Deep sequencing reveals the mitochondrial DNA variation landscapes of breast-to-brain metastasis blood samples

References

• Akouchekian M, Houshmand M, Hemati S, Ansaripour M, Shafa M. 2009. High rate of mutation in mitochondrial DNA displacement loop region in human colorectal cancer. Dis Colon Rectum. 52:526–530.
   PubMed Web of Science ®Google Scholar
• Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N. 1999. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet. 23:147.
   PubMed Web of Science ®Google Scholar
• Bai RK, Leal SM, Covarrubias D, Liu A, Wong LJC. 2007. Mitochondrial genetic background modifies breast cancer risk. Cancer Res. 67:4687–4694.
   PubMed Web of Science ®Google Scholar
• Berman AT, Thukral AD, Hwang WT, Solin LJ, Vapiwala N. 2013. Incidence and patterns of distant metastases for patients with early-stage breast cancer after breast conservation treatment. Clin. Breast Cancer. 13:88–94.
   PubMed Web of Science ®Google Scholar
• Canter JA, Kallianpur AR, Parl FF, Millikan RC. 2005. Mitochondrial DNA G10398A polymorphism and invasive breast cancer in African-American women. Cancer Res. 65:8028–8033.
   PubMed Web of Science ®Google Scholar
• Chen EI. 2012. Mitochondrial dysfunction and cancer metastasis. J ioenerg Biomembr. 44:619–622.
   PubMed Web of Science ®Google Scholar
• Czarnecka AM, Krawczyk T, Plak K, Klemba A, Zdrozny M, Arnold RS, Kofler B, Golik P, Szybinskia A, Lubinski J, et al. 2010. Mitochondrial genotype and breast cancer predisposition. Oncol Rep. 24:1521–1534.
   PubMed Web of Science ®Google Scholar
• Eccles D, Gerty S, Simmonds P, Hammond V, Ennis S, Altman DG. 2007. Prospective study of Outcomes in Sporadic versus Hereditary breast cancer (POSH): study protocol. BMC Cancer. 7:160.
   PubMed Web of Science ®Google Scholar
• Emsley P, Lohkamp B, Scott WG, Cowtan K. 2010. Features and development of Coot. Acta Crystallogr D Biol Crystallogr. 66:486–501.
   PubMed Web of Science ®Google Scholar
• Engel J, Eckel R, Aydemir Ü, Aydemir S, Kerr J, Schlesinger-Raab A, Dirschedl P, Hölzel D. 2003. Determinants and prognoses of locoregional and distant progression in breast cancer. Int J Radiat Oncol Biol Phys. 55:1186–1195.
   PubMed Web of Science ®Google Scholar
• Fagerholm R, Schmidt MK, Khan S, Rafiq S, Tapper W, Aittomäki K, Groco D, Heikkinen T, Muranen TA, Fasching PA, et al. 2015. The SNP rs6500843 in 16p13.3 is associated with survival specifically among chemotherapy-treated breast cancer patients. Oncotarget. 6:7390–7407.
   PubMed Web of Science ®Google Scholar
• Fidler IJ. 2015. The biology of brain metastasis: challenges for therapy. Cancer J. 21:284–293.
   PubMed Web of Science ®Google Scholar
• Fliss MS, Usadel H, Caballero OL, Wu L, Buta MR, Eleff SM, Jen J, Sidransky D. 2000. Facile detection of mitochondrial DNA mutations in tumors and bodily fluids. Science. 287:2017–2019.
   PubMed Web of Science ®Google Scholar
• Fornuskova D, Stiburek L, Wenchich L, Vinsova K, Hansikova H, Zeman J. 2010. Novel insights into the assembly and function of human nuclear-encoded cytochrome c oxidase subunits 4, 5a, 6a, 7a and 7b. Biochem J. 428:363–374.
   PubMed Web of Science ®Google Scholar
• Gao X, Wen X, Esser L, Quinn B, Yu L, Yu CA, Xia D. 2003. Structural basis for the quinone reduction in the bc1 complex: a comparative analysis of crystal structures of mitochondrial cytochrome bc1 with bound substrate and inhibitors at the Qi site. Biochemistry. 42:9067–9080.
   PubMed Web of Science ®Google Scholar
• Gil-Gil MJ, Martinez-Garcia M, Sierra A, Conesa G, Del Barco S, González-Jimenez S, Villà S. 2014. Breast cancer brain metastases: a review of the literature and a current multidisciplinary management guideline. Clin Transl Oncol. 16:436–446.
   PubMed Web of Science ®Google Scholar
• Gouet P, Courcelle E, Stuart DI, Metoz F. 1999. ESPript: analysis of multiple sequence alignments in PostScript. Bioinformatics. 15:305–308.
   PubMed Web of Science ®Google Scholar
• Ishikawa K, Takenaga K, Akimoto M, Koshikawa N, Yamaguchi A, Imanishi H, Nahada K, Honma Y, Hayashi J. 2008. ROS-generating mitochondrial DNA mutations can regulate tumor cell metastasis. Science. 320:661–664.
   PubMed Web of Science ®Google Scholar
• Iwata S, Lee JW, Okada K, Lee JK, Iwata M, Rasmussen B, Link TA, Ramaswamy S, Jap BK. 1998. Complete structure of the 11-subunit bovine mitochondrial cytochrome bc1 complex. Science. 281:64–71.
   PubMed Web of Science ®Google Scholar
• Jeong SY, Seol DW. 2008. The role of mitochondria in apoptosis. BMB Rep. 41:11–22.
   PubMed Web of Science ®Google Scholar
• Ju YS, Alexandrov LB, Gerstung M, Martincorena I, Nik-Zainal S, Ramakrishna M, Davies HR, Papaemmanuil E, Gundem G, Shlien A, et al. 2014. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer. Elife. 3:e02935.
   PubMed Web of Science ®Google Scholar
• Kenny TC, Hart P, Ragazzi M, Sersinghe M, Chipuk J, Sagar MA, Eliceiri KW, LaFramboise T, Grandhi S, Santos J, et al. 2017. Selected mitochondrial DNA landscapes activate the SIRT3 axis of the UPR(mt) to promote metastasis. Oncogene [Epub ahead of print] doi: 10.1038/onc.2017.52.
   PubMed Web of Science ®Google Scholar
• Khan S, Fagerholm R, Rafiq S, Tapper W, Aittomäki K, Liu J, Blomqvist C, Eccles D, Nevanlinna H. 2015. Polymorphism at 19q13.41 predicts breast cancer survival specifically after endocrine therapy. Clin Cancer Res. 21:4086–4096.
   PubMed Web of Science ®Google Scholar
• Larkin M, Blackshields G, Brown N, Chenna R, McGettigan P, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics. 23:2947–2948.
   PubMed Web of Science ®Google Scholar
• Lloyd RE, Keatley K, Littlewood DTJ, Meunier B, Holt WV, An Q, Higgins SC, Polyzoidis S, Stephenson KF, Ashkan K, et al. 2015. Identification and functional prediction of mitochondrial complex III and IV mutations associated with glioblastoma. Neuro-Oncology. 17:942–952.
   PubMed Web of Science ®Google Scholar
• Lloyd RE, McGeehan JE. 2013. Structural analysis of mitochondrial mutations reveals a role for bigenomic protein interactions in human disease. PLoS One. 8:e69003.
   PubMed Web of Science ®Google Scholar
• Milne I, Stephen G, Bayer M, Cock PJ, Pritchard L, Cardle L, Shaw PD, Marshall D. 2013. Using Tablet for visual exploration of second-generation sequencing data. Brief Bioinform. 14:193–202.
   PubMed Web of Science ®Google Scholar
• Muramoto K, Hirata K, Shinzawa-Itoh K, Yoko-o S, Yamashita E, Aoyama H, Tsukihara T, Yoshikawa S. 2007. A histidine residue acting as a controlling site for dioxygen reduction and proton pumping by cytochrome c oxidase. Proc Natl Acad Sci USA. 104:7881–7886.
   PubMed Web of Science ®Google Scholar
• Parrella P, Xiao Y, Fliss M, Sanchez-Cespedes M, Mazzarelli P, Rinaldi M, Nicol T, Gabrielson E, Cuomo D, Cohen D, et al. 2001. Detection of mitochondrial DNA mutations in primary breast cancer and fine-needle aspirates. Cancer Res. 61:7623–7626.
   PubMed Web of Science ®Google Scholar
• Quintens R, Singh S, Lemaire K, de Bock K, Granvik M, Schraenen A, Vroegrijk IOCM, Costa V, van Noten P, Lambrechts D, et al. 2013. Mice deficient in the respiratory chain gene Cox6a2 are protected against high-fat diet-induced obesity and insulin resistance. PLoS One. 8:e56719.
   PubMed Web of Science ®Google Scholar
• Rafiq S, Tapper W, Collins A, Khan S, Politopoulos I, Gerty S, Blomqvist C, Couch FJ, Nevanlinna H, Liu J, Eccles D. 2013. Identification of inherited genetic variations influencing prognosis in early-onset breast cancer. Cancer Res. 73:1883–1891.
   PubMed Web of Science ®Google Scholar
• Rizzuto R, De Stefani D, Raffaello A, Mammucari C. 2012. Mitochondria as sensors and regulators of calcium signalling. Nat Rev Mol Cell Biol. 13:566–578.
   PubMed Web of Science ®Google Scholar
• Rossignol R, Faustin B, Rocher C, Malgat M, Mazat JP, Letellier T. 2003. Mitochondrial threshold effects. Biochem J. 370:751–762.
   PubMed Web of Science ®Google Scholar
• Rostami R, Mittal S, Rostami P, Tavassoli F, Jabbari B. 2016. Brain metastasis in breast cancer: a comprehensive literature review. J Neurooncol. 127:407–414.
   PubMed Web of Science ®Google Scholar
• Schmidt T, Situ AJ, Ulmer TS. 2016. Structural and thermodynamic basis of proline-induced transmembrane complex stabilization. Sci Rep. 6:29809.
   PubMed Web of Science ®Google Scholar
• Schon EA, DiMauro S, Hirano M. 2012. Human mitochondrial DNA: roles of inherited and somatic mutations. Nat Rev Genet. 13:878–890.
   PubMed Web of Science ®Google Scholar
• Sedlák E, Robinson NC. 2009. Sequential dissociation of subunits from bovine heart cytochrome c oxidase by urea. Biochemistry. 48:8143–8150.
   PubMed Web of Science ®Google Scholar
• Sena LA, Chandel NS. 2012. Physiological roles of mitochondrial reactive oxygen species. Mol Cell. 48:158–166.
   PubMed Web of Science ®Google Scholar
• Song Z, Laleve A, Vallières C, McGeehan JE, Lloyd RE, Meunier B. 2016. Human mitochondrial cytochrome b variants studied in yeast: not all are silent polymorphisms. Hum Mutat. 37:933–941.
   PubMed Web of Science ®Google Scholar
• Tamiya G, Makino S, Hayashi M, Abe A, Numakura C, Ueki M, Tanaka A, Ito C, Tohimori K, Ogawa N, et al. 2014. A mutation of COX6A1 causes a recessive axonal or mixed form of Charcot-Marie-Tooth disease. Am J Hum Genet. 95:294–300.
   PubMed Web of Science ®Google Scholar
• Wang C, Youle RJ. 2009. The role of mitochondria in apoptosis*. Annu Rev Genet. 43:95–118.
   PubMed Web of Science ®Google Scholar
• Wang Y, Liu VWS, Tsang PCK, Chiu PM, Cheung ANY, Khoo US, Nagley P, Ngan HYS. 2006. Microsatellite instability in mitochondrial genome of common female cancers. Int J Gynecol Cancer. 16:259–266.
   PubMed Web of Science ®Google Scholar
• Wiseman H, Halliwell B. 1996. Damage to DNA by reactive oxygen and nitrogen species: role in inflammatory disease and progression to cancer. Biochem J. 313:17–29.
   PubMed Web of Science ®Google Scholar
• Zhang P, Samuels DC, Wang J, Zhao S, Shyr Y, Guo Y. 2016. Mitochondria single nucleotide variation across six blood cell types. Mitochondrion. 28:16–22.
   PubMed Web of Science ®Google Scholar
• Zhou A, Rohou A, Schep DG, Bason JV, Montgomery MG, Walker JE, Grigorieffniko N, Rubinstein JL. 2015. Structure and conformational states of the bovine mitochondrial ATP synthase by cryo-EM. Elife. 4:e10180.
   PubMed Web of Science ®Google Scholar
• Zhu J, Vinothkumar KR, Hirst J. 2016. Structure of mammalian respiratory complex I. Nature. 536:354–358.
   PubMed Web of Science ®Google Scholar