Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

Agustin Sgro; Joseph Cursons; Charlene Waryah; Eleanor A Woodward; Momeneh Foroutan; Ruqian Lyu; George C T Yeoh; Peter J Leedman; Pilar Blancafort

doi:10.1186/s13148-023-01482-0

Epigenetic reactivation of tumor suppressor genes with CRISPRa technologies as precision therapy for hepatocellular carcinoma

Clin Epigenetics. 2023 Apr 29;15(1):73. doi: 10.1186/s13148-023-01482-0.

Authors

Agustin Sgro^{1

2

3}, Joseph Cursons⁴, Charlene Waryah^{1

2}, Eleanor A Woodward^{1

2}, Momeneh Foroutan⁴, Ruqian Lyu^{5

6}, George C T Yeoh^{2

7}, Peter J Leedman^{2

8

9}, Pilar Blancafort^{10

11

12}

Affiliations

¹ Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia.
² Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia.
³ School of Human Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia.
⁴ Biomedicine Discovery Institute and the Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
⁵ Bioinformatics and Cellular Genomics, St Vincent's Institute of Medical Research, Fitzroy, Melbourne, VIC, 3065, Australia.
⁶ Melbourne Integrative Genomics/School of Mathematics and Statistics, Faculty of Science, The University of Melbourne, Royal Parade, Parkville, VIC, 3010, Australia.
⁷ School of Molecular Sciences, University of Western Australia, Crawley, Perth, WA, 6009, Australia.
⁸ Laboratory for Cancer Medicine, Harry Perkins Institute of Medical Research, QEII Medical Centre, 6 Verdun St, Nedlands, Perth, WA, 6009, Australia.
⁹ School of Medicine and Pharmacology, The University of Western Australia, Crawley, Perth, WA, 6009, Australia.
¹⁰ Cancer Epigenetics Group, The Harry Perkins Institute of Medical Research, Nedlands, Perth, WA, 6009, Australia. [email protected].
¹¹ Centre for Medical Research, The University of Western Australia, Perth, WA, 6009, Australia. [email protected].
¹² School of Human Sciences, The University of Western Australia, Crawley, Perth, WA, 6009, Australia. [email protected].

Abstract

Background: Epigenetic silencing of tumor suppressor genes (TSGs) is a key feature of oncogenesis in hepatocellular carcinoma (HCC). Liver-targeted delivery of CRISPR-activation (CRISPRa) systems makes it possible to exploit chromatin plasticity, by reprogramming transcriptional dysregulation.

Results: Using The Cancer Genome Atlas HCC data, we identify 12 putative TSGs with negative associations between promoter DNA methylation and transcript abundance, with limited genetic alterations. All HCC samples harbor at least one silenced TSG, suggesting that combining a specific panel of genomic targets could maximize efficacy, and potentially improve outcomes as a personalized treatment strategy for HCC patients. Unlike epigenetic modifying drugs lacking locus selectivity, CRISPRa systems enable potent and precise reactivation of at least 4 TSGs tailored to representative HCC lines. Concerted reactivation of HHIP, MT1M, PZP, and TTC36 in Hep3B cells inhibits multiple facets of HCC pathogenesis, such as cell viability, proliferation, and migration.

Conclusions: By combining multiple effector domains, we demonstrate the utility of a CRISPRa toolbox of epigenetic effectors and gRNAs for patient-specific treatment of aggressive HCC.

Keywords: CRISPRa; Epigenetic drugs; Epigenetic editing toolbox; Genome multiplexing; Hepatocellular carcinoma; Precision medicine; Tumor suppressor genes.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Carcinoma, Hepatocellular* / genetics
Carcinoma, Hepatocellular* / pathology
Cell Line, Tumor
Clustered Regularly Interspaced Short Palindromic Repeats
DNA Methylation
Epigenesis, Genetic
Gene Expression Regulation, Neoplastic
Genes, Tumor Suppressor
Humans
Liver Neoplasms* / genetics
Liver Neoplasms* / pathology