2. Academic Validation
  3. Redistribution of super-enhancers promotes malignancy in human hepatocellular carcinoma

Redistribution of super-enhancers promotes malignancy in human hepatocellular carcinoma

  • J Adv Res. 2025 Jul 4:S2090-1232(25)00504-1. doi: 10.1016/j.jare.2025.07.006.
Jiacheng Huang 1,  Liang Xu 2,  Ye Chen 3,  Mengqing Sun 4,  Yiqing Hu 1,  Caixu Pan 1,  Liangyu Jiang 4,  Menglan Wang 4,  Jing Liu 4,  Heng Dong 4,  Qian Li 4,  Fangtian Bu 4,  Cunjie Chang 4,  Xuliang Chen 5,  Yu Wang 4,  Shusen Zheng 1,  Qi Ling 6,  Jianxiang Chen 7,  Yiting Qiao 8
Affiliations

Affiliations

  • 1 Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Key Laboratory of Organ Transplantation, Zhejiang Province 310003, China; Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Science (2019RU019), China.
  • 2 College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
  • 3 Pediatric Cancer Research Center, National Clinical Research Center for Child Health, Children's Hospital Zhejiang University School of Medicine, Hangzhou 310003, China.
  • 4 School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China.
  • 5 Key Laboratory of Artificial Organs and Computational Medicine in Zhejiang Province, Shulan (Hangzhou) Hospital, Shulan International Medical College, Zhejiang Shuren University, Hangzhou 310015, China.
  • 6 Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Key Laboratory of Organ Transplantation, Zhejiang Province 310003, China; Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Science (2019RU019), China. Electronic address: lingqi@zju.edu.cn.
  • 7 School of Pharmacy and Department of Hepatology, the Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China; Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China. Electronic address: chenjx@hznu.edu.cn.
  • 8 Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China; NHC Key Laboratory of Combined Multi-organ Transplantation, Key Laboratory of Organ Transplantation, Zhejiang Province 310003, China; Key Laboratory of the Diagnosis and Treatment of Organ Transplantation, Research Unit of Collaborative Diagnosis and Treatment For Hepatobiliary and Pancreatic Cancer, Chinese Academy of Medical Science (2019RU019), China; Institute of Organ Transplantation, Zhejiang University, Hangzhou 310003, China; State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Hangzhou 310003, China. Electronic address: yitingqiao@zju.edu.cn.
PMID: 40617410 DOI: 10.1016/j.jare.2025.07.006
Abstract

Introduction: Super-enhancers (SEs) are defined as the regulatory region where intensive transcriptional cofactors bind. Dysregulation of SEs is related to multiple diseases, however, its role in hepatocellular carcinoma (HCC) remains elusive.

Objectives: This work aimed to reveal the dysregulation of SEs in HCC and the therapeutic potential for HCC treatment.

Methods: Fifteen HCC and twelve paracancerous samples underwent chromatin immunoprecipitation (ChIP) Sequencing targeting H3K27ac, and subsequently the SEs were identified by the Rank Ordering of Super-Enhancers algorithm. Differential SEs featured by tumor or paracancerous tissues were identified, and cross-referenced with the differential expression genes and prognosis-related genes in 2 independent public or in-house HCC cohorts. The SE region of HSPA4 was deleted in the genome of HCCLM3 cell by CRISPR-Cas9, named HSPA4-SE-KO cells. The potential druggable transcriptional factors were identified by CRCmapper, GeneMANIA and Drug Gene Interaction Database (DGID).

Results: Five targets, including CDKN2C, HSPA4, GGH, PDGFA, and CAP2, were identified as HCC-gain SEs with oncogenic potential, which were further validated experimentally by SE inhibitors and ChIP targeting H3K27ac and BRD4. Cell proliferation and migration assays further confirmed that silencing of these HCC-gain SEs significantly suppressed the malignant phenotype of HCC cell lines. HSPA4 appeared strongest oncogenic functions among these targets, which was further verified by HCC mouse xenograft models and clinical sample investigation. Moreover, HSPA4-SE-KO cells obtained significantly suppressed HSPA4 expression and retarded tumorigenic capability. Finally, dysregulation of transcriptional factors engaged in the oncogenic role of SEs, and Danthron that targeting RXRA were identified from DGID for HCC treatment.

Conclusion: The dysregulated SE landscape of HCC promoted the malignancy phenotype by the upregulation of oncogenes, and SE-regulatory network might be potential drug targets for HCC treatment. Our study deepened the insight of epigenetic dysregulation in HCC, offering the groundwork for SEs as potential therapeutic targets of HCC treatment.

Keywords

Epigenetics; H3K27ac; Hepatocellular carcinoma; Super-enhancers; Therapeutic targets.

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