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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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Di Y, Wang Z, Xiao J, Zhang X, Ye L, Wen X, Qin J, Lu L, Wang X, He W. ACSL6-activated IL-18R1-NF-κB promotes IL-18-mediated tumor immune evasion and tumor progression. SCIENCE ADVANCES 2024; 10:eadp0719. [PMID: 39292786 PMCID: PMC11409972 DOI: 10.1126/sciadv.adp0719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/09/2024] [Indexed: 09/20/2024]
Abstract
Aberrant activation of IL-18 signaling regulates tumor immune evasion and progression. However, the underlying mechanism remains unclear. Here, we report that long-chain acyl-CoA synthase 6 (ACSL6) is highly expressed in liver cancer and correlated with poor prognosis. ACSL6 promotes tumor growth, metastasis, and immune evasion mediated by IL-18, independent of its metabolic enzyme activity. Mechanistically, upon IL-18 stimulation, ACSL6 is phosphorylated by ERK2 at S674 and recruits IL-18RAP to interact with IL-18R1, thereby reinforcing the IL-18R1-IL-18RAP heterodimer and triggering NF-κB-dependent gene expression to facilitate tumor development. Furthermore, the up-regulation of CXCL1 and CXCL5 by ACSL6 promotes tumor-associated neutrophil and tumor-associated macrophage recruitment, thereby inhibiting cytotoxic CD8+ T cell infiltration. Ablation or S674A mutation of ACSL6 potentiated anti-PD-1 therapeutic efficacy by increasing the effector activity of intertumoral CD8+ T cells. We revealed that ACSL6 is a potential adaptor that activates IL-18-NF-κB axis-mediated tumor immune evasion and provides valuable insights for developing effective immunotherapy strategies for cancer.
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Affiliation(s)
- Yuqin Di
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Ziyang Wang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jing Xiao
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, Guangdong 519000, China
| | - Xiang Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Lvlan Ye
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Xiangqiong Wen
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jiale Qin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Ligong Lu
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People’s Hospital (Zhuhai Clinical Medical College of Jinan University), Zhuhai, Guangdong 519000, China
| | - Xiongjun Wang
- School of Life Sciences, Guangzhou University, Guangzhou, Guangdong 510006, China
| | - Weiling He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
- Department of Gastrointestinal Surgery, Xiang’an Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian 361000, China
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Chan YT, Zhang C, Wu J, Lu P, Xu L, Yuan H, Feng Y, Chen ZS, Wang N. Biomarkers for diagnosis and therapeutic options in hepatocellular carcinoma. Mol Cancer 2024; 23:189. [PMID: 39242496 PMCID: PMC11378508 DOI: 10.1186/s12943-024-02101-z] [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: 07/30/2024] [Accepted: 08/23/2024] [Indexed: 09/09/2024] Open
Abstract
Liver cancer is a global health challenge, causing a significant social-economic burden. Hepatocellular carcinoma (HCC) is the predominant type of primary liver cancer, which is highly heterogeneous in terms of molecular and cellular signatures. Early-stage or small tumors are typically treated with surgery or ablation. Currently, chemotherapies and immunotherapies are the best treatments for unresectable tumors or advanced HCC. However, drug response and acquired resistance are not predictable with the existing systematic guidelines regarding mutation patterns and molecular biomarkers, resulting in sub-optimal treatment outcomes for many patients with atypical molecular profiles. With advanced technological platforms, valuable information such as tumor genetic alterations, epigenetic data, and tumor microenvironments can be obtained from liquid biopsy. The inter- and intra-tumoral heterogeneity of HCC are illustrated, and these collective data provide solid evidence in the decision-making process of treatment regimens. This article reviews the current understanding of HCC detection methods and aims to update the development of HCC surveillance using liquid biopsy. Recent critical findings on the molecular basis, epigenetic profiles, circulating tumor cells, circulating DNAs, and omics studies are elaborated for HCC diagnosis. Besides, biomarkers related to the choice of therapeutic options are discussed. Some notable recent clinical trials working on targeted therapies are also highlighted. Insights are provided to translate the knowledge into potential biomarkers for detection and diagnosis, prognosis, treatment response, and drug resistance indicators in clinical practice.
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Affiliation(s)
- Yau-Tuen Chan
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Cheng Zhang
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Junyu Wu
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Pengde Lu
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lin Xu
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Hongchao Yuan
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Yibin Feng
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Zhe-Sheng Chen
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John's University, 8000 Utopia Parkway, Queens, NY, 11439, USA.
| | - Ning Wang
- School of Chinese Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
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Akbulut S, Kucukakcali Z, Sahin TT, Colak C, Yilmaz S. Role of Epigenetic Factors in Determining the Biological Behavior and Prognosis of Hepatocellular Carcinoma. Diagnostics (Basel) 2024; 14:1925. [PMID: 39272711 PMCID: PMC11394249 DOI: 10.3390/diagnostics14171925] [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: 06/21/2024] [Revised: 08/23/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND The current study's objective is to evaluate the molecular genetic mechanisms influencing the biological behavior of hepatocellular carcinoma (HCC) by analyzing the transcriptomic and epigenetic signatures of the tumors. METHODS Transcriptomic data were downloaded from the NCBI GEO database. We investigated the expression differences between the GSE46444 (48 cirrhotic tissues versus 88 HCC tissues) and GSE63898 (168 cirrhotic tissues versus 228 HCC tissues) data sets using GEO2R. Differentially expressed genes were evaluated using GO and KEGG metabolic pathway analysis websites. Whole genome bisulfite sequencing (WGBS) and Methylated DNA Immunoprecipitation Sequencing (MeDIP-Seq) data sets (26 HCC tissues versus 26 adjacent non-tumoral tissues) were also downloaded from the NCBI SRA database. These data sets were analyzed using Bismark and QSEA, respectively. The methylation differences between the groups were assessed using functional enrichment analysis. RESULTS In the GSE46444 data set, 80 genes were upregulated, and 315 genes were downregulated in the tumor tissue (HCC tissue) compared to the non-tumor cirrhotic tissue. In the GSE63898 data set, 1261 genes were upregulated, and 458 genes were downregulated in the cirrhotic tissue compared to the tumor tissues. WGBS revealed that 20 protein-coding loci were hypermethylated. while the hypomethylated regions were non-protein-coding. The methylated residues of the tumor tissue, non-tumorous cirrhotic tissue, and healthy tissue were comparable. MeDIP-Seq, conducted on tumoral and non-tumoral tissues, identified hypermethylated or hypomethylated areas as protein-coding regions. The functional enrichment analysis indicated that these genes were related to pathways including peroxisome, focal adhesion, mTOR, RAP1, Phospholipase D, Ras, and PI3K/AKT signal transduction. CONCLUSIONS The investigation of transcriptomic and epigenetic mechanisms identified several genes significant in the biological behavior of HCC. These genes present potential targets for the development of targeted therapy.
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Affiliation(s)
- Sami Akbulut
- Liver Transplant Institute and Department of Surgery, Faculty of Medicine, Inonu University, 44280 Malatya, Turkey
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280 Malatya, Turkey
| | - Zeynep Kucukakcali
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280 Malatya, Turkey
| | - Tevfik Tolga Sahin
- Liver Transplant Institute and Department of Surgery, Faculty of Medicine, Inonu University, 44280 Malatya, Turkey
| | - Cemil Colak
- Department of Biostatistics and Medical Informatics, Faculty of Medicine, Inonu University, 44280 Malatya, Turkey
| | - Sezai Yilmaz
- Liver Transplant Institute and Department of Surgery, Faculty of Medicine, Inonu University, 44280 Malatya, Turkey
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Chen T, Xiang L, Zhang W, Xia Z, Chen W. AGXT2 Suppresses the Proliferation and Dissemination of Hepatocellular Carcinoma Cells by Modulating Intracellular Lipid Metabolism. J Hepatocell Carcinoma 2024; 11:1623-1639. [PMID: 39206420 PMCID: PMC11353308 DOI: 10.2147/jhc.s470250] [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: 05/02/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024] Open
Abstract
Purpose Alanine glyoxylate aminotransferase (AGXT) family members are crucial in cancer processes, but their role in hepatocellular carcinoma (HCC) metabolism is unclear. This study investigates AGXT2's function in HCC. Patients and Methods AGTX2 expression was studied using bioinformatics, real-time reverse transcriptase-polymerase chain reaction (RT-qPCR), Western blot, and Enzyme-linked immunosorbent assay (ELISA). A lentivirus-induced AGTX2 overexpression cell model was analyzed with RNA sequencing (RNA-seq) and liquid chromatography-mass spectrometry (LC-MS). Cholesterol levels were confirmed by Oil Red O staining. AGTX2 effects were evaluated through cell cycle analysis, wound healing, and transwell migration assays.Tumorigenic effects were observed in NOD-SCID IL2Rγnull (NTG) mice in subcutaneous experiments. Protein interaction was examined through co-immunoprecipitation methods. Results We observed a significant reduction in AGXT2 mRNA and protein levels in both HCC tumor tissues and serum samples from patients with liver cancer, which was associated with a worse prognosis. The activation of AGXT2 has been shown to effectively decrease cholesterol levels in liver cancer cells, serving as an antagonist in the cholesterol metabolism pathway. An increase in low density lipoprotein receptor (LDLR) mRNA was noted in cells overexpressing AGXT2, accompanied by a decrease in LDLR protein and an elevation in proprotein convertase subtilisin/kexin type 9 (PCSK9) mRNA and protein levels. Molecular docking and co-immunoprecipitation experiments further elucidated the interaction between AGXT2 and LDLR proteins. AGXT2 was observed to suppress the migratory and invasive capabilities of HCC cells, inducing cell cycle arrest in the G2/M phase. AGXT2 activation inhibited subcutaneous liver cancer tumor growth in NTG mice. Conclusion AGXT2 was found to lower cholesterol levels in liver cancer cells, possibly through interactions with the LDLR protein and modulation of PCSK9-mediated LDLR degradation. This mechanism may impede cholesterol transport to liver cancer cells, thereby suppressing their growth and metastasis.
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Affiliation(s)
- Tian Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
| | - Lunjian Xiang
- Hepatobiliary Surgery, Chongqing University Three Gorges Hospital, Chongqing, People’s Republic of China
| | - Wenjin Zhang
- Chongqing Municipality Clinical Research Center for Endocrinology and Metabolic Diseases, Chongqing University Three Gorges Hospital, Chongqing, People’s Republic of China
| | - Zhenyi Xia
- Thoracic surgery, Chongqing University Three Gorges Hospital, Chongqing, People’s Republic of China
| | - Weixian Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China
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Jeong BK, Choi WI, Choi W, Moon J, Lee WH, Choi C, Choi IY, Lee SH, Kim JK, Ju YS, Kim P, Moon YA, Park JY, Kim H. A male mouse model for metabolic dysfunction-associated steatotic liver disease and hepatocellular carcinoma. Nat Commun 2024; 15:6506. [PMID: 39090079 PMCID: PMC11294468 DOI: 10.1038/s41467-024-50660-y] [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: 10/28/2023] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
The lack of an appropriate preclinical model of metabolic dysfunction-associated steatotic liver disease (MASLD) that recapitulates the whole disease spectrum impedes exploration of disease pathophysiology and the development of effective treatment strategies. Here, we develop a mouse model (Streptozotocin with high-fat diet, STZ + HFD) that gradually develops fatty liver, metabolic dysfunction-associated steatohepatitis (MASH), hepatic fibrosis, and hepatocellular carcinoma (HCC) in the context of metabolic dysfunction. The hepatic transcriptomic features of STZ + HFD mice closely reflect those of patients with obesity accompanying type 2 diabetes mellitus, MASH, and MASLD-related HCC. Dietary changes and tirzepatide administration alleviate MASH, hepatic fibrosis, and hepatic tumorigenesis in STZ + HFD mice. In conclusion, a murine model recapitulating the main histopathologic, transcriptomic, and metabolic alterations observed in MASLD patients is successfully established.
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Affiliation(s)
- Byung-Kwan Jeong
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Korea
- Biomedical Research Center, KAIST, Daejeon, Korea
| | - Won-Il Choi
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Korea
- Biomedical Research Center, KAIST, Daejeon, Korea
| | - Wonsuk Choi
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University Medical School, Hwasun, Korea.
| | - Jieun Moon
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Korea
- Biomedical Research Center, KAIST, Daejeon, Korea
| | - Won Hee Lee
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Korea
- Biomedical Research Center, KAIST, Daejeon, Korea
| | - Chan Choi
- Department of Pathology, Chonnam National University Medical School, Hwasun, Korea
| | - In Young Choi
- Hanmi Research Center, Hanmi Pharmaceutical Co. Ltd, Hwaseong, Korea
| | - Sang-Hyun Lee
- Hanmi Research Center, Hanmi Pharmaceutical Co. Ltd, Hwaseong, Korea
| | - Jung Kuk Kim
- Hanmi Research Center, Hanmi Pharmaceutical Co. Ltd, Hwaseong, Korea
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Korea
- Biomedical Research Center, KAIST, Daejeon, Korea
| | - Pilhan Kim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Korea
- Biomedical Research Center, KAIST, Daejeon, Korea
| | - Young-Ah Moon
- Department of Molecular Medicine, Inha University College of Medicine, Incheon, 22212, Korea
| | - Jun Yong Park
- Department of Internal Medicine, Yonsei University College of Medicine, Yonsei Liver Center, Severance Hospital, Seoul, Korea.
| | - Hail Kim
- Graduate School of Medical Science and Engineering, KAIST, Daejeon, 34141, Korea.
- Biomedical Research Center, KAIST, Daejeon, Korea.
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Yang T, Huang L, He J, Luo L, Guo W, Chen H, Jiang X, Huang L, Ma S, Liu X. Establishment of diagnostic model and identification of diagnostic markers between liver cancer and cirrhosis based on multi-chip and machine learning. Clin Exp Pharmacol Physiol 2024; 51:e13907. [PMID: 38965675 DOI: 10.1111/1440-1681.13907] [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: 11/03/2023] [Revised: 05/16/2024] [Accepted: 06/02/2024] [Indexed: 07/06/2024]
Abstract
OBJECTIVE Most cases of hepatocellular carcinoma (HCC) arise as a consequence of cirrhosis. In this study, our objective is to construct a comprehensive diagnostic model that investigates the diagnostic markers distinguishing between cirrhosis and HCC. METHODS Based on multiple GEO datasets containing cirrhosis and HCC samples, we used lasso regression, random forest (RF)-recursive feature elimination (RFE) and receiver operator characteristic analysis to screen for characteristic genes. Subsequently, we integrated these genes into a multivariable logistic regression model and validated the linear prediction scores in both training and validation cohorts. The ssGSEA algorithm was used to estimate the fraction of infiltrating immune cells in the samples. Finally, molecular typing for patients with cirrhosis was performed using the CCP algorithm. RESULTS The study identified 137 differentially expressed genes (DEGs) and selected five significant genes (CXCL14, CAP2, FCN2, CCBE1 and UBE2C) to construct a diagnostic model. In both the training and validation cohorts, the model exhibited an area under the curve (AUC) greater than 0.9 and a kappa value of approximately 0.9. Additionally, the calibration curve demonstrated excellent concordance between observed and predicted incidence rates. Comparatively, HCC displayed overall downregulation of infiltrating immune cells compared to cirrhosis. Notably, CCBE1 showed strong correlations with the tumour immune microenvironment as well as genes associated with cell death and cellular ageing processes. Furthermore, cirrhosis subtypes with high linear predictive scores were enriched in multiple cancer-related pathways. CONCLUSION In conclusion, we successfully identified diagnostic markers distinguishing between cirrhosis and hepatocellular carcinoma and developed a novel diagnostic model for discriminating the two conditions. CCBE1 might exert a pivotal role in regulating the tumour microenvironment, cell death and senescence.
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Affiliation(s)
- Tianpeng Yang
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Lu Huang
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Jiale He
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Lihong Luo
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Weiting Guo
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Huajian Chen
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Xinyue Jiang
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Li Huang
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Shumei Ma
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Xiaodong Liu
- School of Public Health, Wenzhou Medical University, Wenzhou, China
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Iavarone M, Nault JC, Cabibbo G, Torres F, Reig M. Indolent cancer and pattern of progression: Two missing parameters in trial design for hepatology. Hepatology 2024; 79:1452-1462. [PMID: 37399245 PMCID: PMC11095876 DOI: 10.1097/hep.0000000000000527] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/20/2023] [Indexed: 07/05/2023]
Abstract
The indolent and aggressive behaviors of HCC might have a role in clinical trial (CT) results; however, the indolent HCC is less analyzed compared to others cancer. Indolent profile could be characterized as follows: (1) patients with low risk of progression itself due to the HCC molecular profile and/or due to the interaction between cancer cell their microenvironment; (2) patients who achieve objective response or present spontaneous regression; and (3) patients who develop radiological progression with no consequence on either the liver function or general status, and without trigger a change in the tumor stage. Patients with "indolent HCC" generally never develop cancer-related symptoms neither die for HCC-related causes. Thus, we hypothesize that the imbalance in the proportion of "indolent" versus "aggressive HCC" between arms or the underestimation/overestimation of HCC behavior at baseline in single-arm CT could be associated with CT failure or under-overestimation of trial results. The "indolent progression" may also explain the discrepancy between radiological progression-based end points and survival. Moreover, we discuss the related causes that explain the indolent profile of HCC and propose (1) refining the progression-related end point by the pattern of progression to minimize the limitations of the current end points; (2) considering alternative statistical tools for survival analysis such as milestone survival, or restricted mean survival time to capture the value of indolent HCC. According to these considerations, we propose incorporating novel end points into the single arm of phase I/II CT as exploratory analysis or as a secondary end point in phase III CT.
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Affiliation(s)
- Massimo Iavarone
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico—Division of Gastroenterology and Hepatology, Milan, Italy
| | - Jean-Charles Nault
- Centre de Recherche des Cordeliers, Sorbonne Université, Inserm, Université de Paris Cité, team « Functional Genomics of Solid Tumors », Equipe labellisée Ligue Nationale Contre le Cancer, Labex OncoImmunology, Paris, France
- 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 nord, Bobigny, France
| | - Giuseppe Cabibbo
- Section of Gastroenterology & Hepatology, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties, PROMISE, University of Palermo, Palermo, Italy
| | - Ferran Torres
- Biostatistics Unit, Medical School, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Maria Reig
- Liver Oncology Unit. Liver Unit, Hospital Clínic Barcelona, Barcelona, Spain
- BCLC group, FUNDACIO/IDIBAPS, Barcelona, Spain
- CIBEREHD, Madrid, Spain
- Universitat de Barcelona, Barcelona, Spain
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Lombardo D, Franzè MS, Caminiti G, Pollicino T. Hepatitis Delta Virus and Hepatocellular Carcinoma. Pathogens 2024; 13:362. [PMID: 38787214 PMCID: PMC11124437 DOI: 10.3390/pathogens13050362] [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: 03/22/2024] [Revised: 04/14/2024] [Accepted: 04/20/2024] [Indexed: 05/25/2024] Open
Abstract
The hepatitis D virus (HDV) is a compact, enveloped, circular RNA virus that relies on hepatitis B virus (HBV) envelope proteins to initiate a primary infection in hepatocytes, assemble, and secrete new virions. Globally, HDV infection affects an estimated 12 million to 72 million people, carrying a significantly elevated risk of developing cirrhosis, liver failure, and hepatocellular carcinoma (HCC) compared to an HBV mono-infection. Furthermore, HDV-associated HCC often manifests at a younger age and exhibits more aggressive characteristics. The intricate mechanisms driving the synergistic carcinogenicity of the HDV and HBV are not fully elucidated but are believed to involve chronic inflammation, immune dysregulation, and the direct oncogenic effects of the HDV. Indeed, recent data highlight that the molecular profile of HCC associated with HDV is unique and distinct from that of HBV-induced HCC. However, the question of whether the HDV is an oncogenic virus remains unanswered. In this review, we comprehensively examined several crucial aspects of the HDV, encompassing its epidemiology, molecular biology, immunology, and the associated risks of liver disease progression and HCC development.
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Affiliation(s)
| | | | | | - Teresa Pollicino
- Department of Clinical and Experimental Medicine, University Hospital of Messina, 98124 Messina, Italy; (D.L.); (M.S.F.); (G.C.)
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Ma J, Chen Z, Liu S, Chen C, Guan W, Geng M, Xiao H, Mao B, Wang B. Prognostic effect of DNA methylation of BTG2 gene in Chinese hepatocellular carcinoma. Heliyon 2024; 10:e28580. [PMID: 38560180 PMCID: PMC10979207 DOI: 10.1016/j.heliyon.2024.e28580] [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: 08/05/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
Background This study aims to develop a prognostic model for overall survival based on potential methylation sites within B-cell translocation gene 2 (BTG2) in Chinese patients with hepatocellular carcinoma (HCC). Methods This is a retrospective study. The beta values of nine CpG sites and RSEM normalized count values of BTG2 gene were extracted from the Cancer Genome Atlas-Liver Hepatocellular Carcinoma (TCGA-LIHC) (TCGA-LIHC) dataset, with the beta value representing the methylation level by indicating the ratio of the intensity of the methylated bead type to the combined locus intensity. Pyrosequencing was performed to determine the range of methylation values surrounding cg01798157 site in BTG2 gene. A weighted linear model was developed to predict the overall survival (OS). Results The beta value of cg01798157 was significantly negatively associated with the mRNA expression of BTG2 in the TCGA-LIHC dataset (Spearman's rho = -0.5306, P = 2.27 × 10-27). The methylation level of cg01798157 was significantly associated with OS in the cohort of 51 Chinese HCC patients (Hazard ratio = 0.597, 95% CI: 0.434-0.820, P = 0.001). Multivariate Cox regression analysis identified methylation level of cg01798157, cirrhosis, and microvascular invasion as independent prognostic factors. The prognostic efficiency of death risk score was superior to that of cirrhosis or microvascular invasion alone. Conclusions The methylation level of cg01798157 in BTG2 may be an epigenetic biomarker in Chinese patients with resectable HCC.
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Affiliation(s)
- Jungang Ma
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Zhuo Chen
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Shuixia Liu
- Department of Ophthalmology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Chuan Chen
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Wei Guan
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Mingying Geng
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - He Xiao
- Department of Oncology, Daping Hospital, Army Medical University, Chongqing, 400042, China
| | - Bijing Mao
- Department of Oncology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, 401120, China
| | - Bin Wang
- Department of Oncology, The Seventh People's Hospital of Chongqing (Affiliated Central Hospital of Chongqing University of Technology), Chongqing, 400054, China
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11
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Fu Y, Maccioni L, Wang XW, Greten TF, Gao B. Alcohol-associated liver cancer. Hepatology 2024:01515467-990000000-00837. [PMID: 38607725 DOI: 10.1097/hep.0000000000000890] [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: 01/31/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024]
Abstract
Heavy alcohol intake induces a wide spectrum of liver diseases ranging from steatosis, steatohepatitis, cirrhosis, and HCC. Although alcohol consumption is a well-known risk factor for the development, morbidity, and mortality of HCC globally, alcohol-associated hepatocellular carcinoma (A-HCC) is poorly characterized compared to viral hepatitis-associated HCC. Most A-HCCs develop after alcohol-associated cirrhosis (AC), but the direct carcinogenesis from ethanol and its metabolites to A-HCC remains obscure. The differences between A-HCC and HCCs caused by other etiologies have not been well investigated in terms of clinical prognosis, genetic or epigenetic landscape, molecular mechanisms, and heterogeneity. Moreover, there is a huge gap between basic research and clinical practice due to the lack of preclinical models of A-HCC. In the current review, we discuss the pathogenesis, heterogeneity, preclinical approaches, epigenetic, and genetic profiles of A-HCC, and discuss the current insights into and the prospects for future research on A-HCC. The potential effect of alcohol on cholangiocarcinoma and liver metastasis is also discussed.
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Affiliation(s)
- Yaojie Fu
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, USA
| | - Luca Maccioni
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, USA
| | - Xin Wei Wang
- Liver Carcinogenesis Section, Laboratory of Human Carcinogenesis, National Cancer Institute, NIH, Bethesda, Maryland, USA
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Tim F Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
- Gastrointestinal Malignancies Section, Thoracic and Gastrointestinal Malignancies Branch, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Bin Gao
- Laboratory of Liver Diseases, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland, USA
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12
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Contreras-Mancilla J, Cerapio JP, Ruiz E, Fernández R, Casavilca-Zambrano S, Machicado C, Fournié JJ, Pineau P, Bertani S. Hepatocellular carcinoma in Peru: A molecular description of an unconventional clinical presentation. REVISTA DE GASTROENTEROLOGIA DE MEXICO (ENGLISH) 2024; 89:194-204. [PMID: 37164797 DOI: 10.1016/j.rgmxen.2023.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/17/2023] [Indexed: 05/12/2023]
Abstract
INTRODUCTION AND AIM Hepatocellular carcinoma (HCC) is the third most frequent cancer of digestive tract tumors in Peru, with a high mortality rate of 17.7 per 100,000 inhabitants. A significant number of HCC cases in Peru do not follow the classic clinical epidemiology of the disease described in other parts of the world. Those patients present with a distinct transcriptome profile and a singular tumor process, suggesting a particular type of hepatocarcinogenesis in a portion of the Peruvian population. Our aim was to understand the clinical and biologic involvement of the epigenetic profile (methylation) and gene expression (transcriptome) of HCC in Peruvian patients. METHODS HCC and liver transcriptome and DNA methylation profiles were evaluated in 74 Peruvian patients. RESULTS When grouped by age, there was greater DNA methylation in younger patients with HCC but no differences with respect to the transcriptomic profile. A high prevalence of the hepatitis B virus (HBV) (>90%) was also observed in the younger patients with HCC. Enrichment analyses in both molecular profiles pinpointed PRC2 as an important molecular effector of that liver tumor process in Peruvian patients. CONCLUSION HCC in Peruvian patients has a unique molecular profile, associated with the presence of HBV, as well as overall DNA hypermethylation related to undifferentiated liver cells or cellular reprogramming.
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Affiliation(s)
- J Contreras-Mancilla
- Laboratorio de Investigación Traslacional y Biología Computacional, Facultad de Ciencias y Filosofía - LID, Universidad Peruana Cayetano Heredia, Lima, Peru; Laboratorio Mixto Internacional de Oncología Antropológica Molecular (LOAM), IRD, INEN, Lima, Peru
| | - J P Cerapio
- Laboratorio Mixto Internacional de Oncología Antropológica Molecular (LOAM), IRD, INEN, Lima, Peru; Université de Toulouse, UMR 1037 CRCT, INSERM, CNRS, UPS, Toulouse, France; Laboratorio de Excelencia Toulouse-Cáncer (TOUCAN), Toulouse, France
| | - E Ruiz
- Laboratorio Mixto Internacional de Oncología Antropológica Molecular (LOAM), IRD, INEN, Lima, Peru; Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - R Fernández
- Laboratorio Mixto Internacional de Oncología Antropológica Molecular (LOAM), IRD, INEN, Lima, Peru; Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - S Casavilca-Zambrano
- Laboratorio Mixto Internacional de Oncología Antropológica Molecular (LOAM), IRD, INEN, Lima, Peru; Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - C Machicado
- Laboratorio de Investigación Traslacional y Biología Computacional, Facultad de Ciencias y Filosofía - LID, Universidad Peruana Cayetano Heredia, Lima, Peru; Instituto de Biocomputación y Sistemas Complejos (BIFI), Universidad de Zaragoza, Zaragoza, Spain
| | - J J Fournié
- Laboratorio Mixto Internacional de Oncología Antropológica Molecular (LOAM), IRD, INEN, Lima, Peru; Université de Toulouse, UMR 1037 CRCT, INSERM, CNRS, UPS, Toulouse, France; Laboratorio de Excelencia Toulouse-Cáncer (TOUCAN), Toulouse, France
| | - P Pineau
- Laboratorio Mixto Internacional de Oncología Antropológica Molecular (LOAM), IRD, INEN, Lima, Peru; Institut Pasteur, U 993, INSERM, Paris, France
| | - S Bertani
- Laboratorio Mixto Internacional de Oncología Antropológica Molecular (LOAM), IRD, INEN, Lima, Peru; Université de Toulouse, UMR 152 PHARMADEV, IRD, UPS, Toulouse, France.
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13
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Mezzacappa C, Wang Z, Lu L, Risch H, Taddei T, Yu H. Detection of hepatocellular carcinoma methylation markers in salivary DNA. Biosci Rep 2024; 44:BSR20232063. [PMID: 38457142 PMCID: PMC10958141 DOI: 10.1042/bsr20232063] [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: 12/06/2023] [Revised: 02/21/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Alterations to DNA methylation have been identified in both hepatocellular carcinoma (HCC) tumor and circulating DNA from affected individuals. These markers have potential utility in HCC screening. Adherence to HCC screening is poor and acceptable HCC screening tests are needed. METHODS A feasibility study was performed on a subset of case patients and control subjects from a prior study of risk factors for HCC. Case patients (n=12) included adults aged 47-85 years with a first diagnosis of HCC between 2011 and 2016 and without viral hepatitis. Control subjects (n=12) were matched on age, sex, and state of residence. Participants provided saliva samples for DNA genotyping. Log fold change in salivary DNA methylation at 1359 CpG sites representing 25 candidate genes previously associated with HCC was compared across case patients and control subjects. RESULTS The quantity of DNA ranged from 9.65 to 257.79 μg. The purity of DNA isolates was good, with mean OD260/280 ratio of 1.78 (SD: 0.14). Of 25 candidate genes, 16 had at ≥1 CpG site with detectable differences in methylation across HCC case patients and control subjects. Sites differentially methylated in HCC case patients included genes encoding tumor suppressors (PRDM2, RUNX3, p15/16, and RASSF1/5), regulators of cell cycle progression (DAPK1 and TP73), and DNA repair (MGMT and GSTP1). No associations met the significance threshold 3.7 × 10-5 required for multiple comparisons. CONCLUSIONS Salivary DNA may be a feasible alternative to blood samples in the era of novel DNA-based screening tests for HCC. The ease of saliva-based testing supports further investigation of its potential.
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Affiliation(s)
- Catherine Mezzacappa
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
| | - Zhanwei Wang
- University of Hawai’i Cancer Consortium, Honolulu, HI, United States
| | - Lingeng Lu
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States
| | - Harvey Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States
| | - Tamar Taddei
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT, United States
- VA Connecticut Healthcare System, West Haven, CT, United States
| | - Herbert Yu
- University of Hawai’i Cancer Consortium, Honolulu, HI, United States
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States
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14
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Huo W, Hu H, Li T, Yuan L, Zhang J, Feng Y, Wu Y, Fu X, Ke Y, Wang M, Zhang W, Wang L, Chen Y, Gao Y, Li X, Liu J, Huang Z, Hu F, Zhang M, Sun L, Hu D, Zhao Y. Association of methylation risk score with incident type 2 diabetes mellitus: A nested case-control study. J Diabetes 2024; 16:e13512. [PMID: 38062913 PMCID: PMC10940902 DOI: 10.1111/1753-0407.13512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 03/16/2024] Open
Abstract
AIMS To investigate the association of methylation risk score (MRS) and its interactions with environmental factors with type 2 diabetes mellitus (T2DM) risk. METHODS We conducted a nested case-control study with 241 onset cases and 241 matched controls. Conditional logistic regression models were employed to identify risk CpG sites. Simple and weighted MRSs were constructed based on the methylation levels of ATP-binding cassette G1 gene, fat mass and obesity associated gene, potassium voltage-gated channel member 1 gene, and thioredoxin-interacting protein gene previously associated with T2DM to estimate the association of MRS with T2DM risk. Stratified analyses were used to investigate interactions between MRS and environmental factors. RESULTS A total of 10 CpG loci were identified from the aforementioned genes to calculate MRS. After controlling for potential confounding factors, taking tertile 1 as reference, the odds ratios (ORs) and 95% confidence intervals (CIs) for T2DM of tertile 3 was 2.39 (1.36-4.20) for simple MRS and 2.59 (1.45-4.63) for weighted MRS. With per SD score increment in MRS, the OR (95% CI) was 1.66 (1.29-2.14) and 1.60 (1.24-2.08) for simple and weighted MRSs, respectively. J-curved associations were observed between both simple and weighted MRSs and T2DM risks. Additionally, multiplication interactions for smoking and hypertension with simple MRS on the risk of T2DM were found, similarly for smoking and obesity with weighted MRS on the risk of T2DM (all Pinteraction < .05). CONCLUSION Elevated simple and weighted MRSs were associated with increased risk of T2DM. Environmental risk factors may influence the association between MRS and T2DM.
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Affiliation(s)
- Weifeng Huo
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Huifang Hu
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Tianze Li
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Lijun Yuan
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Jinli Zhang
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yifei Feng
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yuying Wu
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Xueru Fu
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yamin Ke
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Mengmeng Wang
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Wenkai Zhang
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Longkang Wang
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yaobing Chen
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yajuan Gao
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Xi Li
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Jiong Liu
- Department of Preventive MedicineSchool of Public Health, Shenzhen University Medical SchoolShenzhenChina
| | - Zelin Huang
- Department of Preventive MedicineSchool of Public Health, Shenzhen University Medical SchoolShenzhenChina
| | - Fulan Hu
- Department of Biostatistics and EpidemiologySchool of Public Health, Shenzhen University Medical SchoolShenzhenChina
| | - Ming Zhang
- Department of Biostatistics and EpidemiologySchool of Public Health, Shenzhen University Medical SchoolShenzhenChina
| | - Liang Sun
- Department of Social Medicine and Health Service ManagementCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Dongsheng Hu
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
| | - Yang Zhao
- Department of Epidemiology and BiostatisticsCollege of Public Health, Zhengzhou UniversityZhengzhouChina
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15
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Jung KH, Lee S, Kim HS, Kim JM, Lee YJ, Park MS, Seo MS, Lee M, Yun M, Park S, Hong SS. Acetyl-CoA synthetase 2 contributes to a better prognosis for liver cancer by switching acetate-glucose metabolism. Exp Mol Med 2024; 56:721-733. [PMID: 38528124 PMCID: PMC10984961 DOI: 10.1038/s12276-024-01185-3] [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: 06/14/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 03/27/2024] Open
Abstract
Acetyl-CoA synthetase 2 (ACSS2)-dependent acetate usage has generally been associated with tumorigenesis and increased malignancy in cancers under nutrient-depleted conditions. However, the nutrient usage and metabolic characteristics of the liver differ from those of other organs; therefore, the mechanism of ACSS2-mediated acetate metabolism may also differ in liver cancer. To elucidate the underlying mechanisms of ACSS2 in liver cancer and acetate metabolism, the relationships between patient acetate uptake and metabolic characteristics and between ACSS2 and tumor malignancies were comprehensively studied in vitro, in vivo and in humans. Clinically, we initially found that ACSS2 expression was decreased in liver cancer patients. Moreover, PET-CT imaging confirmed that lower-grade cancer cells take up more 11C-acetate but less 18F-fluorodeoxyglucose (18F-FDG); however, this trend was reversed in higher-grade cancer. Among liver cancer cells, those with high ACSS2 expression avidly absorbed acetate even in a glucose-sufficient environment, whereas those with low ACSS2 expression did not, thereby showing correlations with their respective ACSS2 expression. Metabolomic isotope tracing in vitro and in vivo revealed greater acetate incorporation, greater lipid anabolic metabolism, and less malignancy in high-ACSS2 tumors. Notably, ACSS2 downregulation in liver cancer cells was associated with increased tumor occurrence in vivo. In human patient cohorts, patients in the low-ACSS2 subgroup exhibited reduced anabolism, increased glycolysis/hypoxia, and poorer prognosis. We demonstrated that acetate uptake by ACSS2 in liver cancer is independent of glucose depletion and contributes to lipid anabolic metabolism and reduced malignancy, thereby leading to a better prognosis for liver cancer patients.
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Affiliation(s)
- Kyung Hee Jung
- Department of Biomedical Sciences, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon, 22332, Korea.
| | - Sujin Lee
- Department of Manufacturing Pharmacy, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Korea
| | - Han Sun Kim
- Department of Manufacturing Pharmacy, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Korea
| | - Jin-Mo Kim
- Department of Manufacturing Pharmacy, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Korea
| | - Yun Ji Lee
- Department of Biomedical Sciences, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon, 22332, Korea
| | - Min Seok Park
- Department of Biomedical Sciences, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon, 22332, Korea
| | - Myeong-Seong Seo
- Department of Biomedical Sciences, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon, 22332, Korea
| | - Misu Lee
- Division of Life Science, College of Life Science and Bioengineering, Incheon National University, Incheon, 21999, Korea
| | - Mijin Yun
- Department of Nuclear Medicine, Severance Hospital, Yonsei University College of Medicine, 134 Shinchon-dong, Seodaemun-gu, Seoul, 03722, Korea.
| | - Sunghyouk Park
- Department of Manufacturing Pharmacy, Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Korea.
| | - Soon-Sun Hong
- Department of Biomedical Sciences, College of Medicine, and Program in Biomedical Science & Engineering, Inha University, 3-ga, Sinheung-dong, Jung-gu, Incheon, 22332, Korea.
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16
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Giraud J, Chalopin D, Ramel E, Boyer T, Zouine A, Derieppe MA, Larmonier N, Adotevi O, Le Bail B, Blanc JF, Laurent C, Chiche L, Derive M, Nikolski M, Saleh M. THBS1 + myeloid cells expand in SLD hepatocellular carcinoma and contribute to immunosuppression and unfavorable prognosis through TREM1. Cell Rep 2024; 43:113773. [PMID: 38350444 DOI: 10.1016/j.celrep.2024.113773] [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: 04/19/2023] [Revised: 11/05/2023] [Accepted: 01/25/2024] [Indexed: 02/15/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is an inflammation-associated cancer arising from viral or non-viral etiologies including steatotic liver diseases (SLDs). Expansion of immunosuppressive myeloid cells is a hallmark of inflammation and cancer, but their heterogeneity in HCC is not fully resolved and might underlie immunotherapy resistance. Here, we present a high-resolution atlas of innate immune cells from patients with HCC that unravels an SLD-associated contexture characterized by influx of inflammatory and immunosuppressive myeloid cells, including a discrete population of THBS1+ regulatory myeloid (Mreg) cells expressing monocyte- and neutrophil-affiliated genes. THBS1+ Mreg cells expand in SLD-associated HCC, populate fibrotic lesions, and are associated with poor prognosis. THBS1+ Mreg cells are CD163+ but distinguished from macrophages by high expression of triggering receptor expressed on myeloid cells 1 (TREM1), which contributes to their immunosuppressive activity and promotes HCC tumor growth in vivo. Our data support myeloid subset-targeted immunotherapies to treat HCC.
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Affiliation(s)
- Julie Giraud
- University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 33000 Bordeaux, France
| | - Domitille Chalopin
- University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 33000 Bordeaux, France; University of Bordeaux, CNRS, IBGC, UMR 5095, 33000 Bordeaux, France
| | - Eloïse Ramel
- University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 33000 Bordeaux, France
| | - Thomas Boyer
- University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 33000 Bordeaux, France
| | - Atika Zouine
- Bordeaux University, CNRS UMS3427, INSERM US05, Flow Cytometry Facility, TransBioMed Core, 33000 Bordeaux, France
| | | | - Nicolas Larmonier
- University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 33000 Bordeaux, France
| | - Olivier Adotevi
- Université Bourgogne Franche-Comté, INSERM, UMR1098, 25000 Besançon, France
| | - Brigitte Le Bail
- Bordeaux University Hospital, Division of Pathology, Pellegrin Hospital, 33000 Bordeaux, France
| | - Jean-Frédéric Blanc
- University of Bordeaux Hospital, Division of Gastrohepatology and Oncology, Haut Leveque Hospital, 33604 Pessac, France
| | - Christophe Laurent
- University of Bordeaux Hospital, Division of Gastrohepatology and Oncology, Haut Leveque Hospital, 33604 Pessac, France
| | - Laurence Chiche
- University of Bordeaux Hospital, Division of Gastrohepatology and Oncology, Haut Leveque Hospital, 33604 Pessac, France
| | | | - Macha Nikolski
- University of Bordeaux, CNRS, IBGC, UMR 5095, 33000 Bordeaux, France
| | - Maya Saleh
- University of Bordeaux, CNRS, ImmunoConcEpT, UMR 5164, 33000 Bordeaux, France; Institut National de la Recherche Scientifique (INRS), Armand Frappier Health & Biotechnology (AFSB) Research Center, Laval, QC H7V 1B7, Canada.
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17
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Sun M, Xu B, Chen C, Zhu Y, Li X, Chen K. Tissue of origin prediction for cancer of unknown primary using a targeted methylation sequencing panel. Clin Epigenetics 2024; 16:25. [PMID: 38336771 PMCID: PMC10854167 DOI: 10.1186/s13148-024-01638-6] [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: 11/20/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
RATIONALE Cancer of unknown primary (CUP) is a group of rare malignancies with poor prognosis and unidentifiable tissue-of-origin. Distinct DNA methylation patterns in different tissues and cancer types enable the identification of the tissue of origin in CUP patients, which could help risk assessment and guide site-directed therapy. METHODS Using genome-wide DNA methylation profile datasets from The Cancer Genome Atlas (TCGA) and machine learning methods, we developed a 200-CpG methylation feature classifier for CUP tissue of origin prediction (MFCUP). MFCUP was further validated with public-available methylation array data of 2977 specimens and targeted methylation sequencing of 78 Formalin-fixed paraffin-embedded (FFPE) samples from a single center. RESULTS MFCUP achieved an accuracy of 97.2% in a validation cohort (n = 5923) representing 25 cancer types. When applied to an Infinium 450 K array dataset (n = 1052) and an Infinium EPIC (850 K) array dataset (n = 1925), MFCUP achieved an overall accuracy of 93.4% and 84.8%, respectively. Based on MFCUP, we established a targeted bisulfite sequencing panel and validated it with FFPE sections from 78 patients of 20 cancer types. This methylation sequencing panel correctly identified tissue of origin in 88.5% (69/78) of samples. We also found that the methylation levels of specific CpGs can distinguish one cancer type from others, indicating their potential as biomarkers for cancer diagnosis and screening. CONCLUSION Our methylation-based cancer classifier and targeted methylation sequencing panel can predict tissue of origin in diverse cancer types with high accuracy.
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Affiliation(s)
- Miaomiao Sun
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Bo Xu
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Chao Chen
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Youjie Zhu
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China
| | - Xiaomo Li
- Research and Development Division, Oriomics Biotech Inc, Hangzhou, China.
| | - Kuisheng Chen
- Department of Pathology, Henan Key Laboratory of Tumor Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China.
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18
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Kurokawa S, Kobori T, Yoneda M, Ogawa Y, Honda Y, Kessoku T, Imajo K, Saito S, Nakajima A, Hotta K. Identification of differentially methylated regions associated with both liver fibrosis and hepatocellular carcinoma. BMC Gastroenterol 2024; 24:57. [PMID: 38302914 PMCID: PMC10832174 DOI: 10.1186/s12876-024-03149-3] [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: 12/02/2022] [Accepted: 01/25/2024] [Indexed: 02/03/2024] Open
Abstract
BACKGROUND Liver fibrosis is a major risk factor for hepatocellular carcinoma (HCC). We have previously reported that differentially methylated regions (DMRs) are correlated with the fibrosis stages of metabolic dysfunction-associated steatotic liver disease (MASLD). In this study, the methylation levels of those DMRs in liver fibrosis and subsequent HCC were examined. METHODS The methylation levels of DMRs were investigated using alcoholic cirrhosis and HCC (GSE60753). The data of hepatitis C virus-infected cirrhosis and HCC (GSE60753), and two datasets (GSE56588 and GSE89852) were used for replication analyses. The transcriptional analyses were performed using GSE114564, GSE94660, and GSE142530. RESULTS Hypomethylated DMR and increased transcriptional level of zinc finger and BTB domain containing 38 (ZBTB38) were observed in HCC. Hypermethylated DMRs, and increased transcriptional levels of forkhead box K1 (FOXK1) and zinc finger CCCH-type containing 3 (ZC3H3) were observed in HCC. The methylation levels of DMR of kazrin, periplakin interacting protein (KAZN) and its expression levels were gradually decreased as cirrhosis progressed to HCC. CONCLUSIONS Changes in the methylation and transcriptional levels of ZBTB38, ZC3H3, FOXK1, and KAZN are important for the development of fibrosis and HCC; and are therefore potential therapeutic targets and diagnostic tools for cirrhosis and HCC.
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Affiliation(s)
- Suguru Kurokawa
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Takuro Kobori
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan
| | - Masato Yoneda
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Yuji Ogawa
- Department of Gastroenterology, National Hospital Organization Yokohama Medical Center, 3-60-2 Harajyuku, Totsuka, Yokohama, 245-8675, Japan
| | - Yasushi Honda
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Takaomi Kessoku
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
- Department of Palliative Medicine, International University of Health and Welfare Narita Hospital, 852, Hatakeda, Narita, 286-8520, Japan
| | - Kento Imajo
- Department of Gastroenterology, Shin-yurigaoka General Hospital, 255 Furusawatsuko, Asao, Kawasaki, 2150-0026, Japan
| | - Satoru Saito
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Atsushi Nakajima
- Department of Gastroenterology and Hepatology, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan
| | - Kikuko Hotta
- Laboratoy of Pathophysiology and Pharmacotherapeutics, Faculty of Pharmacy, Osaka Ohtani University, 3-11-1 Nishikiori-kita, Tondabayashi, Osaka, 584-8540, Japan.
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19
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Bardol T, Pageaux GP, Assenat E, Alix-Panabières C. Circulating Tumor DNA Clinical Applications in Hepatocellular Carcinoma: Current Trends and Future Perspectives. Clin Chem 2024; 70:33-48. [PMID: 37962158 DOI: 10.1093/clinchem/hvad168] [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: 05/23/2023] [Accepted: 09/13/2023] [Indexed: 11/15/2023]
Abstract
BACKGROUND Globally, liver cancers are the second most lethal malignancy after lung cancer (0.83 million deaths in 2020). Hepatocellular carcinoma (HCC) is the predominant type of primary liver cancer and is typically associated with liver fibrosis or cirrhosis. HCC diagnosis relies on histologic examination of surgical specimens or conventional tissue biopsy material. However, standard tissue biopsies are invasive and often do not accurately reflect the tumor heterogeneity. On the other hand, the use of liquid biopsies, represented mainly by circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs), has greatly increased in the past 2 decades. Indeed, liquid biopsies are a noninvasive, repeatable, and sensitive approach to studying tumor biology. CONTENT This review describes current clinical applications of ctDNA analysis in the management of patients with chronic liver disease, cirrhosis, and HCC. There is a substantial clinical potential of ctDNA, but interventional studies are still lacking for the moment. SUMMARY Detection of ctDNA in both asymptomatic individuals and high-risk patients (with chronic liver disease or cirrhosis) contributes to the early diagnosis of HCC. ctDNA analysis also offer tremendous information on the tumor burden and on the risk of early recurrence. The implementation of ctDNA analysis, in association with classical tumor markers (e.g., alpha-fetoprotein), may improve (a) HCC screening in high-risk patients, (b) stratification of the recurrence risk after surgery, and (c) prognosis evaluation of patients with HCC.
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Affiliation(s)
- Thomas Bardol
- Laboratory of Rare Human Circulating Cells, University Hospital Center, University of Montpellier, Montpellier, France
- CREEC, MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
- Department of Digestive Surgery and Transplantation, Digestive and Mini-invasive Surgery Unit, Montpellier University Hospital, Montpellier University, Montpellier, France
| | - Georges-Philippe Pageaux
- Hepatology and Liver Transplant Unit, Saint Eloi University Hospital, Montpellier University, Montpellier, France
| | - Eric Assenat
- Department of Medical Oncology, Saint Eloi University Hospital Center, Montpellier University, Montpellier, France
| | - Catherine Alix-Panabières
- Laboratory of Rare Human Circulating Cells, University Hospital Center, University of Montpellier, Montpellier, France
- CREEC, MIVEGEC, University of Montpellier, CNRS, IRD, Montpellier, France
- European Liquid Biopsy Society (ELBS), Hamburg, Germany
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20
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Shah M, Sarkar D. HCC-Related lncRNAs: Roles and Mechanisms. Int J Mol Sci 2024; 25:597. [PMID: 38203767 PMCID: PMC10779127 DOI: 10.3390/ijms25010597] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatocellular carcinoma (HCC) presents a significant global health threat, particularly in regions endemic to hepatitis B and C viruses, and because of the ongoing pandemic of obesity causing metabolic-dysfunction-related fatty liver disease (MAFLD), a precursor to HCC. The molecular intricacies of HCC, genetic and epigenetic alterations, and dysregulated signaling pathways facilitate personalized treatment strategies based on molecular profiling. Epigenetic regulation, encompassing DNA methyltion, histone modifications, and noncoding RNAs, functions as a critical layer influencing HCC development. Long noncoding RNAs (lncRNAs) are spotlighted for their diverse roles in gene regulation and their potential as diagnostic and therapeutic tools in cancer. In this review, we explore the pivotal role of lncRNAs in HCC, including MAFLD and viral hepatitis, the most prevalent risk factors for hepatocarcinogenesis. The dysregulation of lncRNAs is implicated in HCC progression by modulating chromatin regulation and transcription, sponging miRNAs, and influencing structural functions. The ongoing studies on lncRNAs contribute to a deeper comprehension of HCC pathogenesis and offer promising routes for precision medicine, highlighting the utility of lncRNAs as early biomarkers, prognostic indicators, and therapeutic targets.
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Affiliation(s)
- Mimansha Shah
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Devanand Sarkar
- Department of Human and Molecular Genetics, Massey Comprehensive Cancer Center, and VCU Institute of Molecular Medicine (VIMM), Virginia Commonwealth University, Richmond, VA 23298, USA
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21
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Rayginia TP, Keerthana CK, Shifana SC, Pellissery MJ, Abhishek A, Anto RJ. Phytochemicals as Potential Lead Molecules against Hepatocellular Carcinoma. Curr Med Chem 2024; 31:5199-5221. [PMID: 38213177 DOI: 10.2174/0109298673275501231213063902] [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: 08/03/2023] [Revised: 10/31/2023] [Accepted: 11/16/2023] [Indexed: 01/13/2024]
Abstract
Hepatocellular carcinoma (HCC) is the most prevalent form of liver cancer, accounting for 85-90% of liver cancer cases and is a leading cause of cancer-related mortality worldwide. The major risk factors for HCC include hepatitis C and B viral infections, along with chronic liver diseases, such as cirrhosis, fibrosis, and non-alcoholic steatohepatitis associated with metabolic syndrome. Despite the advancements in modern medicine, there is a continuous rise in the annual global incidence rate of HCC, and it is estimated to reach >1 million cases by 2025. Emerging research in phytomedicine and chemotherapy has established the anti-cancer potential of phytochemicals, owing to their diverse biological activities. In this review, we report the major phytochemicals that have been explored in combating hepatocellular carcinoma and possess great potential to be used as an alternative or in conjunction with the existing HCC treatment modalities. An overview of the pre-clinical observations, mechanism of action and molecular targets of some of these phytochemicals is also incorporated.
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Affiliation(s)
- Tennyson Prakash Rayginia
- Division of Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
- Department of Biotechnology, University of Kerala, Thiruvananthapuram, Kerala, 695011, India
| | - Chenicheri Kizhakkeveettil Keerthana
- Division of Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
- Department of Biotechnology, University of Kerala, Thiruvananthapuram, Kerala, 695011, India
| | | | - Maria Joy Pellissery
- Division of Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Ajmani Abhishek
- Molecular Bioassay Laboratory, Institute of Advanced Virology, Thiruvananthapuram, Kerala, 695317, India
| | - Ruby John Anto
- Division of Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
- Molecular Bioassay Laboratory, Institute of Advanced Virology, Thiruvananthapuram, Kerala, 695317, India
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22
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Wen DS, Huang LC, Bu XY, He MK, Lai ZC, Du ZF, Huang YX, Kan A, Shi M. DNA methylation-activated full-length EMX1 facilitates metastasis through EMX1-EGFR-ERK axis in hepatocellular carcinoma. Cell Death Dis 2023; 14:769. [PMID: 38007497 PMCID: PMC10676392 DOI: 10.1038/s41419-023-06293-y] [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: 05/12/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 11/27/2023]
Abstract
Altered DNA methylation is a crucial epigenetic event in hepatocellular carcinoma (HCC) development and progression. Through methylation-transcriptomic analysis, we identified a set of sixty potential DNA methylation-based epidriver genes. In this set of genes, we focused on the hypermethylation of EMX1, which is frequently observed in hepatobiliary tumors. Despite of its frequent occurrence, the function of EMX1 remains largely unknown. By utilizing bisulfite-next-generation sequencing, we have detected EMX1 DNA hypermethylation on the gene body, which is positively correlated with EMX1 mRNA expression. Further analysis revealed that EMX1 mRNA terminal exon splicing in HCC generated two protein isoforms: EMX1 full length (EMX1-FL) and alternative terminal exon splicing isoform (EMX1-X1). Cellular functional assays demonstrated that gain-of-function EMX1-FL, but not EMX1-X1, induced HCC cells migration and invasion while silencing EMX1-FL inhibited HCC cells motility. This result was further validated by in vivo tumor metastasis models. Mechanistically, EMX1-FL bound to EGFR promoter, promoting EGFR transcription and activating EGFR-ERK signaling to trigger tumor metastasis. Therefore, EGFR may be a potential therapeutic target for EMX1-high expression HCC. Our work illuminated the crucial role of gene body hypermethylation-activated EMX1-FL in promoting tumorigenesis and metastasis in HCC. These findings pave the way for targeting the EMX1-EGFR axis in HCC tumorigenicity and metastasis.
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Affiliation(s)
- Dong-Sheng Wen
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Li-Chang Huang
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Xiao-Yun Bu
- Department of Colorectal Surgery, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, P. R. China
| | - Min-Ke He
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Zhi-Cheng Lai
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Ze-Feng Du
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Ye-Xing Huang
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China
| | - Anna Kan
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China.
| | - Ming Shi
- Department of Hepatobiliary Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, P. R. China.
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23
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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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24
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Singh P, Gupta P, De A, Duseja A. Molecular Characterization of Hepatocellular Carcinoma in Nonalcoholic Steatohepatitis: Implications for Immunotherapy. J Clin Exp Hepatol 2023; 13:1140-1143. [PMID: 37975053 PMCID: PMC10643478 DOI: 10.1016/j.jceh.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 02/24/2023] [Accepted: 03/01/2023] [Indexed: 11/19/2023] Open
Affiliation(s)
- Priya Singh
- Departments of Hepatology, Post-graduate Institute of Medical Education and Research, Chandigarh, India
| | - Parul Gupta
- Departments of Pathology, Post-graduate Institute of Medical Education and Research, Chandigarh, India
| | - Arka De
- Departments of Hepatology, Post-graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ajay Duseja
- Departments of Hepatology, Post-graduate Institute of Medical Education and Research, Chandigarh, India
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25
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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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26
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Jeepalyam S, Sheel A, Ejaz A, Miller E, Manne A. Is Cell-Free DNA Testing in Hepatocellular Carcinoma Ready for Prime Time? Int J Mol Sci 2023; 24:14231. [PMID: 37762533 PMCID: PMC10531802 DOI: 10.3390/ijms241814231] [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: 08/28/2023] [Revised: 09/14/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
Revamping the current biomarker landscape of hepatocellular carcinoma (HCC) with cell-free DNA (cfDNA) could improve overall outcomes. The use of commercially available cfDNA testing (also known as liquid biopsy) is limited by the low prevalence of targetable mutations and does not have any prognostic or predictive value. Thus, current cfDNA testing cannot be relied upon for perioperative risk stratification (POR), including early detection of recurrence, long-term surveillance, predicting outcomes, and treatment response. Prior evidence on cfDNA mutation profiling (non-specific detection or gene panel testing) suggests that it can be a reliable tool for POR and prognostication, but it still requires significant improvements. cfDNA methylation changes or epigenetic markers have not been explored extensively, but early studies have shown potential for it to be a prognostic biomarker tool. The predictive value of cfDNA (mutations and EM) to assist treatment selection (systemic therapy, immune-checkpoint inhibitor vs. tyrosine kinase inhibitor) and to monitor response to systemic and locoregional therapies should be a future area of focus. We highlighted the unmet needs in the HCC management and the current role of cfDNA testing in HCC in addressing them.
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Affiliation(s)
- Sravan Jeepalyam
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS 66103, USA
| | - Ankur Sheel
- Department of Internal Medicine, The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Aslam Ejaz
- Division of Surgical Oncology, Department of Surgery, The Ohio State University Wexner Medical Center, 320 W. 10th Ave., M-260 Starling-Loving Hall, Columbus, OH 43210, USA
| | - Eric Miller
- Department of Radiation Oncology, The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Ashish Manne
- Department of Internal Medicine, Division of Medical Oncology, The Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
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27
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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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28
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Chicherova I, Hernandez C, Mann F, Zoulim F, Parent R. Axon guidance molecules in liver pathology: Journeys on a damaged passport. Liver Int 2023; 43:1850-1864. [PMID: 37402699 DOI: 10.1111/liv.15662] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/09/2023] [Accepted: 06/18/2023] [Indexed: 07/06/2023]
Abstract
BACKGROUND AND AIMS The liver is an innervated organ that develops a variety of chronic liver disease (CLD). Axon guidance cues (AGCs), of which ephrins, netrins, semaphorins and slits are the main representative, are secreted or membrane-bound proteins that can attract or repel axons through interactions with their growth cones that contain receptors recognizing these messengers. While fundamentally implicated in the physiological development of the nervous system, the expression of AGCs can also be reinduced under acute or chronic conditions, such as CLD, that necessitate redeployment of neural networks. METHODS This review considers the ad hoc literature through the neglected canonical neural function of these proteins that is also applicable to the diseased liver (and not solely their observed parenchymal impact). RESULTS AGCs impact fibrosis regulation, immune functions, viral/host interactions, angiogenesis, and cell growth, both at the CLD and HCC levels. Special attention has been paid to distinguishing correlative and causal data in such datasets in order to streamline data interpretation. While hepatic mechanistic insights are to date limited, bioinformatic evidence for the identification of AGCs mRNAs positive cells, protein expression, quantitative regulation, and prognostic data have been provided. Liver-pertinent clinical studies based on the US Clinical Trials database are listed. Future research directions derived from AGC targeting are proposed. CONCLUSION This review highlights frequent implication of AGCs in CLD, linking traits of liver disorders and the local autonomic nervous system. Such data should contribute to diversifying current parameters of patient stratification and our understanding of CLD.
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Affiliation(s)
- Ievgeniia Chicherova
- Cancer Research Centre of Lyon, Inserm Unit 1052, CNRS UMR 5286, University of Lyon, Léon Bérard Anticancer Centre, Lyon, France
| | - Charlotte Hernandez
- Cancer Research Centre of Lyon, Inserm Unit 1052, CNRS UMR 5286, University of Lyon, Léon Bérard Anticancer Centre, Lyon, France
| | - Fanny Mann
- Aix-Marseille University, CNRS, IBDM, Marseille, France
| | - Fabien Zoulim
- Cancer Research Centre of Lyon, Inserm Unit 1052, CNRS UMR 5286, University of Lyon, Léon Bérard Anticancer Centre, Lyon, France
- Hepatogastroenterology Service, Croix-Rousse University Hospital, Hospices Civils de Lyon, Lyon, France
| | - Romain Parent
- Cancer Research Centre of Lyon, Inserm Unit 1052, CNRS UMR 5286, University of Lyon, Léon Bérard Anticancer Centre, Lyon, France
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29
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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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30
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Wang Y, Deng B. Hepatocellular carcinoma: molecular mechanism, targeted therapy, and biomarkers. Cancer Metastasis Rev 2023; 42:629-652. [PMID: 36729264 DOI: 10.1007/s10555-023-10084-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/16/2023] [Indexed: 02/03/2023]
Abstract
Hepatocellular carcinoma (HCC) is a common malignancy and one of the leading causes of cancer-related death. The biological process of HCC is complex, with multiple factors leading to the broken of the balance of inactivation and activation of tumor suppressor genes and oncogenes, the abnormal activation of molecular signaling pathways, the differentiation of HCC cells, and the regulation of angiogenesis. Due to the insidious onset of HCC, at the time of first diagnosis, less than 30% of HCC patients are candidates for radical treatment. Systematic antitumor therapy is the hope for the treatment of patients with middle-advanced HCC. Despite the emergence of new systemic therapies, survival rates for advanced HCC patients remain low. The complex pathogenesis of HCC has inspired researchers to explore a variety of biomolecular targeted therapeutics targeting specific targets. Correct understanding of the molecular mechanism of HCC occurrence is key to seeking effective targeted therapy. Research on biomarkers for HCC treatment is also advancing. Here, we explore the molecular mechanism that are associated with HCC development, summarize targeted therapies for HCC, and discuss potential biomarkers that may drive therapies.
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Affiliation(s)
- Yu Wang
- Department of Infectious Diseases, The First Hospital of China Medical University, 155 Nanjing North Street, Shenyang, 110001, Liaoning Province, China
| | - Baocheng Deng
- Department of Infectious Diseases, The First Hospital of China Medical University, 155 Nanjing North Street, Shenyang, 110001, Liaoning Province, China.
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31
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Yuan T, Edelmann D, Fan Z, Alwers E, Kather JN, Brenner H, Hoffmeister M. Machine learning in the identification of prognostic DNA methylation biomarkers among patients with cancer: A systematic review of epigenome-wide studies. Artif Intell Med 2023; 143:102589. [PMID: 37673571 DOI: 10.1016/j.artmed.2023.102589] [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: 07/21/2022] [Revised: 04/19/2023] [Accepted: 04/30/2023] [Indexed: 09/08/2023]
Abstract
BACKGROUND DNA methylation biomarkers have great potential in improving prognostic classification systems for patients with cancer. Machine learning (ML)-based analytic techniques might help overcome the challenges of analyzing high-dimensional data in relatively small sample sizes. This systematic review summarizes the current use of ML-based methods in epigenome-wide studies for the identification of DNA methylation signatures associated with cancer prognosis. METHODS We searched three electronic databases including PubMed, EMBASE, and Web of Science for articles published until 2 January 2023. ML-based methods and workflows used to identify DNA methylation signatures associated with cancer prognosis were extracted and summarized. Two authors independently assessed the methodological quality of included studies by a seven-item checklist adapted from 'A Tool to Assess Risk of Bias and Applicability of Prediction Model Studies (PROBAST)' and from the 'Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK). Different ML methods and workflows used in included studies were summarized and visualized by a sunburst chart, a bubble chart, and Sankey diagrams, respectively. RESULTS Eighty-three studies were included in this review. Three major types of ML-based workflows were identified. 1) unsupervised clustering, 2) supervised feature selection, and 3) deep learning-based feature transformation. For the three workflows, the most frequently used ML techniques were consensus clustering, least absolute shrinkage and selection operator (LASSO), and autoencoder, respectively. The systematic review revealed that the performance of these approaches has not been adequately evaluated yet and that methodological and reporting flaws were common in the identified studies using ML techniques. CONCLUSIONS There is great heterogeneity in ML-based methodological strategies used by epigenome-wide studies to identify DNA methylation markers associated with cancer prognosis. In theory, most existing workflows could not handle the high multi-collinearity and potentially non-linearity interactions in epigenome-wide DNA methylation data. Benchmarking studies are needed to compare the relative performance of various approaches for specific cancer types. Adherence to relevant methodological and reporting guidelines are urgently needed.
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Affiliation(s)
- Tanwei Yuan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Medical Faculty Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Dominic Edelmann
- Division of Biostatistics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ziwen Fan
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Elizabeth Alwers
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jakob Nikolas Kather
- Else Kroener Fresenius Center for Digital Health, Technical University Dresden, Dresden, Germany; Medical Oncology, National Center of Tumour Diseases (NCT), University Hospital Heidelberg, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany; Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany; German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Kadi D, Yamamoto MF, Lerner EC, Jiang H, Fowler KJ, Bashir MR. Imaging prognostication and tumor biology in hepatocellular carcinoma. JOURNAL OF LIVER CANCER 2023; 23:284-299. [PMID: 37710379 PMCID: PMC10565542 DOI: 10.17998/jlc.2023.08.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/26/2023] [Accepted: 08/29/2023] [Indexed: 09/16/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver malignancy, and represents a significant global health burden with rising incidence rates, despite a more thorough understanding of the etiology and biology of HCC, as well as advancements in diagnosis and treatment modalities. According to emerging evidence, imaging features related to tumor aggressiveness can offer relevant prognostic information, hence validation of imaging prognostic features may allow for better noninvasive outcomes prediction and inform the selection of tailored therapies, ultimately improving survival outcomes for patients with HCC.
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Affiliation(s)
- Diana Kadi
- Department of Radiology, Duke University Medical Center, Durham, NC, USA
| | - Marilyn F. Yamamoto
- Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Emily C. Lerner
- Department of Radiology, Duke University School of Medicine, Durham, NC, USA
| | - Hanyu Jiang
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, China
| | - Kathryn J. Fowler
- Department of Radiology, University of California San Diego, San Diego, CA, USA
| | - Mustafa R. Bashir
- Department of Radiology, Duke University, Durham, NC, USA
- Division of Hepatology, Department of Medicine, Duke University, Durham, NC, USA
- Center for Advanced Magnetic Resonance Development, Duke University, Durham, NC, USA
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Lominadze Z, Shaik MR, Choi D, Zaffar D, Mishra L, Shetty K. Hepatocellular Carcinoma Genetic Classification. Cancer J 2023; 29:249-258. [PMID: 37796642 PMCID: PMC10686192 DOI: 10.1097/ppo.0000000000000682] [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] [Indexed: 10/07/2023]
Abstract
ABSTRACT Hepatocellular carcinoma (HCC) represents a significant global burden, with management complicated by its heterogeneity, varying presentation, and relative resistance to therapy. Recent advances in the understanding of the genetic, molecular, and immunological underpinnings of HCC have allowed a detailed classification of these tumors, with resultant implications for diagnosis, prognostication, and selection of appropriate treatments. Through the correlation of genomic features with histopathology and clinical outcomes, we are moving toward a comprehensive and unifying framework to guide our diagnostic and therapeutic approach to HCC.
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Affiliation(s)
- Zurabi Lominadze
- Division of Gastroenterology and Hepatology, University of Maryland School of Medicine
| | | | - Dabin Choi
- Department of Medicine, University of Maryland Medical Center
| | - Duha Zaffar
- Department of Medicine, University of Maryland Midtown Medical Center
| | - Lopa Mishra
- Feinstein Institutes for Medical Research and Cold Spring Harbor Laboratory; Divisions of Gastroenterology and Hepatology, Northwell Health
| | - Kirti Shetty
- Division of Gastroenterology and Hepatology, University of Maryland School of Medicine
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34
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Liao Y, Wu C, Li Y, Wen J, Zhao D. MIF is a critical regulator of mononuclear phagocytic infiltration in hepatocellular carcinoma. iScience 2023; 26:107273. [PMID: 37520719 PMCID: PMC10371853 DOI: 10.1016/j.isci.2023.107273] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/03/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023] Open
Abstract
Immunotherapy targeting tumor-associated macrophages (TAMs) is a promising approach to treating cancer. However, the limited drug targets and ambiguous mechanisms impede the development of clinical immunotherapy strategies. To elucidate the underlying processes involved in mononuclear phagocyte (MNP) infiltration and phenotypic changes in hepatocellular carcinoma (HCC), we integrated single-cell RNA-sequencing data from 100,030 cells derived from patients with HCC and healthy individuals and compared the phenotypes and origins of the MNPs in the tumor core, tumor periphery, adjacent normal tissue, and healthy liver samples. Using machine learning and multi-omics analyses, we identified 445 infiltration-associated genes and potential drug targets affecting this process. Through in vitro experiments, we found that the expression of macrophage migration inhibitory factor (MIF) is the upstream regulator of secreted phosphoprotein 1 (SPP1) and promote migration in TAMs. Our findings also indicate that MIF promotes tumor metastasis and invasion and is a promising potential target for treating HCC.
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Affiliation(s)
- Yunxi Liao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Chenyang Wu
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
| | - Yang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Jinhua Wen
- Department of Cell Biology, School of Basic Medical Sciences, Peking University, Beijing 100191, China
| | - Dongyu Zhao
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University, Beijing 100191, China
- State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing 100191, China
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35
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Liu Y, Zhang H, Xu Y, Liu YZ, Al-Adra DP, Yeh MM, Zhang Z. Five Critical Gene-Based Biomarkers With Optimal Performance for Hepatocellular Carcinoma. Cancer Inform 2023; 22:11769351231190477. [PMID: 37577174 PMCID: PMC10413891 DOI: 10.1177/11769351231190477] [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: 03/06/2023] [Accepted: 07/11/2023] [Indexed: 08/15/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the most fatal cancers in the world. There is an urgent need to understand the molecular background of HCC to facilitate the identification of biomarkers and discover effective therapeutic targets. Published transcriptomic studies have reported a large number of genes that are individually significant for HCC. However, reliable biomarkers remain to be determined. In this study, built on max-linear competing risk factor models, we developed a machine learning analytical framework to analyze transcriptomic data to identify the most miniature set of differentially expressed genes (DEGs). By analyzing 9 public whole-transcriptome datasets (containing 1184 HCC samples and 672 nontumor controls), we identified 5 critical differentially expressed genes (DEGs) (ie, CCDC107, CXCL12, GIGYF1, GMNN, and IFFO1) between HCC and control samples. The classifiers built on these 5 DEGs reached nearly perfect performance in identification of HCC. The performance of the 5 DEGs was further validated in a US Caucasian cohort that we collected (containing 17 HCC with paired nontumor tissue). The conceptual advance of our work lies in modeling gene-gene interactions and correcting batch effect in the analytic framework. The classifiers built on the 5 DEGs demonstrated clear signature patterns for HCC. The results are interpretable, robust, and reproducible across diverse cohorts/populations with various disease etiologies, indicating the 5 DEGs are intrinsic variables that can describe the overall features of HCC at the genomic level. The analytical framework applied in this study may pave a new way for improving transcriptome profiling analysis of human cancers.
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Affiliation(s)
- Yongjun Liu
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
| | - Heping Zhang
- Yale School of Public Health, Yale University, New Haven, CT, USA
| | - Yuqing Xu
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
| | - Yao-Zhong Liu
- Department of Biostatistics, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - David P Al-Adra
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Matthew M Yeh
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, WA, USA
- Department of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Zhengjun Zhang
- Department of Statistics, University of Wisconsin-Madison, Madison, WI, USA
- Biostatistics and Medical Informatics, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, USA
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36
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Yu X, Lei X. Application of the Multi-Omics Liquid Biopsy Method M2P-HCC in Early Liver Cancer Screening for High-Risk Individuals with Hepatitis B-Related Liver Cancer. Diagnostics (Basel) 2023; 13:2484. [PMID: 37568847 PMCID: PMC10417463 DOI: 10.3390/diagnostics13152484] [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: 06/21/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is one of the most common malignant tumors worldwide, with low rates of early diagnosis and surgical resection. In recent years, with the rapid development of liquid biopsy technology, circulating tumor DNA (ctDNA) has emerged as a research hotspot in the field of precision medicine for liver cancer. Existing studies have demonstrated the suitability of ctDNA for combined detection with other liver cancer diagnostic markers, enabling a multi-index analysis. In recent years, a novel prediction model has been developed for early liver cancer screening based on ctDNA liquid biopsy, M2P-HCC (methylation, mutation, and protein-HCC), mainly incorporating methylation changes, gene mutations, and protein markers associated with liver cancer. Preliminary validation in the HCCscreenTM Investigational (HIT, ChiCTR1800020233) study, which focused on screening early liver cancer in communities with Hepatitis B surface antigen (HBsAg) positivity, yielded promising results with 100% sensitivity and 94% specificity. However, it remains uncertain whether M2P-HCC can be effectively applied in high-risk populations for Hepatitis B-associated liver cancer, warranting further research. METHODS Patients who were under long-term follow-up at the outpatient clinic of the Infectious Diseases Center of West China Hospital of Sichuan University from December 2020 to January 2023 were recruited in this prospective observational study and underwent the M2P-HCC test. The study population consisted of high-risk patients with Hepatitis B-related liver cancer who met the inclusion criteria. Patients with a history of previous malignancy, recent blood transfusion, autoimmune diseases, and human immunodeficiency virus (HIV) infection were excluded. Clinical data were collected at a baseline, and all patients underwent the M2P-HCC blood test. Based on the test results, they were categorized into positive, early-warning, and negative groups. Prospective cohort observation and regular follow-ups were performed for 6-8 months. RESULTS 313 patients met the inclusion criteria and were included in the study. After 6-8 months of follow-up, HCC occurred in 41(13.1%) participants. The M2P-HCC test demonstrated good predictive performance with an area under the curve (AUC) of 0.88 (95% CI: 0.81-0.95, p < 0.001) and a cutoff value of 83 points (sensitivity 82.9% and specificity 85.7%). In contrast, the combination of alpha-fetoprotein (AFP) and ultrasound (US) yielded an inferior predictive performance (AUC 0.76 (95% CI: 0.69-0.84, p < 0.001), sensitivity 58.5%, and specificity 94.1%). Multivariate analyses revealed that M2P-HCC was an independent predictor of increased risk of HCC (OR = 1.16 [1.09-1.22], p < 0.001). CONCLUSIONS M2P-HCC liquid biopsy demonstrated good performance for early liver cancer screening in high-risk populations of Hepatitis B-related liver cancer, exhibiting better sensitivity than the combination of AFP and US.
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Affiliation(s)
| | - Xuezhong Lei
- Center of Infectious Diseases, West China Hospital of Sichuan University, Chengdu 610041, China;
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37
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Vucur M, Ghallab A, Schneider AT, Adili A, Cheng M, Castoldi M, Singer MT, Büttner V, Keysberg LS, Küsgens L, Kohlhepp M, Görg B, Gallage S, Barragan Avila JE, Unger K, Kordes C, Leblond AL, Albrecht W, Loosen SH, Lohr C, Jördens MS, Babler A, Hayat S, Schumacher D, Koenen MT, Govaere O, Boekschoten MV, Jörs S, Villacorta-Martin C, Mazzaferro V, Llovet JM, Weiskirchen R, Kather JN, Starlinger P, Trauner M, Luedde M, Heij LR, Neumann UP, Keitel V, Bode JG, Schneider RK, Tacke F, Levkau B, Lammers T, Fluegen G, Alexandrov T, Collins AL, Nelson G, Oakley F, Mann DA, Roderburg C, Longerich T, Weber A, Villanueva A, Samson AL, Murphy JM, Kramann R, Geisler F, Costa IG, Hengstler JG, Heikenwalder M, Luedde T. Sublethal necroptosis signaling promotes inflammation and liver cancer. Immunity 2023; 56:1578-1595.e8. [PMID: 37329888 DOI: 10.1016/j.immuni.2023.05.017] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 08/30/2022] [Accepted: 05/22/2023] [Indexed: 06/19/2023]
Abstract
It is currently not well known how necroptosis and necroptosis responses manifest in vivo. Here, we uncovered a molecular switch facilitating reprogramming between two alternative modes of necroptosis signaling in hepatocytes, fundamentally affecting immune responses and hepatocarcinogenesis. Concomitant necrosome and NF-κB activation in hepatocytes, which physiologically express low concentrations of receptor-interacting kinase 3 (RIPK3), did not lead to immediate cell death but forced them into a prolonged "sublethal" state with leaky membranes, functioning as secretory cells that released specific chemokines including CCL20 and MCP-1. This triggered hepatic cell proliferation as well as activation of procarcinogenic monocyte-derived macrophage cell clusters, contributing to hepatocarcinogenesis. In contrast, necrosome activation in hepatocytes with inactive NF-κB-signaling caused an accelerated execution of necroptosis, limiting alarmin release, and thereby preventing inflammation and hepatocarcinogenesis. Consistently, intratumoral NF-κB-necroptosis signatures were associated with poor prognosis in human hepatocarcinogenesis. Therefore, pharmacological reprogramming between these distinct forms of necroptosis may represent a promising strategy against hepatocellular carcinoma.
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Affiliation(s)
- Mihael Vucur
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany.
| | - Ahmed Ghallab
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Technical University Dortmund, Dortmund, Germany; Department of Forensic Medicine and Toxicology, Faculty of Veterinary Medicine, South Valley University, Qena, Egypt
| | - Anne T Schneider
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Arlind Adili
- Department of Chronic Inflammation and Cancer, German Cancer Research Institute (DKFZ), Heidelberg, Germany
| | - Mingbo Cheng
- Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Mirco Castoldi
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Michael T Singer
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Veronika Büttner
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Leonie S Keysberg
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Lena Küsgens
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Marlene Kohlhepp
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Boris Görg
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Suchira Gallage
- Department of Chronic Inflammation and Cancer, German Cancer Research Institute (DKFZ), Heidelberg, Germany; The M3 Research Institute, Eberhard Karls University, Tübingen, Germany
| | - Jose Efren Barragan Avila
- Department of Chronic Inflammation and Cancer, German Cancer Research Institute (DKFZ), Heidelberg, Germany
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Claus Kordes
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Anne-Laure Leblond
- Department for pathology and molecular pathology, Zürich University Hospital, Zürich, Switzerland
| | - Wiebke Albrecht
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Technical University Dortmund, Dortmund, Germany
| | - Sven H Loosen
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Carolin Lohr
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Markus S Jördens
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Anne Babler
- Institute of Experimental Medicine and Systems Biology and Department of Nephrology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Sikander Hayat
- Institute of Experimental Medicine and Systems Biology and Department of Nephrology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - David Schumacher
- Institute of Experimental Medicine and Systems Biology and Department of Nephrology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Maria T Koenen
- Department of Medicine, Rhein-Maas-Klinikum, Würselen, Germany
| | - Olivier Govaere
- Department of Imaging and Pathology, KU Leuven and University Hospitals Leuven, Leuven, Belgium
| | - Mark V Boekschoten
- Nutrition, Metabolism and Genomics Group, Division of Human Nutrition and Health, Wageningen University, Wageningen, the Netherlands
| | - Simone Jörs
- Second Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, Germany
| | - Carlos Villacorta-Martin
- Division of Liver Diseases, Liver Cancer Program, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vincenzo Mazzaferro
- Gastrointestinal Surgery and Liver Transplantation Unit, National Cancer Institute, University of Milan, Milan, Italy
| | - Josep M Llovet
- Division of Liver Diseases, Liver Cancer Program, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Translational Research Laboratory, Barcelona-Clínic Liver Cancer Group, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Liver Unit, CIBEREHD, Hospital Clínic, Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), University Hospital RWTH Aachen, Aachen, Germany
| | - Jakob N Kather
- Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, Technical University Dresden, Dresden, Germany
| | - Patrick Starlinger
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, Mayo Clinic, Rochester, MN, USA
| | - Michael Trauner
- Division of Gastroenterology and Hepatology, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Mark Luedde
- Department of Cardiology and Angiology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Lara R Heij
- Visceral and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Ulf P Neumann
- Visceral and Transplant Surgery, University Hospital RWTH Aachen, Aachen, Germany
| | - Verena Keitel
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany; Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Magdeburg, Medical Faculty of Otto Von Guericke University Magdeburg, Magdeburg, Germany
| | - Johannes G Bode
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Rebekka K Schneider
- Department of Cell Biology, Institute for Biomedical Engineering, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Charité-Universitätsmedizin Berlin, Campus Virchow Klinikum and Campus Charité Mitte, Berlin, Germany
| | - Bodo Levkau
- Institute of Molecular Medicine III, University Hospital Dusseldorf, Heinrich Heine University, Dusseldorf, Germany
| | - Twan Lammers
- Department of Nanomedicine and Theranostics, Institute for Experimental Molecular Imaging, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Georg Fluegen
- Department of Surgery (A), University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University, Dusseldorf, Germany
| | - Theodore Alexandrov
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Amy L Collins
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Glyn Nelson
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Derek A Mann
- Newcastle Fibrosis Research Group, Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Christoph Roderburg
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany
| | - Thomas Longerich
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Achim Weber
- Department for pathology and molecular pathology, Zürich University Hospital, Zürich, Switzerland
| | - Augusto Villanueva
- Division of Liver Diseases, Liver Cancer Program, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andre L Samson
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - James M Murphy
- The Walter and Eliza Hall Institute, Parkville, VIC, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology and Department of Nephrology, RWTH Aachen University, Medical Faculty, Aachen, Germany
| | - Fabian Geisler
- Second Department of Internal Medicine, Klinikum Rechts der Isar, Technische Universität München, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany
| | - Jan G Hengstler
- Leibniz Research Centre for Working Environment and Human Factors (IfADo), Technical University Dortmund, Dortmund, Germany
| | - Mathias Heikenwalder
- Department of Chronic Inflammation and Cancer, German Cancer Research Institute (DKFZ), Heidelberg, Germany; The M3 Research Institute, Eberhard Karls University, Tübingen, Germany
| | - Tom Luedde
- Department of Gastroenterology, Hepatology and Infectious Diseases, University Hospital Dusseldorf, Medical Faculty at Heinrich Heine University Dusseldorf, Dusseldorf, Germany.
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Papadakos SP, Stergiou IE, Gkolemi N, Arvanitakis K, Theocharis S. Unraveling the Significance of EPH/Ephrin Signaling in Liver Cancer: Insights into Tumor Progression and Therapeutic Implications. Cancers (Basel) 2023; 15:3434. [PMID: 37444544 DOI: 10.3390/cancers15133434] [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: 06/11/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
Liver cancer is a complex and challenging disease with limited treatment options and dismal prognosis. Understanding the underlying molecular mechanisms driving liver cancer progression and metastasis is crucial for developing effective therapeutic strategies. The EPH/ephrin system, which comprises a family of cell surface receptors and their corresponding ligands, has been implicated in the pathogenesis of HCC. This review paper aims to provide an overview of the current understanding of the role of the EPH/ephrin system in HCC. Specifically, we discuss the dysregulation of EPH/ephrin signaling in HCC and its impact on various cellular processes, including cell proliferation, migration, and invasion. Overall, the EPH/ephrin signaling system emerges as a compelling and multifaceted player in liver cancer biology. Elucidating its precise mechanisms and understanding its implications in disease progression and therapeutic responses may pave the way for novel targeted therapies and personalized treatment approaches for liver cancer patients. Further research is warranted to unravel the full potential of the EPH/ephrin system in liver cancer and its clinical translation.
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Affiliation(s)
- Stavros P Papadakos
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Ioanna E Stergiou
- Department of Pathophysiology, School of Medicine, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Nikolina Gkolemi
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
| | - Konstantinos Arvanitakis
- Division of Gastroenterology and Hepatology, First Department of Internal Medicine, AHEPA University Hospital, Aristotle University of Thessaloniki, St. Kiriakidi 1, 54636 Thessaloniki, Greece
- Basic and Translational Research Unit, Special Unit for Biomedical Research and Education, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Stamatios Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece
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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: 14] [Impact Index Per Article: 14.0] [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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Nepal C, Andersen JB. Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes. Nat Commun 2023; 14:2712. [PMID: 37169774 PMCID: PMC10175279 DOI: 10.1038/s41467-023-38272-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 04/24/2023] [Indexed: 05/13/2023] Open
Abstract
Transcriptional regulation is commonly governed by alternative promoters. However, the regulatory architecture in alternative and reference promoters, and how they differ, remains elusive. In 100 CAGE-seq libraries from hepatocellular carcinoma patients, here we annotate 4083 alternative promoters in 2926 multi-promoter genes, which are largely undetected in normal livers. These genes are enriched in oncogenic processes and predominantly show association with overall survival. Alternative promoters are narrow nucleosome depleted regions, CpG island depleted, and enriched for tissue-specific transcription factors. Globally tumors lose DNA methylation. We show hierarchical retention of intragenic DNA methylation with CG-poor regions rapidly losing methylation, while CG-rich regions retain it, a process mediated by differential SETD2, H3K36me3, DNMT3B, and TET1 binding. This mechanism is validated in SETD2 knockdown cells and SETD2-mutated patients. Selective DNA methylation loss in CG-poor regions makes the chromatin accessible for alternative transcription. We show alternative promoters can control tumor transcriptomes and their regulatory architecture.
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Affiliation(s)
- Chirag Nepal
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, DK-2200, Denmark.
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA.
| | - Jesper B Andersen
- Biotech Research and Innovation Centre (BRIC), Department of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, DK-2200, Denmark.
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Kmeid M, Park YN, Chung T, Pacheco RR, Arslan ME, Lee H. SEPT9 Expression in Hepatic Nodules: An Immunohistochemical Study of Hepatocellular Neoplasm and Metastasis. Appl Immunohistochem Mol Morphol 2023; 31:278-287. [PMID: 36867734 DOI: 10.1097/pai.0000000000001112] [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: 07/30/2022] [Accepted: 01/24/2023] [Indexed: 03/05/2023]
Abstract
The methylated SEPT9 DNA ( mSEPT9 ) in plasma is a US Food and Drug Administration (FDA)-approved screening biomarker in colorectal cancer and is emerging as a promising diagnostic and prognostic biomarker in hepatocellular carcinoma (HCC). We evaluated the SEPT9 protein expression by immunohistochemistry (IHC) in various hepatic tumors from 164 hepatectomies and explants. Cases diagnosed as HCC (n=68), hepatocellular adenoma (n=31), dysplastic nodule (n=24), and metastasis (n=41) were retrieved. SEPT9 stain was performed on representative tissue blocks showing tumor/liver interface. For HCC, archived IHC (SATB2, CK19, CDX2, CK20, and CDH17) slides were also reviewed. The findings were correlated with demographics, risk factors, tumor size, alpha fetoprotein levels at diagnosis, T stage and oncologic outcomes, with significance defined as P <0.05. Percentage of SEPT9 positivity differed significantly among hepatocellular adenoma (3%), dysplastic nodule (0%), HCC (32%), and metastasis (83%, P <0.001). Compared with patients with SEPT9- HCC, those with SEPT9+ HCC were older (70 vs. 63 y, P =0.01). The extent of SEPT9 staining correlated with age ( rs =0.31, P =0.01), tumor grade ( rs =0.30, P =0.01), and extent of SATB2 staining ( rs =0.28, P =0.02). No associations were found between SEPT9 staining and tumor size, T stage, risk factors, CK19, CDX2, CK20, or CDH17 expression, alpha fetoprotein levels at diagnosis, METAVIR fibrosis stage, and oncologic outcome in the HCC cohort. SEPT9 is likely implicated in liver carcinogenesis in a HCC subset. Similar to mSEPT9 DNA measurement in liquid biopsies, SEPT9 staining by IHC may prove helpful as an adjunct diagnostic biomarker with potential prognostic ramifications.
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Affiliation(s)
- Michel Kmeid
- Department of Pathology, Albany Medical Center, Albany, NY
| | | | - Taek Chung
- Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | | | | | - Hwajeong Lee
- Department of Pathology, Albany Medical Center, Albany, NY
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42
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Li M, Zhu C, Xue Y, Miao C, He R, Li W, Zhang B, Yu W, Huang X, Lv M, Xu Y, Huang Q. A DNA methylation signature for the prediction of tumour recurrence in stage II colorectal cancer. Br J Cancer 2023; 128:1681-1689. [PMID: 36828869 PMCID: PMC10133253 DOI: 10.1038/s41416-023-02155-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 01/05/2023] [Accepted: 01/11/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND A major challenge in stage II colorectal carcinoma is to identify patients with increased risk of recurrence. Biomarkers that distinguish patients with poor prognosis from patients without recurrence are currently lacking. This study aims to develop a robust DNA methylation classifier that allows the prediction of recurrence and chemotherapy benefit in patients with stage II colorectal cancer. We performed a genome-wide DNA methylation capture sequencing in 243 stage II colorectal carcinoma samples and identified a relapse-specific DNA methylation signature consisting of eight CpG sites. METHODS Two hundred and forty-three patients with stage II CRC were enrolled in this study. In order to select differential methylation sites among recurrence and non-recurrence stage II CRC samples, DNA methylation profiles of 62 tumour samples including 31 recurrence and 31 nonrecurrence samples were analysed using the Agilent SureSelectXT Human Methyl-Seq, a comprehensive target enrichment system to analyse CpG methylation. Pyrosequencing was applied to quantify the methylation level of candidate DNA methylation sites in 243 patients. Least absolute shrinkage and selection operator (LASSO) method was employed to build the disease recurrence prediction classifier. RESULTS We identified a relapse-related DNA methylation signature consisting of eight CpG sites in stage II CRC by DNA methylation capture sequencing. The classifier showed significantly higher prognostic accuracy than any clinicopathological risk factors. The Kaplan-Meier survival curve showed an association of high-risk score with poor prognosis. In multivariate analysis, the signature was the most significant prognosis factor, with an HR of 2.80 (95% CI, 1.71-4.58, P < 0.001). The signature could identify patients who are suitable candidates for adjuvant chemotherapy. CONCLUSIONS An eight-CpG DNA methylation signature is a reliable prognostic and predictive tool for disease recurrence in patients with stage II CRC.
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Affiliation(s)
- Min Li
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Congcong Zhu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China
| | - Ying Xue
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Changhong Miao
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Department of Anesthesiology, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Ruiping He
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China
| | - Wei Li
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Baolong Zhang
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Wenqiang Yu
- Laboratory of RNA Epigenetics, Institute of Biomedical Sciences, Fudan University, 130 Dong'An Road, 200032, Shanghai, P. R. China
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, P. R. China
| | - Minzhi Lv
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Department of Biostatistics, Clinical Research Unit, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
| | - Ye Xu
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, 270 Dong'An Road, 200032, Shanghai, P. R. China.
- Department of Oncology, Shanghai Medical College, Fudan University, 270 Dong'An Road, 200032, Shanghai, P. R. China.
| | - Qihong Huang
- Cancer Center, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Institute of Clinical Sciences, Zhongshan Hospital, Fudan University, 180 Fenglin Road, 200032, Shanghai, P. R. China.
- Shanghai Respiratory Research Institute, 180 Fenglin Road, 200032, Shanghai, P. R. China.
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Permtermsin C, Lalchungnunga H, Nakjang S, Casement J, Ogle LF, Reeves HL, Strathdee G, Shukla R. Identification of TIAM1 as a Potential Synthetic-Lethal-like Gene in a Defined Subset of Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:6387. [PMID: 37047360 PMCID: PMC10094703 DOI: 10.3390/ijms24076387] [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: 01/31/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
Hepatocellular carcinoma (HCC), the most common type of liver cancer, has very poor outcomes. Current therapies often have low efficacy and significant toxicities. Thus, there is a critical need for the development of novel therapeutic approaches for HCC. We have developed a novel bioinformatics pipeline, which integrates genome-wide DNA methylation and gene expression data, to identify genes required for the survival of specific molecular cancer subgroups but not normal cells. Targeting these genes may induce cancer-specific "synthetic lethality". Initially, five potential HCC molecular subgroups were identified based on global DNA methylation patterns. Subgroup-2 exhibited the most unique methylation profile and two candidate subtype-specific vulnerability or SL-like genes were identified for this subgroup, including TIAM1, a guanine nucleotide exchange factor encoding gene known to activate Rac1 signalling. siRNA targeting TIAM1 inhibited cell proliferation in TIAM1-positive (subgroup-2) HCC cell lines but had no effect on the normal hepatocyte HHL5 cell line. Furthermore, TIAM1-positive/subgroup-2 cell lines were significantly more sensitive to the TIAM1/RAC1 inhibitor NSC23766 compared with TIAM1-negative HCC lines or the normal HHL5 cell line. The results are consistent with a synthetic lethal role for TIAM1 in a methylation-defined HCC subgroup and suggest it may be a viable therapeutic target in this subset of HCC patients.
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Affiliation(s)
- Chalermsin Permtermsin
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
| | - H Lalchungnunga
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
| | - Sirintra Nakjang
- Bioinformatics Support Unit, Newcastle University, Newcastle NE2 4HH, UK
| | - John Casement
- Bioinformatics Support Unit, Newcastle University, Newcastle NE2 4HH, UK
| | - Laura Frances Ogle
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
| | - Helen L Reeves
- Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
- Liver Unit, Freeman Hospital, Newcastle-Upon-Tyne Hospitals NHS Foundation Trust, Newcastle-upon-Tyne NE7 7DN, UK
| | - Gordon Strathdee
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
| | - Ruchi Shukla
- Biosciences Institute, Newcastle University Centre for Cancer, Newcastle University, Newcastle NE2 4HH, UK
- Department of Applied Sciences, Northumbria University, Newcastle NE1 8ST, UK
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44
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Khadirnaikar S, Shukla S, Prasanna SRM. Machine learning based combination of multi-omics data for subgroup identification in non-small cell lung cancer. Sci Rep 2023; 13:4636. [PMID: 36944673 PMCID: PMC10030850 DOI: 10.1038/s41598-023-31426-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/11/2023] [Indexed: 03/23/2023] Open
Abstract
Non-small Cell Lung Cancer (NSCLC) is a heterogeneous disease with a poor prognosis. Identifying novel subtypes in cancer can help classify patients with similar molecular and clinical phenotypes. This work proposes an end-to-end pipeline for subgroup identification in NSCLC. Here, we used a machine learning (ML) based approach to compress the multi-omics NSCLC data to a lower dimensional space. This data is subjected to consensus K-means clustering to identify the five novel clusters (C1-C5). Survival analysis of the resulting clusters revealed a significant difference in the overall survival of clusters (p-value: 0.019). Each cluster was then molecularly characterized to identify specific molecular characteristics. We found that cluster C3 showed minimal genetic aberration with a high prognosis. Next, classification models were developed using data from each omic level to predict the subgroup of unseen patients. Decision‑level fused classification models were then built using these classifiers, which were used to classify unseen patients into five novel clusters. We also showed that the multi-omics-based classification model outperformed single-omic-based models, and the combination of classifiers proved to be a more accurate prediction model than the individual classifiers. In summary, we have used ML models to develop a classification method and identified five novel NSCLC clusters with different genetic and clinical characteristics.
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Affiliation(s)
- Seema Khadirnaikar
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India.
| | - S R M Prasanna
- Department of Electrical Engineering, Indian Institute of Technology Dharwad, Dharwad, India
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Qiao JY, Li W, Zeng RY, Yu YJ, Chen QW, Liu XH, Cheng SX, Zhang XZ. An orally delivered bacteria-based coacervate antidote for alcohol detoxification. Biomaterials 2023; 296:122072. [PMID: 36878091 DOI: 10.1016/j.biomaterials.2023.122072] [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: 10/09/2022] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023]
Abstract
Alcohol intoxication causes serious diseases, whereas current treatments are mostly supportive and unable to convert alcohol into nontoxic products in the digestive tract. To address this issue, an oral intestinal-coating coacervate antidote containing acetic acid bacteria (AAB) and sodium alginate (SA) mixture was constructed. After oral administration, SA reduces absorption of ethanol and promotes the proliferation of AAB, and AAB converts ethanol to acetic acid or carbon dioxide and water by two sequential catalytic reactions in the presence of membrane-bound alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH). In vivo study shows that the bacteria-based coacervate antidote can significantly reduce the blood alcohol concentration (BAC) and effectively alleviates alcoholic liver injury in mice. Given the convenience and effectiveness of oral administration, AAB/SA can be used as a promising candidate antidote for relieving alcohol-induced acute liver injury.
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Affiliation(s)
- Ji-Yan Qiao
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Wen Li
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Run-Yao Zeng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Yun-Jian Yu
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Qi-Wen Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Xin-Hua Liu
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Si-Xue Cheng
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China
| | - Xian-Zheng Zhang
- Key Laboratory of Biomedical Polymers of Ministry of Education & Department of Chemistry, Wuhan University, Wuhan, 430072, China.
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Liu X, Chen J, Li J, Zeng Z, Jiang X, Gao Y, Huang Z, Wu Q, Gong Y, Xie C. Integrated analysis reveals common DNA methylation patterns of alcohol-associated cancers: A pan-cancer analysis. Front Genet 2023; 14:1032683. [PMID: 36861126 PMCID: PMC9968750 DOI: 10.3389/fgene.2023.1032683] [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: 08/31/2022] [Accepted: 01/24/2023] [Indexed: 02/16/2023] Open
Abstract
Background: The role of alcohol in carcinogenesis has received increasing attention in recent years. Evidence shows its impacts on various aspects, including epigenetics alteration. The DNA methylation patterns underlying alcohol-associated cancers are not fully understood. Methods: We investigated the aberrant DNA methylation patterns in four alcohol-associated cancers based on the Illumina HumanMethylation450 BeadChip. Pearson coefficient correlations were identified between differential methylated CpG probes and annotated genes. Transcriptional factor motifs were enriched and clustered using MEME Suite, and a regulatory network was constructed. Results: In each cancer, differential methylated probes (DMPs) were identified, and 172 hypermethylated and 21 hypomethylated pan-cancer DMPs (PDMPs) were examined further. Annotated genes significantly regulated by PDMPs were investigated and enriched in transcriptional misregulation in cancers. The CpG island chr19:58220189-58220517 was hypermethylated in all four cancers and silenced in the transcription factor ZNF154. Various biological effects were exerted by 33 hypermethylated and seven hypomethylated transcriptional factor motifs grouped into five clusters. Eleven pan-cancer DMPs were identified to be associated with clinical outcomes in the four alcohol-associated cancers, which might provide a potential point of view for clinical outcome prediction. Conclusion: This study provides an integrated insight into DNA methylation patterns in alcohol-associated cancers and reveals the corresponding features, influences, and potential mechanisms.
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Affiliation(s)
- Xingyu Liu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiarui Chen
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jiali Li
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zihang Zeng
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xueping Jiang
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yanping Gao
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengrong Huang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qiuji Wu
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yan Gong
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China,Tumor Precision Diagnosis and Treatment Technology and Translational Medicine, Hubei Engineering Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China,*Correspondence: Yan Gong, ; Conghua Xie,
| | - Conghua Xie
- Department of Radiation and Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China,Hubei Cancer Clinical Study Center, Zhongnan Hospital of Wuhan University, Wuhan, China,*Correspondence: Yan Gong, ; Conghua Xie,
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Oura K, Morishita A, Hamaya S, Fujita K, Masaki T. The Roles of Epigenetic Regulation and the Tumor Microenvironment in the Mechanism of Resistance to Systemic Therapy in Hepatocellular Carcinoma. Int J Mol Sci 2023; 24:2805. [PMID: 36769116 PMCID: PMC9917861 DOI: 10.3390/ijms24032805] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Primary liver cancer is the sixth most common cancer and the third most common cause of cancer-related deaths worldwide. Hepatocellular carcinoma (HCC) is a major histologic type with a poor prognosis owing to the difficulty in early detection, the chemotherapy resistance, and the high recurrence rate of the disease. Despite recent advancements in HCC prevention and diagnosis, over 50% of patients are diagnosed at Barcelona Clinic Liver Cancer Stage B or C. Systemic therapies are recommended for unresectable HCC (uHCC) with major vascular invasion, extrahepatic metastases, or intrahepatic lesions that have a limited response to transcatheter arterial chemoembolization, but the treatment outcome tends to be unsatisfactory due to acquired drug resistance. Elucidation of the mechanisms underlying the resistance to systemic therapies and the appropriate response strategies to solve this issue will contribute to improved outcomes in the multidisciplinary treatment of uHCC. In this review, we summarize recent findings on the mechanisms of resistance to drugs such as sorafenib, regorafenib, and lenvatinib in molecularly targeted therapy, with a focus on epigenetic regulation and the tumor microenvironment and outline the approaches to improve the therapeutic outcome for patients with advanced HCC.
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Affiliation(s)
- Kyoko Oura
- Department of Gastroenterology and Neurology, Faculty of Medicine, Kagawa University, Kita 761-0793, Kagawa, Japan
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Cabral LKD, Giraudi PJ, Giannelli G, Dituri F, Negro R, Tiribelli C, Sukowati CHC. Network Analysis for the Discovery of Common Oncogenic Biomarkers in Liver Cancer Experimental Models. Biomedicines 2023; 11:342. [PMID: 36830879 PMCID: PMC9953082 DOI: 10.3390/biomedicines11020342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/12/2023] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a malignancy marked by heterogeneity. This study aimed to discover target molecules for potential therapeutic efficacy that may encompass HCC heterogeneity. In silico analysis using published datasets identified 16 proto-oncogenes as potential pharmacological targets. We used an immortalized hepatocyte (IHH) and five HCC cell lines under two subtypes: S1/TGFβ-Wnt-activated (HLE, HLF, and JHH6) and the S2/progenitor subtype (HepG2 and Huh7). Three treatment modalities, 5 µM 5-Azacytidine, 50 µM Sorafenib, and 20 nM PD-L1 gene silencing, were evaluated in vitro. The effect of treatments on the proto-oncogene targets was assessed by gene expression and Western blot analysis. Our results showed that 10/16 targets were upregulated in HCC cells, where cells belonging to the S2/progenitor subtype had more upregulated targets compared to the S1/TGFβ-Wnt-activated subtype (81% vs. 62%, respectively). Among the targets, FGR was consistently down-regulated in the cell lines following the three different treatments. Sorafenib was effective to down-regulate targets in S2/progenitor subtype while PD-L1 silencing was able to decrease targets in all HCC subtypes, suggesting that this treatment strategy may comprise cellular heterogeneity. This study strengthens the relevance of liver cancer cellular heterogeneity in response to cancer therapies.
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Affiliation(s)
- Loraine Kay D. Cabral
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, 34149 Trieste, Italy; (L.K.D.C.); (P.J.G.); (C.T.)
- Doctoral School in Molecular Biomedicine, University of Trieste, 34127 Trieste, Italy
| | - Pablo J. Giraudi
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, 34149 Trieste, Italy; (L.K.D.C.); (P.J.G.); (C.T.)
| | - Gianluigi Giannelli
- National Institute of Gastroenterology IRCCS “S. De Bellis” Research Hospital, 70013 Bari, Italy; (G.G.); (F.D.); (R.N.)
| | - Francesco Dituri
- National Institute of Gastroenterology IRCCS “S. De Bellis” Research Hospital, 70013 Bari, Italy; (G.G.); (F.D.); (R.N.)
| | - Roberto Negro
- National Institute of Gastroenterology IRCCS “S. De Bellis” Research Hospital, 70013 Bari, Italy; (G.G.); (F.D.); (R.N.)
| | - Claudio Tiribelli
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, 34149 Trieste, Italy; (L.K.D.C.); (P.J.G.); (C.T.)
| | - Caecilia H. C. Sukowati
- Fondazione Italiana Fegato ONLUS, AREA Science Park, Campus Basovizza, 34149 Trieste, Italy; (L.K.D.C.); (P.J.G.); (C.T.)
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency of Indonesia (BRIN), Jakarta Pusat 10340, Indonesia
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Fan L, Tang Y, Li J, Huang W. Increased expression of TBC1D10B as a potential prognostic and immunotherapy relevant biomarker in liver hepatocellular carcinoma. Sci Rep 2023; 13:335. [PMID: 36611046 PMCID: PMC9825366 DOI: 10.1038/s41598-022-20341-1] [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: 02/07/2022] [Accepted: 09/12/2022] [Indexed: 01/09/2023] Open
Abstract
The TBC1 domain family member 10B (EPI64B/TBC1D10B), a member of the RabGAP EPI64 subfamily, contains a TBC domain that confers GTPase-activating protein activity. Even though overexpression of TBC1D10B has been reported to promote tumor invasion and metastasis in gastric adenocarcinoma, the prognostic value of TBC1D10B and its correlation with DNA methylation and immune infiltration in hepatocellular carcinoma are still not known. Transcriptional expression profiles of TBC1D10B between hepatocellular carcinoma tissues and normal tissues were downloaded from The Cancer Genome Atlas and Gene Expression Omnibus. The Clinical Proteomic Tumor Analysis Consortium and the Human Protein Atlas were used to assess the TBC1D10B protein expression. The biological functions of TBC1D10B were evaluated by the Metascape database and by Gene Set Enrichment Analysis (GSEA). Receiver operating characteristic (ROC) curve analysis was used to distinguish hepatocellular carcinoma from adjacent normal tissues. The effect of TBC1D10B on survival was estimated using the Kaplan-Meier method. DNA methylation in the TBC1D10B gene was assessed using the online MEXPRESS and MethSurv tools. The association between TBC1D10B mRNA expression and immune cell infiltration was investigated by the TIMER2 web server, tumor immune estimation resource and single-sample GSEA. This study found that TBC1D10B is highly expressed in hepatocellular carcinoma and that increased TBC1D10B mRNA expression is associated with female sex, lower Body Mass Index, high level of alpha fetal protein, and worse clinical stages. The mRNA and protein levels of TBC1D10B were verified in cells. Functional annotation indicated enrichment with negative regulation of the cell cycle, extracellular matrix, and corresponding pathways in the high-TBC1D10B phenotype. The ROC curve analysis showed that, with a cutoff level of 2.912, the accuracy, sensitive, and specificity in differentiate TBC1D10B hepatocellular carcinoma from adjacent controls were 0.931, 0.920, and 0.802, respectively. Kaplan-Meier survival analysis showed that hepatocellular carcinoma patients with high TBC1D10B had a worse prognosis than those with low TBC1D10B, especially in patients with a weight below 70 kg, height above 170 cm, and histological G2 and G3. We also found that the methylation of TBC1D10B was associated with the prognosis in patients with hepatocellular carcinoma. Moreover, correlation analysis indicated that TBC1D10B mRNA expression was positively correlated with infiltration levels of most immune cells, but negatively correlated with Th17 and cytotoxic cells infiltration. Our study indicates that increased TBC1D10B expression in hepatocellular carcinoma may play a role in tumorigenesis by regulating the cell cycle and extracellular matrix. TBC1D10B may be a novel prognostic and predictive marker and immune therapeutic target in hepatocellular carcinoma patients.
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Affiliation(s)
- Li Fan
- grid.477238.dDepartment of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001 Guangxi China
| | - Yongmei Tang
- grid.477238.dDepartment of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001 Guangxi China
| | - Jingjing Li
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001, Guangxi, China.
| | - Wenjie Huang
- Department of Reproductive Medicine, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, 545001, Guangxi, China.
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50
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Kim M, Delgado E, Ko S. DNA methylation in cell plasticity and malignant transformation in liver diseases. Pharmacol Ther 2023; 241:108334. [PMID: 36535346 PMCID: PMC9841769 DOI: 10.1016/j.pharmthera.2022.108334] [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: 11/02/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
The liver possesses extraordinary regenerative capacity mainly attributable to the ability of hepatocytes (HCs) and biliary epithelial cells (BECs) to self-replicate. This ability is left over from their bipotent parent cell, the hepatoblast, during development. When this innate regeneration is compromised due to the absence of proliferative parenchymal cells, such as during cirrhosis, HCs and BEC can transdifferentiate; thus, adding another layer of complexity to the process of liver repair. In addition, dysregulated lineage maintenance in these two cell populations has been shown to promote malignant growth in experimental conditions. Here, malignant transformation, driven in part by insufficient maintenance of lineage reprogramming, contributes to end-stage liver disease. Epigenetic changes are key drivers for cell fate decisions as well as transformation by finetuning overall transcription and gene expression. In this review, we address how altered DNA methylation contributes to the initiation and progression of hepatic cell fate conversion and cancer formation. We also discussed the diagnostic and therapeutic potential of targeting DNA methylation in liver cancer, its current limitations, and what future research is necessary to facilitate its contribution to clinical translation.
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Affiliation(s)
- Minwook Kim
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Evan Delgado
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Sungjin Ko
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America; Pittsburgh Liver Research Center, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America.
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