Hypoxia increases mutational load of breast cancer cells through frameshift mutations

References

• Chabanon RM, Pedrero M, Lefebvre C, Marabelle A, Soria JC, Postel-Vinay S. Mutational landscape and sensitivity to immune checkpoint blockers. Clin Cancer Res. 2016;22(17):4309–10. doi:10.1158/1078-0432.CCR-16-0903.
   PubMed Web of Science ®Google Scholar
• Francis A, Venkatesh GH, Zaarour RF, Zeinelabdin NA, Nawafleh HH, Prasad P, Buart S, Terry S, Chouaib S. Tumor hypoxia: a key determinant of microenvironment hostility and a major checkpoint during the antitumor response. Crit Rev Immunol. 2018;38(6):505–524. doi:10.1615/CritRevImmunol.2019030168.
   PubMed Web of Science ®Google Scholar
• Terry S, Buart S, Chouaib S. Hypoxic stress-induced tumor and immune plasticity, suppression, and impact on tumor heterogeneity. Front Immunol. 2017;8:1625. doi:10.3389/fimmu.2017.01625.
   PubMed Web of Science ®Google Scholar
• Harris AL. Hypoxia–a key regulatory factor in tumour growth. Nat Rev Cancer. 2002;2(1):38–47. doi:10.1038/nrc704.
   PubMed Web of Science ®Google Scholar
• Dewhirst MW, Cao Y, Moeller B. Cycling hypoxia and free radicals regulate angiogenesis and radiotherapy response. Nat Rev Cancer. 2008;8(6):425–437. doi:10.1038/nrc2397.
   PubMed Web of Science ®Google Scholar
• Chen A, Sceneay J, Gödde N, Kinwel T, Ham S, Thompson EW, Humbert PO, Möller A. Intermittent hypoxia induces a metastatic phenotype in breast cancer. Oncogene. 2018;37(31):4214–4225. doi:10.1038/s41388-018-0259-3.
   PubMed Web of Science ®Google Scholar
• Giglia-Mari G, Zotter A, Vermeulen W. DNA damage response. Cold Spring Harb Perspect Biol. 2011;3(1):a000745. doi:10.1101/cshperspect.a000745.
   PubMed Web of Science ®Google Scholar
• Scanlon SE, Glazer PM. Multifaceted control of DNA repair pathways by the hypoxic tumor microenvironment. DNA Repair (Amst). 2015;32:180–189. doi:10.1016/j.dnarep.2015.04.030.
   PubMed Web of Science ®Google Scholar
• Ng N, Purshouse K, Foskolou IP, Olcina MM, Hammond EM. Challenges to DNA replication in hypoxic conditions. Febs J. 2018;285(9):1563–1571. doi:10.1111/febs.14377.
   PubMed Web of Science ®Google Scholar
• Michiels C, Tellier C, Feron O. Cycling hypoxia: A key feature of the tumor microenvironment. Biochim Biophys Acta. 2016;1866(1):76–86. doi:10.1016/j.bbcan.2016.06.004.
   PubMed Web of Science ®Google Scholar
• Koritzinsky M, Wouters BG. The roles of reactive oxygen species and autophagy in mediating the tolerance of tumor cells to cycling hypoxia. Semin Radiat Oncol. 2013;23(4):252–261. doi:10.1016/j.semradonc.2013.05.006.
   PubMed Web of Science ®Google Scholar
• Chae YK, Anker JF, Bais P, Namburi S, Giles FJ, Chuang JH. Mutations in DNA repair genes are associated with increased neo-antigen load and activated T cell infiltration in lung adenocarcinoma. Oncotarget. 2018;9(8):7949–7960. doi:10.18632/oncotarget.23742.
   PubMedGoogle Scholar
• Germano G, Lamba S, Rospo G, Barault L, Magrì A, Maione F, Russo M, Crisafulli G, Bartolini A, Lerda G, et al. Inactivation of DNA repair triggers neoantigen generation and impairs tumour growth. Nature. 2017;552(7683):116–120. doi:10.1038/nature24673.
   PubMed Web of Science ®Google Scholar
• Luoto KR, Kumareswaran R, Bristow RG. Tumor hypoxia as a driving force in genetic instability. Genome Integr. 2013;4(1):5. doi:10.1186/2041-9414-4-5.
   PubMedGoogle Scholar
• Olive PL, Banáth JP. The comet assay: a method to measure DNA damage in individual cells. Nat Protoc. 2006;1(1):23–29. doi:10.1038/nprot.2006.5.
   PubMed Web of Science ®Google Scholar
• Gyori BM, Venkatachalam G, Thiagarajan PS, Hsu D, Clement MV. OpenComet: an automated tool for comet assay image analysis. Redox Biol. 2014;2:457–465. doi:10.1016/j.redox.2013.12.020.
   PubMed Web of Science ®Google Scholar
• Koboldt DC, Zhang Q, Larson DE, Shen D, McLellan MD, Lin L, Miller CA, Mardis ER, Ding L, Wilson RK, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22(3):568–576. doi:10.1101/gr.129684.111.
   PubMed Web of Science ®Google Scholar
• McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The ensembl variant effect predictor. Genome Biol. 2016;17(1):122. doi:10.1186/s13059-016-0974-4.
   PubMed Web of Science ®Google Scholar
• Mayakonda A, Lin DC, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018;28(11):1747–1756. doi:10.1101/gr.239244.118.
   PubMed Web of Science ®Google Scholar
• Schenck RO, Lakatos E, Gatenbee C, Graham TA, Anderson ARA. NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline. BMC Bioinformatics. 2019;20(1):264. doi:10.1186/s12859-019-2876-4.
   PubMedGoogle Scholar
• Jurtz V, Paul S, Andreatta M, Marcatili P, Peters B, Morten N. Netmhcpan-4.0: improved peptide–mhc class i interaction predictions integrating eluted ligand and peptide binding affinity data. J Immunol. 2017;199(9):3360–3368. doi:10.4049/jimmunol.1700893.
   PubMed Web of Science ®Google Scholar
• Babicki S, Arndt D, Marcu A, Liang Y, Grant JR, Maciejewski A, Wishart DS. Heatmapper: web-enabled heat mapping for all. Nucleic Acids Res. 2016;44(W1):W147–53. doi:10.1093/nar/gkw419.
   PubMed Web of Science ®Google Scholar
• Olcina M, Lecane PS, Hammond EM. Targeting hypoxic cells through the DNA damage response. Clin Cancer Res. 2010;16(23):5624–5629. doi:10.1158/1078-0432.CCR-10-0286.
   PubMed Web of Science ®Google Scholar
• Hammond EM, Denko NC, Dorie MJ, Abraham RT, Giaccia AJ. Hypoxia links ATR and p53 through replication arrest. Mol Cell Biol. 2002;22(6):1834–1843. doi:10.1128/MCB.22.6.1834-1843.2002.
   PubMed Web of Science ®Google Scholar
• Huang LE, Bindra RS, Glazer PM, Harris AL. Hypoxia-induced genetic instability–a calculated mechanism underlying tumor progression. J Mol Med (Berl). 2007;85(2):139–148. doi:10.1007/s00109-006-0133-6.
   PubMed Web of Science ®Google Scholar
• Havel JJ, Chowell D, Chan TA. The evolving landscape of biomarkers for checkpoint inhibitor immunotherapy. Nat Rev Cancer. 2019;19(3):133–150. doi:10.1038/s41568-019-0116-x.
   PubMed Web of Science ®Google Scholar
• Bhandari V, Li CH, Bristow RG, Boutros PC, Consortium PCAWG. Divergent mutational processes distinguish hypoxic and normoxic tumours. Nat Commun. 2020;11(1):737. doi:10.1038/s41467-019-14052-x.
   PubMed Web of Science ®Google Scholar
• Rospo G, Lorenzato A, Amirouchene-Angelozzi N, Magrì A, Cancelliere C, Corti G, Negrino C, Amodio V, Montone M, Bartolini A, et al. Evolving neoantigen profiles in colorectal cancers with DNA repair defects. Genome Med. 2019;11(1):42. doi:10.1186/s13073-019-0654-6.
   PubMedGoogle Scholar
• Turajlic S, Litchfield K, Xu H, Rosenthal R, McGranahan N, Reading JL, Wong YNS, Rowan A, Kanu N, Al Bakir M, et al. Insertion-and-deletion-derived tumour-specific neoantigens and the immunogenic phenotype: a pan-cancer analysis. Lancet Oncol. 2017;18(8):1009–1021. doi:10.1016/S1470-2045(17)30516-8.
   PubMed Web of Science ®Google Scholar
• Davoli T, Uno H, Wooten EC, Elledge SJ. Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy. Science. 2017;355:6322. doi:10.1126/science.aaf8399.
   Web of Science ®Google Scholar
• Tripathi R, Modur V, Senovilla L, Kroemer G, Komurov K. Suppression of tumor antigen presentation during aneuploid tumor evolution contributes to immune evasion. OncoImmunology. 2019;8(11):1657374. doi:10.1080/2162402X.2019.1657374.
   PubMed Web of Science ®Google Scholar
• McGranahan N, Furness AJ, Rosenthal R, Ramskov S, Lyngaa R, Saini SK, Jamal-Hanjani M, Wilson GA, Birkbak NJ, Hiley CT, et al. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade. Science. 2016;351(6280):1463–1469. doi:10.1126/science.aaf1490.
   PubMed Web of Science ®Google Scholar
• Petrova V, Annicchiarico-Petruzzelli M, Melino G, Amelio I. The hypoxic tumour microenvironment. Oncogenesis. 2018;7(1):10. doi:10.1038/s41389-017-0011-9.
   PubMed Web of Science ®Google Scholar
• de Miranda NFCC, Trajanoski Z. Advancing cancer immunotherapy: a vision for the field. Genome Med. 2019;11(1):51. doi:10.1186/s13073-019-0662-6.
   PubMedGoogle Scholar
• Lakatos E, Williams MJ, Schenck RO, Cross WCH, Househam J, Werner B, Gatenbee C, Robertson-Tessi M, Barnes CP, Anderson ARA, et al. Evolutionary dynamics of neoantigens in growing tumours. bioRxiv. 2019;536433.
   Google Scholar
• Shaltiel IA, Krenning L, Bruinsma W, Medema RH. The same, only different - DNA damage checkpoints and their reversal throughout the cell cycle. J Cell Sci. 2015;128(4):607–620. doi:10.1242/jcs.163766.
   PubMed Web of Science ®Google Scholar