SETD1A drives stemness by reprogramming the epigenetic landscape in hepatocellular carcinoma stem cells
Jianxu Chen, Zhijie Xu, Hongbin Huang, Yao Tang, Hong Shan, Fei Xiao
Jianxu Chen, Zhijie Xu, Hongbin Huang, Yao Tang, Hong Shan, Fei Xiao
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Research Article Hepatology Oncology

SETD1A drives stemness by reprogramming the epigenetic landscape in hepatocellular carcinoma stem cells

Abstract

Cancer stem cells (CSCs) are responsible for tumor progression and recurrence. However, the mechanisms regulating hepatocellular carcinoma (HCC) stemness remain unclear. Applying a genome-scale CRISPR knockout screen, we identified that the H3K4 methyltransferase SETD1A and other members of Trithorax group proteins drive cancer stemness in HCC. SET domain containing 1A (SETD1A) was positively correlated with poor clinical outcome in patients with HCC. Combination of SETD1A and serum alpha fetoprotein substantially improved the accuracy of predicting HCC relapse. Mechanistically, SETD1A mediates transcriptional activation of various histone-modifying enzymes, facilitates deposition of trimethylated H3K4 (H3K4me3) and H3K27me3, and activates oncogenic enhancers and super-enhancers, leading to activation of oncogenes and inactivation of tumor suppressor genes simultaneously in liver CSCs. In addition, SETD1A cooperates with polyadenylate-binding protein cytoplasmic 1 to regulate H3K4me3 modification on oncogenes. Our data pinpoint SETD1A as a key epigenetic regulator driving HCC stemness and progression, highlighting the potential of SETD1A as a candidate target for HCC intervention and therapy.

Authors

Jianxu Chen, Zhijie Xu, Hongbin Huang, Yao Tang, Hong Shan, Fei Xiao

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Figure 5

SETD1A cooperates with PABPC1 to promote HCC stemness and progression.

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SETD1A cooperates with PABPC1 to promote HCC stemness and progression. (...
(A) MS identification of PABPC1 as an interaction protein of SETD1A. (B) Western blots of endogenous co-IPs for PABPC1, SETD1A, CXXC1, ASH2L, and WDR5 in PLC and Huh7 cells. (C) Analysis of relative expression of PABPC1 in HCC samples and their matched normal samples using TCGA database. (D) Analysis of overall survival curves of patients with high and low PABPC1 expression levels using TCGA database. (E) ATAC-Seq analysis of the accessibility of PABPC1 locus in the CD24+CD133+ CSCs and CD24–CD133– non-CSCs and the representative SETD1A CUT&Tag profiles in CD24+CD133+ CSCs at PABPC1 locus. (F) Comparison of the proportion of CD24+CD133+ CSCs in SETD1A-knockdown and PABPC1-expressing SETD1A-knockdown HCC cells using flow cytometry (n = 3). (G) The spheroid formation assays showing the effect of PABPC1 overexpression on the stemness of SETD1A-knockdown HCC cells (n = 3). Scale bar represents 500 μm. (H) Cell proliferation assay for the effect of PABPC1 overexpression on the cell proliferation of SETD1A-knockdown HCC cells (n = 3). (I and J) Transwell assay with/without Matrigel assessing the effect of SETD1A-knockdown PABPC1 overexpression on the migration and invasion of SETD1A-knockdown HCC cells (n = 3). Scale bar represents 200 μm. (K) Venn diagram showing the extent of overlap for PABPC1-, SETD1A-, and H3K4me3-bound regions in liver CSCs. (L) GO analysis for biological processes of PABPC1 target genes. (M) GO analysis for biological processes of PABPC1 and SETD1A co-regulation genes. (N) GO analysis for biological processes of PABPC1, H3K4me3, and SETD1A co-regulation genes. Data are presented as mean ± SEM. Statistical analysis was performed by unpaired 2-tailed Student’s t test, or 2-way ANOVA was used with post hoc test. *P < 0.05, **P < 0.01, and ***P < 0.001.