1
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Ma W, Tang W, Kwok JS, Tong AH, Lo CW, Chu AT, Chung BH. A review on trends in development and translation of omics signatures in cancer. Comput Struct Biotechnol J 2024; 23:954-971. [PMID: 38385061 PMCID: PMC10879706 DOI: 10.1016/j.csbj.2024.01.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024] Open
Abstract
The field of cancer genomics and transcriptomics has evolved from targeted profiling to swift sequencing of individual tumor genome and transcriptome. The steady growth in genome, epigenome, and transcriptome datasets on a genome-wide scale has significantly increased our capability in capturing signatures that represent both the intrinsic and extrinsic biological features of tumors. These biological differences can help in precise molecular subtyping of cancer, predicting tumor progression, metastatic potential, and resistance to therapeutic agents. In this review, we summarized the current development of genomic, methylomic, transcriptomic, proteomic and metabolic signatures in the field of cancer research and highlighted their potentials in clinical applications to improve diagnosis, prognosis, and treatment decision in cancer patients.
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Affiliation(s)
- Wei Ma
- Hong Kong Genome Institute, Hong Kong, China
| | - Wenshu Tang
- Hong Kong Genome Institute, Hong Kong, China
| | | | | | | | | | - Brian H.Y. Chung
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Hong Kong Genome Project
- Hong Kong Genome Institute, Hong Kong, China
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China
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2
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Zhu Q, Xie J, Mei W, Zeng C. Methylated circulating tumor DNA in hepatocellular carcinoma: A comprehensive analysis of biomarker potential and clinical implications. Cancer Treat Rev 2024; 128:102763. [PMID: 38763055 DOI: 10.1016/j.ctrv.2024.102763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/30/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
The intricate epigenetic landscape of hepatocellular carcinoma (HCC) is profoundly influenced by alterations in DNA methylation patterns. Understanding these alterations is crucial for unraveling the molecular mechanisms underlying HCC pathogenesis. Methylated circulating tumor DNA (ctDNA) presents itself as an encouraging avenue for biomarker discovery and holds substantial clinical implications in HCC management. This review comprehensively outlines the studies concerning DNA methylation in HCC and underscores the significance of methylated ctDNA within this context. Moreover, a variety of cfDNA methylation-based methodologies, such as 5hmC profiling, bisulfite-based, restriction enzyme-dependent, and enrichment-based methods, provide in-depth insights into the molecular pathology of HCC. Additionally, the integration of methylated ctDNA analysis into clinical practice represents a significant advancement in personalized HCC management. By facilitating cancer screening, prognosis assessment, and treatment response prediction, the utilization of methylated ctDNA signifies a pivotal stride toward enhancing patient care and outcomes in HCC.
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Affiliation(s)
- Qian Zhu
- Department of Gastroenterology, Shenzhen Longhua District Central Hospital, Shenzhen 518110, China
| | - Jiaqi Xie
- Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Wuxuan Mei
- Xianning Medical College, Hubei University of Science and Technology, Xianning 437100, China
| | - Changchun Zeng
- Department of Medical Laboratory, Shenzhen Longhua District Central Hospital, Guangdong Medical University, Shenzhen 518110, China.
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3
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Zhang P, Wan Y, Ma J, Gong J, Zhong Z, Cui Y, Zhang H, Da Y, Ma J, Li C, Liu L, Gong T, Tan Y, Zhang C. Epigenetic silencing of LDHB promotes hepatocellular carcinoma by remodeling the tumor microenvironment. Cancer Immunol Immunother 2024; 73:127. [PMID: 38739169 DOI: 10.1007/s00262-024-03717-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 05/14/2024]
Abstract
Lactate dehydrogenase B (LDHB) reversibly catalyzes the conversion of pyruvate to lactate or lactate to pyruvate and expressed in various malignancies. However, the role of LDHB in modulating immune responses against hepatocellular carcinoma (HCC) remains largely unknown. Here, we found that down-regulation of lactate dehydrogenase B (LDHB) was coupled with the promoter hypermethylation and knocking down the DNA methyltransferase 3A (DNMT 3A) restored LDHB expression levels in HCC cell lines. Bioinformatics analysis of the HCC cohort from The Cancer Genome Atlas revealed a significant positive correlation between LDHB expression and immune regulatory signaling pathways and immune cell infiltrations. Moreover, immune checkpoint inhibitors (ICIs) have shown considerable promise for HCC treatment and patients with higher LDHB expression responded better to ICIs. Finally, we found that overexpression of LDHB suppressed HCC growth in immunocompetent but not in immunodeficient mice, suggesting that the host immune system was involved in the LDHB-medicated tumor suppression. Our findings indicate that DNMT3A-mediated epigenetic silencing of LDHB may contribute to HCC progression through remodeling the tumor immune microenvironment, and LDHB may become a potential prognostic biomarker and therapeutic target for HCC immunotherapy.
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Affiliation(s)
- Peng Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
- Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Jiangxi Medical Academy of Nutrition and Health Management, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
| | - Yi Wan
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
- Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
| | - Jinrong Ma
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
- Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
| | - Jin Gong
- Cancer Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China
| | - Ziwei Zhong
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
- Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
| | - Yuxin Cui
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China
| | - Hongli Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
- Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
| | - Yanyan Da
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
- Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
| | - Junpeng Ma
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
- Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
| | - Chenxi Li
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
- Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
| | - Lijuan Liu
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, 277 Yanta West Road, Xi'an, 710061, China
| | - Tian Gong
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
- Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
- Jiangxi Medical Academy of Nutrition and Health Management, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
- Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China
| | - Youwen Tan
- Jiangxi Medical Academy of Nutrition and Health Management, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China
| | - Chengsheng Zhang
- Center for Molecular Diagnosis and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China.
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China.
- Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China.
- Jiangxi Medical Academy of Nutrition and Health Management, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 17 Yongwai Zhengjie, Nanchang, 330006, China.
- Department of Medical Genetics, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, 1519 Dongyue Dadao, Nanchang, 330209, China.
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4
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Gong Y, Zhou M, Zhu Y, Pan J, Zhou X, Jiang Y, Zeng H, Zheng H, Geng X, Huang D. PVALB Was Identified as an Independent Prognostic Factor for HCC Closely Related to Immunity, and Its Absence Accelerates Tumor Progression by Regulating NK Cell Infiltration. J Hepatocell Carcinoma 2024; 11:813-838. [PMID: 38737383 PMCID: PMC11088852 DOI: 10.2147/jhc.s450479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 04/23/2024] [Indexed: 05/14/2024] Open
Abstract
Purpose Hepatocellular carcinoma is the most common primary liver cancer, with poor prognosis. Complex immune microenvironment of the liver is linked to the development of HCC. PVALB is a calcium-binding protein which has been described as a cancer suppressor gene in thyroid cancer and glioma. Nevertheless, the role of PVALB in HCC is unknown. Materials and Methods We obtained data from TCGA and GSE54236 datasets. MCP-counter, WGCNA and LASSO model were applied to identify PVALB. With UALCAN, MethSurv, and other websites, we probed the expression, methylation and survival of PVALB. LinkedOmics and GSEA were adopted for functional analysis, while TIMER, TISIDB, Kaplan-Meier plotter, TIDE databases were utilized to evaluate the relevance of PVALB to the tumor immune microenvironment and predict immunotherapy efficacy. TargetScan, DIANA, LncRNASNP2 databases and relevant experiments were employed to construct ceRNA network. Finally, molecular docking and drug sensitivity of PVALB were characterized by GeneMANIA, CTD, and so on. Results PVALB was recognized as a gene associated with HCC and NK cell. Its expression was down-regulated in HCC tissue, which lead to adverse prognosis. Besides, the hypomethylation of PVALB was related to its reduced expression. Notably, PVALB was tightly linked to immune, and its reduced expression attenuated the anticancer effect of NK cells via the Fas/FasL pathway, leading to a adverse outcome. The lnc-YY1AP1-3/hsa-miR-6735-5p/PVALB axis may regulate the PVALB expression. Finally, we found immunotherapy might be a viable treatment option. Conclusion In a word, PVALB is a prognostic indicator, whose low expression facilitates HCC progression by impacting NK cell infiltration.
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Affiliation(s)
- Yiyang Gong
- Department of Thyroid Surgery; Second Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Minqin Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Yanting Zhu
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Jingying Pan
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Xuanrui Zhou
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Yike Jiang
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Hong Zeng
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Hao Zheng
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Xitong Geng
- Second College of Clinical Medicine, Nanchang University, Nanchang, People’s Republic of China
| | - Da Huang
- Department of Thyroid Surgery; Second Affiliated Hospital of Nanchang University, Nanchang, People’s Republic of China
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5
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Zuo A, Li J, Weng S, Xu H, Zhang Y, Wang L, Xing Z, Luo P, Cheng Q, Li J, Han X, Liu Z. Integrated Exploration of Epigenetic Dysregulation Reveals a Stemness/EMT Subtype and MMP12 Linked to the Progression and Prognosis in Hepatocellular Carcinoma. J Proteome Res 2024; 23:1821-1833. [PMID: 38652053 DOI: 10.1021/acs.jproteome.4c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Epigenetic dysregulation drives aberrant transcriptional programs playing a critical role in hepatocellular carcinoma (HCC), which may provide novel insights into the heterogeneity of HCC. This study performed an integrated exploration on the epigenetic dysregulation of miRNA and methylation. We discovered and validated three patterns endowed with gene-related transcriptional traits and clinical outcomes. Specially, a stemness/epithelial-mesenchymal transition (EMT) subtype was featured by immune exhaustion and the worst prognosis. Besides, MMP12, a characteristic gene, was highly expressed in the stemness/EMT subtype, which was verified as a pivotal regulator linked to the unfavorable prognosis and further proven to promote tumor proliferation, invasion, and metastasis in vitro experiments. Proteomic analysis by mass spectrometry sequencing also indicated that the overexpression of MMP12 was significantly associated with cell proliferation and adhesion. Taken together, this study unveils innovative insights into epigenetic dysregulation and identifies a stemness/EMT subtype-specific gene, MMP12, correlated with the progression and prognosis of HCC.
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Affiliation(s)
- Anning Zuo
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinyu Li
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Libo Wang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhe Xing
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Peng Luo
- Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Jing Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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6
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Liang C, Long K, Zheng W, Zhong R, Li Z, Zhu S, Gu S, Zhu C, Yang Y. Exploring the role of CDCA4 in liver hepatocellular carcinoma using bioinformatics analysis and experiments. Medicine (Baltimore) 2024; 103:e38028. [PMID: 38701314 PMCID: PMC11062718 DOI: 10.1097/md.0000000000038028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/05/2024] [Indexed: 05/05/2024] Open
Abstract
Liver hepatocellular carcinoma (LIHC) encompasses diverse therapeutic approaches, among which targeted therapy has gained significant prominence in recent years. The identification of numerous targets and the increasing clinical application of targeted drugs have greatly improved LIHC treatment. However, the precise role of CDCA4 (Cell Division Cycle Associated 4), as well as its underlying mechanisms and prognostic implications in LIHC, remains unclear. CDCA4 expression levels in LIHC were analyzed using multiple databases including the cancer genome atlas (TCGA), gene expression profiling interactive analysis (GEPIA), and ULCAN, as well as the datasets E_TABM_36, GSE144269, GSE14520, and GSE54236. The prognostic value of CDCA4 was then evaluated. Subsequently, the association between CDCA4 and immune cells was investigated. Enrichment analysis (GSEA) was utilized to investigate the functional roles and pathways linked to CDCA4. Additionally, the methylation patterns and drug sensitivity of CDCA4 were examined. A predictive model incorporating immune genes related to CDCA4 was developed. The TISCH dataset was used to investigate the single-cell expression patterns of CDCA4. Finally, validation of CDCA4 expression levels was conducted through RT-PCR, Western blotting, and immunohistochemistry. CDCA4 exhibited significant overexpression in LIHC and demonstrated significant correlations with clinical features. High expression of CDCA4 is associated with a poorer prognosis. Analysis of immune infiltration and enrichment revealed its association with the immune microenvironment. Furthermore, its expression is correlated with methylation and mutation patterns. CDCA4 is associated with 19 drugs. Prognostic models utilizing CDCA4 demonstrate favorable effectiveness. T cell subtypes were found to be associated with CDCA4 through single-cell analysis. The conclusive experiment provided evidence of significant upregulation of CDCA4 in LIHC. The high expression of CDCA4 in LIHC is associated with prognostic significance and is highly expressed in T cell subtypes, providing a new therapeutic target and potential therapeutic strategy for LIHC.
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Affiliation(s)
- Changfu Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Kaijun Long
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Wenhao Zheng
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Riqiang Zhong
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Zhangrui Li
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Shengwei Zhu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Shijing Gu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Chuangshi Zhu
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Hainan Medical College, Haikou, China
| | - Yan Yang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital of Hainan Medical College, Haikou, China
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7
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Bin P, Wang C, Zhang H, Yan Y, Ren W. Targeting methionine metabolism in cancer: opportunities and challenges. Trends Pharmacol Sci 2024; 45:395-405. [PMID: 38580603 DOI: 10.1016/j.tips.2024.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/13/2024] [Accepted: 03/13/2024] [Indexed: 04/07/2024]
Abstract
Reprogramming of methionine metabolism is a conserved hallmark of tumorigenesis. Recent studies have revealed mechanisms regulating methionine metabolism within the tumor microenvironment (TME) that drive both cancer development and antitumor immunity evasion. In this review article we summarize advancements in our understanding of tumor regulation of methionine metabolism and therapies in development that target tumor methionine metabolism. We also delineate the challenges of methionine blockade therapies in cancer and discuss emerging strategies to address them.
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Affiliation(s)
- Peng Bin
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; Henry Fok School of Biology and Agriculture, Shaoguan University, Shaoguan 512005, China
| | - Chuanlong Wang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Hangchao Zhang
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yuqi Yan
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Wenkai Ren
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China.
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8
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Peng J, Li H, Tong F, Hu J, Li M, Chen G, Liu D, Liu J, Wang R, Xu H, Li X, Zhong X, Yao J, Cao B. Methylation changes of liver DNA during the formation of gallstones. Epigenomics 2024. [PMID: 38444389 DOI: 10.2217/epi-2023-0391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024] Open
Abstract
Aim: To explore the overall methylation changes in liver tissues during the formation of gallstones, as well as the key pathways and genes involved in the process. Methods: Reduced-representation bisulfite sequencing and RNA sequencing were conducted on the liver tissues of mice with gallstones and control normal mice. Results: A total of 8705 differentially methylated regions in CpG and 1410 differentially expressed genes were identified. The joint analysis indicated that aberrant DNA methylation may be associated with dysregulated gene expression in key pathways such as cholesterol metabolism and bile secretion. Conclusion: We propose for the first time that methylation changes in some key pathway genes in liver tissue may be involved in the formation of gallstones.
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Affiliation(s)
- Junbin Peng
- Medical School of Anhui University Of Science & Technology, Huainan, 232001, Anhui, China
| | - Haojie Li
- Medical School of Anhui University Of Science & Technology, Huainan, 232001, Anhui, China
| | - Fang Tong
- Medical School of Anhui University Of Science & Technology, Huainan, 232001, Anhui, China
| | - Jinlong Hu
- Department of General Surgery, Anhui No.2 Provincial People's Hospital, Hefei, 230041, Anhui, China
- Anhui Province Key Laboratory of Occupational Health, Anhui No.2 Provincial People's Hospital, Hefei, 230041, China
| | - Min Li
- Department of General Surgery, Anhui No.2 Provincial People's Hospital, Hefei, 230041, Anhui, China
| | - Gan Chen
- Department of General Surgery, Anhui No.2 Provincial People's Hospital, Hefei, 230041, Anhui, China
| | - Dongquan Liu
- Department of General Surgery, Anhui No.2 Provincial People's Hospital, Hefei, 230041, Anhui, China
| | - Jinshan Liu
- Anhui Medical University, Hefei, 230032, Anhui, China
| | - Rui Wang
- Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Hongyu Xu
- Anhui Medical University, Hefei, 230032, Anhui, China
| | - Xuanxuan Li
- Bengbu Medical College, Bengbu, 233030, Anhui, China
| | - Xinguo Zhong
- Department of General Surgery, Anhui No.2 Provincial People's Hospital, Hefei, 230041, Anhui, China
| | - Jiaming Yao
- Department of General Surgery, Anhui No.2 Provincial People's Hospital, Hefei, 230041, Anhui, China
| | - Baoqiang Cao
- Medical School of Anhui University Of Science & Technology, Huainan, 232001, Anhui, China
- Department of General Surgery, Anhui No.2 Provincial People's Hospital, Hefei, 230041, Anhui, China
- Anhui Province Key Laboratory of Occupational Health, Anhui No.2 Provincial People's Hospital, Hefei, 230041, China
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9
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Zhu D, Zeng S, Su C, Li J, Xuan Y, Lin Y, Xu E, Fan Q. The interaction between DNA methylation and tumor immune microenvironment: from the laboratory to clinical applications. Clin Epigenetics 2024; 16:24. [PMID: 38331927 PMCID: PMC10854038 DOI: 10.1186/s13148-024-01633-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
DNA methylation is a pivotal epigenetic modification that affects gene expression. Tumor immune microenvironment (TIME) comprises diverse immune cells and stromal components, creating a complex landscape that can either promote or inhibit tumor progression. In the TIME, DNA methylation has been shown to play a critical role in influencing immune cell function and tumor immune evasion. DNA methylation regulates immune cell differentiation, immune responses, and TIME composition Targeting DNA methylation in TIME offers various potential avenues for enhancing immune cytotoxicity and reducing immunosuppression. Recent studies have demonstrated that modification of DNA methylation patterns can promote immune cell infiltration and function. However, challenges persist in understanding the precise mechanisms underlying DNA methylation in the TIME, developing selective epigenetic therapies, and effectively integrating these therapies with other antitumor strategies. In conclusion, DNA methylation of both tumor cells and immune cells interacts with the TIME, and thus affects clinical efficacy. The regulation of DNA methylation within the TIME holds significant promise for the advancement of tumor immunotherapy. Addressing these challenges is crucial for harnessing the full potential of epigenetic interventions to enhance antitumor immune responses and improve patient outcomes.
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Affiliation(s)
- Daoqi Zhu
- School of Traditional Chinese Medicine, Southern Medical University, No. 1023 Shatai North Road, Guangzhou, 510515, China
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, No.111 Liuhua Road, Guangzhou, 510010, China
| | - Siying Zeng
- School of Traditional Chinese Medicine, Southern Medical University, No. 1023 Shatai North Road, Guangzhou, 510515, China
| | - Chao Su
- School of Traditional Chinese Medicine, Southern Medical University, No. 1023 Shatai North Road, Guangzhou, 510515, China
| | - Jingjun Li
- Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Yiwen Xuan
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, No.111 Liuhua Road, Guangzhou, 510010, China
| | - Yongkai Lin
- Department of Endocrinology, The First Affiliated Hospital, Traditional Chinese Medicine University of Guangzhou, Guangzhou, 510405, China
| | - Enwu Xu
- Department of Thoracic Surgery, General Hospital of Southern Theater Command, PLA, No.111 Liuhua Road, Guangzhou, 510010, China.
| | - Qin Fan
- School of Traditional Chinese Medicine, Southern Medical University, No. 1023 Shatai North Road, Guangzhou, 510515, China.
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10
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Draškovič T, Hauptman N. Discovery of novel DNA methylation biomarker panels for the diagnosis and differentiation between common adenocarcinomas and their liver metastases. Sci Rep 2024; 14:3095. [PMID: 38326602 PMCID: PMC10850119 DOI: 10.1038/s41598-024-53754-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/05/2024] [Indexed: 02/09/2024] Open
Abstract
Differentiation between adenocarcinomas is sometimes challenging. The promising avenue for discovering new biomarkers lies in bioinformatics using DNA methylation analysis. Utilizing a 2853-sample identification dataset and a 782-sample independent verification dataset, we have identified diagnostic DNA methylation biomarkers that are hypermethylated in cancer and differentiate between breast invasive carcinoma, cholangiocarcinoma, colorectal cancer, hepatocellular carcinoma, lung adenocarcinoma, pancreatic adenocarcinoma and stomach adenocarcinoma. The best panels for cancer type exhibit sensitivity of 77.8-95.9%, a specificity of 92.7-97.5% for tumors, a specificity of 91.5-97.7% for tumors and normal tissues and a diagnostic accuracy of 85.3-96.4%. We have shown that the results can be extended from the primary cancers to their liver metastases, as the best panels diagnose and differentiate between pancreatic adenocarcinoma liver metastases and breast invasive carcinoma liver metastases with a sensitivity and specificity of 83.3-100% and a diagnostic accuracy of 86.8-91.9%. Moreover, the panels could detect hypermethylation of selected regions in the cell-free DNA of patients with liver metastases. At the same time, these were unmethylated in the cell-free DNA of healthy donors, confirming their applicability for liquid biopsies.
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Affiliation(s)
- Tina Draškovič
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia
| | - Nina Hauptman
- Faculty of Medicine, Institute of Pathology, University of Ljubljana, Ljubljana, Slovenia.
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11
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Leng X, Xie S, Tao D, Wang Z, Shi J, Yi M, Tan X, Zhang X, Liu Y, Yang Y. Mouse Tspyl5 promotes spermatogonia proliferation through enhancing Pcna-mediated DNA replication. Reprod Fertil Dev 2024; 36:RD23042. [PMID: 38185096 DOI: 10.1071/rd23042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
CONTEXT The human TSPY1 (testis-specific protein, Y-linked 1) gene is critical for spermatogenesis and male fertility. However, there have been difficulties with studying the mechanism underlying its function, partly due to the presence of the Tspy1 pseudogene in mice. AIMS TSPYL5 (TSPY-like 5), an autosomal homologous gene of TSPY1 showing a similar expression pattern in both human and mouse testes, is also speculated to play a role in male spermatogenesis. It is beneficial to understand the role of TSPY1 in spermatogenesis by investigating Tspyl5 functions. METHODS Tspyl5 -knockout mice were generated to investigate the effect of TSPYL5 knockout on spermatogenesis. KEY RESULTS Tspyl5 deficiency caused a decline in fertility and decreased the numbers of spermatogonia and spermatozoa in aged male mice. Trancriptomic detection of spermatogonia derived from aged Tspyl5 -knockout mice revealed that the Pcna -mediated DNA replication pathway was downregulated. Furthermore, Tspyl5 was proven to facilitate spermatogonia proliferation and upregulate Pcna expression by promoting the ubiquitination-degradation of the TRP53 protein. CONCLUSIONS Our findings suggest that Tspyl5 is a positive regulator for the maintenance of the spermatogonia pool by enhancing Pcna -mediated DNA replication. IMPLICATIONS This observation provides an important clue for further investigation of the spermatogenesis-related function of TSPY1 .
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Affiliation(s)
- Xiangyou Leng
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Shengyu Xie
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Dachang Tao
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Zhaokun Wang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Jiaying Shi
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Ming Yi
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Xiaolan Tan
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Xinyue Zhang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu, China
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12
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Qin R, Jin T, Xu F. Biomarkers predicting the efficacy of immune checkpoint inhibitors in hepatocellular carcinoma. Front Immunol 2023; 14:1326097. [PMID: 38187399 PMCID: PMC10770866 DOI: 10.3389/fimmu.2023.1326097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
In recent years, immune checkpoint inhibitors (ICIs) have emerged as a transformative approach in treating advanced hepatocellular carcinoma (HCC). Despite their success, challenges persist, including concerns about their effectiveness, treatment costs, frequent occurrence of treatment-related adverse events, and tumor hyperprogression. Therefore, it is imperative to identify indicators capable of predicting the efficacy of ICIs treatment, enabling optimal patient selection to maximize clinical benefits while minimizing unnecessary toxic side effects and economic losses. This review paper categorizes prognostic biomarkers of ICIs treatment into the following categories: biochemical and cytological indicators, tumor-related markers, imaging and personal features, etiology, gut microbiome, and immune-related adverse events (irAEs). By organizing these indicators systematically, we aim to guide biomarker exploration and inform clinical treatment decisions.
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Affiliation(s)
| | - Tianqiang Jin
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Feng Xu
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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13
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Zou Q, Cao S. miR-4270 suppresses hepatocellular carcinoma progression by inhibiting DNMT3A-mediated methylation of HGFAC promoter. PeerJ 2023; 11:e16566. [PMID: 38077422 PMCID: PMC10704985 DOI: 10.7717/peerj.16566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/12/2023] [Indexed: 12/18/2023] Open
Abstract
Background miR-4270 is a regulatory factor has been linked with the progression of various cancers, such as nasopharyngeal carcinoma, hepatocellular carcinoma (HCC), and gastric cancer. However, the underlying mechanisms through which miR-4270 modulates HCC development are not fully understood. Methods miR-4270 expression levels were analyzed in various HCC cell lines and tissue samples. An online bioinformatics tool was then utilized to predict the miR-4270 target gene. The binding relationship between miR-4270 and its target gene DNMT3A was verified using dual-luciferase reporter and Ago2-RIP assays. Then, co-immunoprecipitation (Co-IP) and chromatin immunoprecipitation (ChIP) assays were conducted to investigate the association between DNMT3A and the hepatocyte growth factor activator (HGFAC) promoter region. To assess the methylation level of the HGFAC promoter, methylation-specific PCR (MSP) was employed. Furthermore, rescue analyses were carried out to evaluate the functional relevance of miR-4270 and HGFAC in the modulation of the malignant properties of HCC cells. Finally, HepG2 cells overexpressing miR-4270 were subcutaneously injected into nude mice to estimate the impact of miR-4270 on the xenograft tumor growth of HCC. Results A substantial miR-4270 downregulation was revealed in HCC patient samples and cell lines. miR-4270 upregulation suppressed both cell proliferation and invasion while promoting apoptosis. At the molecular level, miR-4270 was found to bind to the 3'untranslated region (3'UTR) of DNMT3A, thereby inhibiting DNMT3A-mediated methylation of the HGFAC promoter. Functional assays indicated that inhibition of miR-4270 stimulated HCC cell growth, an effect counteracted by overexpression of HGFAC. In vivo assays further verified that miR-4270 effectively suppressed the progression of HCC xenograft tumors. Conclusions miR-4270 was found to mitigate the malignant characteristics of HCC by inhibiting DNMT3A-mediated methylation of the HGFAC promoter, suggesting a potential therapeutic avenue for the management of HCC.
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Affiliation(s)
- Qiang Zou
- Department of Interventional Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin’s Clinical Research Center for Cancer, Tianjin, China
| | - Shasha Cao
- Department of Neonatology, Zibo Maternal and Child Health Hospital, Zibo, China
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14
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van der Meeren PE, de Wilde RF, Sprengers D, IJzermans JNM. Benefit and harm of waiting time in liver transplantation for HCC. Hepatology 2023:01515467-990000000-00646. [PMID: 37972979 DOI: 10.1097/hep.0000000000000668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023]
Abstract
Liver transplantation is the most successful treatment for limited-stage HCC. The waiting time for liver transplantation (LT) can be a critical factor affecting the oncological prognosis and outcome of patients with HCC. Efficient strategies to optimize waiting time are essential to maximize the benefits of LT and to reduce the harm of delay in transplantation. The ever-increasing demand for donor livers emphasizes the need to improve the organization of the waiting list for transplantation and to optimize organ availability for patients with and without HCC. Current progress in innovations to expand the donor pool includes the implementation of living donor LT and the use of grafts from extended donors. By expanding selection criteria, an increased number of patients are eligible for transplantation, which necessitates criteria to prevent futile transplantations. Thus, the selection criteria for LT have evolved to include not only tumor characteristics but biomarkers as well. Enhancing our understanding of HCC tumor biology through the analysis of subtypes and molecular genetics holds significant promise in advancing the personalized approach for patients. In this review, the effect of waiting time duration on outcome in patients with HCC enlisted for LT is discussed.
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Affiliation(s)
- Pam Elisabeth van der Meeren
- Department of Surgery, Division of HPB & Transplant Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Roeland Frederik de Wilde
- Department of Surgery, Division of HPB & Transplant Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Dave Sprengers
- Department of Gastroenterology & Hepatology, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Jan Nicolaas Maria IJzermans
- Department of Surgery, Division of HPB & Transplant Surgery, Erasmus MC Transplant Institute, University Medical Center Rotterdam, Rotterdam, the Netherlands
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15
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Zhang Y, Wang JW, Su X, Li JE, Wei XF, Yang JR, Gao S, Fan YC, Wang K. F-box protein 43 promoter methylation as a novel biomarker for hepatitis B virus-associated hepatocellular carcinoma. Front Microbiol 2023; 14:1267844. [PMID: 38029156 PMCID: PMC10652413 DOI: 10.3389/fmicb.2023.1267844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) has a high prevalence and poor prognosis worldwide. Therefore, it is urgent to find effective and timely diagnostic markers. The objective of this study was to evaluate the diagnostic value of F-box protein 43 promoter methylation in peripheral blood mononuclear cells (PBMCs) for HCC. Method A total of 247 participants were included in this study, comprising individuals with 123 hepatitis B virus-associated HCC, 79 chronic hepatitis B, and 45 healthy controls. F-box protein 43 methylation and mRNA levels in PBMCs were detected by MethyLight and quantitative real-time PCR. Result F-box protein 43 promoter methylation levels were significantly lower in HCC PBMCs than the chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Relative mRNA expression levels of F-box protein 43 in HCC PBMCs were significantly higher than those in chronic hepatitis B (P < 0.001) and healthy control PBMCs (P < 0.001). Receiver operating characteristic analysis of F-box protein 43 promoter methylation levels yielded an area under curve (AUC) of 0.793 with 76.42% sensitivity and 68.35% specificity when differentiating HCC from chronic hepatitis. These values for the F-box protein 43 promoter methylation level were superior to those of the alpha-fetoprotein serum (AFP) level (AUC: 0.780, sensitivity: 47.97%, and specificity: 96.20%), with increments in values for the combination of F-box protein 43 promoter methylation AFP levels (AUC: 0.888, sensitivity: 76.42%, and specificity: 86.08%). Conclusion Hypomethylation of the F-box protein 43 promoter in PBMCs is a promising biochemical marker for HBV-associated HCC.
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Affiliation(s)
- Ying Zhang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jing-Wei Wang
- Department of Hepatology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
| | - Xing Su
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jin-E Li
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Xue-Fei Wei
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Jie-Ru Yang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
| | - Shuai Gao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, China
- Department of Hepatology, Qilu Hospital (Qingdao) of Shandong University, Qingdao, China
- Hepatology Institute of Shandong University, Shandong University, Jinan, China
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16
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Liu C, Tang H, Hu N, Li T. Methylomics and cancer: the current state of methylation profiling and marker development for clinical care. Cancer Cell Int 2023; 23:242. [PMID: 37840147 PMCID: PMC10577916 DOI: 10.1186/s12935-023-03074-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
Epigenetic modifications have long been recognized as an essential level in transcriptional regulation linking behavior and environmental conditions or stimuli with biological processes and disease development. Among them, methylation is the most abundant of these reversible epigenetic marks, predominantly occurring on DNA, RNA, and histones. Methylation modification is intimately involved in regulating gene transcription and cell differentiation, while aberrant methylation status has been linked with cancer development in several malignancies. Early detection and precise restoration of dysregulated methylation form the basis for several epigenetics-based therapeutic strategies. In this review, we summarize the current basic understanding of the regulation and mechanisms responsible for methylation modification and cover several cutting-edge research techniques for detecting methylation across the genome and transcriptome. We then explore recent advances in clinical diagnostic applications of methylation markers of various cancers and address the current state and future prospects of methylation modifications in therapies for different diseases, especially comparing pharmacological methylase/demethylase inhibitors with the CRISPRoff/on methylation editing systems. This review thus provides a resource for understanding the emerging role of epigenetic methylation in cancer, the use of methylation-based biomarkers in cancer detection, and novel methylation-targeted drugs.
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Affiliation(s)
- Chengyin Liu
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Georgetown University, Washington, DC, USA
| | - Han Tang
- BioChain (Beijing) Science & Technology Inc., Beijing, People's Republic of China
| | - Nana Hu
- BioChain (Beijing) Science & Technology Inc., Beijing, People's Republic of China
| | - Tianbao Li
- Department of Molecular Medicine, The University of Texas Health, San Antonio, USA.
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17
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Romualdo GR, Heidor R, Bacil GP, Moreno FS, Barbisan LF. Past, present, and future of chemically induced hepatocarcinogenesis rodent models: Perspectives concerning classic and new cancer hallmarks. Life Sci 2023; 330:121994. [PMID: 37543357 DOI: 10.1016/j.lfs.2023.121994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/25/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023]
Abstract
Hepatocellular carcinoma (HCC), the main primary liver cancer, accounts for 5 % of all incident cases and 8.4 % of all cancer-related deaths worldwide. HCC displays a spectrum of environmental risk factors (viral chronic infections, aflatoxin exposure, alcoholic- and nonalcoholic fatty liver diseases) that result in molecular complexity and heterogeneity, contributing to a rising epidemiological burden, poor prognosis, and non-satisfactory treatment options. The emergence of HCC (i.e., hepatocarcinogenesis) is a multistep and complex process that addresses many (epi)genetic alterations and phenotypic traits, the so-called cancer hallmarks. "Polymorphic microbiomes", "epigenetic reprogramming", "senescent cells" and "unlocking phenotypic plasticity" are trending hallmarks/enabling features in cancer biology. As the main molecular drivers of HCC are still undruggable, chemically induced in vivo models of hepatocarcinogenesis are useful tools in preclinical research. Thus, this narrative review aimed at recapitulating the basic features of chemically induced rodent models of hepatocarcinogenesis, eliciting their permanent translational value regarding the "classic" and the "new" cancer hallmarks/enabling features. We gathered state-of-art preclinical evidence on non-cirrhotic, inflammation-, alcoholic liver disease- and nonalcoholic fatty liver-associated HCC models, demonstrating that these bioassays indeed express the recently added hallmarks, as well as reflect the interplay between classical and new cancer traits. Our review demonstrated that these protocols remain valuable for translational preclinical application, as they recapitulate trending features of cancer science. Further "omics-based" approaches are warranted while multimodel investigations are encouraged in order to avoid "model-biased" responses.
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Affiliation(s)
- Guilherme Ribeiro Romualdo
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Multimodel Drug Screening Platform - Laboratory of Chemically Induced and Experimental Carcinogenesis (MDSP-LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Biosciences Institute, Department of Structural and Functional Biology, Laboratory of Chemically Induced and Experimental Carcinogenesis (LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Botucatu Medical School, Botucatu, SP, Brazil
| | - Renato Heidor
- University of São Paulo (USP), Faculty of Pharmaceutical Sciences, Department of Food and Experimental Nutrition, Laboratory of Diet, Nutrition, and Cancer, São Paulo, SP, Brazil
| | - Gabriel Prata Bacil
- São Paulo State University (UNESP), Biosciences Institute, Department of Structural and Functional Biology, Laboratory of Chemically Induced and Experimental Carcinogenesis (LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Botucatu Medical School, Botucatu, SP, Brazil
| | - Fernando Salvador Moreno
- University of São Paulo (USP), Faculty of Pharmaceutical Sciences, Department of Food and Experimental Nutrition, Laboratory of Diet, Nutrition, and Cancer, São Paulo, SP, Brazil
| | - Luís Fernando Barbisan
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Multimodel Drug Screening Platform - Laboratory of Chemically Induced and Experimental Carcinogenesis (MDSP-LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Biosciences Institute, Department of Structural and Functional Biology, Laboratory of Chemically Induced and Experimental Carcinogenesis (LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Botucatu Medical School, Botucatu, SP, Brazil.
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18
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Ugonabo O, Udoh UAS, Rajan PK, Reeves H, Arcand C, Nakafuku Y, Joshi T, Finley R, Pierre SV, Sanabria JR. The Current Status of the Liver Liquid Biopsy in MASH Related HCC: Overview and Future Directions. Biomolecules 2023; 13:1369. [PMID: 37759769 PMCID: PMC10526956 DOI: 10.3390/biom13091369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Metabolic dysfunction-associated steatohepatitis (MASH) is one of the major risk factors for chronic liver disease and hepatocellular carcinoma (HCC). The incidence of MASH in Western countries continues to rise, driving HCC as the third cause of cancer-related death worldwide. HCC has become a major global health challenge, partly from the obesity epidemic promoting metabolic cellular disturbances but also from the paucity of biomarkers for its early detection. Over 50% of HCC cases are clinically present at a late stage, where curative measures are no longer beneficial. Currently, there is a paucity of both specific and sensitive biological markers for the early-stage detection of HCC. The search for biological markers in the diagnosis of early HCC in high-risk populations is intense. We described the potential role of surrogates for a liver biopsy in the screening and monitoring of patients at risk for nesting HCC.
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Affiliation(s)
- Onyinye Ugonabo
- Department of Medicine, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (O.U.); (T.J.)
| | - Utibe-Abasi Sunday Udoh
- Marshall Institute for Interdisciplinary Research, Marshall University School of Medicine, Huntington, WV 25703, USA; (U.-A.S.U.); (P.K.R.); (Y.N.); (S.V.P.)
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Pradeep Kumar Rajan
- Marshall Institute for Interdisciplinary Research, Marshall University School of Medicine, Huntington, WV 25703, USA; (U.-A.S.U.); (P.K.R.); (Y.N.); (S.V.P.)
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Heather Reeves
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Christina Arcand
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Yuto Nakafuku
- Marshall Institute for Interdisciplinary Research, Marshall University School of Medicine, Huntington, WV 25703, USA; (U.-A.S.U.); (P.K.R.); (Y.N.); (S.V.P.)
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Tejas Joshi
- Department of Medicine, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (O.U.); (T.J.)
| | - Rob Finley
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
| | - Sandrine V. Pierre
- Marshall Institute for Interdisciplinary Research, Marshall University School of Medicine, Huntington, WV 25703, USA; (U.-A.S.U.); (P.K.R.); (Y.N.); (S.V.P.)
| | - Juan Ramon Sanabria
- Marshall Institute for Interdisciplinary Research, Marshall University School of Medicine, Huntington, WV 25703, USA; (U.-A.S.U.); (P.K.R.); (Y.N.); (S.V.P.)
- Department of Surgery, Marshall University School of Medicine, Marshall University, Huntington, WV 25701, USA; (H.R.); (C.A.); (R.F.)
- Department of Nutrition and Metabolomic Core Facility, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
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19
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Fu S, Debes JD, Boonstra A. DNA methylation markers in the detection of hepatocellular carcinoma. Eur J Cancer 2023; 191:112960. [PMID: 37473464 DOI: 10.1016/j.ejca.2023.112960] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver malignancy and has a poor prognosis. Epigenetic modification has been shown to be deregulated during HCC development by dramatically impacting the differentiation, proliferation, and function of cells. One important epigenetic modification is DNA methylation during which methyl groups are added to cytosines without changing the DNA sequence itself. Studies found that methylated DNA markers can be specific for detection of HCC. On the basis of these findings, the utility of methylated DNA markers as novel biomarkers for early-stage HCC has been measured in blood, and indeed superior sensitivity and specificity have been found in several studies when compared to current surveillance methods. However, a variety of factors currently limit the immediate application of these exciting biomarkers. In this review, we provide a detailed rationalisation of the approach and basis for the use of methylation biomarkers for HCC detection and summarise recent studies on methylated DNA markers in HCC focusing on the importance of the aetiological cause of liver disease in the mechanisms leading to cancer.
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Affiliation(s)
- Siyu Fu
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands
| | - José D Debes
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands; Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - André Boonstra
- Erasmus MC University Medical Center, Department of Gastroenterology and Hepatology, Rotterdam, the Netherlands.
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20
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Long G, Zhao L, Tang B, Zhou L, Mi X, Su W, Xiao L. A robust panel based on genomic methylation sites for recurrence-free survival in early hepatocellular carcinoma. Heliyon 2023; 9:e19434. [PMID: 37809660 PMCID: PMC10558510 DOI: 10.1016/j.heliyon.2023.e19434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
Purpose Altered gene methylation precedes altered gene expression and the onset of disease. This study aimed to develop a potential model for predicting recurrence of early to mid-stage hepatocellular carcinoma (HCC) using methylation loci. Methods We used data from early to mid-stage HCC patients (TNM I-II) in the TCGA-LIHC dataset and lasso-cox regression model to identify an 18-DNA methylation site panel from which to calculate the riskScore of patients. The correlation of high/low riskScore with recurrence-free survival (RFS) and immune microenvironment in HCC patients was analyzed by bioinformatics. It was also validated in the GSE56588 dataset and the final dynamic nomogram was constructed. Results The results showed that riskScore was significantly correlated with RFS in HCC patients. The differential mutated genes between the two groups of HCC patients with high/low riskScore were mainly enriched in the TP53 signaling pathway. The immune microenvironment was better in HCC patients in the low-riskScore group compared to the high-riskScore group. This was validated in the GSE56588 dataset. Based on the subgroup stratification analysis of the relationship between high/low riskScore and RFS, as well as univariate and multivariate cox analyses, the riskScore was found to be independent of clinical indicators. We found that riskScore, vascular invasion and cirrhosis status could effectively differentiate RFS in HCC patients, and we also constructed prediction model based on these three factors. The model we constructed were validated in the TCGA-LIHC database and a web calculator was built for clinical use. Conclusion The methylation riskScore is a predictor of RFS independent of clinical factors and can be used as a marker to predict recurrence in HCC patients.
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Affiliation(s)
- Guo Long
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Lihua Zhao
- Department of Translational Medicine, Genecast Biotechnology Co., Ltd, Wuxi City, Jiangsu, China
| | - Biao Tang
- Hepatobiliary and Pancreatic Surgery Department, The Central Hospital of Yongzhou, Yongzhou, China
| | - Ledu Zhou
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xingyu Mi
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Wenxin Su
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Liang Xiao
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
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Wang Y, Hu P, Wang F, Xi S, Wu S, Sun L, Du Y, Zheng J, Yang H, Tang M, Gao H, Luo H, Lv Y, Yan J, Ou X, Li Y. UHRF1 inhibition epigenetically reprograms cancer stem cells to suppress the tumorigenic phenotype of hepatocellular carcinoma. Cell Death Dis 2023; 14:381. [PMID: 37380646 DOI: 10.1038/s41419-023-05895-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 06/11/2023] [Accepted: 06/15/2023] [Indexed: 06/30/2023]
Abstract
Cancer stem cells (CSCs) contribute to tumor initiation, progression, and recurrence in many types of cancer, including hepatocellular carcinoma (HCC). Epigenetic reprogramming of CSCs has emerged as a promising strategy for inducing the transition from malignancy to benignity. Ubiquitin-like with PHD and ring finger domains 1 (UHRF1) is required for DNA methylation inheritance. Here, we investigated the role and mechanism of UHRF1 in regulating CSC properties and evaluated the impact of UHRF1 targeting on HCC. Hepatocyte-specific Uhrf1 knockout (Uhrf1HKO) strongly suppressed tumor initiation and CSC self-renewal in both diethylnitrosamine (DEN)/CCl4-induced and Myc-transgenic HCC mouse models. Ablation of UHRF1 in human HCC cell lines yielded consistent phenotypes. Integrated RNA-seq and whole genome bisulfite sequencing revealed widespread hypomethylation induced by UHRF1 silencing epigenetically reprogrammed cancer cells toward differentiation and tumor suppression. Mechanistically, UHRF1 deficiency upregulated CEBPA and subsequently inhibited GLI1 and Hedgehog signaling. Administration of hinokitiol, a potential UHRF1 inhibitor, significantly reduced tumor growth and CSC phenotypes in mice with Myc-driven HCC. Of pathophysiological significance, the expression levels of UHRF1, GLI1, and key axis proteins consistently increased in the livers of mice and patients with HCC. These findings highlight the regulatory mechanism of UHRF1 in liver CSCs and have important implications for the development of therapeutic strategies for HCC.
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Affiliation(s)
- Yanchen Wang
- Harbin Institute of Technology, Harbin, China
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Pengchao Hu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Fenfen Wang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Shaoyan Xi
- Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou, China
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shasha Wu
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Liangzhan Sun
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yuyang Du
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jingyi Zheng
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hui Yang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Mao Tang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Han Gao
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Hao Luo
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yue Lv
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jingsong Yan
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xijun Ou
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yan Li
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
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22
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Wei T, Li J, Zhang J, Zhang Q, Liu X, Chen Q, Wen L, Ma K, Chen W, Zhao J, Zhang C, Huang J, Xie Y, Qin H, Qian D, Liang T. Loss of Mettl3 enhances liver tumorigenesis by inducing hepatocyte dedifferentiation and hyperproliferation. Cell Rep 2023; 42:112704. [PMID: 37379215 DOI: 10.1016/j.celrep.2023.112704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/20/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023] Open
Abstract
While a few works have shown that Mettl3 plays oncogenic roles in hepatocellular carcinoma (HCC), its function in early HCC tumorigenesis remains unclear. In Mettl3flox/flox; Alb-Cre knockout mice, Mettl3 loss leads to aberrant hepatocyte homeostasis and liver damage. Importantly, Mettl3 deletion dramatically accelerates liver tumorigenesis in various HCC mouse models. Depletion of Mettl3 in adult Mettl3flox/flox mice through TBG-Cre administration also enhances liver tumor development, while overexpression of Mettl3 inhibits hepatocarcinogenesis. Mechanistically, aggravated tumorigenesis upon Mettl3 deletion is a consequence of hepatocyte dedifferentiation and hyperproliferation via m6A-mediated modulation on Hnf4α and cell cycle genes. In contrast, by using Mettl3flox/flox; Ubc-Cre mice, depletion of Mettl3 in established HCC ameliorates tumor progression. Additionally, Mettl3 is overexpressed in HCC tumors compared with adjacent non-tumor tissues. The present findings define a tumor-suppressive role of Mettl3 in liver tumorigenesis, indicating its potentially opposite stage-dependent functions in HCC initiation versus progression.
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Affiliation(s)
- Tao Wei
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Jin Li
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Jian Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Xiaoyu Liu
- Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Chen
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Liang Wen
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Ke Ma
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Wen Chen
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Jianhui Zhao
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Cheng Zhang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Jinyan Huang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Yali Xie
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Hao Qin
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Danfeng Qian
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310003, China; Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, Zhejiang 310003, China; Cancer Center, Zhejiang University, Hangzhou, Zhejiang 310014, China.
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23
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Wu R, Wu C, Zhu B, Li J, Zhao W. Screening and validation of potential markers associated with uterine corpus endometrial carcinoma and polycystic ovary syndrome based on bioinformatics methods. Front Mol Biosci 2023; 10:1192313. [PMID: 37363398 PMCID: PMC10288877 DOI: 10.3389/fmolb.2023.1192313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/01/2023] [Indexed: 06/28/2023] Open
Abstract
Background: Endometrial cancer (UCEC) is a commonly occurring tumor in females, and polycystic ovary syndrome (PCOS) is closely related to UCEC, but the molecular mechanisms remain unclear. This article aims to explore potential molecular mechanisms in UCEC and PCOS, as well as identify prognostic genes for UCEC. Methods: Bioinformatics methods were employed to screen for DEGs in UCEC and PCOS. The shared DEGs were analyzed by constructing a protein-protein interaction (PPI) network using the String database and Cytoscape software. The enrichment analysis was performed using Metascape. The shared DEGs associated with the prognosis of UCEC were identified through univariate and lasso Cox regression methods. A multivariate Cox regression model was constructed and internally validated. The expression and test efficiency of the key prognostic genes were verified using external datasets for UCEC and PCOS. Furthermore, the Gepia database was utilized to analyze the expression of key prognostic genes and their correlation with the disease-free survival (RFS) of UCEC. Tumor mutation burden (TMB), immune infiltration, and the correlation of immune cells were assessed for the prognostic genes of UCEC. Results: There were 151 shared DEGs identified between UCEC and PCOS through bioinformatics screening. These shared DEGs were primarily enriched in leukocyte activation. Following model construction and verification, nine genes were determined to be prognostic for UCEC from the shared DEGs. Among them, TSPYL5, KCNJ15, RTN1, HMOX1, DCAF12L1, VNN2, and ANXA1 were confirmed as prognostic genes in UCEC through external validation. Additionally, RTN1 was identified as a key gene in both UCEC and PCOS. Gepia analysis revealed that higher expression of RTN1 was associated with RFS in UCEC. Immune infiltration analysis of the shared DEGs demonstrated significant differences in the expression of various immune cells between UCEC high and low TMB groups. The seven key prognostic genes in UCEC exhibited regulatory relationships with immune cells. Conclusion: This study identified TSPYL5, KCNJ15, RTN1, HMOX1, DCAF12L1, VNN2, and ANXA1 as the key prognostic DEGs of UCEC. These genes are associated with UCEC survival, TMB, immune cell infiltration, and immune cell regulation. Among them, RTN1 may serve as a potential biomarker for both UCEC and PCOS.
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Affiliation(s)
- Ruishan Wu
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China
| | - Cailin Wu
- Department of Gynecology, The University of HongKong–Shenzhen Hospital, Shenzhen, China
| | - Bingming Zhu
- Department of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jin Li
- Department of Pain Management, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Wenzhong Zhao
- NHC Key Laboratory of Male Reproduction and Genetics, Guangdong Provincial Reproductive Science Institute (Guangdong Provincial Fertility Hospital), Guangzhou, China
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24
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Kopystecka A, Patryn R, Leśniewska M, Budzyńska J, Kozioł I. The Use of ctDNA in the Diagnosis and Monitoring of Hepatocellular Carcinoma-Literature Review. Int J Mol Sci 2023; 24:ijms24119342. [PMID: 37298294 DOI: 10.3390/ijms24119342] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver cancer and is one of the leading causes of cancer-related deaths worldwide. Despite advances in medicine, it is still a cancer with a very poor prognosis. Both imaging and liver biopsy still have important limitations, especially in very small nodules and those which show atypical imaging features. In recent years, liquid biopsy and molecular analysis of tumor breakdown products have become an attractive source of new biomarkers. Patients with liver and biliary malignancies, including hepatocellular carcinoma (HCC), may greatly benefit from ctDNA testing. These patients are often diagnosed at an advanced stage of the disease, and relapses are common. Molecular analysis may indicate the best cancer treatment tailored to particular patients with specific tumor DNA mutations. Liquid biopsy is a minimally invasive technique that facilitates the early detection of cancer. This review summarizes the knowledge of ctDNA in liquid biopsy as an indicator for early diagnosis and monitoring of hepatocellular cancer.
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Affiliation(s)
- Agnieszka Kopystecka
- Students' Scientific Circle on Medical Law, Department of Humanities and Social Medicine, Medical University of Lublin, 20-093 Lublin, Poland
| | - Rafał Patryn
- Department of Humanities and Social Medicine, Medical University of Lublin, 20-093 Lublin, Poland
| | - Magdalena Leśniewska
- Students' Scientific Circle on Medical Law, Department of Humanities and Social Medicine, Medical University of Lublin, 20-093 Lublin, Poland
| | - Julia Budzyńska
- Students' Scientific Circle on Medical Law, Department of Humanities and Social Medicine, Medical University of Lublin, 20-093 Lublin, Poland
| | - Ilona Kozioł
- Students' Scientific Circle on Medical Law, Department of Humanities and Social Medicine, Medical University of Lublin, 20-093 Lublin, Poland
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25
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Ortiz-Barahona V, Soler M, Davalos V, García-Prieto CA, Janin M, Setien F, Fernández-Rebollo I, Bech-Serra JJ, De La Torre C, Guil S, Villanueva A, Zhang PH, Yang L, Guarnacci M, Schumann U, Preiss T, Balaseviciute U, Montal R, Llovet JM, Esteller M. Epigenetic inactivation of the 5-methylcytosine RNA methyltransferase NSUN7 is associated with clinical outcome and therapeutic vulnerability in liver cancer. Mol Cancer 2023; 22:83. [PMID: 37173708 PMCID: PMC10176850 DOI: 10.1186/s12943-023-01785-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 05/08/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND RNA modifications are important regulators of transcript activity and an increasingly emerging body of data suggests that the epitranscriptome and its associated enzymes are altered in human tumors. METHODS Combining data mining and conventional experimental procedures, NSUN7 methylation and expression status was assessed in liver cancer cell lines and primary tumors. Loss-of-function and transfection-mediated recovery experiments coupled with RNA bisulfite sequencing and proteomics determined the activity of NSUN7 in downstream targets and drug sensitivity. RESULTS In this study, the initial screening for genetic and epigenetic defects of 5-methylcytosine RNA methyltransferases in transformed cell lines, identified that the NOL1/NOP2/Sun domain family member 7 (NSUN7) undergoes promoter CpG island hypermethylation-associated with transcriptional silencing in a cancer-specific manner. NSUN7 epigenetic inactivation was common in liver malignant cells and we coupled bisulfite conversion of cellular RNA with next-generation sequencing (bsRNA-seq) to find the RNA targets of this poorly characterized putative RNA methyltransferase. Using knock-out and restoration-of-function models, we observed that the mRNA of the coiled-coil domain containing 9B (CCDC9B) gene required NSUN7-mediated methylation for transcript stability. Most importantly, proteomic analyses determined that CCDC9B loss impaired protein levels of its partner, the MYC-regulator Influenza Virus NS1A Binding Protein (IVNS1ABP), creating sensitivity to bromodomain inhibitors in liver cancer cells exhibiting NSUN7 epigenetic silencing. The DNA methylation-associated loss of NSUN7 was also observed in primary liver tumors where it was associated with poor overall survival. Interestingly, NSUN7 unmethylated status was enriched in the immune active subclass of liver tumors. CONCLUSION The 5-methylcytosine RNA methyltransferase NSUN7 undergoes epigenetic inactivation in liver cancer that prevents correct mRNA methylation. Furthermore, NSUN7 DNA methylation-associated silencing is associated with clinical outcome and distinct therapeutic vulnerability.
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Affiliation(s)
- Vanessa Ortiz-Barahona
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Marta Soler
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Veronica Davalos
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Carlos A García-Prieto
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Catalonia, Spain
| | - Maxime Janin
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Fernando Setien
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Irene Fernández-Rebollo
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Joan J Bech-Serra
- Proteomics Unit, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Carolina De La Torre
- Proteomics Unit, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
| | - Sonia Guil
- Regulatory RNA and Chromatin Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain
- Germans Trias i Pujol Health Science Research Institute, Barcelona, Catalonia, Spain
| | - Alberto Villanueva
- Chemoresistance and Predictive Factors Group, Program Against Cancer Therapeutic Resistance (ProCURE), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | - Pei-Hong Zhang
- Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Li Yang
- Center for Molecular Medicine, Children's Hospital, Fudan University and Shanghai Key Laboratory of Medical Epigenetics, International Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Marco Guarnacci
- Shine-Dalgarno Centre for RNA Innovation, Australian National University, Canberra, Australia
| | - Ulrike Schumann
- Shine-Dalgarno Centre for RNA Innovation, Australian National University, Canberra, Australia
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst (Sydney), Queensland, NSW, 2010, Australia
| | - Ugne Balaseviciute
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Catalonia, Spain
| | - Robert Montal
- Hospital Arnau de Vilanova, IRBLleida, University of Lleida (UdL), Catalonia, Spain
| | - Josep M Llovet
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, University of Barcelona, Catalonia, Spain
- ICAHN School of Medicine at Mount Sinai, New York, NY, USA
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, 08010, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Josep Carreras Leukaemia Research Institute, Badalona, Barcelona, Catalonia, 08916, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, 08010, Spain.
- Centro de Investigacion Biomedica en Red Cancer, Madrid, 28029, Spain.
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, 08907, Spain.
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26
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Chen M, Fang Y, Liang M, Zhang N, Zhang X, Xu L, Ren X, Zhang Q, Zhou Y, Peng S, Yu J, Zeng J, Li X. The activation of mTOR signalling modulates DNA methylation by enhancing DNMT1 translation in hepatocellular carcinoma. J Transl Med 2023; 21:276. [PMID: 37088830 PMCID: PMC10124003 DOI: 10.1186/s12967-023-04103-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 04/03/2023] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND Both dysregulation of mechanistic target of rapamycin (mTOR) signalling and DNA methylation patterns have been shown to be closely associated with tumor progression and serve as promising targets for hepatocellular carcinoma (HCC) therapy. Although their respective roles in HCC have been extensively revealed, the existence of molecular interactions between them remains largely unknown. METHODS The association of DNA methylation and mTOR signalling in HCC tissues and cell lines was assessed. A Kaplan‒Meier analysis was applied to estimate the overall survival (OS) and recurrence-free survival (RFS) of HCC patients. The modulation of DNMT1 by mTOR in HCC cell lines was determined. The effect of the drug combination in cell lines and mouse models was examined. RESULTS The results showed that the DNA methylation level was positively associated with the activation of mTOR signalling in HCC tissues and cell lines. Moreover, HCC patients with higher DNA methylation levels and enhanced activation of mTOR signalling exhibited the worst prognosis. Then, we screened methylation-related enzymes and found that the activation of mTOR signalling increased DNMT1 expression and activity. In addition, mTOR enhanced the translational efficiency of DNMT1 in a 4E-BP1-dependent manner, which is based on the pyrimidine rich translational element (PRTE)-containing 5'UTR of DNMT1. Moreover, we demonstrated that the combined inhibition of mTOR and DNMT synergistically inhibited HCC growth in vitro and in vivo. CONCLUSIONS In addition to some already identified pro-cancer downstream molecules, the activation of mTOR signalling was found to promote DNA methylation by increasing the translation of DNMT1. Furthermore, combined targeting of mTOR and DNMT1 has been demonstrated to have a more effective tumor suppressive function in HCC.
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Affiliation(s)
- Mengke Chen
- Department of Oncology, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
- Institute of Precision Medicine, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
| | - Yi Fang
- Institute of Precision Medicine, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
| | - Meinong Liang
- Institute of Precision Medicine, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
| | - Ning Zhang
- Department of Gastroenterology, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
| | - Xinyue Zhang
- Department of Oncology, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
- Institute of Precision Medicine, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
| | - Lixia Xu
- Department of Oncology, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
| | - Xuxin Ren
- Department of Oncology, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
- Institute of Precision Medicine, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
| | | | - Yufeng Zhou
- Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Sui Peng
- Institute of Precision Medicine, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
| | - Jun Yu
- Institute of Precision Medicine, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China
| | - Judeng Zeng
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Hong Kong, China.
| | - Xiaoxing Li
- Department of Oncology, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China.
- Institute of Precision Medicine, Sun Yat-Sen University First Affiliated Hospital, Guangzhou, China.
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Tian GA, Xu WT, Zhang XL, Zhou YQ, Sun Y, Hu LP, Jiang SH, Nie HZ, Zhang ZG, Zhu L, Li J, Yang XM, Yao LL. CCBE1 promotes mitochondrial fusion by inhibiting the TGFβ-DRP1 axis to prevent the progression of hepatocellular carcinoma. Matrix Biol 2023; 117:31-45. [PMID: 36849082 DOI: 10.1016/j.matbio.2023.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 02/21/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
The extracellular matrix (ECM), as an important component of the tumor microenvironment, exerts various roles in tumor formation. Mitochondrial dynamic disorder is closely implicated in tumorigenesis, including hyperfission in HCC. We aimed to determine the influence of the ECM-related protein CCBE1 on mitochondrial dynamics in HCC. Here, we found that CCBE1 was capable of promoting mitochondrial fusion in HCC. Initially, CCBE1 expression was found to be significantly downregulated in tumors compared with nontumor tissues, which resulted from hypermethylation of the CCBE1 promoter in HCC. Furthermore, CCBE1 overexpression or treatment with recombinant CCBE1 protein dramatically inhibited HCC cell proliferation, migration, and invasion in vitro and in vivo. Mechanistically, CCBE1 functioned as an inhibitor of mitochondrial fission by preventing the location of DRP1 on mitochondria through inhibiting its phosphorylation at Ser616 by directly binding with TGFβR2 to inhibit TGFβ signaling activity. In addition, a higher percentage of specimens with higher DRP1 phosphorylation was present in patients with lower CCBE1 expression than in patients with higher CCBE1 expression, which further confirmed the inhibitory effect of CCBE1 on DRP1 phosphorylation at Ser616. Collectively, our study highlights the crucial roles of CCBE1 in mitochondrial homeostasis, suggesting strong evidence for this process as a potential therapeutic strategy for HCC.
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Affiliation(s)
- Guang-Ang Tian
- Department of Central Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University, School of Medicine, 243 Huaihai West Road, Shanghai 200030, PR China; State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Wen-Ting Xu
- Department of Pathology, The International Peace Maternity & Child Health Hospital of China Welfare Institute, School of Medicine, Shanghai Jiao Tong University, 910 Hengshan Road, Shanghai 200030, PR China
| | - Xue-Li Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Yao-Qi Zhou
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Yue Sun
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Li-Peng Hu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Shu-Heng Jiang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Hui-Zhen Nie
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Zhi-Gang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China
| | - Lei Zhu
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China.
| | - Jun Li
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China.
| | - Xiao-Mei Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China.
| | - Lin-Li Yao
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, PR China.
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Campani C, Zucman-Rossi J, Nault JC. Genetics of Hepatocellular Carcinoma: From Tumor to Circulating DNA. Cancers (Basel) 2023; 15:cancers15030817. [PMID: 36765775 PMCID: PMC9913369 DOI: 10.3390/cancers15030817] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 02/01/2023] Open
Abstract
Hepatocellular carcinoma (HCC) accounts for 90% of primary hepatic malignancies and is one of the major causes of cancer-related death. Over the last 15 years, the molecular landscape of HCC has been deciphered, with the identification of the main driver genes of liver carcinogenesis that belong to six major biological pathways, such as telomere maintenance, Wnt/b-catenin, P53/cell cycle regulation, oxidative stress, epigenetic modifiers, AKT/mTOR and MAP kinase. The combination of genetic and transcriptomic data composed various HCC subclasses strongly related to risk factors, pathological features and prognosis. However, translation into clinical practice is not achieved, mainly because the most frequently mutated genes are undruggable. Moreover, the results derived from the analysis of a single tissue sample may not adequately catch the intra- and intertumor heterogeneity. The analysis of circulating tumor DNA (ctDNA) is broadly developed in other types of cancer for early diagnosis, prognosis and monitoring under systemic treatment in order to identify primary and secondary mechanisms of resistance. The aim of this review is to describe recent data about the HCC molecular landscape and to discuss how ctDNA could be used in the future for HCC detection and management.
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Affiliation(s)
- Claudia Campani
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris Cité, Team «Functional Genomics of Solid Tumors», 75006 Paris, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, 75006 Paris, France
- Internal Medicine and Hepatology Unit, Department of Experimental and Clinical Medicine, University of Firenze, 50134 Firenze, Italy
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris Cité, Team «Functional Genomics of Solid Tumors», 75006 Paris, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, 75006 Paris, France
- Hôpital Européen Georges Pompidou, APHP, 75015 Paris, France
| | - Jean-Charles Nault
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris Cité, Team «Functional Genomics of Solid Tumors», 75006 Paris, France
- Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, 75006 Paris, France
- Liver Unit, Hôpital Avicenne, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, 93000 Bobigny, France
- Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris Nord, 93000 Bobigny, France
- Correspondence: ; Tel.: +33-6-1067-9461
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Tang Z, Yang Y, Zhang Q, Liang T. Epigenetic dysregulation-mediated COL12A1 upregulation predicts worse outcome in intrahepatic cholangiocarcinoma patients. Clin Epigenetics 2023; 15:13. [PMID: 36694230 PMCID: PMC9875497 DOI: 10.1186/s13148-022-01413-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/18/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Collagen type XII alpha 1 chain (COL12A1) is associated with human cancer progression. Nevertheless, the expression pattern and the function of COL12A1 in intrahepatic cholangiocarcinoma (iCCA) remain unknown. The present study was performed to assess the role of COL12A1 in iCCA. RESULTS A total of 1669 genes, differentially expressed between iCCA and nontumor liver tissue samples, were identified as potential tumor-specific biomarkers for iCCA patients. Of these, COL12A1 was significantly upregulated in clinical iCCA tissue samples and correlated with epithelial-mesenchymal transition gene set enrichment score and advanced tumor stage in clinical iCCA. COL12A1-high expression was associated with the poor prognoses of iCCA patients (n = 421) from four independent cohorts. Promoter hypermethylation-induced downregulation of miR-424-5p resulted in COL12A1 upregulation in clinical iCCA. Experimental knockout of COL12A1 inhibited the proliferation, invasiveness and growth of iCCA cells. MiR-424-5p had a therapeutic potential in iCCA via directly targeting COL12A1. CONCLUSIONS Promoter hypermethylation-induced miR-424-5p downregulation contributes to COL12A1 upregulation in iCCA. COL12A1 is a promising druggable target for epigenetic therapy of iCCA.
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Affiliation(s)
- Zengwei Tang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310003, Zhejiang, China
- Zhejiang University Cancer Center, Hangzhou, 310058, Zhejiang, China
| | - Yuan Yang
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Qi Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310003, Zhejiang, China
- Zhejiang University Cancer Center, Hangzhou, 310058, Zhejiang, China
| | - Tingbo Liang
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, 310003, Zhejiang, China.
- Zhejiang Clinical Research Center of Hepatobiliary and Pancreatic Diseases, Hangzhou, 310003, Zhejiang, China.
- Zhejiang University Cancer Center, Hangzhou, 310058, Zhejiang, China.
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Tao S, Liang S, Zeng T, Yin D. Epigenetic modification-related mechanisms of hepatocellular carcinoma resistance to immune checkpoint inhibition. Front Immunol 2023; 13:1043667. [PMID: 36685594 PMCID: PMC9845774 DOI: 10.3389/fimmu.2022.1043667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) constitutes most primary liver cancers and is one of the most lethal and life-threatening malignancies globally. Unfortunately, a substantial proportion of HCC patients are identified at an advanced stage that is unavailable for curative surgery. Thus, palliative therapies represented by multi-tyrosine kinase inhibitors (TKIs) sorafenib remained the front-line treatment over the past decades. Recently, the application of immune checkpoint inhibitors (ICIs), especially targeting the PD-1/PD-L1/CTLA-4 axis, has achieved an inspiring clinical breakthrough for treating unresectable solid tumors. However, many HCC patients with poor responses lead to limited benefits in clinical applications, which has quickly drawn researchers' attention to the regulatory mechanisms of immune checkpoints in HCC immune evasion. Evasion of immune surveillance by cancer is attributed to intricate reprogramming modulation in the tumor microenvironment. Currently, more and more studies have found that epigenetic modifications, such as chromatin structure remodeling, DNA methylation, histone post-translational modifications, and non-coding RNA levels, may contribute significantly to remodeling the tumor microenvironment to avoid immune clearance, affecting the efficacy of immunotherapy for HCC. This review summarizes the rapidly emerging progress of epigenetic-related changes during HCC resistance to ICIs and discusses the mechanisms of underlying epigenetic therapies available for surmounting immune resistance. Finally, we summarize the clinical advances in combining epigenetic therapies with immunotherapy, aiming to promote the formation of immune combination therapy strategies.
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Affiliation(s)
- Shengwei Tao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Shuhang Liang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Taofei Zeng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Dalong Yin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
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Huang F, Yang G, Jiang H, Chen X, Yang Y, Yu Q, Pan B, Wang B, Guo W, Yang W, Zhang C. Role of Plasma methylated SEPT9 for Predicting Microvascular Invasion and Tumor Proliferation in Hepatocellular Carcinoma. Technol Cancer Res Treat 2022; 21:15330338221144510. [PMID: 36573042 PMCID: PMC9806378 DOI: 10.1177/15330338221144510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background: Methylated SEPT9 (mSEPT9) has a role in the occurrence and development of hepatocellular carcinoma (HCC). Here, we studied the significance of plasma mSEPT9 for predicting prognosis-associated pathological parameters in patients with HCC. Methods: We retrospectively analyzed data from 205 subjects, including 111 HCC patients, 53 patients with at-risk liver disease (ARD) and 41 healthy donors (HDs). Analysis of plasma mSEPT9 was performed using methylation-specific polymerase chain reaction. Levels of mSEPT9 among different groups were compared using a nonparametric Mann-Whitney U test or a one-way ANOVA test. Correlations between pretreatment plasma mSEPT9 and clinicopathological characteristics were analyzed using the Chi-square. Univariate and multivariate analyses were used to identify factors related to microvascular invasion (MVI). Performance of variables for MVI prediction was evaluated by receiver operating characteristics curve. Results: A specific increase of plasma mSEPT9 in HCC was found when compared with ARD and HDs (HCC vs ARD, P = 1.1 × 10-5 and HCC vs HDs, P = 3.7 × 10-10). Pretreatment plasma mSEPT9 was significantly correlated tumor number (P = .004), tumor size (P = 4.6 × 10-5), MVI (P = .002) and Barcelona Clinic Liver Cancer stage (P = .012). Levels of plasma mSEPT9 correlated significantly with Ki67 expression in tumor (r = 0.356, P = 1.3 × 10-4). Univariate and multivariate analyses showed that plasma mSEPT9 and serum protein induced by vitamin K absence or antagonist-II (PIVKA-II) were independent predictors for MVI. A combination of these 2 markers exhibited a larger areas under the curve (areas under the curve [AUC] = 0.72) than mSEPT9 or PIVKA alone (AUC = 0.67 and 0.65), especially in early-stage HCC. Conclusions: Plasma mSEPT9 is a promising noninvasive biomarker for predicting MVI and tumor proliferation in HCC. Integration plasma mSEPT9 detection into clinical settings might facilitate the patient management.
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Affiliation(s)
- Fei Huang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Guowei Yang
- Department of Interventional Radiology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Huiqin Jiang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xinning Chen
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yihui Yang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qian Yu
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Baishen Pan
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China,Branch of National Clinical Research Center for Laboratory Medicine, Shanghai, China
| | - Beili Wang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Guo
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China,Cancer Centre, Zhongshan Hospital, Fudan University, Shanghai, China,Department of Laboratory Medicine, Wusong Branch, Zhongshan Hospital, Fudan University, Shanghai, China,Branch of National Clinical Research Center for Laboratory Medicine, Shanghai, China,Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China
| | - Wenjing Yang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China,Wenjing Yang, Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, 111 Yi Xue Yuan Road, Shanghai 200032, China.
| | - Chunyan Zhang
- Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, Shanghai, China,Department of Laboratory Medicine, Xiamen Branch, Zhongshan Hospital, Fudan University, Xiamen, China,Chunyan Zhang, Department of Laboratory Medicine, Zhongshan Hospital, Fudan University, 111 Yi Xue Yuan Road, Shanghai 200032, China.
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Antropova E, Khlebodarova T, Demenkov P, Venzel A, Ivanisenko N, Gavrilenko A, Ivanisenko T, Adamovskaya A, Revva P, Lavrik I, Ivanisenko V. Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins. Vavilovskii Zhurnal Genet Selektsii 2022; 26:733-742. [PMID: 36714033 PMCID: PMC9840909 DOI: 10.18699/vjgb-22-89] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023] Open
Abstract
Hepatitis C virus (HCV) is a risk factor that leads to hepatocellular carcinoma (HCC) development. Epigenetic changes are known to play an important role in the molecular genetic mechanisms of virus-induced oncogenesis. Aberrant DNA methylation is a mediator of epigenetic changes that are closely associated with the HCC pathogenesis and considered a biomarker for its early diagnosis. The ANDSystem software package was used to reconstruct and evaluate the statistical significance of the pathways HCV could potentially use to regulate 32 hypermethylated genes in HCC, including both oncosuppressor and protumorigenic ones identified by genome-wide analysis of DNA methylation. The reconstructed pathways included those affecting protein-protein interactions (PPI), gene expression, protein activity, stability, and transport regulations, the expression regulation pathways being statistically significant. It has been shown that 8 out of 10 HCV proteins were involved in these pathways, the HCV NS3 protein being implicated in the largest number of regulatory pathways. NS3 was associated with the regulation of 5 tumor-suppressor genes, which may be the evidence of its central role in HCC pathogenesis. Analysis of the reconstructed pathways has demonstrated that following the transcription factor inhibition caused by binding to viral proteins, the expression of a number of oncosuppressors (WT1, MGMT, SOCS1, P53) was suppressed, while the expression of others (RASF1, RUNX3, WIF1, DAPK1) was activated. Thus, the performed gene-network reconstruction has shown that HCV proteins can influence not only the methylation status of oncosuppressor genes, but also their transcriptional regulation. The results obtained can be used in the search for pharmacological targets to develop new drugs against HCV-induced HCC.
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Affiliation(s)
- E.A. Antropova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, Russia
| | - T.M. Khlebodarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - P.S. Demenkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.S. Venzel
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - N.V. Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.D. Gavrilenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
| | - T.V. Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.V. Adamovskaya
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
| | - P.M. Revva
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - I.N. Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - V.A. Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
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Schlosser S, Tümen D, Volz B, Neumeyer K, Egler N, Kunst C, Tews HC, Schmid S, Kandulski A, Müller M, Gülow K. HCC biomarkers - state of the old and outlook to future promising biomarkers and their potential in everyday clinical practice. Front Oncol 2022; 12:1016952. [PMID: 36518320 PMCID: PMC9742592 DOI: 10.3389/fonc.2022.1016952] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 11/04/2022] [Indexed: 08/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most common and deadly tumors worldwide. Management of HCC depends on reliable biomarkers for screening, diagnosis, and monitoring of the disease, as well as predicting response towards therapy and safety. To date, imaging has been the established standard technique in the diagnosis and follow-up of HCC. However, imaging techniques have their limitations, especially in the early detection of HCC. Therefore, there is an urgent need for reliable, non/minimal invasive biomarkers. To date, alpha-fetoprotein (AFP) is the only serum biomarker used in clinical practice for the management of HCC. However, AFP is of relatively rather low quality in terms of specificity and sensitivity. Liquid biopsies as a source for biomarkers have become the focus of clinical research. Our review highlights alternative biomarkers derived from liquid biopsies, including circulating tumor cells, proteins, circulating nucleic acids, and exosomes, and their potential for clinical application. Using defined combinations of different biomarkers will open new perspectives for diagnosing, treating, and monitoring HCC.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Karsten Gülow
- Department of Internal Medicine I, Gastroenterology, Hepatology, Endocrinology, Rheumatology, and Infectious Diseases, University Hospital Regensburg, Regensburg, Germany
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Study on the Prognostic Values of TTC36 Correlated with Immune Infiltrates and Its Methylation in Hepatocellular Carcinoma. J Immunol Res 2022; 2022:7267131. [PMID: 35846428 PMCID: PMC9286891 DOI: 10.1155/2022/7267131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/22/2022] [Accepted: 06/24/2022] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) remains an incurable disease with a very poor clinical outcome. The purpose of this article was to investigate whether the expression or methylation of tetrapeptide repeat domain 36 (TTC36) could be used as a prognostic marker in hepatocellular carcinoma. TCGA database was used to obtain information on HCC gene expression and the associated clinical features of HCC patients. Differentially expressed genes (DEGs) were screened between 374 HCC specimens and 50 nontumor specimens. The expression and prognostic value of TTC36 were analyzed. The correlations between TTC36 and cancer immune infiltrates were investigated via TIMER. In this study, HCC specimens and nontumor specimens were compared and 35 DEGs were found between them. Among the 35 DEGs, the expression of TTC36 was significantly reduced in HCC samples compared with nontumor samples. Survival tests revealed that patients with low TTC36 expression had a shorter overall survival than patients with high TTC36 expression. TTC36 was found to be an independent predictive factor for HCC in both univariate and multivariate regression analyses. TTC36 was negatively regulated by TTC36 methylation, leading to its low expression in HCC tissues. Immune analysis revealed that TTC36 expression has significant correlations with B cell, T cell CD4+, neutrophil, macrophage, and myeloid dendritic cell. Finally, TTC36 expression was dramatically reduced in HCC cells, and overexpression greatly suppressed HCC cell proliferation and invasion, according to our experimental results. Overall, our data suggested that TTC36 could be applied as a prognostic marker for predicting outcome and immune infiltration in HCC.
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Yang Z, Tian H, Li L, Li C, Xu J, Bie F, Chen Y, Tian Y, Bai G, Peng Y, Yang J, Fan T, Xiao C, Liu W, Liu L, Li R, Sun S, Zheng B, Tan F, Ying J, Li C, Gao S, He J. PSC subtyping based on TTF-1 and p40 expression reveals distinct molecular characteristics and therapeutic strategies. Int J Cancer 2022; 151:717-729. [PMID: 35612583 DOI: 10.1002/ijc.34137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 04/26/2022] [Accepted: 05/11/2022] [Indexed: 11/10/2022]
Abstract
Pulmonary sarcomatoid carcinoma (PSC) is a unique form of poorly differentiated non-small cell lung cancer (NSCLC) and is notorious for its highly malignant nature and dismal prognosis. To introduce effective treatment for PSC patients, precise subtyping of PSC is demanding. In our study, TTF-1 and P40 immunohistochemistry (IHC) staining were applied to 56 PSC patients with multi-omics data. According to IHC results, we categorized these patients into three subgroups and profiled their molecular contexture using bioinformatic skills. IHC results classified these patients into three subgroups: TTF-1 positive subgroup (n=27), P40 positive subgroup (n=15), and double-negative subgroup (n=14). Spindle cell samples accounted for 35.71% (5/14) of double-negative patients, higher than others (p=0.034). The three subgroups were heterogeneous in the genomic alteration spectrum, showing significant differences in the RTK/RAS pathway (p=0.004) and the cell cycle pathway (p=0.030). The methylation profile of the double-negative subgroup was between the other two subgroups. In similarity analysis, the TTF-1 and p40 subgroups were closely related to LUAD and LUSC, respectively. The TTF-1 positive subgroup had the highest leukocyte fraction (LF) among several cancer types, and the tumor mutation burden (TMB) of the p40 positive subgroup ranked third in the TMB list, suggesting the applicability of immunotherapy for PSC. The study established a new subtyping method of PSC based on IHC results and reveals 3 subgroups with distinct molecular features, providing evidence for refined stratification in the treatment of PSC. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - He Tian
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chao Li
- Department of Thoracic Surgery, Rizhao Central Hospital, Rizhao, China
| | - Jiachen Xu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fenglong Bie
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Chen
- Department of Thoracic Surgery I, the Third Affiliated Hospital of Kunming Medical University (Yunnan Cancer Hospital, Yunnan Cancer Center), Kunming, China
| | - Yanhua Tian
- Department of Thoracic Surgery/Head & Neck Medical Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Guangyu Bai
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Peng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Junhui Yang
- Genetron Health (Beijing) Co. Ltd., Beijing, China
| | - Tao Fan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chu Xiao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenchao Liu
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Liu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Renda Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Sijin Sun
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Zheng
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fengwei Tan
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunxiang Li
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie He
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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Sun D, Gan X, Liu L, Yang Y, Ding D, Li W, Jiang J, Ding W, Zhao L, Hou G, Yu J, Wang J, Yang F, Yuan S, Zhou W. DNA hypermethylation modification promotes the development of hepatocellular carcinoma by depressing the tumor suppressor gene ZNF334. Cell Death Dis 2022; 13:446. [PMID: 35534462 PMCID: PMC9085879 DOI: 10.1038/s41419-022-04895-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/19/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022]
Abstract
DNA methylation plays a pivotal role in the development and progression of tumors. However, studies focused on the dynamic changes of DNA methylation in the development of hepatocellular carcinoma (HCC) are rare. To systematically illustrate the dynamic DNA methylation alternation from premalignant to early-stage liver cancer with the same genetic background, this study enrolled 5 HBV-related patients preceded with liver cirrhosis, pathologically identified as early-stage HCC with dysplastic nodules. Liver fibrosis tissues, dysplastic nodules and early HCC tissues from these patients were used to measure DNA methylation. Here, we report significant differences in the DNA methylation spectrum among the three types of tissues. In the early stage of HCC, DNA hypermethylation of tumor suppressor genes is predominant. Additionally, DNA hypermethylation in the early stage of HCC changes the binding ability of transcription factor TP53 to the promoter of tumor suppressor gene ZNF334, and inhibits the expression of ZNF334 at the transcription level. Furthermore, through a series of in vivo and in vitro experiments, we have clarified the exacerbation effect of tumor suppressor gene ZNF334 deletion in the occurrence of HCC. Combined with clinical data, we found that the overall survival and relapse-free survival of patients with high ZNF334 expression are significantly longer. Thus, we partly elucidated a sequential alternation of DNA methylation modification during the occurrence of HCC, and clarified the biological function and regulatory mechanism of the tumor suppressor gene ZNF334, which is regulated by related DNA methylation sites. Our study provides a new target and clinical evidence for the early diagnosis and sheds light on the precise treatment of liver cancer.
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Affiliation(s)
- Dapeng Sun
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Xiaojie Gan
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Lei Liu
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Yuan Yang
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Dongyang Ding
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Wen Li
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Junyao Jiang
- grid.428926.30000 0004 1798 2725Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou, 510530 China
| | - Wenbin Ding
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Linghao Zhao
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Guojun Hou
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Jian Yu
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Jie Wang
- grid.428926.30000 0004 1798 2725Center for Health Research, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou, 510530 China
| | - Fu Yang
- grid.73113.370000 0004 0369 1660The department of Medical Genetics, Naval Medical University, Shanghai, 200438 China
| | - Shengxian Yuan
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
| | - Weiping Zhou
- grid.73113.370000 0004 0369 1660The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, 225 Changhai Road Shanghai, Shanghai, 200438 China
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37
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Recalde M, Gárate-Rascón M, Herranz JM, Elizalde M, Azkona M, Unfried JP, Boix L, Reig M, Sangro B, Fernández-Barrena MG, Fortes P, Ávila MA, Berasain C, Arechederra M. DNA Methylation Regulates a Set of Long Non-Coding RNAs Compromising Hepatic Identity during Hepatocarcinogenesis. Cancers (Basel) 2022; 14:cancers14092048. [PMID: 35565178 PMCID: PMC9102946 DOI: 10.3390/cancers14092048] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/13/2022] [Accepted: 04/17/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Hepatocarcinogenesis is a long process which implies the loss of hepatic functions. Our effort is to understand the mechanisms implicated in this pathological process in order to contribute to the development of new diagnostic markers and therapeutic targets. In this study we have identified a set of lncRNAs significantly downregulated in hepatocellular carcinoma (HCC) in correlation with the grade of tumor dedifferentiation and patients’ worse prognosis. Mechanistically, our results show that they are related with hepatic differentiation and at least a subset of those lncRNAs are essential to ensure the expression of other hepato-specific genes required for liver function. Moreover, we demonstrate that the expression of these lncRNAs in HCC is silenced by DNA methylation. All in all, we uncover connected epigenetic alterations involved in the progression of liver cancer and identify potential new biomarkers. Abstract Background: Long noncoding RNAs (lncRNAs) are emerging as key players in cancer, including hepatocellular carcinoma (HCC). Here we identify the mechanism implicated in the HCC inhibition of a set of lncRNAs, and their contribution to the process of hepatocarcinogenesis. Methods and Results: The top-ranked 35 lncRNAs downregulated in HCC (Top35 LNDH) were validated in several human HCC cohorts. We demonstrate that their inhibition is associated with promoter hypermethylation in HCC compared to control tissue, and in HCC human cell lines compared to primary hepatocytes. Moreover, demethylating treatment of HCC human cell lines induced the expression of these lncRNAs. The Top35 LNDH were preferentially expressed in the adult healthy liver compared to other tissues and fetal liver and were induced in well-differentiated HepaRG cells. Remarkably, their knockdown compromised the expression of other hepato-specific genes. Finally, the expression of the Top35 LNDH positively correlates with the grade of tumor differentiation and, more importantly, with a better patient prognosis. Conclusions: Our results demonstrate that the selected Top35 LNDH are not only part of the genes that compose the hepatic differentiated signature but participate in its establishment. Moreover, their downregulation through DNA methylation occurs during the process of hepatocarcinogenesis compromising hepatocellular differentiation and HCC patients’ prognosis.
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Affiliation(s)
- Miriam Recalde
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - María Gárate-Rascón
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - José María Herranz
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
| | - María Elizalde
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - María Azkona
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
| | - Juan P. Unfried
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain;
| | - Loreto Boix
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Barcelona Clinic Liver Cancer (BCLC) Group, Liver Unit, Hospital Clínic de Barcelona, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - María Reig
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Barcelona Clinic Liver Cancer (BCLC) Group, Liver Unit, Hospital Clínic de Barcelona, IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Bruno Sangro
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Hepatology Unit, Navarra University Clinic, 31008 Pamplona, Spain
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Maite G. Fernández-Barrena
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Puri Fortes
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain;
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Matías A. Ávila
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
| | - Carmen Berasain
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Correspondence: (C.B.); (M.A.); Tel.: +34-948194700 (C.B. & M.A.)
| | - María Arechederra
- Program of Hepatology, Centre of Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain; (M.R.); (M.G.-R.); (J.M.H.); (M.E.); (M.A.); (M.G.F.-B.); (M.A.Á.)
- National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd, Carlos III Health Institute), 28029 Madrid, Spain; (L.B.); (M.R.); (B.S.); (P.F.)
- IdiSNA, Navarra Institute for Health Research, 31008 Pamplona, Spain
- Correspondence: (C.B.); (M.A.); Tel.: +34-948194700 (C.B. & M.A.)
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38
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Llovet JM, Pinyol R, Kelley RK, El-Khoueiry A, Reeves HL, Wang XW, Gores GJ, Villanueva A. Molecular pathogenesis and systemic therapies for hepatocellular carcinoma. NATURE CANCER 2022; 3:386-401. [PMID: 35484418 PMCID: PMC9060366 DOI: 10.1038/s43018-022-00357-2] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/25/2022] [Indexed: 12/11/2022]
Abstract
Hepatocellular carcinoma (HCC) remains one of the most prevalent and deadliest cancers. The poor outcome associated with HCC is dramatically changing due to the advent of effective systemic therapies. Here we discuss the molecular pathogenesis of HCC, molecular classes and determinants of heterogeneity. In addition, effective single-agent and combination systemic therapies involving immunotherapies as standard of care are analyzed. Finally, we propose a flowchart of sequential therapies, explore mechanisms of resistance and address the need for predictive biomarkers.
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Affiliation(s)
- Josep M Llovet
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.
| | - Roser Pinyol
- Liver Cancer Translational Research Laboratory, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Robin K Kelley
- Helen Diller Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Anthony El-Khoueiry
- Keck School of Medicine, USC Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Helen L Reeves
- Newcastle University Translational and Clinical Research Institute and Newcastle University Centre for Cancer, Medical School, Newcastle Upon Tyne, UK
- Hepatopancreatobiliary Multidisciplinary Team, Newcastle upon Tyne NHS Foundation Trust, Freeman Hospital, Newcastle upon Tyne, UK
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Gregory J Gores
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Augusto Villanueva
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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39
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Desjonqueres E, Campani C, Marra F, Zucman-Rossi J, Nault JC. Preneoplastic lesions in the liver: Molecular insights and relevance for clinical practice. Liver Int 2022; 42:492-506. [PMID: 34982503 DOI: 10.1111/liv.15152] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/12/2022]
Abstract
Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA) are the most frequent primary liver cancers, accounting for approximately 80% and 15%, respectively. HCC carcinogenesis occurs mostly in cirrhosis and is a complex multi-step process, from precancerous lesions (low-grade and high-grade dysplastic nodules) to progressed HCC. During the different stages of liver carcinogenesis, there is an accumulation of pathological, genetic and epigenetic changes leading to initiation, malignant transformation and finally tumour progression. In contrast, a small subset of HCC occurs in normal liver from the transformation of hepatocellular adenoma (HCA), a benign hepatocellular tumour. The recent molecular classification enables to stratify HCAs according to their risk of complication, in particular malignant transformation, associated with mutations in exon 3 of the catenin beta 1 (CTNNB1) gene. Cholangiocarcinoma (CCA) derives from the multistep malignant transformation of preneoplastic lesions, like biliary intraepithelial neoplasia (BilIN) and intraductal papillary neoplasm of the bile duct (IPNB), for which a pre-operative diagnosis remains difficult. Different genetic alterations are involved in BilIN and IPNB progression, leading to the development of tubular or intestinal adenocarcinoma. The aims of this review are to describe the main clinical and molecular features of preneoplastic lesions leading to the development of HCC and CCA, their implications in clinical practice and the perspectives for future research.
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Affiliation(s)
- Elvire Desjonqueres
- Service d'hépatologie, Hôpital Avicenne, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, Bobigny, France.,Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris 13, Communauté d'Universités et Etablissements Sorbonne Paris Cité, Paris, France.,Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Paris, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France
| | - Claudia Campani
- Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris 13, Communauté d'Universités et Etablissements Sorbonne Paris Cité, Paris, France.,Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Paris, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France.,Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Fabio Marra
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Paris, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France.,Hôpital Européen Georges Pompidou, APHP, Paris, France
| | - Jean-Charles Nault
- Service d'hépatologie, Hôpital Avicenne, Hôpitaux Universitaires Paris-Seine-Saint-Denis, Assistance-Publique Hôpitaux de Paris, Bobigny, France.,Unité de Formation et de Recherche Santé Médecine et Biologie Humaine, Université Paris 13, Communauté d'Universités et Etablissements Sorbonne Paris Cité, Paris, France.,Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris, team « Functional Genomics of Solid Tumors », Paris, France.,Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France
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40
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Gallon J, Coto-Llerena M, Ercan C, Bianco G, Paradiso V, Nuciforo S, Taha-Melitz S, Meier MA, Boldanova T, Pérez-Del-Pulgar S, Rodríguez-Tajes S, von Flüe M, Soysal SD, Kollmar O, Llovet JM, Villanueva A, Terracciano LM, Heim MH, Ng CKY, Piscuoglio S. Epigenetic priming in chronic liver disease impacts the transcriptional and genetic landscapes of hepatocellular carcinoma. Mol Oncol 2021; 16:665-682. [PMID: 34863035 PMCID: PMC8807355 DOI: 10.1002/1878-0261.13154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 10/18/2021] [Accepted: 12/02/2021] [Indexed: 01/05/2023] Open
Abstract
Hepatocellular carcinomas (HCCs) usually arise from chronic liver disease (CLD). Precancerous cells in chronically inflamed environments may be 'epigenetically primed', sensitising them to oncogenic transformation. We investigated whether epigenetic priming in CLD may affect HCC outcomes by influencing the genomic and transcriptomic landscapes of HCC. Analysis of DNA methylation arrays from 10 paired CLD-HCC identified 339 shared dysregulated CpG sites and 18 shared differentially methylated regions compared with healthy livers. These regions were associated with dysregulated expression of genes with relevance in HCC, including ubiquitin D (UBD), cytochrome P450 family 2 subfamily C member 19 (CYP2C19) and O-6-methylguanine-DNA methyltransferase (MGMT). Methylation changes were recapitulated in an independent cohort of nine paired CLD-HCC. High CLD methylation score, defined using the 124 dysregulated CpGs in CLD and HCC in both cohorts, was associated with poor survival, increased somatic genetic alterations and TP53 mutations in two independent HCC cohorts. Oncogenic transcriptional and methylation dysregulation is evident in CLD and compounded in HCC. Epigenetic priming in CLD sculpts the transcriptional landscape of HCC and creates an environment favouring the acquisition of genetic alterations, suggesting that the extent of epigenetic priming in CLD could influence disease outcome.
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Affiliation(s)
- John Gallon
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Switzerland
| | - Mairene Coto-Llerena
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital Basel, Switzerland
| | - Caner Ercan
- Institute of Medical Genetics and Pathology, University Hospital Basel, Switzerland
| | - Gaia Bianco
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Switzerland
| | - Viola Paradiso
- Institute of Medical Genetics and Pathology, University Hospital Basel, Switzerland
| | - Sandro Nuciforo
- Hepatology Laboratory, Department of Biomedicine, University of Basel, Switzerland
| | - Stephanie Taha-Melitz
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Switzerland.,Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | - Marie-Anne Meier
- Hepatology Laboratory, Department of Biomedicine, University of Basel, Switzerland
| | - Tujana Boldanova
- Hepatology Laboratory, Department of Biomedicine, University of Basel, Switzerland.,Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | | | | | - Markus von Flüe
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | - Savas D Soysal
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | - Otto Kollmar
- Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | - Josep M Llovet
- Translational Research in Hepatic Oncology, Liver Unit, IDIBAPS, Hospital Clínic, University of Barcelona, Spain.,Liver Cancer Program, Divisions of Liver Diseases and Hematology/Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Augusto Villanueva
- Liver Cancer Program, Divisions of Liver Diseases and Hematology/Medical Oncology, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Luigi M Terracciano
- Department of Pathology, Humanitas Clinical and Research Center, IRCCS, Milan, Italy.,Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Markus H Heim
- Hepatology Laboratory, Department of Biomedicine, University of Basel, Switzerland.,Clarunis, Department of Visceral Surgery, University Centre for Gastrointestinal and Liver Diseases, St. Clara Hospital and University Hospital Basel, Switzerland
| | - Charlotte K Y Ng
- Department for BioMedical Research, University of Bern, Switzerland.,SIB, Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Salvatore Piscuoglio
- Visceral Surgery and Precision Medicine Research Laboratory, Department of Biomedicine, University of Basel, Switzerland.,Institute of Medical Genetics and Pathology, University Hospital Basel, Switzerland
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41
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Jawarkar RD, Bakal RL, Khatale PN, Lewaa I, Jain CM, Manwar JV, Jaiswal MS. QSAR, pharmacophore modeling and molecular docking studies to identify structural alerts for some nitrogen heterocycles as dual inhibitor of telomerase reverse transcriptase and human telomeric G-quadruplex DNA. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2021. [DOI: 10.1186/s43094-021-00380-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA are amongst the favorable target for researchers to discover novel and more effective anticancer agents. To understand and elucidate structure activity relationship and mechanism of inhibition of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA, a QSAR modeling and molecular docking were conducted.
Results
Two robust QSAR model were obtained which consist of full set QSAR model (R2: 0.8174, CCCtr: 0.8995, Q2loo: 0.7881, Q2LMO: 0.7814) and divided set QSAR model (R2: 0.8217, CCCtr: 0.9021, Q2loo: 0.7886, Q2LMO: 0.7783, Q2-F1: 0.7078, Q2-F2: 0.6865, Q2-F3: 0.7346) for envisaging the inhibitory activity of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA. The analysis reveals that carbon atom exactly at 3 bonds from aromatic carbon atom, nitrogen atom exactly at six bonds from planer nitrogen atom, aromatic carbon atom within 2 A0 from the center of mass of molecule and occurrence of element hydrogen within 2 A0 from donar atom are the key pharmacophoric features important for dual inhibition of TERT and human telomeric G-quadruplex DNA. To validate this analysis, pharmacophore modeling and the molecular docking is performed. Molecular docking analysis support QSAR analysis and revealed that, dual inhibition of TERT and human telomeric DNA is mainly contributed from hydrophobic and hydrogen bonding interactions.
Conclusion
The findings of molecular docking, pharmacophore modelling, and QSAR are all consistent and in strong agreement. The validated QSAR analyses can detect structural alerts, pharmacophore modelling can classify a molecule's consensus pharmacophore involving hydrophobic and acceptor regions, whereas docking analysis can reveal the mechanism of dual inhibition of telomerase reverse transcriptase (TERT) and human telomeric G-quadruplex DNA. The combination of QSAR, pharmacophore modeling and molecular docking may be useful for the future drug design of dual inhibitors to combat the devastating issue of resistance.
Graphical abstract
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Desaulniers D, Vasseur P, Jacobs A, Aguila MC, Ertych N, Jacobs MN. Integration of Epigenetic Mechanisms into Non-Genotoxic Carcinogenicity Hazard Assessment: Focus on DNA Methylation and Histone Modifications. Int J Mol Sci 2021; 22:10969. [PMID: 34681626 PMCID: PMC8535778 DOI: 10.3390/ijms222010969] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/30/2021] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
Epigenetics involves a series of mechanisms that entail histone and DNA covalent modifications and non-coding RNAs, and that collectively contribute to programing cell functions and differentiation. Epigenetic anomalies and DNA mutations are co-drivers of cellular dysfunctions, including carcinogenesis. Alterations of the epigenetic system occur in cancers whether the initial carcinogenic events are from genotoxic (GTxC) or non-genotoxic (NGTxC) carcinogens. NGTxC are not inherently DNA reactive, they do not have a unifying mode of action and as yet there are no regulatory test guidelines addressing mechanisms of NGTxC. To fil this gap, the Test Guideline Programme of the Organisation for Economic Cooperation and Development is developing a framework for an integrated approach for the testing and assessment (IATA) of NGTxC and is considering assays that address key events of cancer hallmarks. Here, with the intent of better understanding the applicability of epigenetic assays in chemical carcinogenicity assessment, we focus on DNA methylation and histone modifications and review: (1) epigenetic mechanisms contributing to carcinogenesis, (2) epigenetic mechanisms altered following exposure to arsenic, nickel, or phenobarbital in order to identify common carcinogen-specific mechanisms, (3) characteristics of a series of epigenetic assay types, and (4) epigenetic assay validation needs in the context of chemical hazard assessment. As a key component of numerous NGTxC mechanisms of action, epigenetic assays included in IATA assay combinations can contribute to improved chemical carcinogen identification for the better protection of public health.
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Affiliation(s)
- Daniel Desaulniers
- Environmental Health Sciences and Research Bureau, Hazard Identification Division, Health Canada, AL:2203B, Ottawa, ON K1A 0K9, Canada
| | - Paule Vasseur
- CNRS, LIEC, Université de Lorraine, 57070 Metz, France;
| | - Abigail Jacobs
- Independent at the Time of Publication, Previously US Food and Drug Administration, Rockville, MD 20852, USA;
| | - M. Cecilia Aguila
- Toxicology Team, Division of Human Food Safety, Center for Veterinary Medicine, US Food and Drug Administration, Department of Health and Human Services, Rockville, MD 20852, USA;
| | - Norman Ertych
- German Centre for the Protection of Laboratory Animals (Bf3R), German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany;
| | - Miriam N. Jacobs
- Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton OX11 0RQ, UK;
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Mattos ÂZ, Debes JD, Dhanasekaran R, Benhammou JN, Arrese M, Patrício ALV, Zilio AC, Mattos AA. Hepatocellular carcinoma in nonalcoholic fatty liver disease: A growing challenge. World J Hepatol 2021; 13:1107-1121. [PMID: 34630878 PMCID: PMC8473502 DOI: 10.4254/wjh.v13.i9.1107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/21/2021] [Accepted: 07/26/2021] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common cause of liver disease worldwide, and its prevalence increases continuously. As it predisposes to hepatocellular carcinoma both in the presence and in the absence of cirrhosis, it is not surprising that the incidence of NAFLD-related hepatocellular carcinoma would also rise. Some of the mechanisms involved in hepatocarcinogenesis are particular to individuals with fatty liver, and they help explain why liver cancer develops even in patients without cirrhosis. Genetic and immune-mediated mechanisms seem to play an important role in the development of hepatocellular carcinoma in this population. Currently, it is consensual that patients with NAFLD-related cirrhosis should be surveilled with ultrasonography every 6 mo (with or without alpha-fetoprotein), but it is known that they are less likely to follow this recommendation than individuals with other kinds of liver disease. Moreover, the performance of the methods of surveillance are lower in NAFLD than they are in other liver diseases. Furthermore, it is not clear which subgroups of patients without cirrhosis should undergo surveillance. Understanding the mechanisms of hepatocarcinogenesis in NAFLD could hopefully lead to the identification of biomarkers to be used in the surveillance for liver cancer in these individuals. By improving surveillance, tumors could be detected in earlier stages, amenable to curative treatments.
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Affiliation(s)
- Ângelo Z Mattos
- Graduate Program in Medicine: Hepatology, Federal University of Health Sciences of Porto Alegre, Porto Alegre 90020-090, Rio Grande do Sul, Brazil
| | - Jose D Debes
- Department of Medicine, Division of Infectious Diseases and of Gastroenterology, University of Minnesota, Minneapolis, MN 55455, United States
| | - Renu Dhanasekaran
- Division of Gastroenterology and Hepatology, Stanford University, Stanford, CA 94305, United States
| | - Jihane N Benhammou
- The Vatche and Tamar Manoukian Division of Digestive Diseases, University of California, Los Angeles, CA 90095, United States
| | - Marco Arrese
- Department of Gastroenterology, Pontificia Universidad Católica de Chile, Santiago 3580000, Chile
| | - André Luiz V Patrício
- Gastroenterology and Hepatology Unit, Irmandade Santa Casa de Misericórdia de Porto Alegre, Porto Alegre 90020-090, Rio Grande do Sul, Brazil
| | - Amanda C Zilio
- Gastroenterology and Hepatology Unit, Irmandade Santa Casa de Misericórdia de Porto Alegre, Porto Alegre 90020-090, Rio Grande do Sul, Brazil
| | - Angelo A Mattos
- Graduate Program in Medicine: Hepatology, Federal University of Health Sciences of Porto Alegre, Porto Alegre 90020-090, Rio Grande do Sul, Brazil
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Qiu L, Yang X, Wu J, Huang C, Miao Y, Fu Z. HIST2H2BF Potentiates the Propagation of Cancer Stem Cells via Notch Signaling to Promote Malignancy and Liver Metastasis in Colorectal Carcinoma. Front Oncol 2021; 11:677646. [PMID: 34476209 PMCID: PMC8406628 DOI: 10.3389/fonc.2021.677646] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/18/2021] [Indexed: 11/17/2022] Open
Abstract
Background Growing evidence demonstrates that the initiation and progression of colorectal carcinoma (CRC) is related to the presence of cancer stem cells (CSCs). However, the mechanism through which the stem cell features of CRC cells are maintained is poorly understood. In this study, we identified the oncogenic histone cluster 2 H2B family member F (HIST2H2BF) and aimed to investigate the function of upregulated HIST2H2BF expression in maintaining the stem cell features of CRC cells, which accelerate the progression of CRC. Methods HIST2H2BF expression was quantified using real-time polymerase chain reaction, immunohistochemistry, and western blotting. The correlation between CpG island methylation status and HIST2H2BF re-expression was assessed through bisulfite sequencing polymerase chain reaction, methylation-specific polymerase chain reaction, and 5-Aza-dC treatment. Functional assays were performed on CRC cells and mice to investigate the HIST2H2BF-induced stem cell-like and cancer properties of CRC. Using the Notch pathway inhibitor FLI-06, the regulatory effect of HIST2H2BF on downstream Notch signaling was confirmed. Results HIST2H2BF was highly expressed in CRC tissues and cell lines. The reactivation of HIST2H2BF in CRC stems at least in part from the hypomethylated CpG islands. CRC patients with high HIST2H2BF expression have poor survival outcomes. Functional studies have shown that HIST2H2BF promotes CSC phenotype, malignancy, and liver metastasis through the activation of Notch signaling in CRC. Blockage of the Notch pathway reduced the stem cell-like and cancer properties. Conclusion Our study suggests that HIST2H2BF upregulation enhances the CSC phenotype, malignancy, and liver metastasis through the activation of Notch signaling in CRC. These results identified a new perspective on the mechanism by which the stem cell features of CRC cells are maintained and highlighted the potential novel therapeutic targets for CRC.
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Affiliation(s)
- Lei Qiu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of General Surgery, The Second People's Hospital of Lianyungang, Lianyungang Tumor Hospital, Lianyungang Hospital Affiliated to Bengbu Medical University, Lianyungang, China
| | - Xiuwei Yang
- Department of General Surgery, The Second People's Hospital of Lianyungang, Lianyungang Tumor Hospital, Lianyungang Hospital Affiliated to Bengbu Medical University, Lianyungang, China
| | - Jingyu Wu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Changzhi Huang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yongchang Miao
- Department of General Surgery, The Second People's Hospital of Lianyungang, Lianyungang Tumor Hospital, Lianyungang Hospital Affiliated to Bengbu Medical University, Lianyungang, China
| | - Zan Fu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
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Sun R, Du C, Li J, Zhou Y, Xiong W, Xiang J, Liu J, Xiao Z, Fang L, Li Z. Systematic Investigation of DNA Methylation Associated With Platinum Chemotherapy Resistance Across 13 Cancer Types. Front Pharmacol 2021; 12:616529. [PMID: 33995018 PMCID: PMC8117351 DOI: 10.3389/fphar.2021.616529] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Platinum resistance poses a significant problem for oncology clinicians. As a result, the role of epigenetics and DNA methylation in platinum-based chemoresistance has gained increasing attention from researchers in recent years. A systematic investigation of aberrant methylation patterns related to platinum resistance across various cancer types is urgently needed. Methods: We analyzed the platinum chemotherapy response-related methylation patterns from different perspectives of 618 patients across 13 cancer types and integrated transcriptional and clinical data. Spearman’s test was used to evaluate the correlation between methylation and gene expression. Cox analysis, the Kaplan-Meier method, and log-rank tests were performed to identify potential risk biomarkers based on differentially methylated positions (DMPs) and compare survival based on DMP values. Support vector machines and receiver operating characteristic curves were used to identify the platinum-response predictive DMPs. Results: A total of 3,703 DMPs (p value < 0.001 and absolute delta beta >0.10) were identified, and the DMP numbers of each cancer type varied. A total of 39.83% of DMPs were hypermethylated and 60.17% were hypomethylated in platinum-resistant patients. Among them, 405 DMPs (Benjamini and Hochberg adjusted p value < 0.05) were found to be associated with prognosis in tumor patients treated with platinum-based regimens, and 664 DMPs displayed the potential to predict platinum chemotherapy response. In addition, we defined six DNA DMPs consisting of four gene members (mesothelin, protein kinase cAMP-dependent type II regulatory subunit beta, msh homeobox 1, and par-6 family cell polarity regulator alpha) that may have favorable prognostic and predictive values for platinum chemotherapy. Conclusion: The methylation-transcription axis exists and participates in the complex biological mechanism of platinum resistance in various cancers. Six DMPs and four associated genes may have the potential to serve as promising epigenetic biomarkers for platinum-based chemotherapy and guide clinical selection of optimal treatment.
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Affiliation(s)
- Ruizheng Sun
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Chao Du
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Jiaxin Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Yanhong Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Juanjuan Xiang
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Jiheng Liu
- Department of Hematology and Oncology, The First Hospital of Changsha, Changsha, China
| | - Zhigang Xiao
- Department of General Surgery, Hunan Provincial People's Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Li Fang
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
| | - Zheng Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China.,The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
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Labgaa I, Villanueva A, Dormond O, Demartines N, Melloul E. The Role of Liquid Biopsy in Hepatocellular Carcinoma Prognostication. Cancers (Basel) 2021; 13:cancers13040659. [PMID: 33562173 PMCID: PMC7914891 DOI: 10.3390/cancers13040659] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/01/2021] [Accepted: 02/01/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Hepatocellular carcinoma (HCC) is one of the deadliest cancer. Clinical guidelines for the management of HCC endorse algorithms deriving from clinical variables whose performances to prognosticate HCC is limited. Liquid biopsy is the molecular analysis of tumor by-products released into the bloodstream. It offers minimally-invasive access to circulating analytes like DNA, RNA, exosomes and cells. This technology demonstrated promising results for various applications in cancers, including prognostication. This review aimed to provide a comprehensive overview of the contribution of liquid biopsy in HCC prognostication. The results suggested that liquid biopsy may be a polyvalent and valuable tool to prognosticate HCC. Abstract Showing a steadily increasing cancer-related mortality, the epidemiological evolution of hepatocellular carcinoma (HCC) is concerning. Numerous strategies have attempted to prognosticate HCC but their performance is modest; this is partially due to the heterogeneous biology of this cancer. Current clinical guidelines endorse classifications and scores that use clinical variables, such as the Barcelona Clinic Liver Cancer (BCLC) classification. These algorithms are unlikely to fully recapitulate the genomic complexity of HCC. Integrating molecular readouts on a patient-basis, following a precision-medicine perspective, might be an option to refine prognostic systems. The limited access to HCC tissue samples is an important limitation to these approaches but it could be partially circumvented by using liquid biopsy. This concept consists of the molecular analysis of products derived from a solid tumor and released into biological fluids, mostly into the bloodstream. It offers an easy and minimally-invasive access to DNA, RNA, extracellular vesicles and cells that can be analyzed with next-generation sequencing (NGS) technologies. This review aims to investigate the potential contributions of liquid biopsy in HCC prognostication. The results identified prognostic values for each of the components of liquid biopsy, suggesting that this technology may help refine HCC prognostication.
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Affiliation(s)
- Ismail Labgaa
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), CH-1011 Lausanne, Switzerland; (I.L.); (O.D.); (E.M.)
| | - Augusto Villanueva
- Division of Liver Diseases, Liver Cancer Program, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
- Division of Hematology/Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Olivier Dormond
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), CH-1011 Lausanne, Switzerland; (I.L.); (O.D.); (E.M.)
| | - Nicolas Demartines
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), CH-1011 Lausanne, Switzerland; (I.L.); (O.D.); (E.M.)
- Correspondence:
| | - Emmanuel Melloul
- Department of Visceral Surgery, Lausanne University Hospital (CHUV), University of Lausanne (UNIL), CH-1011 Lausanne, Switzerland; (I.L.); (O.D.); (E.M.)
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