GATA4 loss of function in liver cancer impedes precursor to hepatocyte transition
Francis O. Enane, Wai Ho Shuen, Xiaorong Gu, Ebrahem Quteba, Bartlomiej Przychodzen, Hideki Makishima, Juraj Bodo, Joanna Ng, Chit Lai Chee, Rebecca Ba, Lip Seng Koh, Janice Lim, Rachael Cheong, Marissa Teo, Zhenbo Hu, Kwok Peng Ng, Jaroslaw Maciejewski, Tomas Radivoyevitch, Alexander Chung, London Lucien Ooi, Yu Meng Tan, Peng-Chung Cheow, Pierce Chow, Chung Yip Chan, Kiat Hon Lim, Lisa Yerian, Eric Hsi, Han Chong Toh, Yogen Saunthararajah
Francis O. Enane, Wai Ho Shuen, Xiaorong Gu, Ebrahem Quteba, Bartlomiej Przychodzen, Hideki Makishima, Juraj Bodo, Joanna Ng, Chit Lai Chee, Rebecca Ba, Lip Seng Koh, Janice Lim, Rachael Cheong, Marissa Teo, Zhenbo Hu, Kwok Peng Ng, Jaroslaw Maciejewski, Tomas Radivoyevitch, Alexander Chung, London Lucien Ooi, Yu Meng Tan, Peng-Chung Cheow, Pierce Chow, Chung Yip Chan, Kiat Hon Lim, Lisa Yerian, Eric Hsi, Han Chong Toh, Yogen Saunthararajah
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Research Article Genetics Oncology

GATA4 loss of function in liver cancer impedes precursor to hepatocyte transition

Abstract

The most frequent chromosomal structural loss in hepatocellular carcinoma (HCC) is of the short arm of chromosome 8 (8p). Genes on the remaining homologous chromosome, however, are not recurrently mutated, and the identity of key 8p tumor-suppressor genes (TSG) is unknown. In this work, analysis of minimal commonly deleted 8p segments to identify candidate TSG implicated GATA4, a master transcription factor driver of hepatocyte epithelial lineage fate. In a murine model, liver-conditional deletion of 1 Gata4 allele to model the haploinsufficiency seen in HCC produced enlarged livers with a gene expression profile of persistent precursor proliferation and failed hepatocyte epithelial differentiation. HCC mimicked this gene expression profile, even in cases that were morphologically classified as well differentiated. HCC with intact chromosome 8p also featured GATA4 loss of function via GATA4 germline mutations that abrogated GATA4 interactions with a coactivator, MED12, or by inactivating mutations directly in GATA4 coactivators, including ARID1A. GATA4 reintroduction into GATA4-haploinsufficient HCC cells or ARID1A reintroduction into ARID1A-mutant/GATA4-intact HCC cells activated hundreds of hepatocyte genes and quenched the proliferative precursor program. Thus, disruption of GATA4-mediated transactivation in HCC suppresses hepatocyte epithelial differentiation to sustain replicative precursor phenotype.

Authors

Francis O. Enane, Wai Ho Shuen, Xiaorong Gu, Ebrahem Quteba, Bartlomiej Przychodzen, Hideki Makishima, Juraj Bodo, Joanna Ng, Chit Lai Chee, Rebecca Ba, Lip Seng Koh, Janice Lim, Rachael Cheong, Marissa Teo, Zhenbo Hu, Kwok Peng Ng, Jaroslaw Maciejewski, Tomas Radivoyevitch, Alexander Chung, London Lucien Ooi, Yu Meng Tan, Peng-Chung Cheow, Pierce Chow, Chung Yip Chan, Kiat Hon Lim, Lisa Yerian, Eric Hsi, Han Chong Toh, Yogen Saunthararajah

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Figure 4

A baseline difference in chromatin at precursor/proliferation genes with high versus hepatocyte epithelial-differentiation genes with low expression in HCC.

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A baseline difference in chromatin at precursor/proliferation genes with...
(A) Precursor genes were identified by their differential expression at early/intermediate (precursor) versus terminal stages of liver development. Hierarchical clustering by GenePattern analysis (FDR < 0.01) (GEO GSE13149) (23). Gene names are listed in Supplemental Table 1. (B) High expression of precursor and low expression of epithelial-differentiation genes in HCC versus nonmalignant liver (FDR < 0.01). Gene names are listed in Supplemental Table 3. (C) Genes highly expressed in HCC, including MYC target genes, have chromatin that is open/poised for gene activation in the ultimate baseline, ESCs; in contrast, less expressed genes, including known hepatocyte epithelial-differentiation genes, have closed chromatin with low H3K4me3 levels. Aligned H1 ESC H3K4me3 ChIP-Seq data (ENCFF775QSF) were imported, analyzed, and visualized to show number of reads with or without 2,000 bp from the transcription start site using Easeq (80). (D) Close-up of H3K4me3 at cytochrome genes with low (CYP1A2) versus high (CYP2R1) expression in HCC. (E) Quantification of data shown in C. Plotted are medians and interquartile range (box) and minimum/maximum (whiskers). (F) This difference in baseline chromatin state was also evident by CpG methylation analysis. Methylation values (β values) by Illumina 450-k CpG array for CpG linked with these genes in ESC (n = 19) and normal liver (n = 4) (β values from GEO GSE31848) (81). MYC target genes, 356 genes/5716 CpG (82); hepatocyte epithelial-differentiation genes, 600 genes/9238 CpG; genes significantly highly expressed in HCC, 700 genes/10528 CpG; genes significantly less expressed in HCC 700, genes/11616 CpG.