1
|
Cherubini A, Ostadreza M, Jamialahmadi O, Pelusi S, Rrapaj E, Casirati E, Passignani G, Norouziesfahani M, Sinopoli E, Baselli G, Meda C, Dongiovanni P, Dondossola D, Youngson N, Tourna A, Chokshi S, Bugianesi E, Della Torre S, Prati D, Romeo S, Valenti L. Author Correction: Interaction between estrogen receptor-α and PNPLA3 p.I148M variant drives fatty liver disease susceptibility in women. Nat Med 2024; 30:1212. [PMID: 38267549 PMCID: PMC11031389 DOI: 10.1038/s41591-024-02817-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Affiliation(s)
- Alessandro Cherubini
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Mahnoosh Ostadreza
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Oveis Jamialahmadi
- Department of Molecular and Clinical Medicine, Gothenburg University, Gothenburg, Sweden
| | - Serena Pelusi
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Eniada Rrapaj
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elia Casirati
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Giulia Passignani
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marjan Norouziesfahani
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elena Sinopoli
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Guido Baselli
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Clara Meda
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Paola Dongiovanni
- Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniele Dondossola
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- General and Liver Transplant Surgery, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico and University of Milan, Centre of Preclinical Research, Milan, Italy
| | - Neil Youngson
- Foundation for Liver Research, The Roger Williams Institute of Hepatology, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Aikaterini Tourna
- Foundation for Liver Research, The Roger Williams Institute of Hepatology, London, UK
| | - Shilpa Chokshi
- Foundation for Liver Research, The Roger Williams Institute of Hepatology, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Elisabetta Bugianesi
- Department of Medical Sciences, Division of Gastroenterology, University of Turin, Turin, Italy
| | - Sara Della Torre
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Milan, Italy
| | - Daniele Prati
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Romeo
- Department of Molecular and Clinical Medicine, Gothenburg University, Gothenburg, Sweden
- Cardiology Department, Sahlgrenska Hospital, Gothenburg, Sweden
- Department of Medical and Surgical Science, Magna Græcia University, Catanzaro, Italy
| | - Luca Valenti
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.
| |
Collapse
|
2
|
Cherubini A, Ostadreza M, Jamialahmadi O, Pelusi S, Rrapaj E, Casirati E, Passignani G, Norouziesfahani M, Sinopoli E, Baselli G, Meda C, Dongiovanni P, Dondossola D, Youngson N, Tourna A, Chokshi S, Bugianesi E, Della Torre S, Prati D, Romeo S, Valenti L. Interaction between estrogen receptor-α and PNPLA3 p.I148M variant drives fatty liver disease susceptibility in women. Nat Med 2023; 29:2643-2655. [PMID: 37749332 PMCID: PMC10579099 DOI: 10.1038/s41591-023-02553-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/21/2023] [Indexed: 09/27/2023]
Abstract
Fatty liver disease (FLD) caused by metabolic dysfunction is the leading cause of liver disease and the prevalence is rising, especially in women. Although during reproductive age women are protected against FLD, for still unknown and understudied reasons some develop rapidly progressive disease at the menopause. The patatin-like phospholipase domain-containing 3 (PNPLA3) p.I148M variant accounts for the largest fraction of inherited FLD variability. In the present study, we show that there is a specific multiplicative interaction between female sex and PNPLA3 p.I148M in determining FLD in at-risk individuals (steatosis and fibrosis, P < 10-10; advanced fibrosis/hepatocellular carcinoma, P = 0.034) and in the general population (P < 10-7 for alanine transaminase levels). In individuals with obesity, hepatic PNPLA3 expression was higher in women than in men (P = 0.007) and in mice correlated with estrogen levels. In human hepatocytes and liver organoids, PNPLA3 was induced by estrogen receptor-α (ER-α) agonists. By chromatin immunoprecipitation and luciferase assays, we identified and characterized an ER-α-binding site within a PNPLA3 enhancer and demonstrated via CRISPR-Cas9 genome editing that this sequence drives PNPLA3 p.I148M upregulation, leading to lipid droplet accumulation and fibrogenesis in three-dimensional multilineage spheroids with stellate cells. These data suggest that a functional interaction between ER-α and PNPLA3 p.I148M variant contributes to FLD in women.
Collapse
Affiliation(s)
- Alessandro Cherubini
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Mahnoosh Ostadreza
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Oveis Jamialahmadi
- Department of Molecular and Clinical Medicine, Gothenburg University, Gothenburg, Sweden
| | - Serena Pelusi
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Eniada Rrapaj
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elia Casirati
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Giulia Passignani
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marjan Norouziesfahani
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Elena Sinopoli
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Guido Baselli
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Clara Meda
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Paola Dongiovanni
- Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniele Dondossola
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- General and Liver Transplant Surgery, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico and University of Milan, Centre of Preclinical Research, Milan, Italy
| | - Neil Youngson
- Foundation for Liver Research, The Roger Williams Institute of Hepatology, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Aikaterini Tourna
- Foundation for Liver Research, The Roger Williams Institute of Hepatology, London, UK
| | - Shilpa Chokshi
- Foundation for Liver Research, The Roger Williams Institute of Hepatology, London, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Elisabetta Bugianesi
- Department of Medical Sciences, Division of Gastroenterology, University of Turin, Turin, Italy
| | - Sara Della Torre
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Milan, Italy
| | - Daniele Prati
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Romeo
- Department of Molecular and Clinical Medicine, Gothenburg University, Gothenburg, Sweden
- Cardiology Department, Sahlgrenska Hospital, Gothenburg, Sweden
- Department of Medical and Surgical Science, Magna Græcia University, Catanzaro, Italy
| | - Luca Valenti
- Precision Medicine-Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.
| |
Collapse
|
3
|
Assante G, Chandrasekaran S, Ng S, Tourna A, Chung CH, Isse KA, Banks JL, Soffientini U, Filippi C, Dhawan A, Liu M, Rozen SG, Hoare M, Campbell P, Ballard JWO, Turner N, Morris MJ, Chokshi S, Youngson NA. Correction: Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease. Genome Med 2023; 15:38. [PMID: 37202796 DOI: 10.1186/s13073-023-01190-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023] Open
Affiliation(s)
- Gabriella Assante
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Sriram Chandrasekaran
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stanley Ng
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Aikaterini Tourna
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Carolina H Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kowsar A Isse
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Jasmine L Banks
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Ugo Soffientini
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Celine Filippi
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Anil Dhawan
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Mo Liu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Steven G Rozen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Matthew Hoare
- CRUK Cambridge Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | | | - J William O Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Nigel Turner
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | | | - Shilpa Chokshi
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Neil A Youngson
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK.
- Faculty of Life Sciences and Medicine, King's College London, London, UK.
- UNSW Sydney, Sydney, Australia.
| |
Collapse
|
4
|
Assante G, Tourna A, Carpani R, Ferrari F, Prati D, Peyvandi F, Blasi F, Bandera A, Le Guennec A, Chokshi S, Patel VC, Cox IJ, Valenti L, Youngson NA. Reduced circulating FABP2 in patients with moderate to severe COVID-19 may indicate enterocyte functional change rather than cell death. Sci Rep 2022; 12:18792. [PMID: 36335131 PMCID: PMC9637119 DOI: 10.1038/s41598-022-23282-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 10/25/2022] [Indexed: 11/08/2022] Open
Abstract
The gut is of importance in the pathology of COVID-19 both as a route of infection, and gut dysfunction influencing the severity of disease. Systemic changes caused by SARS-CoV-2 gut infection include alterations in circulating levels of metabolites, nutrients and microbial products which alter immune and inflammatory responses. Circulating plasma markers for gut inflammation and damage such as zonulin, lipopolysaccharide and β-glycan increase in plasma along with severity of disease. However, Intestinal Fatty Acid Binding Protein / Fatty Acid Binding Protein 2 (I-FABP/FABP2), a widely used biomarker for gut cell death, has paradoxically been shown to be reduced in moderate to severe COVID-19. We also found this pattern in a pilot cohort of mild (n = 18) and moderately severe (n = 19) COVID-19 patients in Milan from March to June 2020. These patients were part of the first phase of COVID-19 in Europe and were therefore all unvaccinated. After exclusion of outliers, patients with more severe vs milder disease showed reduced FABP2 levels (median [IQR]) (124 [368] vs. 274 [558] pg/mL, P < 0.01). A reduction in NMR measured plasma relative lipid-CH3 levels approached significance (median [IQR]) (0.081 [0.011] vs. 0.073 [0.024], P = 0.06). Changes in circulating lipid levels are another feature commonly observed in severe COVID-19 and a weak positive correlation was observed in the more severe group between reduced FABP2 and reduced relative lipid-CH3 and lipid-CH2 levels. FABP2 is a key regulator of enterocyte lipid import, a process which is inhibited by gut SARS-CoV-2 infection. We propose that the reduced circulating FABP2 in moderate to severe COVID-19 is a marker of infected enterocyte functional change rather than gut damage, which could also contribute to the development of hypolipidemia in patients with more severe disease.
Collapse
Affiliation(s)
- G Assante
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College, London, UK
| | - A Tourna
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College, London, UK
| | - R Carpani
- Fondazione IRCSS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - F Ferrari
- Fondazione IRCSS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - D Prati
- Fondazione IRCSS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
| | - F Peyvandi
- Fondazione IRCSS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
- Department of Pathophysiology and Transplantation, Università Degli Studi Di Milano, Milan, Italy
| | - F Blasi
- Fondazione IRCSS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
- Department of Pathophysiology and Transplantation, Università Degli Studi Di Milano, Milan, Italy
| | - A Bandera
- Fondazione IRCSS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy
- Department of Pathophysiology and Transplantation, Università Degli Studi Di Milano, Milan, Italy
| | - A Le Guennec
- Randall Centre for Cell & Molecular Biophysics, King's College, London, UK
| | - S Chokshi
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College, London, UK
| | - V C Patel
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK
- Faculty of Life Sciences & Medicine, King's College, London, UK
- Institute of Liver Studies, King's College Hospital, London, UK
| | - I J Cox
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK.
- Faculty of Life Sciences & Medicine, King's College, London, UK.
| | - L Valenti
- Fondazione IRCSS Ca' Granda Ospedale Maggiore Policlinico, Milano, Italy.
- Department of Pathophysiology and Transplantation, Università Degli Studi Di Milano, Milan, Italy.
| | - N A Youngson
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, UK.
- Faculty of Life Sciences & Medicine, King's College, London, UK.
| |
Collapse
|
5
|
Assante G, Chandrasekaran S, Ng S, Tourna A, Chung CH, Isse KA, Banks JL, Soffientini U, Filippi C, Dhawan A, Liu M, Rozen SG, Hoare M, Campbell P, Ballard JWO, Turner N, Morris MJ, Chokshi S, Youngson NA. Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease. Genome Med 2022; 14:67. [PMID: 35739588 PMCID: PMC9219160 DOI: 10.1186/s13073-022-01071-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 06/16/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The incidence of non-alcoholic fatty liver disease (NAFLD)-associated hepatocellular carcinoma (HCC) is increasing worldwide, but the steps in precancerous hepatocytes which lead to HCC driver mutations are not well understood. Here we provide evidence that metabolically driven histone hyperacetylation in steatotic hepatocytes can increase DNA damage to initiate carcinogenesis. METHODS Global epigenetic state was assessed in liver samples from high-fat diet or high-fructose diet rodent models, as well as in cultured immortalized human hepatocytes (IHH cells). The mechanisms linking steatosis, histone acetylation and DNA damage were investigated by computational metabolic modelling as well as through manipulation of IHH cells with metabolic and epigenetic inhibitors. Chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) and transcriptome (RNA-seq) analyses were performed on IHH cells. Mutation locations and patterns were compared between the IHH cell model and genome sequence data from preneoplastic fatty liver samples from patients with alcohol-related liver disease and NAFLD. RESULTS Genome-wide histone acetylation was increased in steatotic livers of rodents fed high-fructose or high-fat diet. In vitro, steatosis relaxed chromatin and increased DNA damage marker γH2AX, which was reversed by inhibiting acetyl-CoA production. Steatosis-associated acetylation and γH2AX were enriched at gene clusters in telomere-proximal regions which contained HCC tumour suppressors in hepatocytes and human fatty livers. Regions of metabolically driven epigenetic change also had increased levels of DNA mutation in non-cancerous tissue from NAFLD and alcohol-related liver disease patients. Finally, genome-scale network modelling indicated that redox balance could be a key contributor to this mechanism. CONCLUSIONS Abnormal histone hyperacetylation facilitates DNA damage in steatotic hepatocytes and is a potential initiating event in hepatocellular carcinogenesis.
Collapse
Affiliation(s)
- Gabriella Assante
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Sriram Chandrasekaran
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, 48109, USA
- Center for Bioinformatics and Computational Medicine, Ann Arbor, MI, 48109, USA
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Stanley Ng
- Wellcome Trust Sanger Institute, Cambridge, UK
| | - Aikaterini Tourna
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Carolina H Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Kowsar A Isse
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Jasmine L Banks
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | - Ugo Soffientini
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Celine Filippi
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Anil Dhawan
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Mo Liu
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Steven G Rozen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore, Singapore
| | - Matthew Hoare
- CRUK Cambridge Institute, Cambridge, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | | | - J William O Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia
| | - Nigel Turner
- UNSW Sydney, Sydney, Australia
- Cellular Bioenergetics Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia
| | | | - Shilpa Chokshi
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK
- King's College London, Faculty of Life Sciences and Medicine, London, UK
| | - Neil A Youngson
- Institute of Hepatology, Foundation for Liver Research, 111 Coldharbour Lane, London, SE5 9NT, UK.
- King's College London, Faculty of Life Sciences and Medicine, London, UK.
- UNSW Sydney, Sydney, Australia.
| |
Collapse
|
6
|
Yamashita H, Tourna A, Akita M, Itoh T, Chokshi S, Ajiki T, Fukumoto T, Youngson NA, Zen Y. Epigenetic upregulation of TET2 is an independent poor prognostic factor for intrahepatic cholangiocarcinoma. Virchows Arch 2021; 480:1077-1085. [PMID: 34905094 PMCID: PMC9033729 DOI: 10.1007/s00428-021-03251-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/19/2021] [Accepted: 12/05/2021] [Indexed: 11/28/2022]
Abstract
Mutations in IDH1/2 and the epigenetic silencing of TET2 occur in leukaemia or glioma in a mutually exclusive manner. Although intrahepatic cholangiocarcinoma (iCCA) may harbour IDH1/2 mutations, the contribution of TET2 to carcinogenesis remains unknown. In the present study, the expression and promoter methylation of TET2 were investigated in iCCA. The expression of TET2 was assessed in 52 cases of iCCA (small-duct type, n = 33; large-duct type, n = 19) by quantitative PCR, immunohistochemistry (IHC) and a sequencing-based methylation assay, and its relationships with clinicopathological features and alterations in cancer-related genes (e.g., KRAS and IDH1) were investigated. In contrast to non-neoplastic bile ducts, which were negative for TET2 on IHC, 42 cases (81%) of iCCA showed the nuclear overexpression of TET2. Based on IHC scores (area × intensity), these cases were classified as TET2-high (n = 25) and TET2-low (n = 27). The histological type, tumour size, lymph node metastasis and frequency of mutations in cancer-related genes did not significantly differ between the two groups. Overall and recurrence-free survival were significantly worse in patients with TET2-high iCCA than in those with TET2-low iCCA. A multivariate analysis identified the high expression of TET2 as an independent prognostic factor (HR = 2.94; p = 0.007). The degree of methylation at two promoter CpG sites was significantly less in TET2-high iCCA than in TET2-low iCCA or non-cancer tissue. In conclusion, in contrast to other IDH-related neoplasms, TET2 overexpression is common in iCCA of both subtypes, and its high expression, potentially induced by promoter hypomethylation, is an independent poor prognostic factor.
Collapse
Affiliation(s)
- Hironori Yamashita
- Institute of Liver Studies, King's College Hospital, London, UK.,King's College London, London, UK.,Institute of Hepatology, Foundation for Liver Research, London, UK.,Department of Hepato-Biliary-Pancreatic Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | | | - Masayuki Akita
- Department of Hepato-Biliary-Pancreatic Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tomoo Itoh
- Department of Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shilpa Chokshi
- Institute of Hepatology, Foundation for Liver Research, London, UK
| | - Tetsuo Ajiki
- Department of Hepato-Biliary-Pancreatic Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takumi Fukumoto
- Department of Hepato-Biliary-Pancreatic Surgery, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Neil A Youngson
- Institute of Hepatology, Foundation for Liver Research, London, UK. .,Faculty of Life Sciences and Medicine, King's College London, London, UK. .,School of Medical Sciences, UNSW Sydney, Sydney, Australia.
| | - Yoh Zen
- Institute of Liver Studies, King's College Hospital, London, UK. .,King's College London, London, UK.
| |
Collapse
|
7
|
Cespiati A, Youngson NA, Tourna A, Valenti L. Genetics and Epigenetics in the Clinic: Precision Medicine in the Management of Fatty Liver Disease. Curr Pharm Des 2020; 26:998-1009. [PMID: 31969087 DOI: 10.2174/1381612826666200122151251] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/16/2019] [Indexed: 11/22/2022]
Abstract
This narrative review will discuss the current evidence supporting the possible application of precision or personalized medicine to the management of nonalcoholic or "metabolic" fatty liver disease (NAFLD), based on recent progress in the understanding of the genetics and epigenetics of the disease. The prevalence of NAFLD, which can progress to cirrhosis and hepatocellular carcinoma, is constantly increasing worldwide. Accurate noninvasive predictors of liver disease progression, as well as of cardiovascular complications of NAFLD, are urgently needed. Evidence is now reporting that the genetic and epigenetic factors involved in NAFLD development can be used to develop risk scores for liver-related complications, which may show the possibility to implement programs for targeted screening and surveillance of complications. Moreover, genetic and epigenetic factors identifying specific sub-phenotypes of NAFLD can predict the individual response to pharmacological therapies. Finally, we describe opportunities for gene-targeted therapeutic approaches in NAFLD, where the genetic variants represent therapeutic targets for precision therapy approaches.
Collapse
Affiliation(s)
- Annalisa Cespiati
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Neil A Youngson
- The Institute of Hepatology London, Foundation for Liver Research, London, United Kingdom.,School of Medical Sciences, UNSW Sydney, New South Wales, Australia
| | - Aikaterini Tourna
- The Institute of Hepatology London, Foundation for Liver Research, London, United Kingdom
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Translational Medicine - Department of Transfusion Medicine and Hematology, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| |
Collapse
|
8
|
Repana D, Nulsen J, Dressler L, Bortolomeazzi M, Venkata SK, Tourna A, Yakovleva A, Palmieri T, Ciccarelli FD. The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens. Genome Biol 2019; 20:1. [PMID: 30606230 PMCID: PMC6317252 DOI: 10.1186/s13059-018-1612-0] [Citation(s) in RCA: 336] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 12/12/2018] [Indexed: 02/06/2023] Open
Abstract
The Network of Cancer Genes (NCG) is a manually curated repository of 2372 genes whose somatic modifications have known or predicted cancer driver roles. These genes were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34,905 cancer donors and multiple primary sites. This represents a more than 1.5-fold content increase compared to the previous version. NCG also annotates properties of cancer genes, such as duplicability, evolutionary origin, RNA and protein expression, miRNA and protein interactions, and protein function and essentiality. NCG is accessible at http://ncg.kcl.ac.uk/ .
Collapse
Affiliation(s)
- Dimitra Repana
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Joel Nulsen
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Lisa Dressler
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Michele Bortolomeazzi
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Santhilata Kuppili Venkata
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Aikaterini Tourna
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Anna Yakovleva
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Tommaso Palmieri
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| | - Francesca D. Ciccarelli
- Cancer Systems Biology Laboratory, The Francis Crick Institute, London, NW1 1AT UK
- School of Cancer and Pharmaceutical Sciences, King’s College London, London, SE1 1UL UK
| |
Collapse
|