1
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Wang YH, Masson E, Liao Z, Férec C, Zou WB, Chen JM. Strengths and limitations of AlphaMissense in CPA1 missense variant classification. Gut 2024:gutjnl-2024-332120. [PMID: 38471746 DOI: 10.1136/gutjnl-2024-332120] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024]
Affiliation(s)
- Ya-Hui Wang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Masson
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
- CHRU Brest, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
| | - Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, Naval Medical University, Shanghai, China
- Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- Univ Brest, Inserm, EFS, UMR 1078, GGB, F-29200 Brest, France
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2
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Qian Z, Liang J, Huang R, Song W, Ying J, Bi X, Zhao J, Shi Z, Liu W, Liu J, Li Z, Zhou J, Huang Z, Zhang Y, Zhao D, Wu J, Wang L, Chen X, Mao R, Zhou Y, Guo L, Hu H, Ge D, Li X, Luo Z, Yao J, Li T, Chen Q, Wang B, Wei Z, Chen K, Qu C, Cai J, Jiao Y, Bao L, Zhao H. HBV integrations reshaping genomic structures promote hepatocellular carcinoma. Gut 2024:gutjnl-2023-330414. [PMID: 38395437 DOI: 10.1136/gutjnl-2023-330414] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/01/2024] [Indexed: 02/25/2024]
Abstract
OBJECTIVE Hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC), mostly characterised by HBV integrations, is prevalent worldwide. Previous HBV studies mainly focused on a few hotspot integrations. However, the oncogenic role of the other HBV integrations remains unclear. This study aimed to elucidate HBV integration-induced tumourigenesis further. DESIGN Here, we illuminated the genomic structures encompassing HBV integrations in 124 HCCs across ages using whole genome sequencing and Nanopore long reads. We classified a repertoire of integration patterns featured by complex genomic rearrangement. We also conducted a clustered regularly interspaced short palindromic repeat (CRISPR)-based gain-of-function genetic screen in mouse hepatocytes. We individually activated each candidate gene in the mouse model to uncover HBV integration-mediated oncogenic aberration that elicits tumourigenesis in mice. RESULTS These HBV-mediated rearrangements are significantly enriched in a bridge-fusion-bridge pattern and interchromosomal translocations, and frequently led to a wide range of aberrations including driver copy number variations in chr 4q, 5p (TERT), 6q, 8p, 16q, 9p (CDKN2A/B), 17p (TP53) and 13q (RB1), and particularly, ultra-early amplifications in chr8q. Integrated HBV frequently contains complex structures correlated with the translocation distance. Paired breakpoints within each integration event usually exhibit different microhomology, likely mediated by different DNA repair mechanisms. HBV-mediated rearrangements significantly correlated with young age, higher HBV DNA level and TP53 mutations but were less prevalent in the patients subjected to prior antiviral therapies. Finally, we recapitulated the TONSL and TMEM65 amplification in chr8q led by HBV integration using CRISPR/Cas9 editing and demonstrated their tumourigenic potentials. CONCLUSION HBV integrations extensively reshape genomic structures and promote hepatocarcinogenesis (graphical abstract), which may occur early in a patient's life.
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Affiliation(s)
- Zhaoyang Qian
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
| | - Junbo Liang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Rong Huang
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Wei Song
- Department of Biochemistry and Molecular Biology, State Key Laboratory of Common Mechanism Research for Major Diseases, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Jianming Ying
- Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinyu Bi
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianjun Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhenyu Shi
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Wenjie Liu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianmei Liu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiyu Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianguo Zhou
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhen Huang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yefan Zhang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dongbing Zhao
- Department of Pancreatic and Gastric Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianxiong Wu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liming Wang
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiao Chen
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rui Mao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanchi Zhou
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lei Guo
- Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Hanjie Hu
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Dazhuang Ge
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xingchen Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiwen Luo
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinjie Yao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tengyan Li
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qichen Chen
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bingzhi Wang
- Department of Pathology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhewen Wei
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Kun Chen
- Department of Immunology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chunfeng Qu
- Department of Immunology, State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianqiang Cai
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li Bao
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Tianjin, China
- Key Laboratory of Cancer Prevention and Therapy, Tianjin, China
- Liver Cancer Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Hong Zhao
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Gene Editing Screening and R&D of Digestive System Tumor Drugs, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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3
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Cording S, Lhermitte L, Malamut G, Berrabah S, Trinquand A, Guegan N, Villarese P, Kaltenbach S, Meresse B, Khater S, Dussiot M, Bras M, Cheminant M, Tesson B, Bole-Feysot C, Bruneau J, Molina TJ, Sibon D, Macintyre E, Hermine O, Cellier C, Asnafi V, Cerf-Bensussan N. Oncogenetic landscape of lymphomagenesis in coeliac disease. Gut 2022; 71:497-508. [PMID: 33579790 PMCID: PMC8862029 DOI: 10.1136/gutjnl-2020-322935] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/26/2021] [Accepted: 01/27/2021] [Indexed: 12/16/2022]
Abstract
OBJECTIVE Enteropathy-associated T-cell lymphoma (EATL) is a rare but severe complication of coeliac disease (CeD), often preceded by low-grade clonal intraepithelial lymphoproliferation, referred to as type II refractory CeD (RCDII). Knowledge on underlying oncogenic mechanisms remains scarce. Here, we analysed and compared the mutational landscape of RCDII and EATL in order to identify genetic drivers of CeD-associated lymphomagenesis. DESIGN Pure populations of RCDII-cells derived from intestinal biopsies (n=9) or sorted from blood (n=2) were analysed by whole exome sequencing, comparative genomic hybridisation and RNA sequencing. Biopsies from RCDII (n=50), EATL (n=19), type I refractory CeD (n=7) and uncomplicated CeD (n=18) were analysed by targeted next-generation sequencing. Moreover, functional in vitro studies and drug testing were performed in RCDII-derived cell lines. RESULTS 80% of RCDII and 90% of EATL displayed somatic gain-of-functions mutations in the JAK1-STAT3 pathway, including a remarkable p.G1097 hotspot mutation in the JAK1 kinase domain in approximately 50% of cases. Other recurrent somatic events were deleterious mutations in nuclear factor kappa-light-chain-enhancer of activated B-cells (NF-κB) regulators TNFAIP3 and TNIP3 and potentially oncogenic mutations in TET2, KMT2D and DDX3X. JAK1 inhibitors, and the proteasome inhibitor bortezomib could block survival and proliferation of malignant RCDII-cell lines. CONCLUSION Mutations activating the JAK1-STAT3 pathway appear to be the main drivers of CeD-associated lymphomagenesis. In concert with mutations in negative regulators of NF-κB, they may favour the clonal emergence of malignant lymphocytes in the cytokine-rich coeliac intestine. The identified mutations are attractive therapeutic targets to treat RCDII and block progression towards EATL.
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Affiliation(s)
- Sascha Cording
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR 1163, Paris, France
| | - Ludovic Lhermitte
- Université de Paris, Institut Necker-Enfants Malades, INSERM UMR 1151, Paris, France,Laboratory of Onco-Haematology, AP-HP, Hôpital Necker Enfants-Malades, Paris, France
| | - Georgia Malamut
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR 1163, Paris, France,Department of Gastroenterology, AP-HP, Hôpital Cochin, Paris, France
| | - Sofia Berrabah
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR 1163, Paris, France
| | - Amélie Trinquand
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR 1163, Paris, France,Haematology Department, National Children’s Research Centre, Children’s Health Ireland at Crumlin, Dublin, Ireland
| | - Nicolas Guegan
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR 1163, Paris, France
| | - Patrick Villarese
- Université de Paris, Institut Necker-Enfants Malades, INSERM UMR 1151, Paris, France,Laboratory of Onco-Haematology, AP-HP, Hôpital Necker Enfants-Malades, Paris, France
| | - Sophie Kaltenbach
- Department of Cytogenetics, AP-HP, Hôpital Necker Enfants-Malades, Paris, France
| | - Bertrand Meresse
- Université de Lille, CHU Lille, INSERM UMR 1286 – INFINITE – Institute for Translational Research in Inflammation, Lille, France
| | - Sherine Khater
- Department of Gastroenterology, AP-HP, Hôpital Européen Georges Pompidou, Paris, France
| | - Michael Dussiot
- Université de Paris, Imagine Institute, Laboratory of Molecular Mechanisms of Hematological Disorders and Therapeutic Implications, INSERM UMR 1163, Paris, France
| | - Marc Bras
- Université de Paris, Imagine Institute, Bioinformatics Platform, Paris, France
| | - Morgane Cheminant
- Université de Paris, Imagine Institute, Laboratory of Molecular Mechanisms of Hematological Disorders and Therapeutic Implications, INSERM UMR 1163, Paris, France,Clinical Haematology, AP-HP, Hôpital Necker Enfants-Malades, Paris, France
| | | | | | - Julie Bruneau
- Department of Pathology, AP-HP, Hôpital Necker Enfants-Malades, Paris, France
| | - Thierry Jo Molina
- Université de Paris, Imagine Institute, Laboratory of Molecular Mechanisms of Hematological Disorders and Therapeutic Implications, INSERM UMR 1163, Paris, France,Department of Pathology, AP-HP, Hôpital Necker Enfants-Malades, Paris, France
| | - David Sibon
- Clinical Haematology, AP-HP, Hôpital Necker Enfants-Malades, Paris, France
| | - Elizabeth Macintyre
- Université de Paris, Institut Necker-Enfants Malades, INSERM UMR 1151, Paris, France,Laboratory of Onco-Haematology, AP-HP, Hôpital Necker Enfants-Malades, Paris, France
| | - Olivier Hermine
- Université de Paris, Imagine Institute, Laboratory of Molecular Mechanisms of Hematological Disorders and Therapeutic Implications, INSERM UMR 1163, Paris, France,Clinical Haematology, AP-HP, Hôpital Necker Enfants-Malades, Paris, France
| | - Christophe Cellier
- Department of Gastroenterology, AP-HP, Hôpital Européen Georges Pompidou, Paris, France
| | - Vahid Asnafi
- Université de Paris, Institut Necker-Enfants Malades, INSERM UMR 1151, Paris, France,Laboratory of Onco-Haematology, AP-HP, Hôpital Necker Enfants-Malades, Paris, France
| | - Nadine Cerf-Bensussan
- Université de Paris, Imagine Institute, Laboratory of Intestinal Immunity, INSERM UMR 1163, Paris, France
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4
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Wu H, Boulling A, Cooper DN, Li ZS, Liao Z, Chen JM, Férec C. In vitro and in silico evidence against a significant effect of the SPINK1 c.194G>A variant on pre-mRNA splicing. Gut 2017; 66:2195-2196. [PMID: 28320769 DOI: 10.1136/gutjnl-2017-313948] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 02/21/2017] [Accepted: 02/22/2017] [Indexed: 12/08/2022]
Affiliation(s)
- Hao Wu
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China.,Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France.,Etablissement Français du Sang (EFS)-Bretagne, Brest, France.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Arnaud Boulling
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France.,Etablissement Français du Sang (EFS)-Bretagne, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France.,Etablissement Français du Sang (EFS)-Bretagne, Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
| | - Claude Férec
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France.,Etablissement Français du Sang (EFS)-Bretagne, Brest, France.,Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France.,Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Universitaire (CHU) Brest, Hôpital Morvan, Brest, France
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5
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Ho DWH, Chan LK, Chiu YT, Xu IMJ, Poon RTP, Cheung TT, Tang CN, Tang VWL, Lo ILO, Lam PWY, Yau DTW, Li MX, Wong CM, Ng IOL. TSC1/2 mutations define a molecular subset of HCC with aggressive behaviour and treatment implication. Gut 2017; 66:1496-1506. [PMID: 27974549 PMCID: PMC5530480 DOI: 10.1136/gutjnl-2016-312734] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 11/07/2016] [Accepted: 11/23/2016] [Indexed: 12/12/2022]
Abstract
OBJECTIVE We investigated the mutational landscape of mammalian target of rapamycin (mTOR) signalling cascade in hepatocellular carcinomas (HCCs) with chronic HBV background, aiming to evaluate and delineate mutation-dependent mechanism of mTOR hyperactivation in hepatocarcinogenesis. DESIGN We performed next-generation sequencing on human HCC samples and cell line panel. Systematic mutational screening of mTOR pathway-related genes was undertaken and mutant genes were evaluated based on their recurrence. Protein expressions of tuberous sclerosis complex (TSC)1, TSC2 and pRPS6 were assessed by immunohistochemistry in human HCC samples. Rapamycin sensitivity was estimated by colony-formation assay in HCC cell lines and the treatment was further tested using our patient-derived tumour xenograft (PDTX) models. RESULTS We identified and confirmed multiple mTOR components as recurrently mutated in HBV-associated HCCs. Of significance, we detected frequent (16.2%, n=18/111) mutations of TSC1 and TSC2 genes in the HCC samples. The spectrum of TSC1/2 mutations likely disrupts the endogenous gene functions in suppressing the downstream mTOR activity through different mechanisms and leads to more aggressive tumour behaviour. Mutational disruption of TSC1 and TSC2 was also observed in HCC cell lines and our PDTX models. TSC-mutant cells exhibited reduced colony-forming ability on rapamycin treatment. With the use of biologically relevant TSC2-mutant PDTXs, we demonstrated the therapeutic benefits of the hypersensitivity towards rapamycin treatment. CONCLUSIONS Taken together, our findings suggest the significance of previously undocumented mutation-dependent mTOR hyperactivation and frequent TSC1/2 mutations in HBV-associated HCCs. They define a molecular subset of HCC having genetic aberrations in mTOR signalling, with potential significance of effective specific drug therapy.
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Affiliation(s)
- Daniel W H Ho
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Lo K Chan
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yung T Chiu
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Iris M J Xu
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Ronnie T P Poon
- State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, Hong Kong,Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Tan T Cheung
- Department of Surgery, The University of Hong Kong, Hong Kong, Hong Kong
| | - Chung N Tang
- Department of Surgery, Pamela Youde Hospital, Hong Kong, Hong Kong
| | - Victor W L Tang
- Department of Pathology, Pamela Youde Hospital, Hong Kong, Hong Kong
| | - Irene L O Lo
- Department of Surgery, Queen Elizabeth Hospital, Hong Kong, Hong Kong
| | - Polly W Y Lam
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, Hong Kong
| | - Derek T W Yau
- Department of Pathology, Queen Elizabeth Hospital, Hong Kong, Hong Kong
| | - Miao X Li
- Department of Psychiatry and Center for Genomics Science, The University of Hong Kong, Hong Kong, Hong Kong
| | - Chun M Wong
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
| | - Irene O L Ng
- Department of Pathology, The University of Hong Kong, Hong Kong, Hong Kong,State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, Hong Kong
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6
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Buchanan DD, Clendenning M, Zhuoer L, Stewart JR, Joseland S, Woodall S, Arnold J, Semotiuk K, Aronson M, Holter S, Gallinger S, Jenkins MA, Sweet K, Macrae FA, Winship IM, Parry S, Rosty C. Lack of evidence for germline RNF43 mutations in patients with serrated polyposis syndrome from a large multinational study. Gut 2017; 66:1170-1172. [PMID: 27582512 DOI: 10.1136/gutjnl-2016-312773] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 08/04/2016] [Accepted: 08/07/2016] [Indexed: 12/08/2022]
Affiliation(s)
- Daniel D Buchanan
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Mark Clendenning
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Li Zhuoer
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Jenna R Stewart
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Sharelle Joseland
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Sonja Woodall
- New Zealand Familial Gastrointestinal Cancer Service, Auckland, New Zealand
| | - Julie Arnold
- New Zealand Familial Gastrointestinal Cancer Service, Auckland, New Zealand
| | - Kara Semotiuk
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Melyssa Aronson
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Spring Holter
- Zane Cohen Centre for Digestive Diseases, Familial Gastrointestinal Cancer Registry, Mt Sinai Hospital, Toronto, Ontario, Canada
| | - Steven Gallinger
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Parkville, Victoria, Australia
| | - Kevin Sweet
- Division of Human Genetics, Ohio State University Medical Centre, Columbus, Ohio, USA
| | - Finlay A Macrae
- Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia.,Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Australia.,Department of Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia.,Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Australia
| | - Susan Parry
- New Zealand Familial Gastrointestinal Cancer Service, Auckland, New Zealand
| | - Christophe Rosty
- Colorectal Oncogenomics Group, Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Parkville, Victoria, Australia.,Envoi Specialist Pathologists, Herston, Queensland, Australia.,School of Medicine, The University of Queensland, Herston, Queensland, Australia
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7
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Mennonna D, Maccalli C, Romano MC, Garavaglia C, Capocefalo F, Bordoni R, Severgnini M, De Bellis G, Sidney J, Sette A, Gori A, Longhi R, Braga M, Ghirardelli L, Baldari L, Orsenigo E, Albarello L, Zino E, Fleischhauer K, Mazzola G, Ferrero N, Amoroso A, Casorati G, Parmiani G, Dellabona P. T cell neoepitope discovery in colorectal cancer by high throughput profiling of somatic mutations in expressed genes. Gut 2017; 66:454-463. [PMID: 26681737 PMCID: PMC5534766 DOI: 10.1136/gutjnl-2015-309453] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 11/04/2015] [Accepted: 11/06/2015] [Indexed: 12/25/2022]
Abstract
OBJECTIVE Patient-specific (unique) tumour antigens, encoded by somatically mutated cancer genes, generate neoepitopes that are implicated in the induction of tumour-controlling T cell responses. Recent advancements in massive DNA sequencing combined with robust T cell epitope predictions have allowed their systematic identification in several malignancies. DESIGN We undertook the identification of unique neoepitopes in colorectal cancers (CRCs) by using high-throughput sequencing of cDNAs expressed by standard cancer cell cultures, and by related cancer stem/initiating cells (CSCs) cultures, coupled with a reverse immunology approach not requiring human leukocyte antigen (HLA) allele-specific epitope predictions. RESULTS Several unique mutated antigens of CRC, shared by standard cancer and related CSC cultures, were identified by this strategy. CD8+ and CD4+ T cells, either autologous to the patient or derived from HLA-matched healthy donors, were readily expanded in vitro by peptides spanning different cancer mutations and specifically recognised differentiated cancer cells and CSC cultures, expressing the mutations. Neoepitope-specific CD8+ T cell frequency was also increased in a patient, compared with healthy donors, supporting the occurrence of clonal expansion in vivo. CONCLUSIONS These results provide a proof-of-concept approach for the identification of unique neoepitopes that are immunogenic in patients with CRC and can also target T cells against the most aggressive CSC component.
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Affiliation(s)
- Daniele Mennonna
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | - Cristina Maccalli
- Division of Experimental Oncology, San Raffaele Scientific Institute, Milan, Italy
| | - Michele C Romano
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | - Claudio Garavaglia
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | - Filippo Capocefalo
- Division of Experimental Oncology, San Raffaele Scientific Institute, Milan, Italy
| | - Roberta Bordoni
- Institute for Biomedical Technologies, National Research Council, Segrate, Italy
| | - Marco Severgnini
- Institute for Biomedical Technologies, National Research Council, Segrate, Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies, National Research Council, Segrate, Italy
| | - John Sidney
- La Jolla Institute for Allergy & Immunology, La Jolla, California, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy & Immunology, La Jolla, California, USA
| | - Alessandro Gori
- Institute of Molecular Recognition Chemistry, National Research Council, Milan, Italy
| | - Renato Longhi
- Institute of Molecular Recognition Chemistry, National Research Council, Milan, Italy
| | - Marco Braga
- Department of Surgery, San Raffaele Scientific Institute, Milan, Italy
| | - Luca Ghirardelli
- Department of Surgery, San Raffaele Scientific Institute, Milan, Italy
| | - Ludovica Baldari
- Department of Surgery, San Raffaele Scientific Institute, Milan, Italy
| | - Elena Orsenigo
- Department of Surgery, San Raffaele Scientific Institute, Milan, Italy
| | - Luca Albarello
- Department of Pathology, San Raffaele Scientific Institute, Milano, Italy
| | - Elisabetta Zino
- Unit of Molecular and Functional Immunogenetics, San Raffaele Scientific Institute, Milan, Italy
| | - Katharina Fleischhauer
- Unit of Molecular and Functional Immunogenetics, San Raffaele Scientific Institute, Milan, Italy,Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany
| | - Gina Mazzola
- Department of Medical Sciences, Center for Transplantation Biology and Immunogenetics, University of Turin, Turin, Italy
| | - Norma Ferrero
- Department of Medical Sciences, Center for Transplantation Biology and Immunogenetics, University of Turin, Turin, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, Center for Transplantation Biology and Immunogenetics, University of Turin, Turin, Italy
| | - Giulia Casorati
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
| | - Giorgio Parmiani
- Division of Experimental Oncology, San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Dellabona
- Division of Immunology, Transplantation and Infectious Diseases, San Raffaele Scientific Institute, Milan, Italy
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8
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Huang KK, McPherson JR, Tay ST, Das K, Tan IB, Ng CCY, Chia NY, Zhang SL, Myint SS, Hu L, Rajasegaran V, Huang D, Loh JL, Gan A, Sairi ANH, Sam XX, Dominguez LT, Lee M, Soo KC, Ooi LLPJ, Ong HS, Chung A, Chow PKH, Wong WK, Selvarajan S, Ong CK, Lim KH, Nandi T, Rozen S, Teh BT, Quek R, Tan P. SETD2 histone modifier loss in aggressive GI stromal tumours. Gut 2016; 65:1960-1972. [PMID: 26338826 DOI: 10.1136/gutjnl-2015-309482] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 07/31/2015] [Accepted: 08/15/2015] [Indexed: 12/29/2022]
Abstract
BACKGROUND GI stromal tumours (GISTs) are clinically heterogenous exhibiting varying degrees of disease aggressiveness in individual patients. OBJECTIVES We sought to identify genetic alterations associated with high-risk GIST, explore their molecular consequences, and test their utility as prognostic markers. DESIGNS Exome sequencing of 18 GISTs was performed (9 patients with high-risk/metastatic and 5 patients with low/intermediate-risk), corresponding to 11 primary and 7 metastatic tumours. Candidate alterations were validated by prevalence screening in an independent patient cohort (n=120). Functional consequences of SETD2 mutations were investigated in primary tissues and cell lines. Transcriptomic profiles for 8 GISTs (4 SETD2 mutated, 4 SETD2 wild type) and DNA methylation profiles for 22 GISTs (10 SETD2 mutated, 12 SETD2 wild type) were analysed. Statistical associations between molecular, clinicopathological factors, and relapse-free survival were determined. RESULTS High-risk GISTs harboured increased numbers of somatic mutations compared with low-risk GISTs (25.2 mutations/high-risk cases vs 6.8 mutations/low-risk cases; two sample t test p=3.1×10-5). Somatic alterations in the SETD2 histone modifier gene occurred in 3 out of 9 high-risk/metastatic cases but no low/intermediate-risk cases. Prevalence screening identified additional SETD2 mutations in 7 out of 80 high-risk/metastatic cases but no low/intermediate-risk cases (n=29). Combined, the frequency of SETD2 mutations was 11.2% (10/89) and 0% (0/34) in high-risk and low-risk GISTs respectively. SETD2 mutant GISTs exhibited decreased H3K36me3 expression while SETD2 silencing promoted DNA damage in GIST-T1 cells. In gastric GISTs, SETD2 mutations were associated with overexpression of HOXC cluster genes and a DNA methylation signature of hypomethylated heterochromatin. Gastric GISTs with SETD2 mutations, or GISTs with hypomethylated heterochromatin, showed significantly shorter relapse-free survival on univariate analysis (log rank p=4.1×10-5). CONCLUSIONS Our data suggest that SETD2 is a novel GIST tumour suppressor gene associated with disease progression. Assessing SETD2 genetic status and SETD2-associated epigenomic phenotypes may guide risk stratification and provide insights into mechanisms of GIST clinical aggressiveness.
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Affiliation(s)
- Kie Kyon Huang
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - John R McPherson
- Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Su Ting Tay
- Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Kakoli Das
- Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Iain Beehuat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.,Genome Institute of Singapore, Singapore, Singapore
| | - Cedric Chuan Young Ng
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Na-Yu Chia
- Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Shen Li Zhang
- Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Swe Swe Myint
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Longyu Hu
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Vikneswari Rajasegaran
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Dachuan Huang
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Jia Liang Loh
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Anna Gan
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Alisa Noor Hidayah Sairi
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Xin Xiu Sam
- Department of Pathology, Singapore General Hospital, 11 Hospital Drive, Singapore, Singapore
| | | | - Minghui Lee
- Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Khee Chee Soo
- Division of Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - London Lucien Peng Jin Ooi
- Department of Hepatopancreaticobiliary & Transplant Surgery, Singapore General Hospital, Singapore, Singapore
| | - Hock Soo Ong
- Department of Upper GI & Bariatric Surgery, Singapore General Hospital, Singapore, Singapore
| | - Alexander Chung
- Department of Hepatopancreaticobiliary & Transplant Surgery, Singapore General Hospital, Singapore, Singapore
| | - Pierce Kah-Hoe Chow
- Division of Surgical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore.,Office of Clinical Sciences, Duke-NUS Graduate Medical School, Singapore, Singapore.,Program in Translational and Clinical Liver Research, National Cancer Center Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Wai Keong Wong
- Department of Upper GI & Bariatric Surgery, Singapore General Hospital, Singapore, Singapore
| | | | - Choon Kiat Ong
- Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Kiat Hon Lim
- Department of Pathology, Singapore General Hospital, 11 Hospital Drive, Singapore, Singapore
| | | | - Steve Rozen
- Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Bin Tean Teh
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.,Laboratory of Cancer Epigenome, Division of Medical Sciences, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Richard Quek
- Division of Medical Oncology, National Cancer Centre Singapore, 11 Hospital Drive, Singapore, Singapore
| | - Patrick Tan
- Cancer Science Institute of Singapore, National University of Singapore, Center for Translational Medicine, Singapore, Singapore.,Program in Cancer and Stem Cell Biology, Duke-NUS Graduate Medical School, Singapore, Singapore.,Genome Institute of Singapore, Singapore, Singapore
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9
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Zou WB, Masson E, Boulling A, Cooper DN, Li ZS, Liao Z, Férec C, Chen JM. Digging deeper into the intronic sequences of the SPINK1 gene. Gut 2016; 65:1055-6. [PMID: 26884424 DOI: 10.1136/gutjnl-2016-311428] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 01/21/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Masson
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Universitaire (CHU) Brest, Hôpital Morvan, Brest, France
| | - Arnaud Boulling
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Claude Férec
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Universitaire (CHU) Brest, Hôpital Morvan, Brest, France Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
| | - Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
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10
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Zou WB, Boulling A, Masson E, Cooper DN, Liao Z, Li ZS, Férec C, Chen JM. Clarifying the clinical relevance of SPINK1 intronic variants in chronic pancreatitis. Gut 2016; 65:884-6. [PMID: 26719302 DOI: 10.1136/gutjnl-2015-311168] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 12/03/2015] [Indexed: 12/08/2022]
Affiliation(s)
- Wen-Bin Zou
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Arnaud Boulling
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France
| | - Emmanuelle Masson
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Universitaire (CHU) Brest, Hôpital Morvan, Brest, France
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Zhao-Shen Li
- Department of Gastroenterology, Changhai Hospital, the Second Military Medical University, Shanghai, China Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Claude Férec
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France Laboratoire de Génétique Moléculaire et d'Histocompatibilité, Centre Hospitalier Universitaire (CHU) Brest, Hôpital Morvan, Brest, France Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
| | - Jian-Min Chen
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1078, Brest, France Etablissement Français du Sang (EFS)-Bretagne, Brest, France Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale (UBO), Brest, France
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11
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Zeissig S, Petersen BS, Tomczak M, Melum E, Huc-Claustre E, Dougan SK, Laerdahl JK, Stade B, Forster M, Schreiber S, Weir D, Leichtner AM, Franke A, Blumberg RS. Early-onset Crohn's disease and autoimmunity associated with a variant in CTLA-4. Gut 2015; 64:1889-97. [PMID: 25367873 PMCID: PMC4512923 DOI: 10.1136/gutjnl-2014-308541] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 10/09/2014] [Indexed: 12/17/2022]
Abstract
OBJECTIVE IBD is a group of complex, systemic disorders associated with intestinal inflammation and extraintestinal manifestations. Recent studies revealed Mendelian forms of IBD, which contributed significantly to our understanding of disease pathogenesis and the heritability of IBD. DESIGN We performed exome sequencing in a family with Crohn's disease (CD) and severe autoimmunity, analysed immune cell phenotype and function in affected and non-affected individuals, and performed in silico and in vitro analyses of cytotoxic T lymphocyte-associated protein 4 (CTLA-4) structure and function. RESULTS A novel missense variant was identified in CTLA4 encoding CTLA-4, a coinhibitory protein expressed by T cells and required for regulation of T cell activation. The residue affected by the mutation, CTLA-4 Tyr60, is evolutionarily highly conserved, and the identified Y60C variant is predicted to affect protein folding and structural stability and demonstrated to cause impaired CTLA-4 dimerisation and CD80 binding. Intestinal inflammation and autoimmunity in carriers of CTLA-4 Y60C exhibit incomplete penetrance with a spectrum of clinical presentations ranging from asymptomatic carrier status to fatal autoimmunity and intestinal inflammation. In a clinically affected CTLA-4 Y60C carrier, T cell proliferation was increased in vitro and associated with an increased ratio of memory to naive T cells in vivo, consistent with impaired regulation of T cell activation. CONCLUSIONS Our results support the concept that variants in CTLA4 provide the basis for a novel Mendelian form of early-onset CD associated with systemic autoimmunity. Incomplete penetrance of autoimmunity further indicates the presence of other genetic and/or environmental modifiers.
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Affiliation(s)
- Sebastian Zeissig
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Kiel, Germany,Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michal Tomczak
- Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Espen Melum
- Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA,Norwegian PSC Research Center, Division of Cancer, Surgery and Transplantation, Oslo University Hospital, Rikshospitalet, Oslo, Norway,K.G. Jebsen Inflammation Research Centre, Research Institute of Internal Medicine, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Emilie Huc-Claustre
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Kiel, Germany
| | - Stephanie K Dougan
- Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jon K Laerdahl
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway,Bioinformatics Core Facility, Department of Informatics, University of Oslo, Oslo, Norway
| | - Björn Stade
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Michael Forster
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Kiel, Kiel, Germany,Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Dascha Weir
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Alan M Leichtner
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Richard S Blumberg
- Division of Gastroenterology, Hepatology and Endoscopy, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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12
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Masamune A, Nakano E, Hamada S, Kakuta Y, Kume K, Shimosegawa T. Common variants at PRSS1-PRSS2 and CLDN2-MORC4 loci associate with chronic pancreatitis in Japan. Gut 2015; 64:1345-6. [PMID: 26002935 DOI: 10.1136/gutjnl-2015-309802] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/04/2015] [Indexed: 01/30/2023]
Affiliation(s)
- Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Eriko Nakano
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Shin Hamada
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoichi Kakuta
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kiyoshi Kume
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai, Japan
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