Induction of apobec3 exacerbates dna replication stress and chromosomal instability in early breast and lung cancer evolution

Subramanian Venkatesan, Mihaela Angelova, Clare Puttick, Haoran Zhai, Deborah R. Caswell, Wei Ting Lu, Michelle Dietzen, Panagiotis Galanos, Konstantinos Evangelou, Roberto Bellelli, Emilia L. Lim, Thomas B.K. Watkins, Andrew Rowan, Vitor H. Teixeira, Yue Zhao, Haiquan Chen, Bryan Ngo, Lykourgos Panagiotis Zalmas, Maise Al Bakir, Sebastijan HoborEva Grönroos, Adam Pennycuick, Ersilia Nigro, Brittany B. Campbell, William L. Brown, Ayse U. Akarca, Teresa Marafioti, Y. Wu Mary, Michael Howell, Simon J. Boulton, Cosetta Bertoli, Tim R. Fenton, Robertus A.M. De Bruin, Apolinar Maya-Mendoza, Eric Santoni-Rugiu, Robert E. Hynds, Vassilis G. Gorgoulis, Mariam Jamal-Hanjani, Nicholas McGranahan, Reuben S. Harris, Sam M. Janes, Jirina Bartkova, Samuel F. Bakhoum, Jiri Bartek, Nnennaya Kanu, Charles Swanton

Research output: Contribution to journalArticlepeer-review

10 Scopus citations

Abstract

APOBEC3 enzymes are cytosine deaminases implicated in cancer. Precisely when APOBEC3 expression is induced during cancer development remains to be defined. Here we show that specific APOBEC3 genes are upregulated in breast ductal carcinoma in situ, and in preinvasive lung cancer lesions coincident with cellular proliferation. We observe evidence of APOBEC3-mediated subclonal mutagenesis propagated from TRACERx preinvasive to invasive nonsmall cell lung cancer (NSCLC) lesions. We find that APOBEC3B exacerbates DNA replication stress and chromosomal instability through incomplete replication of genomic DNA, manifested by accumulation of mitotic ultrafine bridges and 53BP1 nuclear bodies in the Gj phase of the cell cycle. Analysis of TRACERx NSCLC clinical samples and mouse lung cancer models revealed APOBEC3B expression driving replication stress and chromosome missegregation. We propose that APOBEC3 is functionally implicated in the onset of chromosomal instability and somatic mutational heterogeneity in preinvasive disease, providing fuel for selection early in cancer evolution. Significance : This study reveals the dynamics and drivers of APOBEC3 gene expression in preinvasive disease and the exacerbation of cellular diversity by APOBEC3B through DNA replication stress to promote chromosomal instability early in cancer evolution.

Original languageEnglish (US)
Pages (from-to)2456-2473
Number of pages18
JournalCancer discovery
Volume11
Issue number10
DOIs
StatePublished - 2021

Bibliographical note

Funding Information:
other support from H. Pappas, grants from Hellenic Foundation for Research and Innovation, and grants from NKUA-SARG during the conduct of the study. A. Pennycuick reports grants from Wellcome Trust during the conduct of the study; in addition, he has a patent for United Kingdom Patent Application No. 1819452.2 pending. S.J. Boulton reports personal fees from Artios Pharma Ltd during the conduct of the study. T.R. Fenton reports being on the Clinical and Scientific Advisory Board of APOBEC Discovery Ltd. E. Santoni-Rugiu reports personal fees from Pfizer, Takeda, Roche, and Bayer; also grants from Roche, and non-financial support from Takeda outside the submitted work. V.G. Gorgoulis reports grants from European Union, grants from National Public Investment Program of the Ministry of Development and Investment/General 27 Secretariat for Research and Technology, other support from Welfare Foundation for Social & Cultural Sciences, other support from H. Pappas, grants from Hellenic Foundation for Research and Innovation, and grants from NKUA-SARG during the conduct of the study. M. Jamal-Hanjani reports grants from Cancer Research UK during the conduct of the study. N. McGranahan reports personal fees from Achilles Therapeutics outside the submitted work; in addition, he has a patent for PCT/GB2018/052004 pending, a patent for PCT/EP2016/071471 pending, a patent for PCT/GB2018/052004 pending, and a patent for PCT/GB2020/050221 pending. R.S. Harris reports other support from ApoGen Biotechnologies during the conduct of the study; other support from ApoGen Biotechnologies outside the submitted work. S.M. Janes reports grants from Wellcome and grants from CRUK during the conduct of the study; personal fees from AstraZeneca, personal fees from Johnson & Johnson, personal fees from Bard1 Lifesciences, and grants from GRAIL Inc outside the submitted work. S.F. Bakhoum reports personal fees and other support from Volastra Therapeutics outside the submitted work; in addition, he has a patent for Targeting cGAS-STING signaling in cancer pending. C. Swanton reports grants from Pfizer, Boehringer-Ingelheim, and Archer Dx Inc; grants and personal fees from Bristol Myers Squibb, AstraZen-eca, Roche-Ventana, Ono Pharmaceuticals; personal fees from Glaxo-SmithKline, Novartis, Celgene, Illumina, MSD, Amgen, Sarah Canon Research Institute, Genentech, Bicycle Therapeutics, and Medicxi; personal fees and other support from GRAIL; other support from Epic Biosciences, Apogen Biotechnologies; and personal fees and other support from Achilles Therapeutics outside the submitted work; in addition, he has a patent for Immune checkpoint intervention in cancer (PCT/EP2016/071471) issued, a patent for Method for treating cancer based on identification of clonal neoantigens (PCT/ EP2016/059401) issued, a patent for Methods for lung cancer detection (PCT/US2017/028013) issued, a patent for Method of detecting tumor recurrence (PCT/GB2017/053289) issued, a patent for Method for treating cancer (PCT/EP2016/059401) issued, a patent for Method of treating cancer by targeting insertion/deletion mutations (PCT/GB2018/051893) issued, a patent for Method of identifying insertion/deletion mutation targets (PCT/GB2018/051892) issued, a patent for Method for determining whether an HLA allele is lost in a tumor (PCT/GB2018/052004) issued, a patent for Method for identifying responders to cancer treatment (PCT/GB2018/051912) issued, and a patent for Method of predicting survival rates for cancer patients (PCT/GB2020/050221) issued; and he is Royal Society Napier Research Professor (RP150154). His work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001169), the UK Medical Research Council (FC001169), and the Wellcome Trust (FC001169). C. Swanton is funded by Cancer Research UK (TRACERx, PEACE and CRUK Cancer Immunotherapy Catalyst Network), Cancer Research UK Lung Cancer Centre of Excellence, the Rosetrees Trust, Butterfield and Stoneygate Trusts, NovoNordisk Foundation (ID16584), Royal Society Research Professorship Enhancement Award (RP/EA/180007), the NIHR BRC at University College London Hospitals, the CRUK-UCL Centre, Experimental Cancer Medicine Centre and the Breast Cancer Research Foundation (BCRF). This research is supported by a Stand Up To Cancer-LUNGevity-American Lung Association Lung Cancer Interception Dream Team Translational Research Grant (SU2C-AACR-DT23-17). Stand Up To Cancer (SU2C) is a program of the Entertainment Industry Foundation. Research grants are administered by the American Association for Cancer Research, the Scientific Partner of SU2C. C. Swanton also receives funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007–2013) Consolidator Grant (FP7-THESEUS-617844), European Commission ITN (FP7-PloidyNet 607722), an ERC Advanced Grant (PROTEUS) from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (835297) and Chromavision from the European Union’s Horizon 2020 research and innovation programme (665233). No disclosures were reported by the other authors.

Funding Information:
We thank the members of the TRACERx consortium for participating in this study. The results published here are in part based upon data generated by TCGA pilot project established by the NCI and the National Human Genome Research Institute. R.E. Hynds is a Wellcome Trust Sir Henry Wellcome Fellow (WT209199/Z/17/Z) and received grant funding from the Roy Castle Lung Cancer Foundation that supported this work. P. Galanos is funded by KBVU grant R167-A11068. The work in the Boulton lab is supported by a European Research Council (ERC) Advanced Investigator Grant (TelMetab) and Wellcome Trust Senior Investigator and Collaborative Grants. T. Marafioti is supported by the UK National Institute of Health Research University College London Hospital Biomedical Research Centre and A.U. Akarca is supported by Cancer Research UK–UCL Centre Cancer Immuno-therapy Accelerator Award. R.A.M. de Bruin and C. Bertoli are supported by core funding to the MRC-UCL University Unit (Ref. MC_EX_G0800785) and funded by R.A.M. de Bruin’s Cancer Research UK Programme Foundation Award. Cancer studies in the Harris lab are supported by NCI P01-CA234228. R.S. Harris is the Margaret Harvey Schering Land Grant Chair for Cancer Research, a Distinguished McKnight University Professor, and an Investigator of the Howard Hughes Medical Institute. K. Evangelou and V.G. Gorgoulis were financially supported by the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grants agreement no. 722729 (SYNTRAIN); the National Public Investment Program of the Ministry of Development and Investment/General Secretariat for Research and Technology, in the framework of the Flagship Initiative to address SARS-CoV-2 (2020ΣE01300001); the Welfare Foundation for Social and Cultural Sciences (KIKPE), Greece; H. Pappas donation; grant no. 775 from the Hellenic Foundation for Research and Innovation (HFRI); and NKUA-SARG grants 70/3/9816, 70/3/12128, and 70/3/15603 S.F. Bakhoum is supported by the Office of the Director, the NIH under Award Number DP5OD026395 High-Risk High-Reward Program, the NCI Breast Cancer SPORE (P50CA247749) and R01 (R01CA256188-01), the Burroughs Wellcome Fund Career Award for Medical Scientists, the Parker Institute for Immunotherapy at MSKCC, the Josie Robertson Foundation, and the MSKCC core grant P30-CA008748. J. Bartek and his team were funded by grants from the Danish Cancer Society (R1123-A7785-15-S2 and R167-A11068), the Novo Nordisk Foundation (16854 and 0060590), the Lundbeck foundation (R266-2017-4289 and R322-2019-2577), the Swedish Research council (VR-MH 2014-46602-117891-30), The Swedish Cancer Foundation/Cancerfonden (170176), and the Danish national research foundation (project CARD, DNRF 125). N. Kanu receives funding from Cancer Research UK. C. Swanton is a Royal Society Napier Research Professor (RP150154). This work was supported by the Francis Crick Institute that receives its core funding from Cancer Research UK (FC001169), the UK Medical Research Council (FC001169), and the Wellcome Trust (FC001169). This research was funded in whole, or in part, by the Wellcome Trust (FC001169). For the purpose of open access, the authors have applied a CC by copyright license to any author-accepted manuscript version arising from this submission. This work was supported by Breast Cancer Research Foundation (BCRF), the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) Consolidator Grant (FP7-THESEUS-617844), an ERC Advanced Grant (PROTEUS) from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (835297), Novo Nordisk Foundation (ID16584), and the National Institute for Health Research (NIHR) Biomedical Research Centre at University College London Hospitals. The authors thank Dr. Silvestro Conti-cello and Dr. Uday Munagala (ISPRO, Italy) for critical discussions. The authors thank Dr. Stephen Elledge (Harvard University) for providing miR-146a-EGFP plasmid, and Dr. Julian Downward and Dr. Miriam Molina (The Francis Crick Institute, UK) for providing TIIP-ER-KRAS V12 cells. We also thank Dr. Sarah Clarke (University College London, UK) for their assistance with normal lung and CIS FFPE blocks. We also thank Laura Tovini and Dr. Sarah McClelland (Barts Cancer Institute, London) for their helpful advice on the Image-Stream. We also thank Dr. Christoffer L. Halvorsen (Danish Cancer Society Research Center, Denmark), Dr. Robert Strauss (Danish Cancer Society Research Center, Denmark), Dr. Agostina Bertolin (The Francis Crick Institute, UK), and Dr. David Moore (The Francis Crick Institute, UK) for helpful suggestions. Finally, the authors gratefully acknowledge members of Experimental Histopathology, Light Microscopy, Flow Cytometry, Cell Services and Genomics Equipment Park at the Francis Crick Institute (The Francis Crick Institute, UK).

Publisher Copyright:
© 2021 American Association for Cancer Research.

PubMed: MeSH publication types

  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

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