes efficient mitochondrial DNA base excision repair in colorectal cancer cells. Cancer Res. 2006, 66:3485-3494.
10. Croteau D.L., Stierum R.H., Bohr V.A. Mitochondrial DNA repair pathways. Mutat. Res. 1999, 434:137-148.
11. 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 2007, 110:1991-1999.
12. Evans M.F., Adamson C.S., Simmons-Arnold L., Cooper K. Touchdown General Primer (GP5+/GP6+) PCR and optimized sample DNA concentration support the sensitive detection of human papillomavirus. BMC Clin. Pathol. 2005, 5:10.
13. Fang H., Lu J., Wei J., Shen L.J., Ding Z., Li H., Bai Y. Mitochondrial DNA mutations in the D-loop region may not be frequent in cervical cancer: a discussion on pitfalls in mitochondrial DNA studies. J. Cancer Res. Clin. Oncol. 2009, 135:649-651.
14. Fang H., Shen L., Chen T., He J., Ding Z., Wei J., Qu J., Chen G., Lu J., Bai Y. Cancer type-specific modulation of mitochondrial haplogroups in breast, colorectal and thyroid cancer. BMC Cancer 2010, 10:421.
15. Faridi R., Zahra A., Khan K., Idrees M. Oncogenic potential of Human Papillomavirus (HPV) and its relation with cervical cancer. Virol. J. 2011, 8:269.
16. Feng S., Xiong L., Ji Z., Cheng W., Yang H. Correlation between increased copy number of mitochondrial DNA and clinicopathological stage in colorectal cancer. Oncol. Lett. 2012, 2:899-903.
17. Franco E.L., Tota J. Invited commentary: human papillomavirus infection and risk of cervical precancer - using the right methods to answer the right questions. Am. J. Epidemiol. 2010, 171:164-168.
18. Goia-Rusanu C.D., Iancu I.V., Botezatu A., Socolov D., Huica I., Plesa A., Anton G. Mitochondrial DNA mutations in patients with HRHPV-related cervical lesions. Roum. Arch. Microbiol. Immunol. 2011, 70:5-10.
19. Gravitt P.E., Peyton C.L., Alessi T.Q., Wheeler C.M., Coutlee F., Hildesheim A., Schiffman M.H., Scott D.R., Apple R.J. Improved amplification of genital human papillomaviruses. J. Clin. Microbiol. 2000, 38:357-361.
20. Guardado-Estrada M., Medina-Martinez I., Juarez-Torres E., Roman-Bassaure E., Macias L., Alfaro A., Alcantara-Vazquez A., Alonso P., Gomez G., Cruz-Talonia F., Serna L., Munoz-Cortez S., Borges-Ibanez M., Espinosa A., Kofman S., Berumen J. The Amerindian mtDNA haplogroup B2 enhances the risk of HPV for cervical cancer: de-regulation of mitochondrial genes may be involved. J. Hum. Genet. 2012, 57:269-276.
21. Kedzia W., Malkowska-Walczak B., Jozefiak A., Wadowicka A., Guglas B., Pruski D., Kedzia H., Spaczynski M. Preinvasive vulvar and cervical cancer in a 32-year-old woman, DNA HPV 16 positive with mtDNA mutation - case study. Ginekol. Pol. 2009, 80:533-537.
22. Kelley L.A., Sternberg M.J. Protein structure prediction on the Web: a case study using the Phyre server. Nat. Protoc. 2009, 4:363-371.
23. Klemba A., Kowalewska M., Kukwa W., Tonska K., Szybinska A., Mossakowska M., Scinska A., Golik P., Koper K., Radziszewski J., Kukwa A., Czarnecka A.M., Bartnik E. Mitochondrial genotype in vulvar carcinoma - cuckoo in the nest. J. Biomed. Sci. 2010, 17:73.
24. Kloss-Brandstatter A., Schafer G., Erhart G., Huttenhofer A., Coassin S., Seifarth C., Summerer M., Bektic J., Klocker H., Kronenberg F. Somatic mutations throughout the entire mitochondrial genome are associated with elevated PSA levels in prostate cancer patients. Am. J. Hum. Genet. 2010, 87:802-812.
25. Krzywinski M., Schein J., Birol I., Connors J., Gascoyne R., Horsman D., Jones S.J., Marra M.A. Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19:1639-1645.
26. Kwok C.S., Quah T.C., Ariffin H., Tay S.K., Yeoh A.E. Mitochondrial D-loop polymorphisms and mitochondrial DNA content in childhood acute lymphoblastic leukemia. J. Pediatr. Hematol. Oncol. 2011, 33:e239-e244.
27. Larsen N.B., Rasmussen M., Rasmussen L.J. Nuclear and mitochondrial DNA repair: similar pathways?. Mitochondrion 2005, 5:89-108.
28. Lievre A., Chapusot C., Bouvier A.M., Zinzindohoue F., Piard F., Roignot P., Arnould L., Beaune P., Faivre J., Laurent-Puig P. Clinical value of mitochondrial mutations in colorectal cancer. J. Clin. Oncol. 2005, 23:3517-3525.
29. Lim S.W., Kim H.R., Kim H.Y., Huh J.W., Kim Y.J., Shin J.H., Suh S.P., Ryang D.W., Shin M.G. High-frequency minisatellite instability of the mitochondrial genome in colorectal cancer tissue associated with clinicopathological values. Int. J. Cancer 2011, 131:1332-1341.
30. Lu J., Sharma L.K., Bai Y. Implications of mitochondrial DNA mutations and mitochondrial dysfunction in tumorigenesis. Cell Res. 2009, 19:802-815.
31. Miller F.J., Rosenfeldt F.L., Zhang C., Linnane A.W., Nagley P. Precise determination of mitochondrial DNA copy number in human skeletal and cardiac muscle by a PCR-based assay: lack of change of copy number with age. Nucleic Acids Res. 2003, 31:e61.
32. Mondal R., Ghosh S.K., Choudhury J.H., Seram A., Sinha K., Hussain M., Laskar R.S., Rabha B., Dey P., Ganguli S., Nathchoudhury M., Talukdar F.R., Chaudhuri B., Dhar B. Mitochondrial DNA copy number and risk of oral cancer: a report from northeast India. PLoS One 2013, 8:e57771.
33. Parmley J.L., Hurst L.D. How do synonymous mutations affect fitness?. Bioessays 2007, 29:515-519.
34. Pavicic W.H., Laguens M., Richard S.M. Analysis association between mitochondrial genome instability and xenobiotic metabolizing genes in human breast cancer. Mol. Med. 2009, 15:160-165.
35. Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. UCSF chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 2004, 25:1605-1612.
36. Rai E., Sharma S., Koul A., Bhat A.K., Bhanwer A.J., Bamezai R.N. Interaction between the UCP2-866G/A, mtDNA 10398G/A and PGC1alpha p.Thr394Thr and p.Gly482Ser polymorphisms in type 2 diabetes susceptibility in North Indian population. Hum. Genet. 2007, 122:535-540.
37. Rani D.S., Dhandapany P.S., Nallari P., Govindaraj P., Singh L., Thangaraj K. Mitochondrial DNA haplogroup 'R' is associated with Noonan syndrome of south India. Mitochondrion 2009, 10:166-173.
38. Richard S.M., Bailliet G., Paez G.L., Bianchi M.S., Peltomaki P., Bianchi N.O. Nuclear and mitochondrial genome instability in human breast cancer. Cancer Res. 2000, 60:4231-4237.
39. Rieder M.J., Taylor S.L., Tobe V.O., Nickerson D.A. Automating the identification of DNA variations using quality-based fluorescence re-sequencing: analysis of the human mitochondrial genome. Nucleic Acids Res. 1998, 26:967-973.
40. Sauna Z.E., Kimchi-Sarfaty C. Understanding the contribution of synonymous mutations to human disease. Nat. Rev. Genet. 2011, 12:683-691.
41. Schon E.A., DiMauro S., Hirano M. Human mitochondrial DNA: roles of inherited and somatic mutations. Nat. Rev. Genet. 2012, 13:878-890.
42. Sharawat S.K., Bakhshi R., Vishnubhatla S., Bakhshi S. Mitochondrial D-loop variations in paediatric acute myeloid leukaemia: a potential prognostic marker. Br. J. Haematol. 2010, 149:391-398.
43. Sharma H., Singh A., Sharma C., Jain S.K., Singh N. Mutations in the mitochondrial DNA D-loop region are frequent in cervical cancer. Cancer Cell Int. 2005, 5:34.
44. Singh K.K., Kulawiec M. Mitochondrial DNA polymorphism and risk of cancer. Methods Mol. Biol. 2009, 471:291-303.
45. Teng S., Srivastava A.K., Wang L. Sequence feature-based prediction of protein stability changes upon amino acid substitutions. BMC Genomics 2010, 11(Suppl. 2):S5.
46. Thangaraj K., Nandan A., Sharma V., Sharma V.K., Eaaswarkhanth M., Patra P.K., Singh S., Rekha S., Dua M., Verma N., Reddy A.G., Singh L. Deep rooting in-situ expansion of mtDNA Haplogroup R8 in South Asia. PLoS One 2009, 4:e6545.
47. Venselaar H., Te Beek T.A., Kuipers R.K., Hekkelman M.L., Vriend G. Protein structure analysis of mutations causing inheritable diseases. An e-science approach with life scientist friendly interfaces. BMC Bioinforma. 2010, 11:548.
48. Wallace D.C. Mitochondria and cancer. Nat. Rev. Cancer 2012, 12:685-698.
49. Wallace D.C., Fan W. Energetics, epigenetics, mitochondrial genetics. Mitochondrion 2010, 10:12-31.
50. Wang Y., Liu V.W., Ngan H.Y., Nagley P. Frequent occurrence of mitochondrial microsatellite instability in the D-loop region of human cancers. Ann. N. Y. Acad. Sci. 2005, 1042:123-129.
51. Wang Y., Liu V.W., Tsang P.C., Chiu P.M., Cheung A.N., Khoo U.S., Nagley P., Ngan H.Y. Microsatellite instability in mitochondrial genome of common female cancers. Int. J. Gynecol. Cancer 2006, 16(Suppl. 1):259-266.
52. Wang X., Yan Q., Guan M.X. Combination of the loss of cmnm5U34 with the lack of s2U34 modifications of tRNALys, tRNAGlu, and tRNAGln altered mitochondrial biogenesis and respiration. J. Mol. Biol. 2010, 395:1038-1048.
53. Warowicka A., Kwasniewska A., Gozdzicka-Jozefiak A. Alterations in mtDNA: a qualitative and quantitative study associated with cervical cancer development. Gynecol. Oncol. 2013, 129:193-198.
54. Weissman L., de Souza-Pinto N.C., Stevnsner T., Bohr V.A. DNA repair, mitochondria, and neurodegeneration. Neuroscience 2007, 145:1318-1329.
55. Xu L., Hu Y., Chen B., Tang W., Han X., Yu H., Xiao C. Mitochondrial polymorphisms as risk factors for endometrial cancer in southwest China. Int. J. Gynecol. Cancer 2006, 16:1661-1667.
56. Zhai K., Chang L., Zhang Q., Liu B., Wu Y. Mitochondrial C150T polymorphism increases the risk of cervical cancer and HPV infection. Mitochondrion 2011, 11:559-563.
57. Zhao Y., Wang J., Chen X., Wu Q. Significance of mutation in the D-loop region in cervical cancer. West Indian Med. J. 2010, 59:291-294.
58. Zheng J., Ji Y., Guan M.X. Mitochondrial tRNA mutations associated with deafness. Mitochondrion 2012, 12:406-413.