Objective Hepatocellular carcinoma (HCC) is the fastest-growing cause of cancer-related mortality with chronic viral hepatitis and non-alcoholic steatohepatitis (NASH) as major aetiologies. Treatment options for HCC are unsatisfactory and chemopreventive approaches are absent. Chronic hepatitis C (CHC) results in epigenetic alterations driving HCC risk and persisting following cure. Here, we aimed to investigate epigenetic modifications as targets for liver cancer chemoprevention.
Design Liver tissues from patients with NASH and CHC were analysed by ChIP-Seq (H3K27ac) and RNA-Seq. The liver disease-specific epigenetic and transcriptional reprogramming in patients was modelled in a liver cell culture system. Perturbation studies combined with a targeted small molecule screen followed by in vivo and ex vivo validation were used to identify chromatin modifiers and readers for HCC chemoprevention.
Results In patients, CHC and NASH share similar epigenetic and transcriptomic modifications driving cancer risk. Using a cell-based system modelling epigenetic modifications in patients, we identified chromatin readers as targets to revert liver gene transcription driving clinical HCC risk. Proof-of-concept studies in a NASH-HCC mouse model showed that the pharmacological inhibition of chromatin reader bromodomain 4 inhibited liver disease progression and hepatocarcinogenesis by restoring transcriptional reprogramming of the genes that were epigenetically altered in patients.
Conclusion Our results unravel the functional relevance of metabolic and virus-induced epigenetic alterations for pathogenesis of HCC development and identify chromatin readers as targets for chemoprevention in patients with chronic liver diseases.
- hepatocellular carcinoma
- gene expression
- hepatitis C
- non-alcoholic steatohepatitis
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FJ, NH, EC and SL contributed equally.
BCF and TFB contributed equally.
Contributors TFB initiated and coordinated the study. TFB, BCF, FJ, NH, EC, SL, KG and YH designed experiments and analysed data. NH, EC, SL, MAO, CT, AARS, KG, AO, MS and GA performed experiments. FJ performed the computational analyses of NGS data. HES performed PLS drug screen analyses. KKT contributed to the concept and approach of the study. CS and CB performed sequencing of ChIPmentation experiments. ID, AO, HES, SJP, MBZ, NF, AS, AM, KG, AARS and YH analysed data. PT, MS, KC, HA and PP provided clinical liver tissue samples. RM and AS analysed the histopathology of mouse liver tissues. NH, FJ, EC, FHTD, BCF, MBZ, SJP, AM, CS and TFB wrote the manuscript.
Funding This work was supported by the European Union (ERC-AdG2014 HEPCIR #671231 (TFB and YH) and H2020 HEPCAR #667273, ERC PoC-HEPCAN #862551 to TFB). ARC, Paris and Institut Hospitalo-Universitaire, Strasbourg (TheraHCC and TheraHCC2.0 IHUARC IHU201301187 and IHUC201901299 TFB), the Foundation of the University of Strasbourg and Roche Institute (HEPKIN), the Agence Nationale de Recherches sur le Sida et les Hépatites Virales (2017/1633), the US Department of Defense (W81XWH-16-1-0363 to TFB and YH), the Cancéropôle du Grand-Est, the National Institutes of Health (DK099558 and T32CA073145-20 to SL, R01CA233794 to YH and TFB, NCI 1R21CA209940-01A1 to TFB), AMED (19fk0210020h0003 to KC), AASLD Foundation (Pinnacle Research Award) and the Massachusetts General Hospital Department of Surgery (KKT) and the Cancer Prevention & Research Institute of Texas RR180016 to YH. This work has been published under the framework of the LABEX ANR-10-LABX-0028_HEPSYS and PLAN CANCER 2014-2019 HCCMICTAR and benefits from a funding from the state managed by the French National Research Agency as part of the Investments for the Future Program, INCa (National Institute for Cancer) and INSERM.
Competing interests The University of Strasbourg, INSERM, the IHU Strasbourg and Mount Sinai Hospital have filed a patent application on the clinical gene signature-based human cell culture model and uses thereof with YH and TFB as co-inventors (WO 2016174130 A1), which has been licensed to Alentis Therapeutics, Basel, Switzerland.
Patient and public involvement Patients and/or the public were not involved in the design, conduct, reporting or dissemination plans of this research.
Patient consent for publication Not required.
Ethics approval The protocols were approved by the Ethics Committee of the Strasbourg University Hospitals (DC-2016–2616), Mount Sinai Hospital, New York (HS13-00159), Basel University Hospital (EKNZ 2014–362) and Hiroshima University Hospitals (E-1049–1).
Provenance and peer review Not commissioned; externally peer reviewed.
Data availability statement Data, i.e. raw reads from ChIP-seq and RNA-seq experiments in fastq files, are available in a public, open access repository without restrictions on the use or distribution of the data. The Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra) project accession number for accessing the data produced for this study is PRJNA606244.
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