Diverse mutational landscapes in human lymphocytes

Heather E. Machado, Emily Mitchell, Nina F. Øbro, Kirsten Kübler, Megan Davies, Daniel Leongamornlert, Alyssa Cull, Francesco Maura, Mathijs A. Sanders, Alex T.J. Cagan, Craig McDonald, Miriam Belmonte, Mairi S. Shepherd, Felipe A. Vieira Braga, Robert J. Osborne, Krishnaa Mahbubani, Iñigo Martincorena, Elisa Laurenti, Anthony R. Green, Gad GetzPaz Polak, Kourosh Saeb-Parsy, Daniel J. Hodson, David G. Kent, Peter J. Campbell*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

35 Citations (Scopus)
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Abstract

The lymphocyte genome is prone to many threats, including programmed mutation during differentiation1, antigen-driven proliferation and residency in diverse microenvironments. Here, after developing protocols for expansion of single-cell lymphocyte cultures, we sequenced whole genomes from 717 normal naive and memory B and T cells and haematopoietic stem cells. All lymphocyte subsets carried more point mutations and structural variants than haematopoietic stem cells, with higher burdens in memory cells than in naive cells, and with T cells accumulating mutations at a higher rate throughout life. Off-target effects of immunological diversification accounted for approximately half of the additional differentiation-associated mutations in lymphocytes. Memory B cells acquired, on average, 18 off-target mutations genome-wide for every on-target IGHV mutation during the germinal centre reaction. Structural variation was 16-fold higher in lymphocytes than in stem cells, with around 15% of deletions being attributable to off-target recombinase-activating gene activity. DNA damage from ultraviolet light exposure and other sporadic mutational processes generated hundreds to thousands of mutations in some memory cells. The mutation burden and signatures of normal B cells were broadly similar to those seen in many B-cell cancers, suggesting that malignant transformation of lymphocytes arises from the same mutational processes that are active across normal ontogeny. The mutational landscape of normal lymphocytes chronicles the off-target effects of programmed genome engineering during immunological diversification and the consequences of differentiation, proliferation and residency in diverse microenvironments.

Original languageEnglish
Pages (from-to)724-732
Number of pages9
JournalNature
Volume608
Issue number7924
DOIs
Publication statusPublished - 25 Aug 2022

Bibliographical note

Funding Information:
G.G. receives research funds from Pharmacyclics and IBM. G.G. is an inventor on multiple patents related to bioinformatics methods (MuTect, MutSig, ABSOLUTE, MSMutSig, MSMuTect, POLYSOLVER and TensorQTL). G.G. is a founder, consultant and holds privately held equity in Scorpion Therapeutics. D.J.H. receives research funding from AstraZeneca and D.G.K. receives research funding from STRM.bio. All other authors declare no competing interests.

Funding Information:
This work was supported by the WBH Foundation and Wellcome Trust. Investigators at the Sanger Institute are supported by a core grant from the Wellcome Trust. M.S.S. was the recipient of a Biotechnology and Biological Sciences Research Council Industrial Collaborative Awards in Science and Engineering PhD Studentship. The D.G.K. laboratory is supported by a Blood Cancer UK Bennett Fellowship (15008), an ERC Starting Grant (ERC-2016-STG–715371), a CR-UK Programme Foundation award (DCRPGF\100008) and an MRC-AMED joint award (MR/V005502/1). D.G.K., E.L. and A.R.G. are supported by a core support grant to the Wellcome MRC Cambridge Stem Cell Institute, Blood Cancer UK, the NIHR Cambridge Biomedical Research Centre, and the CRUK Cambridge Cancer Centre. E.L. is supported by a Sir Henry Dale fellowship from Wellcome/Royal Society (107630/Z/15/Z), BBSRC (BB/P002293/1), and core support grants by Wellcome and MRC to the Wellcome-MRC Cambridge Stem Cell Institute (203151/Z/16/Z). K.K. and G.G. are supported by a GDAN grant (grant number U24CA210999). G.G. is partly supported by the Paul C. Zamecnik Chair in Oncology at the Massachusetts General Hospital Cancer Center. We thank F. Abascal, T. Coorens, T. Butler and S. Brunner for valuable guidance in data analysis; the CASM laboratory, including L. O’Neill and C. Latimer, for sample and data management, and CASM IT for technical support. This research was supported by the Cambridge NIHR BRC Cell Phenotyping Hub and staff, including E. Perez and N. Savinykh, who provided advice and support in flow cytometry and cell sorting. We are especially grateful to the tissue donors and their families and to the Cambridge Biorepository for Translational Medicine for the gift of tissue from transplant organ donors.

Funding Information:
This work was supported by the WBH Foundation and Wellcome Trust. Investigators at the Sanger Institute are supported by a core grant from the Wellcome Trust. M.S.S. was the recipient of a Biotechnology and Biological Sciences Research Council Industrial Collaborative Awards in Science and Engineering PhD Studentship. The D.G.K. laboratory is supported by a Blood Cancer UK Bennett Fellowship (15008), an ERC Starting Grant (ERC-2016-STG–715371), a CR-UK Programme Foundation award (DCRPGF\100008) and an MRC-AMED joint award (MR/V005502/1). D.G.K., E.L. and A.R.G. are supported by a core support grant to the Wellcome MRC Cambridge Stem Cell Institute, Blood Cancer UK, the NIHR Cambridge Biomedical Research Centre, and the CRUK Cambridge Cancer Centre. E.L. is supported by a Sir Henry Dale fellowship from Wellcome/Royal Society (107630/Z/15/Z), BBSRC (BB/P002293/1), and core support grants by Wellcome and MRC to the Wellcome-MRC Cambridge Stem Cell Institute (203151/Z/16/Z). K.K. and G.G. are supported by a GDAN grant (grant number U24CA210999). G.G. is partly supported by the Paul C. Zamecnik Chair in Oncology at the Massachusetts General Hospital Cancer Center. We thank F. Abascal, T. Coorens, T. Butler and S. Brunner for valuable guidance in data analysis; the CASM laboratory, including L. O’Neill and C. Latimer, for sample and data management, and CASM IT for technical support. This research was supported by the Cambridge NIHR BRC Cell Phenotyping Hub and staff, including E. Perez and N. Savinykh, who provided advice and support in flow cytometry and cell sorting. We are especially grateful to the tissue donors and their families and to the Cambridge Biorepository for Translational Medicine for the gift of tissue from transplant organ donors.

Publisher Copyright:
© 2022, The Author(s).

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