Abstract
Mitochondrial dysfunction is regarded as a hallmark of cancer progression. In the current study, we evaluated mitochondrial genome instability and copy number in colorectal cancer using Next Generation Sequencing approach and qPCR, respectively. The results revealed higher levels of heteroplasmy and depletion of the relative mtDNA copy number in colorectal adenocarcinoma. Adenocarcinoma samples also presented an increased number of mutations in nuclear genes encoding proteins which functions are related with mitochondria fusion, fission and localization. Moreover, we found a set of mitochondrial and nuclear genes, which cooperate in the same mitochondrial function simultaneously mutated in adenocarcinoma. In summary, these results support an important role for mitochondrial function and genomic instability in colorectal tumorigenesis.
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Jemal A, Bray F, Center MM, Ferlay J, Ward E, Forman D. Global cancer statistics. CA Cancer J Clin. 2011;61(2):69–90. doi:10.3322/caac.20107.
INCA. Estimativa 2014—Incidência de Câncer no Brasil. Rio de Janeiro, RJ. 2014. Accessed 04/28/15.
Cunningham D, Atkin W, Lenz HJ, Lynch HT, Minsky B, Nordlinger B. Colorectal cancer. Lancet. 2010;375(9719):1030–47. doi:10.1016/S0140-6736(10)60353-4.
Fearon ER, Vogelstein B. A genetic model for colorectal tumorigenesis. Cell. 1990;61(5):759–67.
Weinberg F, Hamanaka R, Wheaton WW, Weinberg S, Joseph J, Lopez M, et al. Mitochondrial metabolism and ROS generation are essential for Kras-mediated tumorigenicity. Proc Natl Acad Sci U S A. 2010;107(19):8788–93. doi:10.1073/pnas.1003428107.
Giannoni E, Buricchi F, Raugei G, Ramponi G, Chiarugi P. Intracellular reactive oxygen species activate Src tyrosine kinase during cell adhesion and anchorage-dependent cell growth. Mol Cell Biol. 2005;25(15):6391–403. doi:10.1128/MCB.25.15.6391-6403.2005.
Gaude E, Frezza C. Defects in mitochondrial metabolism and cancer. Cancer Metab. 2014;2:10. doi:10.1186/2049-3002-2-10.
Warburg O. On the origin of cancer cells. Science. 1956;123(3191):309–14.
Fantin VR, St-Pierre J, Leder P. Attenuation of LDH-A expression uncovers a link between glycolysis, mitochondrial physiology, and tumor maintenance. Cancer Cell. 2006;9(6):425–34. doi:10.1016/j.ccr.2006.04.023.
Tan AS, Baty JW, Dong LF, Bezawork-Geleta A, Endaya B, Goodwin J, et al. Mitochondrial genome acquisition restores respiratory function and tumorigenic potential of cancer cells without mitochondrial DNA. Cell Metab. 2015;21(1):81–94. doi:10.1016/j.cmet.2014.12.003.
Wallace DC. Structure and evolution of organelle genomes. Microbiol Rev. 1982;46(2):208–40.
Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, et al. Sequence and organization of the human mitochondrial genome. Nature. 1981;290(5806):457–65.
Singh RK, Srivastava A, Kalaiarasan P, Manvati S, Chopra R, Bamezai RN. mtDNA germ line variation mediated ROS generates retrograde signaling and induces pro-cancerous metabolic features. Sci Rep. 2014;4:6571. doi:10.1038/srep06571.
Ishikawa K, Hayashi J. A novel function of mtDNA: its involvement in metastasis. Ann N Y Acad Sci. 2010;1201:40–3. doi:10.1111/j.1749-6632.2010.05616.x.
Kaipparettu BA, Ma Y, Park JH, Lee TL, Zhang Y, Yotnda P, et al. Crosstalk from non-cancerous mitochondria can inhibit tumor properties of metastatic cells by suppressing oncogenic pathways. PLoS One. 2013;8(5):e61747. doi:10.1371/journal.pone.0061747.
He Y, Wu J, Dressman DC, Iacobuzio-Donahue C, Markowitz SD, Velculescu VE, et al. Heteroplasmic mitochondrial DNA mutations in normal and tumour cells. Nature. 2010;464(7288):610–4. doi:10.1038/nature08802.
Larman TC, DePalma SR, Hadjipanayis AG, Protopopov A, Zhang J, Gabriel SB, et al. Spectrum of somatic mitochondrial mutations in five cancers. Proc Natl Acad Sci U S A. 2012;109(35):14087–91. doi:10.1073/pnas.1211502109.
Lee JH, Hwang I, Kang YN, Choi IJ, Kim DK. Genetic characteristics of mitochondrial DNA was associated with colorectal carcinogenesis and its prognosis. PLoS One. 2015;10(3):e0118612. doi:10.1371/journal.pone.0118612.
Lim SW, Kim HR, Kim HY, Huh JW, Kim YJ, Shin JH, et al. High-frequency minisatellite instability of the mitochondrial genome in colorectal cancer tissue associated with clinicopathological values. Int J Cancer. 2012;131(6):1332–41. doi:10.1002/ijc.27375.
Ye K, Lu J, Ma F, Keinan A, Gu Z. Extensive pathogenicity of mitochondrial heteroplasmy in healthy human individuals. Proc Natl Acad Sci U S A. 2014;111(29):10654–9. doi:10.1073/pnas.1403521111.
Taylor RW, Taylor GA, Durham SE, Turnbull DM. The determination of complete human mitochondrial DNA sequences in single cells: implications for the study of somatic mitochondrial DNA point mutations. Nucl Acids Res. 2001;29(15):E74–4.
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7(4):248–9. doi:10.1038/nmeth0410-248.
Li B, Krishnan VG, Mort ME, Xin F, Kamati KK, Cooper DN, et al. Automated inference of molecular mechanisms of disease from amino acid substitutions. Bioinformatics. 2009;25(21):2744–50. doi:10.1093/bioinformatics/btp528.
Untergasser A, Cutcutache I, Koressaar T, Ye J, Remme M. Primer3—new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115. doi:10.1093/nar/gks596.
Koressaar T, Remm M. Enhancements and modifications of primer design program Primer3. Bioinformatics. 2007;23(10):1289–91. doi:10.1093/bioinformatics/btm091.
Venegas V, Wang J, Dimmock D, Wong LJ. Real-time quantitative PCR analysis of mitochondrial DNA content. Current protocols in human genetics / editorial board, Jonathan L Haines [et al]. 2011;Chapter 19:Unit 19 7. doi:10.1002/0471142905.hg1907s68.
Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754–60. doi:10.1093/bioinformatics/btp324.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. doi:10.1093/bioinformatics/btp352.
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43(5):491–8. doi:10.1038/ng.806.
Gasparre G, Porcelli AM, Lenaz G, Romeo G. Relevance of mitochondrial genetics and metabolism in cancer development. Cold Spring Harb Perspect Biol. 2013;5(2). doi:10.1101/cshperspect.a011411.
Iommarini L, Kurelac I, Capristo M, Calvaruso MA, Giorgio V, Bergamini C, et al. Different mtDNA mutations modify tumor progression in dependence of the degree of respiratory complex I impairment. Hum Mol Genet. 2014;23(6):1453–66. doi:10.1093/hmg/ddt533.
Tan AS, Baty JW, Berridge MV. The role of mitochondrial electron transport in tumorigenesis and metastasis. Biochim Biophys Acta. 2014;1840(4):1454–63. doi:10.1016/j.bbagen.2013.10.016.
Polyak K, Li Y, Zhu H, Lengauer C, Willson JK, Markowitz SD, et al. Somatic mutations of the mitochondrial genome in human colorectal tumours. Nat Genet. 1998;20(3):291–3. doi:10.1038/3108.
Blok MJ, Spruijt L, de Coo IF, Schoonderwoerd K, Hendrickx A, Smeets HJ. Mutations in the ND5 subunit of complex I of the mitochondrial DNA are a frequent cause of oxidative phosphorylation disease. J Med Genet. 2007;44(4):e74. doi:10.1136/jmg.2006.045716.
Naini AB, Lu J, Kaufmann P, Bernstein RA, Mancuso M, Bonilla E, et al. Novel mitochondrial DNA ND5 mutation in a patient with clinical features of MELAS and MERRF. Arch Neurol. 2005;62(3):473–6. doi:10.1001/archneur.62.3.473.
Danovi D, Cremona CA, Machado-da-Silva G, Basu S, Noon LA, Parrinello S, et al. A genetic screen for anchorage-independent proliferation in mammalian cells identifies a membrane-bound neuregulin. PLoS One. 2010;5(7):e11774. doi:10.1371/journal.pone.0011774.
Zhou S, Kachhap S, Sun W, Wu G, Chuang A, Poeta L, et al. Frequency and phenotypic implications of mitochondrial DNA mutations in human squamous cell cancers of the head and neck. Proc Natl Acad Sci U S A. 2007;104(18):7540–5. doi:10.1073/pnas.0610818104.
Zhang C, Huang VH, Simon M, Sharma LK, Fan W, Haas R, et al. Heteroplasmic mutations of the mitochondrial genome cause paradoxical effects on mitochondrial functions. FASEB J. 2012;26(12):4914–24. doi:10.1096/fj.12-206532.
Porcelli AM, Ghelli A, Ceccarelli C, Lang M, Cenacchi G, Capristo M, et al. The genetic and metabolic signature of oncocytic transformation implicates HIF1alpha destabilization. Hum Mol Genet. 2010;19(6):1019–32. doi:10.1093/hmg/ddp566.
Koshikawa N, Hayashi J, Nakagawara A, Takenaga K. Reactive oxygen species-generating mitochondrial DNA mutation up-regulates hypoxia-inducible factor-1alpha gene transcription via phosphatidylinositol 3-kinase-Akt/protein kinase C/histone deacetylase pathway. J Biol Chem. 2009;284(48):33185–94. doi:10.1074/jbc.M109.054221.
Kurelac I, MacKay A, Lambros MB, Di Cesare E, Cenacchi G, Ceccarelli C. Somatic complex I disruptive mitochondrial DNA mutations are modifiers of tumorigenesis that correlate with low genomic instability in pituitary adenomas. Hum Mol Genet. 2013;22(2):226–38. doi:10.1093/hmg/dds422.
Levinger L, Morl M, Florentz C. Mitochondrial tRNA 3′ end metabolism and human disease. Nucleic Acids Res. 2004;32(18):5430–41. doi:10.1093/nar/gkh884.
Coenen MJ, Antonicka H, Ugalde C, Sasarman F, Rossi R, Heister JG, et al. Mutant mitochondrial elongation factor G1 and combined oxidative phosphorylation deficiency. N Engl J Med. 2004;351(20):2080–6. doi:10.1056/NEJMoa041878.
Smeitink JA, Elpeleg O, Zntonicka H, Diepstra H, Saada A, Smits P, et al. Distinct clinical phenotypes associated with a mutation in the mitochondrial translation elongation factor EFTs. Am J Hum Genet. 2006;79(5):869–77. doi:10.1086/508434.
Desai SP, Bhatia SN, Toner M, Irimia D. Mitochondrial localization and the persistent migration of epithelial cancer cells. Biophys J. 2013;104(9):2077–88. doi:10.1016/j.bpj.2013.03.025.
Zhao J, Zhang J, Yu M, Xie Y, Huang Y, Wolff DW, et al. Mitochondrial dynamics regulates migration and invasion of breast cancer cells. Oncogene. 2013;32(40):4814–24. doi:10.1038/onc.2012.494.
Yu M, Shi Y, Wei X, Yang Y, Zang F, Niu R. Mitochondrial DNA depletion promotes impaired oxidative status and adaptive resistance to apoptosis in T47D breast cancer cells. Eur J Cancer Prev. 2009;18(6):445–57. doi:10.1097/CEJ.0b013e32832f9bd6.
Guha M, Avadhani NG. Mitochondrial retrograde signaling at the crossroads of tumor bioenergetics, genetics and epigenetics. Mitochondrion. 2013;13(6):577–91. doi:10.1016/j.mito.2013.08.007.
Yu M. Generation, function and diagnostic value of mitochondrial DNA copy number alterations in human cancers. Life Sci. 2011;89(3-4):65–71. doi:10.1016/j.lfs.2011.05.010.
Cui H, Huang P, Wang Z, Zhang Y, Zhang Z, Xu W, et al. Association of decreased mitochondrial DNA content with the progression of colorectal cancer. BMC Cancer. 2013;13:110. doi:10.1186/1471-2407-13-110.
Kirches E. Mitochondrial and nuclear genes of mitochondrial components in cancer. Curr Genom. 2009;10(4):281–93. doi:10.2174/138920209788488517.
Elachouri G, Vidoni S, Zanna C, Pattyn A, Boukhaddaoui H, Gaget K, et al. OPA1 links human mitochondrial genome maintenance to mtDNA replication and distribution. Genome Res. 2011;21(1):12–20. doi:10.1101/gr.108696.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19(9):1639–45. doi:10.1101/gr.092759.109.
Acknowledgments
We thank Adriana Aparecida Marques and Life Technologies (Brazil) for the technical support. We also thank Vinicius Kannen Cardoso for the scientific insights.
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All procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and/or national research committee and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards.
Funding
This work was funding by The National Council for Scientific and Technological Development (CNPq), grant #573754/2008-0; by grants #2008/57877-3 and #2013/08135-2, São Paulo Research Foundation (FAPESP); and by Research Support of the University Sao Paulo, CISBi-NAP/USP #12.1.25441.01.2.
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de Araujo, L.F., Fonseca, A.S., Muys, B.R. et al. Mitochondrial genome instability in colorectal adenoma and adenocarcinoma. Tumor Biol. 36, 8869–8879 (2015). https://doi.org/10.1007/s13277-015-3640-7
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DOI: https://doi.org/10.1007/s13277-015-3640-7