Somatic mutations and clonal dynamics in healthy and cirrhotic human liver

Simon F. Brunner, Nicola D. Roberts, Luke A. Wylie, Luiza Moore, Sarah J. Aitken, Susan E. Davies, Mathijs A. Sanders, Pete Ellis, Chris Alder, Yvette Hooks, Federico Abascal, Michael R. Stratton, Inigo Martincorena, Matthew Hoare () and Peter J. Campbell ()
Additional contact information
Simon F. Brunner: Wellcome Trust Sanger Institute
Nicola D. Roberts: Wellcome Trust Sanger Institute
Luke A. Wylie: Wellcome Trust Sanger Institute
Luiza Moore: Wellcome Trust Sanger Institute
Sarah J. Aitken: CRUK Cambridge Institute
Susan E. Davies: University of Cambridge, Addenbrooke’s Hospital
Mathijs A. Sanders: Wellcome Trust Sanger Institute
Pete Ellis: Wellcome Trust Sanger Institute
Chris Alder: Wellcome Trust Sanger Institute
Yvette Hooks: Wellcome Trust Sanger Institute
Federico Abascal: Wellcome Trust Sanger Institute
Michael R. Stratton: Wellcome Trust Sanger Institute
Inigo Martincorena: Wellcome Trust Sanger Institute
Matthew Hoare: CRUK Cambridge Institute
Peter J. Campbell: Wellcome Trust Sanger Institute

Nature, 2019, vol. 574, issue 7779, 538-542

Abstract: Abstract The most common causes of chronic liver disease are excess alcohol intake, viral hepatitis and non-alcoholic fatty liver disease, with the clinical spectrum ranging in severity from hepatic inflammation to cirrhosis, liver failure or hepatocellular carcinoma (HCC). The genome of HCC exhibits diverse mutational signatures, resulting in recurrent mutations across more than 30 cancer genes1–7. Stem cells from normal livers have a low mutational burden and limited diversity of signatures8, which suggests that the complexity of HCC arises during the progression to chronic liver disease and subsequent malignant transformation. Here, by sequencing whole genomes of 482 microdissections of 100–500 hepatocytes from 5 normal and 9 cirrhotic livers, we show that cirrhotic liver has a higher mutational burden than normal liver. Although rare in normal hepatocytes, structural variants, including chromothripsis, were prominent in cirrhosis. Driver mutations, such as point mutations and structural variants, affected 1–5% of clones. Clonal expansions of millimetres in diameter occurred in cirrhosis, with clones sequestered by the bands of fibrosis that surround regenerative nodules. Some mutational signatures were universal and equally active in both non-malignant hepatocytes and HCCs; some were substantially more active in HCCs than chronic liver disease; and others—arising from exogenous exposures—were present in a subset of patients. The activity of exogenous signatures between adjacent cirrhotic nodules varied by up to tenfold within each patient, as a result of clone-specific and microenvironmental forces. Synchronous HCCs exhibited the same mutational signatures as background cirrhotic liver, but with higher burden. Somatic mutations chronicle the exposures, toxicity, regeneration and clonal structure of liver tissue as it progresses from health to disease.

Date: 2019
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DOI: 10.1038/s41586-019-1670-9

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