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Peruhova M, Banova-Chakarova S, Miteva DG, Velikova T. Genetic screening of liver cancer: State of the art. World J Hepatol 2024; 16:716-730. [PMID: 38818292 PMCID: PMC11135278 DOI: 10.4254/wjh.v16.i5.716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/14/2024] [Accepted: 04/09/2024] [Indexed: 05/22/2024] Open
Abstract
Liver cancer, primarily hepatocellular carcinoma, remains a global health challenge with rising incidence and limited therapeutic options. Genetic factors play a pivotal role in the development and progression of liver cancer. This state-of-the-art paper provides a comprehensive review of the current landscape of genetic screening strategies for liver cancer. We discuss the genetic underpinnings of liver cancer, emphasizing the critical role of risk-associated genetic variants, somatic mutations, and epigenetic alterations. We also explore the intricate interplay between environmental factors and genetics, highlighting how genetic screening can aid in risk stratification and early detection via using liquid biopsy, and advancements in high-throughput sequencing technologies. By synthesizing the latest research findings, we aim to provide a comprehensive overview of the state-of-the-art genetic screening methods for liver cancer, shedding light on their potential to revolutionize early detection, risk assessment, and targeted therapies in the fight against this devastating disease.
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Affiliation(s)
- Milena Peruhova
- Department of Gastroenterology, University Hospital "Heart and Brain", Burgas 8000, Bulgaria
| | - Sonya Banova-Chakarova
- Department of Gastroenterology, University Hospital "Heart and Brain", Burgas 8000, Bulgaria.
| | - Dimitrina Georgieva Miteva
- Department of Genetics, Faculty of Biology, Sofia University" St. Kliment Ohridski, Sofia 1164, Bulgaria
| | - Tsvetelina Velikova
- Medical Faculty, Sofia University St. Kliment Ohridski, Sofia 1407, Bulgaria
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2
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Ma H, Hong Y, Xu Z, Weng Z, Yang Y, Jin D, Chen Z, Yue J, Zhou X, Xu Z, Fei F, Li J, Song W. N 6-methyladenosine (m 6A) modification in hepatocellular carcinoma. Biomed Pharmacother 2024; 173:116365. [PMID: 38452654 DOI: 10.1016/j.biopha.2024.116365] [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: 12/21/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 03/09/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is one of the deadliest cancers of human, the tumor-related death of which ranks third among the common malignances. N6-methyladenosine (m6A) methylation, the most abundant internal modification of RNA in mammals, participates in the metabolism of mRNA and interrelates with ncRNAs. In this paper, we overviewed the complex function of m6A regulators in HCC, including regulating the tumorigenesis, progression, prognosis, stemness, metabolic reprogramming, autophagy, ferroptosis, drug resistance and tumor immune microenvironment (TIME). Furthermore, we elucidated the interplay between m6A modification and non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). Finally, we summarized the potential of m6A regulators as diagnostic biomarkers. What's more, we reviewed the inhibitors targeting m6A enzymes as promising therapeutic targets of HCC. We aimed to help understand the function of m6A methylation in HCC systematically and comprehensively so that more effective strategies for HCC treatment will be developed.
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Affiliation(s)
- Hehua Ma
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yuxin Hong
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhenzhen Xu
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Zuyi Weng
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Yuanxun Yang
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Dandan Jin
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Zhiyou Chen
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jing Yue
- Department of Gynaecology and Obstetrics, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Xuan Zhou
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Zhi Xu
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Fei Fei
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China
| | - Juan Li
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
| | - Wei Song
- Phase I Clinical Trials Unit, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing 210008, China.
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3
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Abi Zamer B, Rah B, Jayakumar MN, Abumustafa W, Hamad M, Muhammad JS. DNA methylation-mediated epigenetic regulation of oncogenic RPS2 as a novel therapeutic target and biomarker in hepatocellular carcinoma. Biochem Biophys Res Commun 2024; 696:149453. [PMID: 38181486 DOI: 10.1016/j.bbrc.2023.149453] [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: 11/19/2023] [Revised: 12/21/2023] [Accepted: 12/27/2023] [Indexed: 01/07/2024]
Abstract
Ribosomal Protein S2 (RPS2) has emerged as a potential prognostic biomarker due to its involvement in key cellular processes and its altered expression pattern in certain types of cancer. However, its role in hepatocellular carcinoma (HCC) has yet to be investigated. Herein, we analyzed RPS2 mRNA expression and promoter methylation in HCC patient samples and HepG2 cells. Subsequently, loss-of-function experiments were conducted to determine the function of RPS2 in HCC cells in vitro. Our results revealed that RPS2 mRNA expression is significantly elevated, and its promoter is hypomethylated in HCC patient samples compared to controls. In addition, 5-Azacytidine treatment in HepG2 cells decreased RPS2 promoter methylation level and increased its mRNA expression. RPS2 knockdown in HepG2 cells suppressed cell proliferation and promoted apoptosis. Functional pathway analysis of genes positively and negatively associated with RPS2 expression in HCC showed enrichment in ribosomal biogenesis, translation machinery, cell cycle regulation, and DNA processing. Furthermore, utilizing drug-protein 3D docking, we found that doxorubicin, sorafenib, and 5-Fluorouracil, showed high affinity to the active sites of RPS2, and in vitro treatment with these drugs reduced RPS2 expression. For the first time, we report on DNA methylation-mediated epigenetic regulation of RPS2 and its oncogenic role in HCC. Our findings suggest that RPS2 plays a significant role in the development and progression of HCC, hence its potential prognostic and therapeutic utility. Moreover, as epigenetic changes happen early in cancer development, RPS2 may serve as a potential biomarker for tumor progression.
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Affiliation(s)
- Batoul Abi Zamer
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Research Institute of Medical and Health Sciences, University of Sharjah, United Arab Emirates
| | - Bilal Rah
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Manju Nidagodu Jayakumar
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Wafaa Abumustafa
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Research Institute of Medical and Health Sciences, University of Sharjah, United Arab Emirates
| | - Mawieh Hamad
- Research Institute of Medical and Health Sciences, University of Sharjah, United Arab Emirates; Department of Medical Laboratory Sciences, College of Health Sciences, University of Sharjah, United Arab Emirates
| | - Jibran Sualeh Muhammad
- Department of Basic Medical Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates; Research Institute of Medical and Health Sciences, University of Sharjah, United Arab Emirates.
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4
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Franco-Juárez EX, González-Villasana V, Camacho-Moll ME, Rendón-Garlant L, Ramírez-Flores PN, Silva-Ramírez B, Peñuelas-Urquides K, Cabello-Ruiz ED, Castorena-Torres F, Bermúdez de León M. Mechanistic Insights about Sorafenib-, Valproic Acid- and Metformin-Induced Cell Death in Hepatocellular Carcinoma. Int J Mol Sci 2024; 25:1760. [PMID: 38339037 PMCID: PMC10855535 DOI: 10.3390/ijms25031760] [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: 10/09/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 02/12/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is among the main causes of death by cancer worldwide, representing about 80-90% of all liver cancers. Treatments available for advanced HCC include atezolizumab, bevacizumab, sorafenib, among others. Atezolizumab and bevacizumab are immunological options recently incorporated into first-line treatments, along with sorafenib, for which great treatment achievements have been reached. However, sorafenib resistance is developed in most patients, and therapeutical combinations targeting cancer hallmark mechanisms and intracellular signaling have been proposed. In this review, we compiled evidence of the mechanisms of cell death caused by sorafenib administered alone or in combination with valproic acid and metformin and discussed them from a molecular perspective.
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Affiliation(s)
- Edgar Xchel Franco-Juárez
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey 64720, Nuevo Leon, Mexico; (E.X.F.-J.); (M.E.C.-M.); (P.N.R.-F.); (K.P.-U.)
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66451, Nuevo Leon, Mexico; (V.G.-V.); (L.R.-G.); (E.D.C.-R.)
| | - Vianey González-Villasana
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66451, Nuevo Leon, Mexico; (V.G.-V.); (L.R.-G.); (E.D.C.-R.)
| | - María Elena Camacho-Moll
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey 64720, Nuevo Leon, Mexico; (E.X.F.-J.); (M.E.C.-M.); (P.N.R.-F.); (K.P.-U.)
| | - Luisa Rendón-Garlant
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66451, Nuevo Leon, Mexico; (V.G.-V.); (L.R.-G.); (E.D.C.-R.)
| | - Patricia Nefertari Ramírez-Flores
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey 64720, Nuevo Leon, Mexico; (E.X.F.-J.); (M.E.C.-M.); (P.N.R.-F.); (K.P.-U.)
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Nuevo Leon, Mexico;
| | - Beatriz Silva-Ramírez
- Departamento de Inmunogenética, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey 64720, Nuevo Leon, Mexico;
| | - Katia Peñuelas-Urquides
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey 64720, Nuevo Leon, Mexico; (E.X.F.-J.); (M.E.C.-M.); (P.N.R.-F.); (K.P.-U.)
| | - Ethel Daniela Cabello-Ruiz
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66451, Nuevo Leon, Mexico; (V.G.-V.); (L.R.-G.); (E.D.C.-R.)
| | - Fabiola Castorena-Torres
- Tecnológico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey 64710, Nuevo Leon, Mexico;
| | - Mario Bermúdez de León
- Departamento de Biología Molecular, Centro de Investigación Biomédica del Noreste, Instituto Mexicano del Seguro Social, Monterrey 64720, Nuevo Leon, Mexico; (E.X.F.-J.); (M.E.C.-M.); (P.N.R.-F.); (K.P.-U.)
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Chen G, Xu W, Long Z, Chong Y, Lin B, Jie Y. Single-cell Technologies Provide Novel Insights into Liver Physiology and Pathology. J Clin Transl Hepatol 2024; 12:79-90. [PMID: 38250462 PMCID: PMC10794276 DOI: 10.14218/jcth.2023.00224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/25/2023] [Accepted: 07/12/2023] [Indexed: 01/23/2024] Open
Abstract
The liver is the largest glandular organ in the body and has a unique distribution of cells and biomolecules. However, the treatment outcome of end-stage liver disease is extremely poor. Single-cell sequencing is a new advanced and powerful technique for identifying rare cell populations and biomolecules by analyzing the characteristics of gene expression between individual cells. These cells and biomolecules might be used as potential targets for immunotherapy of liver diseases and contribute to the development of precise individualized treatment. Compared to whole-tissue RNA sequencing, single-cell RNA sequencing (scRNA-seq) or other single-cell histological techniques have solved the problem of cell population heterogeneity and characterize molecular changes associated with liver diseases with higher accuracy and resolution. In this review, we comprehensively summarized single-cell approaches including transcriptomic, spatial transcriptomic, immunomic, proteomic, epigenomic, and multiomic technologies, and described their application in liver physiology and pathology. We also discussed advanced techniques and recent studies in the field of single-cell; our review might provide new insights into the pathophysiological mechanisms of the liver to achieve precise and individualized treatment of liver diseases.
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Affiliation(s)
| | | | - Zhicong Long
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yutian Chong
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Bingliang Lin
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yusheng Jie
- Department of Infectious Diseases, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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6
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Pierdomenico M, Bacchetta L, Benassi B. The ethanolic extract of Corylus avellana L. drives a microRNA-based cytotoxic effect on HepG2 hepatocarcinoma cells. Nat Prod Res 2023:1-8. [PMID: 38013231 DOI: 10.1080/14786419.2023.2287170] [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: 08/16/2023] [Accepted: 11/19/2023] [Indexed: 11/29/2023]
Abstract
An ethanolic extract of Corylus avellana L. hazelnut was characterised by liquid chromatography coupled to high resolution mass spectrometry. We here evaluated the in vitro cytotoxic response to such extract in HepG2 cells and tried to depict the underlying mechanism(s) in terms of microRNA-34b/c involvement. Following long-term exposure (144h) of HepG2 cells with 0.04-0.4 mg/ml of hazelnut extract, we demonstrated that miR-34 precursor RNA and both mature miR-34b and miR-34c molecules underwent a significant stimulation (>2-fold change, p < 0.05) in cells treated with the highest concentration. The epigenetic modulation was accompanied by the inhibition of cell proliferation, the decrease of viability and activation of apoptosis at 144h of treatment with 0.4 mg/ml of hazelnut.These in vitro findings demonstrate the cytotoxic effect of the C. avellana extract in HepG2 cells and open the way to in vivo validation of possible application of hazelnut-based extracts, and/or its metabolites, as promising epigenetics drugs.
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Affiliation(s)
- Maria Pierdomenico
- Division of Health Protection Technologies, ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Loretta Bacchetta
- Division of Biotechnologies and Agroindustry, ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Barbara Benassi
- Division of Health Protection Technologies, ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
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7
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Chavda V, Zajac KK, Gunn JL, Balar P, Khadela A, Vaghela D, Soni S, Ashby CR, Tiwari AK. Ethnic differences in hepatocellular carcinoma prevalence and therapeutic outcomes. Cancer Rep (Hoboken) 2023; 6 Suppl 1:e1821. [PMID: 37344125 PMCID: PMC10440848 DOI: 10.1002/cnr2.1821] [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: 12/31/2022] [Revised: 03/17/2023] [Accepted: 04/10/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. The incidence of HCC is affected by genetic and non-genetic factors. Genetically, mutations in the genes, tumor protein P53 (TP53), catenin beta 1 (CTNNB1), AT-rich interaction domain 1A (ARIC1A), cyclin dependent kinase inhibitor 2A (CDKN2A), mannose 6-phosphate (M6P), smooth muscle action against decapentaplegic (SMAD2), retinoblastoma gene (RB1), cyclin D, antigen presenting cells (APC), AXIN1, and E-cadherin, have been shown to contribute to the occurrence of HCC. Non-genetic factors, including alcohol consumption, exposure to aflatoxin, age, gender, presence of hepatitis B (HBV), hepatitis C (HCV), and non-alcoholic fatty liver disease (NAFLD), increase the risk of HCC. RECENT FINDINGS The severity of the disease and its occurrence vary based on geographical location. Furthermore, men and minorities have been shown to be disproportionately affected by HCC, compared with women and non-minorities. Ethnicity has been reported to significantly affect tumorigenesis and clinical outcomes in patients diagnosed with HCC. Generally, differences in gene expression and/or the presence of comorbid medical diseases affect or influence the progression of HCC. Non-Caucasian HCC patients are significantly more likely to have poorer survival outcomes, compared to their Caucasian counterparts. Finally, there are a number of factors that contribute to the success rate of treatments for HCC. CONCLUSION Assessment and treatment of HCC must be consistent using evidence-based guidelines and standardized outcomes, as well as international clinical practice guidelines for global consensus. Standardizing the assessment approach and method will enable comparison and improvement of liver cancer research through collaboration between researchers, healthcare providers, and advocacy groups. In this review, we will focus on discussing epidemiological factors that result in deviations and changes in treatment approaches for HCC.
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Affiliation(s)
- Vivek Chavda
- Department of Pharmaceutics and Pharmaceutical TechnologyL M College of PharmacyAhmedabadIndia
| | - Kelsee K. Zajac
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical SciencesUniversity of ToledoOhioUSA
| | - Jenna Lynn Gunn
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical SciencesUniversity of ToledoOhioUSA
| | - Pankti Balar
- Pharmacy SectionL M College of PharmacyAhmedabadIndia
| | - Avinash Khadela
- Department of PharmacologyL M College of PharmacyAhmedabadIndia
| | - Dixa Vaghela
- Pharmacy SectionL M College of PharmacyAhmedabadIndia
| | - Shruti Soni
- PharmD SectionL M College of PharmacyAhmedabadIndia
| | - Charles R. Ashby
- Department of Pharmaceutical Sciences, College of PharmacySt. John's UniversityNew YorkNew YorkUSA
| | - Amit K. Tiwari
- Department of Pharmacology and Experimental Therapeutics, College of Pharmacy and Pharmaceutical SciencesUniversity of ToledoOhioUSA
- Department of Cancer Biology, College of Medicine and Life SciencesUniversity of ToledoToledoOhioUSA
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Salama BM, Helmy MW, Fouad H, Shamaa MM, Houssen ME. The Synergistic Antitumor Effect of Decitabine and Vorinostat Combination on HepG2 Human Hepatocellular Carcinoma Cell Line via Epigenetic Modulation of Autophagy-Apoptosis Molecular Crosstalk. Curr Issues Mol Biol 2023; 45:5935-5949. [PMID: 37504291 PMCID: PMC10378248 DOI: 10.3390/cimb45070375] [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: 06/04/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/29/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a worldwide health issue. Epigenetic alterations play a crucial role in HCC tumorigenesis. Using epigenetic modulators for HCC treatment confers a promising therapeutic effect. The aim of this study was to explore the effect of a decitabine (DAC) and vorinostat (VOR) combination on the crosstalk between apoptosis and autophagy in the HCC HepG2 cell line at 24 h and 72 h. Median inhibitory concentrations (IC50s) of VOR and DAC were assessed in the HepG2 cell line. The activity of caspase-3 was evaluated colorimetrically, and Cyclin D1(CCND1), Bcl-2, ATG5, ATG7, and P62 levels were assessed using ELISA at different time intervals (24 h and 72 h), while LC3IIB and Beclin-1gene expression were measured by using qRT-PCR. The synergistic effect of VOR and DAC was confirmed due to the observed combination indices (CIs) and dose reduction indices (DRIs). The combined treatment with both drugs inhibited the proliferation marker (CCND1), and enhanced apoptosis compared with each drug alone at 24 h and 72 h (via active caspase-3 upregulation and Bcl-2 downregulation). Moreover, the combination induced autophagy as an early event via upregulation of Beclin-1, LC3IIB, ATG5, and ATG7 gene expression. The initial induction of autophagy started to decrease after 72 h due to Beclin-1 downregulation, and there was decreased expression of LC3IIB compared with the value at 24 h. Herein, epigenetic modulation via the VOR/DAC combination showed an antitumor effect through the coordination of an autophagy-apoptosis crosstalk and promotion of autophagy-induced apoptosis, which ultimately led to the cellular death of HCC cancer cells.
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Affiliation(s)
- Basant M Salama
- Department of Biochemistry, Faculty of Pharmacy, Damanhour University, Damanhour 22511, Egypt
| | - Maged W Helmy
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Damanhour University, Damanhour 22511, Egypt
- Pharmacology and Toxicology Department, Clinical and Biological Sciences Division, College of Pharmacy, Arab Academy for Science, Technology and Maritime Transport, Alexandria 1029, Egypt
| | - Hosny Fouad
- Pharmacology Department, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
- Department of Biochemistry, Clinical and Biological Science Division, College of Pharmacy, Arab Academy for Science, Technology and Maritime Transport, Alexandria 1029, Egypt
| | - Marium M Shamaa
- Department of Biochemistry, Clinical and Biological Science Division, College of Pharmacy, Arab Academy for Science, Technology and Maritime Transport, Alexandria 1029, Egypt
| | - Maha E Houssen
- Department of Biochemistry, Faculty of Pharmacy, Damanhour University, Damanhour 22511, Egypt
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9
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Aravena TI, Valdés E, Ayala N, D’Afonseca V. A Computational Approach to Predict the Role of Genetic Alterations in Methyltransferase Histones Genes With Implications in Liver Cancer. Cancer Inform 2023; 22:11769351231161480. [PMID: 37008071 PMCID: PMC10064455 DOI: 10.1177/11769351231161480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/16/2023] [Indexed: 04/04/2023] Open
Abstract
Histone methyltransferases (HMTs) comprise a subclass of epigenetic regulators. Dysregulation of these enzymes results in aberrant epigenetic regulation, commonly observed in various tumor types, including hepatocellular adenocarcinoma (HCC). Probably, these epigenetic changes could lead to tumorigenesis processes. To predict how histone methyltransferase genes and their genetic alterations (somatic mutations, somatic copy number alterations, and gene expression changes) are involved in hepatocellular adenocarcinoma processes, we performed an integrated computational analysis of genetic alterations in 50 HMT genes present in hepatocellular adenocarcinoma. Biological data were obtained through the public repository with 360 samples from patients with hepatocellular carcinoma. Through these biological data, we identified 10 HMT genes (SETDB1, ASH1L, SMYD2, SMYD3, EHMT2, SETD3, PRDM14, PRDM16, KMT2C, and NSD3) with a significant genetic alteration rate (14%) within 360 samples. Of these 10 HMT genes, KMT2C and ASH1L have the highest mutation rate in HCC samples, 5.6% and 2.8%, respectively. Regarding somatic copy number alteration, ASH1L and SETDB1 are amplified in several samples, while SETD3, PRDM14, and NSD3 showed a high rate of large deletion. Finally, SETDB1, SETD3, PRDM14, and NSD3 could play an important role in the progression of hepatocellular adenocarcinoma since alterations in these genes lead to a decrease in patient survival, unlike patients who present these genes without genetic alterations. Our computational analysis provides new insights that help to understand how HMTs are associated with hepatocellular carcinoma, as well as provide a basis for future experimental investigations using HMTs as genetic targets against hepatocellular carcinoma.
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Affiliation(s)
- Tania Isabella Aravena
- Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
| | - Elizabeth Valdés
- Facultad de Ciencias Agrarias y Forestales, Universidad Católica del Maule, Talca, Chile
| | - Nicolás Ayala
- Departamento de Genética, Microbiología y Estadística, Universidad de Barcelona, España
| | - Vívian D’Afonseca
- Departamento de Ciencias Preclínicas, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
- Vívian D’Afonseca, Universidad Católica del Maule, Av. San Miguel 3605, Talca, 3460000, Chile.
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10
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Chen J, Zhao Y, Zhang F, Li J, Boland JA, Cheng NC, Liu K, Tiffen JC, Bertolino P, Bowen DG, Krueger A, Lisowski L, Alexander IE, Vadas MA, El-Omar E, Gamble JR, McCaughan GW. Liver-specific deletion of miR-181ab1 reduces liver tumour progression via upregulation of CBX7. Cell Mol Life Sci 2022; 79:443. [PMID: 35867177 PMCID: PMC9307539 DOI: 10.1007/s00018-022-04452-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/23/2022] [Accepted: 06/26/2022] [Indexed: 11/30/2022]
Abstract
MiR-181 expression levels increased in hepatocellular carcinoma (HCC) compared to non-cancerous tissues. MiR-181 has been widely reported as a possible driver of tumourigenesis but also acts as a tumour suppressor. In addition, the miR-181 family regulates the development and function of immune and vascular cells, which play vital roles in the progression of tumours. More complicatedly, many genes have been identified as miR-181 targets to mediate the effects of miR-181. However, the role of miR-181 in the development of primary tumours remains largely unexplored. We aimed to examine the function of miR-181 and its vital mediators in the progression of diethylnitrosamine-induced primary liver cancers in mice. The size of liver tumours was significantly reduced by 90% in global (GKO) or liver-specific (LKO) 181ab1 knockout mice but not in hematopoietic and endothelial lineage-specific knockout mice, compared to WT mice. In addition, the number of tumours was significantly reduced by 50% in GKO mice. Whole-genome RNA-seq analysis and immunohistochemistry showed that epithelial-mesenchymal transition was partially reversed in GKO tumours compared to WT tumours. The expression of CBX7, a confirmed miR-181 target, was up-regulated in GKO compared to WT tumours. Stable CBX7 expression was achieved with an AAV/Transposase Hybrid-Vector System and up-regulated CBX7 expression inhibited liver tumour progression in WT mice. Hepatic CBX7 deletion restored the progression of LKO liver tumours. MiR-181a expression was the lowest and CBX7 expression the highest in iClust2 and 3 subclasses of human HCC compared to iClust1. Gene expression profiles of GKO tumours overlapped with low-proliferative peri-portal-type HCCs. Liver-specific loss of miR-181ab1 inhibited primary liver tumour progression via up-regulating CBX7 expression, but tumour induction requires both hepatic and non-hepatic miR-181. Also, miR-181ab1-deficient liver tumours may resemble low-proliferative periportal-type human HCC.
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Affiliation(s)
- Jinbiao Chen
- Liver Injury and Cancer Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Yang Zhao
- Vascular Biology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, People's Republic of China
| | - Fan Zhang
- UNSW Microbiome Research Centre, School of Clinical Medicine, UNSW Medicine and Health, St George and Sutherland Clinical Campuses, Kogarah, NSW, 2217, Australia
| | - Jia Li
- Vascular Biology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,Centre for Motor Neuron Disease, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jade A Boland
- Liver Injury and Cancer Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Ngan Ching Cheng
- Liver Injury and Cancer Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,Vascular Biology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Ken Liu
- Liver Injury and Cancer Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia.,Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW, 2050, Australia
| | - Jessamy C Tiffen
- Melanoma Epigenetics Lab Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Patrick Bertolino
- Liver Immunology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - David G Bowen
- Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW, 2050, Australia.,Liver Immunology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Andreas Krueger
- Molecular Immunology, Faculty of Biology and Chemistry, Justus Liebig University Gießen, Schubertstr 81, 35392, Giessen, Germany.,Institute for Molecular Medicine, Frankfurt Cancer Institute, Goethe-University, Frankfurt, Germany
| | - Leszek Lisowski
- Translational Vectorology Research Unit, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, 2145, Australia.,Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine, Warsaw, Poland
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney and Sydney Children's Hospitals Network, Westmead, NSW, 2145, Australia
| | - Mathew A Vadas
- Vascular Biology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Emad El-Omar
- UNSW Microbiome Research Centre, School of Clinical Medicine, UNSW Medicine and Health, St George and Sutherland Clinical Campuses, Kogarah, NSW, 2217, Australia
| | - Jennifer R Gamble
- Vascular Biology Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia
| | - Geoffrey W McCaughan
- Liver Injury and Cancer Program Centenary Institute and Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2050, Australia. .,Royal Prince Alfred Hospital, Missenden Road, Camperdown, NSW, 2050, Australia.
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11
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Habash NW, Sehrawat TS, Shah VH, Cao S. Epigenetics of alcohol-related liver diseases. JHEP REPORTS : INNOVATION IN HEPATOLOGY 2022; 4:100466. [PMID: 35462859 PMCID: PMC9018389 DOI: 10.1016/j.jhepr.2022.100466] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/14/2022] [Accepted: 02/22/2022] [Indexed: 02/07/2023]
Abstract
Alcohol-related liver disease (ARLD) is a primary cause of chronic liver disease in the United States. Despite advances in the diagnosis and management of ARLD, it remains a major public health problem associated with significant morbidity and mortality, emphasising the need to adopt novel approaches to the study of ARLD and its complications. Epigenetic changes are increasingly being recognised as contributing to the pathogenesis of multiple disease states. Harnessing the power of innovative technologies for the study of epigenetics (e.g., next-generation sequencing, DNA methylation assays, histone modification profiling and computational techniques like machine learning) has resulted in a seismic shift in our understanding of the pathophysiology of ARLD. Knowledge of these techniques and advances is of paramount importance for the practicing hepatologist and researchers alike. Accordingly, in this review article we will summarise the current knowledge about alcohol-induced epigenetic alterations in the context of ARLD, including but not limited to, DNA hyper/hypo methylation, histone modifications, changes in non-coding RNA, 3D chromatin architecture and enhancer-promoter interactions. Additionally, we will discuss the state-of-the-art techniques used in the study of ARLD (e.g. single-cell sequencing). We will also highlight the epigenetic regulation of chemokines and their proinflammatory role in the context of ARLD. Lastly, we will examine the clinical applications of epigenetics in the diagnosis and management of ARLD.
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Key Words
- 3C, chromosome conformation capture
- 4C, chromosome conformation capture-on-chip
- AH, alcohol-related hepatitis
- ARLD, alcohol-related liver disease
- ASH, alcohol-related steatohepatitis
- ATAC, assay for transposase-accessible chromatin
- Acetylation
- Alcohol liver disease
- BET, bromodomain and extraterminal motif
- BETi, BET inhibitor
- BRD, bromodomain
- CCL2, C-C motif chemokine ligand 2
- CTCF, CCCTC-binding factor
- CXCL, C-X-C motif chemokine ligand
- Chromatin architecture
- Computational biology
- DNA methylation
- DNMT, DNA methyltransferase
- E-P, enhancer-promoter
- Epidrugs
- Epigenetics
- FKBP5, FK506-binding protein 5
- HCC, hepatocellular carcinoma
- HDAC, histone deacetylase
- HIF1α, hypoxia inducible factor-1α
- HMGB1, high-mobility group box protein 1
- HNF4α, hepatocyte nuclear factor 4α
- HSC, hepatic stellate cell
- Hi-C, chromosome capture followed by high-throughput sequencing
- Histones
- IL, interleukin
- LPS, lipopolysaccharide
- MALAT1, metastasis-associated lung adenocarcinoma transcript 1
- MECP2, methyl-CpG binding protein 2
- NAFLD, non-alcohol-related fatty liver disease
- PPARG, peroxisome proliferator activated receptor-γ
- SAA, salvianolic acid A
- SIRT, sirtuin
- SREBPs, sterol regulatory element-binding proteins
- Single cell epigenome
- TAD, topologically associating domain
- TEAD, TEA domain transcription factor
- TLR, Toll-like receptor
- TNF, tumour necrosis factor
- YAP, Yes-associated protein
- lncRNA, long non-coding RNA
- miRNA, microRNA
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Affiliation(s)
| | | | - Vijay H. Shah
- Corresponding authors. Address: Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA. Tel. 507-255-6028, fax: 507-255-6318.
| | - Sheng Cao
- Corresponding authors. Address: Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First St SW, Rochester, MN 55905, USA. Tel. 507-255-6028, fax: 507-255-6318.
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12
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Cai Q, Gan C, Tang C, Wu H, Gao J. Mechanism and Therapeutic Opportunities of Histone Modifications in Chronic Liver Disease. Front Pharmacol 2021; 12:784591. [PMID: 34887768 PMCID: PMC8650224 DOI: 10.3389/fphar.2021.784591] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/08/2021] [Indexed: 02/05/2023] Open
Abstract
Chronic liver disease (CLD) represents a global health problem, accounting for the heavy burden of disability and increased health care utilization. Epigenome alterations play an important role in the occurrence and progression of CLD. Histone modifications, which include acetylation, methylation, and phosphorylation, represent an essential part of epigenetic modifications that affect the transcriptional activity of genes. Different from genetic mutations, histone modifications are plastic and reversible. They can be modulated pharmacologically without changing the DNA sequence. Thus, there might be chances to establish interventional solutions by targeting histone modifications to reverse CLD. Here we summarized the roles of histone modifications in the context of alcoholic liver disease (ALD), metabolic associated fatty liver disease (MAFLD), viral hepatitis, autoimmune liver disease, drug-induced liver injury (DILI), and liver fibrosis or cirrhosis. The potential targets of histone modifications for translation into therapeutics were also investigated. In prospect, high efficacy and low toxicity drugs that are selectively targeting histone modifications are required to completely reverse CLD and prevent the development of liver cirrhosis and malignancy.
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Affiliation(s)
- Qiuyu Cai
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Can Gan
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Chengwei Tang
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Hao Wu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Jinhang Gao
- Laboratory of Gastroenterology and Hepatology, West China Hospital, Sichuan University, Chengdu, China
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
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