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Xi B, Liu S, Zhu Y, Zhang D, Zhang Y, Liu A. Case report: Genetic analysis of a novel intronic inversion variant in the SPTB gene associated with hereditary spherocytosis. Front Genet 2023; 14:1309040. [PMID: 38111681 PMCID: PMC10726134 DOI: 10.3389/fgene.2023.1309040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023] Open
Abstract
Background: Hereditary spherocytosis (HS) is a congenital haemolytic anaemia attributed to dysregulation or abnormal quantities of erythrocyte membrane proteins. Currently, the most common erythrocytic gene, spectrin β (SPTB), variants are located in exons and give rise to mRNA defects. However, the genetic characteristics and pathogenic mechanisms of SPTB intronic variants are not completely understood. This study aimed to analyse a rare intronic inversion variant in the SPTB gene associated with HS, and explore the impact of the variant on SPTB mRNA splicing. Method: The clinical manifestations of the patient were summarised and analysed for spherocytosis phenotype diagnosis. The pathogenic variant was identified in the proband using targeted next-generation and Sanger sequencing. RNA sequencing was performed to analyse whether SPTB gene splicing and expression were affected. Results: Targeted next-generation sequencing identified a novel disease-associated intronic inversion variant of the SPTB gene in the proband. The inversion variant was located between intron 19 and 20, and contained the entire exon 20 and partial sequences of adjacent introns. Sanger sequencing confirmed that the intronic inversion variant only appeared in the genome of the proband, not in his parents. RNA sequencing revealed that the variant could result in the skipping of exon 20 and reduced expression of SPTB mRNA. Conclusion: This study identifies a rare intronic inversion variant in the SPTB gene associated with hereditary spherocytosis. The pathogenic variant can lead to exon 20 skipping and decreased SPTB gene expression. This finding has not been previously reported in any literature. This study can expand the intronic variant spectrum of the SPTB gene, deepen our understanding of HS pathogenesis, and contribute to the genetic diagnosis and clinical management of patients.
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Affiliation(s)
- Bixin Xi
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Siying Liu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yongbing Zhu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dedong Zhang
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhang
- Department of Gynaecology, Wuhan Children’s Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aiguo Liu
- Department of Pediatrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Zhao H, Yu X, Cheng J, Chen D, Xu Q, Sheng J, Shi Y. Citrullinemia type II accompanied by mental derangement combined with multidrug resistance 3 decrease, case report. Heliyon 2023; 9:e21760. [PMID: 38027652 PMCID: PMC10663841 DOI: 10.1016/j.heliyon.2023.e21760] [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: 09/05/2022] [Revised: 06/02/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Background Here we report a rare case of citrullinemia type II (CTLN2) accompanied by mental derangement with a deficiency of multidrug resistance 3 (MDR3) in the liver. Case presentation The clinical data of a 17-year-old girl were collected. Liver puncture was performed, and hepatic expression of MDR3 was determined by immunohistochemistry. Serum amino acids of the patient and her parents wwere determined by a chemical isotope labeling liquid chromatography-mass spectrometry (CIL LC-MS). Genetic mutations of ABCB4 and SLC25A13 were screened by whole-exome sequencing. Immunohistochemical analysis showed a remarkably lower expression of MDR3. Mutation in ABCB4 gene was not found and whole-exome sequencing revealed the SLC25A13 mutation 852-855 del. Elevated serum levels of citrulline, homocitrulline, and homoarginine in the patient and her mother were found. Conclusions We reported a rare case of CTLN2 combined with MDR3 deficiency, without mutation of ABCB4. The link between MDR3 down-expression and CTLN2 warrants further investigation. Meanwhile, clinicians need to further rule out the possibility of CTLN2 if MDR3 decreases in adolescent patients with mental disorders and abnormal liver function.
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Affiliation(s)
| | | | - Jinlin Cheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Deying Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Qiaomai Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Jifang Sheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Yu Shi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
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3
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Dumont M, Weber-Lassalle N, Joly-Beauparlant C, Ernst C, Droit A, Feng BJ, Dubois S, Collin-Deschesnes AC, Soucy P, Vallée M, Fournier F, Lemaçon A, Adank MA, Allen J, Altmüller J, Arnold N, Ausems MGEM, Berutti R, Bolla MK, Bull S, Carvalho S, Cornelissen S, Dufault MR, Dunning AM, Engel C, Gehrig A, Geurts-Giele WRR, Gieger C, Green J, Hackmann K, Helmy M, Hentschel J, Hogervorst FBL, Hollestelle A, Hooning MJ, Horváth J, Ikram MA, Kaulfuß S, Keeman R, Kuang D, Luccarini C, Maier W, Martens JWM, Niederacher D, Nürnberg P, Ott CE, Peters A, Pharoah PDP, Ramirez A, Ramser J, Riedel-Heller S, Schmidt G, Shah M, Scherer M, Stäbler A, Strom TM, Sutter C, Thiele H, van Asperen CJ, van der Kolk L, van der Luijt RB, Volk AE, Wagner M, Waisfisz Q, Wang Q, Wang-Gohrke S, Weber BHF, Devilee P, Tavtigian S, Bader GD, Meindl A, Goldgar DE, Andrulis IL, Schmutzler RK, Easton DF, Schmidt MK, Hahnen E, Simard J. Uncovering the Contribution of Moderate-Penetrance Susceptibility Genes to Breast Cancer by Whole-Exome Sequencing and Targeted Enrichment Sequencing of Candidate Genes in Women of European Ancestry. Cancers (Basel) 2022; 14:cancers14143363. [PMID: 35884425 PMCID: PMC9317824 DOI: 10.3390/cancers14143363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 01/27/2023] Open
Abstract
Rare variants in at least 10 genes, including BRCA1, BRCA2, PALB2, ATM, and CHEK2, are associated with increased risk of breast cancer; however, these variants, in combination with common variants identified through genome-wide association studies, explain only a fraction of the familial aggregation of the disease. To identify further susceptibility genes, we performed a two-stage whole-exome sequencing study. In the discovery stage, samples from 1528 breast cancer cases enriched for breast cancer susceptibility and 3733 geographically matched unaffected controls were sequenced. Using five different filtering and gene prioritization strategies, 198 genes were selected for further validation. These genes, and a panel of 32 known or suspected breast cancer susceptibility genes, were assessed in a validation set of 6211 cases and 6019 controls for their association with risk of breast cancer overall, and by estrogen receptor (ER) disease subtypes, using gene burden tests applied to loss-of-function and rare missense variants. Twenty genes showed nominal evidence of association (p-value < 0.05) with either overall or subtype-specific breast cancer. Our study had the statistical power to detect susceptibility genes with effect sizes similar to ATM, CHEK2, and PALB2, however, it was underpowered to identify genes in which susceptibility variants are rarer or confer smaller effect sizes. Larger sample sizes would be required in order to identify such genes.
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Affiliation(s)
- Martine Dumont
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Nana Weber-Lassalle
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Charles Joly-Beauparlant
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Corinna Ernst
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Arnaud Droit
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Bing-Jian Feng
- Department of Dermatology, University of Utah, Salt Lake City, UT 84103, USA; (B.-J.F.); (D.E.G.)
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
| | - Stéphane Dubois
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Annie-Claude Collin-Deschesnes
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Penny Soucy
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Maxime Vallée
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Frédéric Fournier
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Audrey Lemaçon
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
| | - Muriel A. Adank
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Jamie Allen
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (J.A.); (H.T.)
| | - Norbert Arnold
- Institute of Clinical Molecular Biology, Department of Gynaecology and Obstetrics, University Hospital of Schleswig-Holstein, Campus Kiel, Christian-Albrechts University Kiel, 24105 Kiel, Germany;
| | - Margreet G. E. M. Ausems
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, 3584 Utrecht, The Netherlands;
| | - Riccardo Berutti
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; (R.B.); (T.M.S.)
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Shelley Bull
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Sara Carvalho
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Sten Cornelissen
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
| | - Michael R. Dufault
- Precision Medicine and Computational Biology, Sanofi Genzyme, Cambridge, MA 02142, USA;
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Christoph Engel
- Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, 04107 Leipzig, Germany;
| | - Andrea Gehrig
- Centre of Familial Breast and Ovarian Cancer, Department of Medical Genetics, Institute of Human Genetics, University of Würzburg, 97074 Würzburg, Germany;
| | | | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; (C.G.); (A.P.)
- Research Unit Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany
| | - Jessica Green
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Karl Hackmann
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany;
| | - Mohamed Helmy
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore 138632, Singapore
- Department of Computer Science, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
| | - Julia Hentschel
- Institute of Human Genetics, University Leipzig, 04103 Leipzig, Germany;
| | - Frans B. L. Hogervorst
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Antoinette Hollestelle
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Maartje J. Hooning
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Judit Horváth
- Institute of Human Genetics, University of Münster, 48149 Münster, Germany;
| | - M. Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center, 3015 Rotterdam, The Netherlands;
| | - Silke Kaulfuß
- Institute of Human Genetics, University Medical Center Göttingen, 37075 Göttingen, Germany;
| | - Renske Keeman
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
| | - Da Kuang
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
| | - Craig Luccarini
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Wolfgang Maier
- German Center for Neurodegenerative Diseases (DZNE), Department of Neurodegenerative Diseases and Geriatric Psychiatry, Medical Faculty, University Hospital Bonn, 53127 Bonn, Germany;
| | - John W. M. Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, 3015 Rotterdam, The Netherlands; (A.H.); (M.J.H.); (J.W.M.M.)
| | - Dieter Niederacher
- Department of Gynecology and Obstetrics, University Hospital Düsseldorf, Heinrich-Heine University Düsseldorf, 40225 Düsseldorf, Germany;
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany;
| | - Claus-Eric Ott
- Institute of Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 13353 Berlin, Germany;
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; (C.G.); (A.P.)
- Department of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Paul D. P. Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Alfredo Ramirez
- Division for Neurogenetics and Molecular Psychiatry, Medical Faculty, University of Cologne, 50937 Cologne, Germany;
| | - Juliane Ramser
- Division of Gynaecology and Obstetrics, Klinikum Rechts der Isar der Technischen Universität München, 81675 Munich, Germany; (J.R.); (A.M.)
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany;
| | - Gunnar Schmidt
- Institute of Human Genetics, Hannover Medical School, 30625 Hannover, Germany;
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Martin Scherer
- Department of Primary Medical Care, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Antje Stäbler
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany;
| | - Tim M. Strom
- Institute of Human Genetics, Technische Universität München, 81675 Munich, Germany; (R.B.); (T.M.S.)
| | - Christian Sutter
- Institute of Human Genetics, University Hospital Heidelberg, 69120 Heidelberg, Germany;
| | - Holger Thiele
- Cologne Center for Genomics (CCG), Faculty of Medicine, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany; (J.A.); (H.T.)
| | - Christi J. van Asperen
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands; (C.J.v.A.); (R.B.v.d.L.)
| | - Lizet van der Kolk
- Family Cancer Clinic, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (M.A.A.); (F.B.L.H.); (L.v.d.K.)
| | - Rob B. van der Luijt
- Department of Clinical Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands; (C.J.v.A.); (R.B.v.d.L.)
- Department of Medical Genetics, University Medical Center, 3584 Utrecht, The Netherlands
| | - Alexander E. Volk
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany;
| | - Michael Wagner
- Department of Neurodegenerative Diseases and Geriatric Psychiatry, University Hospital Bonn, 53127 Bonn, Germany;
| | - Quinten Waisfisz
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, 1081 Amsterdam, The Netherlands;
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
| | - Shan Wang-Gohrke
- Department of Gynaecology and Obstetrics, University of Ulm, 89081 Ulm, Germany;
| | - Bernhard H. F. Weber
- Institute of Human Genetics, Regensburg University, 93053 Regensburg, Germany;
- Institute of Clinical Human Genetics, University Hospital Regensburg, 93053 Regensburg, Germany
| | | | | | - Peter Devilee
- Department of Pathology, Department of Human Genetics, Leiden University Medical Center, 2333 Leiden, The Netherlands;
| | - Sean Tavtigian
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Gary D. Bader
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
- The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada;
- Department of Computer Science, University of Toronto, Toronto, ON M5S 3E1, Canada
- Princess Margaret Research Institute, University Health Network, Toronto, ON M5G 0A3, Canada
| | - Alfons Meindl
- Division of Gynaecology and Obstetrics, Klinikum Rechts der Isar der Technischen Universität München, 81675 Munich, Germany; (J.R.); (A.M.)
| | - David E. Goldgar
- Department of Dermatology, University of Utah, Salt Lake City, UT 84103, USA; (B.-J.F.); (D.E.G.)
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, USA;
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, ON M5G 1X5, Canada; (S.B.); (J.G.); (G.D.B.); (I.L.A.)
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada;
| | - Rita K. Schmutzler
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; (J.A.); (M.K.B.); (S.C.); (P.D.P.P.); (Q.W.); (D.F.E.)
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge CB1 8RN, UK; (A.M.D.); (C.L.); (M.S.)
| | - Marjanka K. Schmidt
- Division of Molecular Pathology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands; (S.C.); (R.K.); (M.K.S.)
- Division of Psychosocial Research and Epidemiology, The Netherlands Cancer Institute—Antoni van Leeuwenhoek Hospital, 1066 Amsterdam, The Netherlands
| | - Eric Hahnen
- Center for Familial Breast and Ovarian Cancer, Center for Integrated Oncology (CIO), Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; (N.W.-L.); (C.E.); (R.K.S.); (E.H.)
| | - Jacques Simard
- Genomics Center, CHU de Québec-Université Laval Research Center, 2705 Laurier Boulevard, Quebec City, QC GIV 4G2, Canada; (M.D.); (C.J.-B.); (A.D.); (S.D.); (A.-C.C.-D.); (P.S.); (M.V.); (F.F.); (A.L.)
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +418-654-2264
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Development of vascular disease models to explore disease causation and pathomechanisms of rare vascular diseases. Semin Immunopathol 2022; 44:259-268. [PMID: 35233690 PMCID: PMC8887661 DOI: 10.1007/s00281-022-00925-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/10/2022] [Indexed: 12/15/2022]
Abstract
As the field of medicine is striving forward heralded by a new era of next-generation sequencing (NGS) and integrated technologies such as bioprinting and biological material development, the utility of rare monogenetic vascular disease modeling in this landscape is starting to emerge. With their genetic simplicity and broader applicability, these patient-specific models are at the forefront of modern personalized medicine. As a collective, rare diseases are a significant burden on global healthcare systems, and rare vascular diseases make up a significant proportion of this. High costs are due to a lengthy diagnostic process, affecting all ages from infants to adults, as well as the severity and chronic nature of the disease. Their complex nature requires sophisticated disease models and integrated approaches involving multidisciplinary teams. Here, we review these emerging vascular disease models, how they contribute to our understanding of the pathomechanisms in rare vascular diseases and provide useful platforms for therapeutic discovery.
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5
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Brandão LAC, de Moura RR, Marzano AV, Moltrasio C, Tricarico PM, Crovella S. Variant Enrichment Analysis to Explore Pathways Functionality in Complex Autoinflammatory Skin Disorders through Whole Exome Sequencing Analysis. Int J Mol Sci 2022; 23:2278. [PMID: 35216413 PMCID: PMC8877088 DOI: 10.3390/ijms23042278] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/31/2022] [Accepted: 02/14/2022] [Indexed: 12/04/2022] Open
Abstract
The challenge of unravelling the molecular basis of multifactorial disorders nowadays cannot rely just on association studies searching for potential causative variants shared by groups of patients and not present in healthy individuals; indeed, association studies have as a main limitation the lack of information on the interactions between the disease-causing variants. Thus, new genomic analysis tools focusing on disrupted pathways rather than associated gene variants are required to better understand the complexity of a disease. Therefore, we developed the Variant Enrichment Analysis (VEA) workflow, a tool applicable for whole exome sequencing data, able to find differences between the numbers of genetic variants in a given pathway in comparison with a reference dataset. In this study, we applied VEA to discover novel pathways altered in patients with complex autoinflammatory skin disorders, namely PASH (n = 9), 3 of whom are overlapping with SAPHO) and PAPASH (n = 3). With this approach we have been able to identify pathways related to neutrophil and endothelial cells homeostasis/activations, as disrupted in our patients. We hypothesized that unregulated neutrophil transendothelial migration could elicit increased neutrophil infiltration and tissue damage. Based on our findings, VEA, in our experimental dataset, allowed us to predict novel pathways impaired in subjects with autoinflammatory skin disorders.
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Affiliation(s)
- Lucas André Cavalcanti Brandão
- Department of Advanced Diagnostics, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (L.A.C.B.); (P.M.T.)
| | - Ronald Rodrigues de Moura
- Department of Advanced Diagnostics, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (L.A.C.B.); (P.M.T.)
| | - Angelo Valerio Marzano
- Dermatology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.V.M.); (C.M.)
- Department of Physiopathology and Transplantation, Università degli Studi di Milano, 20122 Milan, Italy
| | - Chiara Moltrasio
- Dermatology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (A.V.M.); (C.M.)
- Department of Medical Surgical and Health Sciences, University of Trieste, 34137 Trieste, Italy
| | - Paola Maura Tricarico
- Department of Advanced Diagnostics, Institute for Maternal and Child Health, IRCCS “Burlo Garofolo”, 34137 Trieste, Italy; (L.A.C.B.); (P.M.T.)
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, University of Qatar, Doha 2713, Qatar;
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6
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Wang Y, Liu Z, Yang G, Gao Q, Xiao L, Li J, Guo C, Troutwine BR, Gray RS, Xie L, Zhang H. Coding Variants Coupled With Rapid Modeling in Zebrafish Implicate Dynein Genes, dnaaf1 and zmynd10, as Adolescent Idiopathic Scoliosis Candidate Genes. Front Cell Dev Biol 2020; 8:582255. [PMID: 33251213 PMCID: PMC7672046 DOI: 10.3389/fcell.2020.582255] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 10/07/2020] [Indexed: 12/11/2022] Open
Abstract
Adolescent idiopathic scoliosis (AIS) is the most common pediatric spine disorder affecting ∼3% of children worldwide. Human genetic studies suggest a complex polygenic disease model for AIS with large genetic and phenotypic heterogeneity. However, the overall genetic etiology of AIS remains poorly understood. To identify additional AIS susceptibility loci, we performed whole-exome sequencing (WES) on a cohort of 195 Southern Chinese AIS patients. Bioinformatics analysis identified 237 novel rare variants associated with AIS, located in 232 new susceptibility loci. Enrichment analysis of these variants revealed 10 gene families associated with our AIS cohort. We screened these gene families by comparing our candidate gene list with IS candidate genes in the Human Phenotype Ontology (HPO) database and previous reported studies. Two candidate gene families, axonemal dynein and axonemal dynein assembly factors, were retained for their associations with ciliary architecture and function. The damaging effects of candidate variants in dynein genes dnali1, dnah1, dnaaf, and zmynd10, as well as in one fibrillin-related gene tns1, were functionally analyzed in zebrafish using targeted CRISPR/Cas9 screening. Knockout of two candidate genes, dnaaf1 or zmynd10, recapitulated scoliosis in viable adult zebrafish. Altogether, our results suggest that the disruption of one or more dynein-associated factors may correlate with AIS susceptibility in the Southern Chinese population.
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Affiliation(s)
- Yunjia Wang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Department of Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin, Dell Medical School, Austin, TX, United States
| | - Zhenhao Liu
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China.,Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, National Health and Family Planning Commission, Xiangya Hospital, Central South University, Changsha, China
| | - Guanteng Yang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Qile Gao
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Lige Xiao
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jiong Li
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Chaofeng Guo
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Benjamin R Troutwine
- Department of Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin, Dell Medical School, Austin, TX, United States
| | - Ryan S Gray
- Department of Pediatrics, Dell Pediatric Research Institute, The University of Texas at Austin, Dell Medical School, Austin, TX, United States
| | - Lu Xie
- Shanghai Center for Bioinformation Technology, Shanghai Academy of Science and Technology, Shanghai, China
| | - Hongqi Zhang
- Department of Spine Surgery and Orthopaedics, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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7
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Silva SL, Fonseca M, Pereira MLM, Silva SP, Barbosa RR, Serra-Caetano A, Blanco E, Rosmaninho P, Pérez-Andrés M, Sousa AB, Raposo AASF, Gama-Carvalho M, Victorino RMM, Hammarstrom L, Sousa AE. Monozygotic Twins Concordant for Common Variable Immunodeficiency: Strikingly Similar Clinical and Immune Profile Associated With a Polygenic Burden. Front Immunol 2019; 10:2503. [PMID: 31824477 PMCID: PMC6882918 DOI: 10.3389/fimmu.2019.02503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/07/2019] [Indexed: 01/10/2023] Open
Abstract
Monozygotic twins provide a unique opportunity to better understand complex genetic diseases and the relative contribution of heritable factors in shaping the immune system throughout life. Common Variable Immunodeficiency Disorders (CVID) are primary antibody defects displaying wide phenotypic and genetic heterogeneity, with monogenic transmission accounting for only a minority of the cases. Here, we report a pair of monozygotic twins concordant for CVID without a family history of primary immunodeficiency. They featured a remarkably similar profile of clinical manifestations and immunological alterations at diagnosis (established at age 37) and along the subsequent 15 years of follow-up. Interestingly, whole-exome sequencing failed to identify a monogenic cause for CVID, but unraveled a combination of heterozygous variants, with a predicted deleterious impact. These variants were found in genes involved in relevant immunological pathways, such as JUN, PTPRC, TLR1, ICAM1, and JAK3. The potential for combinatorial effects translating into the observed disease phenotype is inferred from their roles in immune pathways, namely in T and B cell activation. The combination of these genetic variants is also likely to impose a significant constraint on environmental influences, resulting in a similar immunological phenotype in both twins, despite exposure to different living conditions. Overall, these cases stress the importance of integrating NGS data with clinical and immunological phenotypes at the single-cell level, as provided by multi-dimensional flow-cytometry, in order to understand the complex genetic landscape underlying the vast majority of patients with CVID, as well as those with other immunodeficiencies.
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Affiliation(s)
- Susana L Silva
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal.,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Mariana Fonseca
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal
| | - Marcelo L M Pereira
- Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Sara P Silva
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal.,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Rita R Barbosa
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Serra-Caetano
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal
| | - Elena Blanco
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca (USAL), Salamanca, Spain.,Biomedical Research Networking Centre on Cancer-CIBER-CIBERONC, Number CB16/12/00400, Institute of Health Carlos III, Madrid, Spain
| | - Pedro Rosmaninho
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal
| | - Martin Pérez-Andrés
- Department of Medicine, Cancer Research Centre (IBMCC, USAL-CSIC), Cytometry Service (NUCLEUS), Institute of Biomedical Research of Salamanca (IBSAL), University of Salamanca (USAL), Salamanca, Spain.,Biomedical Research Networking Centre on Cancer-CIBER-CIBERONC, Number CB16/12/00400, Institute of Health Carlos III, Madrid, Spain
| | - Ana Berta Sousa
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal.,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | - Alexandre A S F Raposo
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal
| | - Margarida Gama-Carvalho
- Faculty of Sciences, BioISI-Biosystems & Integrative Sciences Institute, University of Lisboa, Lisbon, Portugal
| | - Rui M M Victorino
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal.,Centro Hospitalar Universitário Lisboa Norte, Hospital de Santa Maria, Lisbon, Portugal
| | | | - Ana E Sousa
- Faculdade de Medicina, Instituto de Medicina Molecular João Lobo Antunes, Universidade de Lisboa, Lisbon, Portugal.,Centro de Imunodeficiências Primárias, Centro Académico de Medicina de Lisboa, Centro Hospitalar Universitário Lisboa Norte and Faculdade de Medicina da Universidade de Lisboa and Instituto de Medicina Molecular, Lisbon, Portugal
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8
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Saad M, Wijsman EM. Association score testing for rare variants and binary traits in family data with shared controls. Brief Bioinform 2019; 20:245-253. [PMID: 28968627 DOI: 10.1093/bib/bbx107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 11/12/2022] Open
Abstract
Genome-wide association studies have been an important approach used to localize trait loci, with primary focus on common variants. The multiple rare variant-common disease hypothesis may explain the missing heritability remaining after accounting for identified common variants. Advances of sequencing technologies with their decreasing costs, coupled with methodological advances in the context of association studies in large samples, now make the study of rare variants at a genome-wide scale feasible. The resurgence of family-based association designs because of their advantage in studying rare variants has also stimulated more methods development, mainly based on linear mixed models (LMMs). Other tests such as score tests can have advantages over the LMMs, but to date have mainly been proposed for single-marker association tests. In this article, we extend several score tests (χcorrected2, WQLS, and SKAT) to the multiple variant association framework. We evaluate and compare their statistical performances relative with the LMM. Moreover, we show that three tests can be cast as the difference between marker allele frequencies (AFs) estimated in each of the group of affected and unaffected subjects. We show that these tests are flexible, as they can be based on related, unrelated or both related and unrelated subjects. They also make feasible an increasingly common design that only sequences a subset of affected subjects (related or unrelated) and uses for comparison publicly available AFs estimated in a group of healthy subjects. Finally, we show the great impact of linkage disequilibrium on the performance of all these tests.
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Affiliation(s)
- Mohamad Saad
- Department of Biostatistics, University of Washington, Seattle, USA.,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, USA.,Qatar Computing Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Ellen M Wijsman
- Department of Biostatistics, University of Washington, Seattle, USA.,Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, USA
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9
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Genetic and experimental evidence for the involvement of the CD6 lymphocyte receptor in psoriasis. Cell Mol Immunol 2017; 15:898-906. [PMID: 29225340 DOI: 10.1038/cmi.2017.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 12/16/2022] Open
Abstract
Psoriasis is a chronic inflammatory skin disease with a strong genetic background and is triggered by environmental factors. Available evidence supports CD6, a lymphocyte surface receptor mostly expressed by T cells, as a putative target in autoimmunity. Accordingly, a humanized anti-CD6 antibody has been assayed for the treatment of certain autoimmune disorders, including psoriasis. Here, we present novel evidence in mice and humans for a direct involvement of CD6 in psoriasis pathophysiology. First, an attenuated form of imiquimod-induced psoriasis-like skin inflammation was demonstrated in CD6-deficient mice, as deduced from lower epidermal thickness and local reduced production of pro-inflammatory cytokines, namely, interleukin-17A. Thus, isolated CD4+CD62L+ T cells from CD6-deficient mice displayed decreased in vitro T-helper type 17 polarization. Second, a statistically significant association between CD6 single-nucleotide polymorphisms (rs17824933, rs11230563 and rs12360861) and more severe forms of psoriasis was demonstrated in a cohort of 304 patients at three public hospitals from the metropolitan area of Barcelona. Taken together, these results provide new supportive evidence of the contribution of the CD6 lymphocyte receptor in psoriasis at both experimental and clinical levels.
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10
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Shin S, Moh IH, Woo YS, Jung SW, Kim JB, Park JW, Suk KT, Kim HS, Hong M, Park SH, Lee MS. Evidence from a familial case suggests maternal inheritance of primary biliary cholangitis. World J Gastroenterol 2017; 23:7191-7197. [PMID: 29093628 PMCID: PMC5656467 DOI: 10.3748/wjg.v23.i39.7191] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 08/23/2017] [Accepted: 09/05/2017] [Indexed: 02/06/2023] Open
Abstract
Primary biliary cholangitis (PBC) is an idiopathic autoimmune liver disease characterized by chronic cholestasis and destruction of the intrahepatic bile ducts. Similar to other autoimmune diseases, the pathogenesis of PBC is considered to be a complex etiologic phenomenon involving the interaction of genetic and environmental factors. Although a number of common variants associated with PBC have been reported from genome-wide association studies, a precise genetic mechanism underlying PBC has yet to be identified. Here, we describe a family with four sisters who were diagnosed with PBC. After the diagnosis of the index patient who was in an advanced stage of PBC, one sister presented with acute hepatitis, and two sisters were subsequently diagnosed with PBC. Notably, one half-sister with a different mother exhibited no evidence of PBC following clinical investigation. Our report suggests the possibility of a maternal inheritance of PBC susceptibility. Moreover, judging from the high-penetrance of the disease observed in this family, we inferred that a pathogenic genetic variant might be the cause of PBC development. We describe a family that exhibited diverse clinical presentations of PBC that included asymptomatic stages with mildly increased liver enzyme levels and symptomatic stages with acute hepatitis or advanced liver fibrosis. Additional studies are needed to investigate the role of genetic factors in the pathogenesis of this rare autoimmune disease.
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Affiliation(s)
- Saeam Shin
- Department of Laboratory Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
| | - In Ho Moh
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
| | - Young Sik Woo
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
| | - Sung Won Jung
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
| | - Jin Bae Kim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
| | - Ji Won Park
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
| | - Ki Tae Suk
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
| | - Hyoung Su Kim
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
| | - Mineui Hong
- Department of Pathology, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
| | - Sang Hoon Park
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
| | - Myung Seok Lee
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Kangnam Sacred Heart Hospital, Hallym University College of Medicine, Seoul 07441, South Korea
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11
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Jouenne F, Chauvot de Beauchene I, Bollaert E, Avril MF, Caron O, Ingster O, Lecesne A, Benusiglio P, Terrier P, Caumette V, Pissaloux D, de la Fouchardière A, Cabaret O, N'Diaye B, Velghe A, Bougeard G, Mann GJ, Koscielny S, Barrett JH, Harland M, Newton-Bishop J, Gruis N, Van Doorn R, Gauthier-Villars M, Pierron G, Stoppa-Lyonnet D, Coupier I, Guimbaud R, Delnatte C, Scoazec JY, Eggermont AM, Feunteun J, Tchertanov L, Demoulin JB, Frebourg T, Bressac-de Paillerets B. Germline CDKN2A/P16INK4A mutations contribute to genetic determinism of sarcoma. J Med Genet 2017; 54:607-612. [PMID: 28592523 DOI: 10.1136/jmedgenet-2016-104402] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 03/13/2017] [Accepted: 03/14/2017] [Indexed: 01/01/2023]
Abstract
BACKGROUND Sarcomas are rare mesenchymal malignancies whose pathogenesis is poorly understood; both environmental and genetic risk factors could contribute to their aetiology. METHODS AND RESULTS We performed whole-exome sequencing (WES) in a familial aggregation of three individuals affected with soft-tissue sarcoma (STS) without TP53 mutation (Li-Fraumeni-like, LFL) and found a shared pathogenic mutation in CDKN2A tumour suppressor gene. We searched for individuals with sarcoma among 474 melanoma-prone families with a CDKN2A-/+ genotype and for CDKN2A mutations in 190 TP53-negative LFL families where the index case was a sarcoma. Including the initial family, eight independent sarcoma cases carried a germline mutation in the CDKN2A/p16INK4A gene. In five out of seven formalin-fixed paraffin-embedded sarcomas, heterozygosity was lost at germline CDKN2A mutations sites demonstrating complete loss of function. As sarcomas are rare in CDKN2A/p16INK4A carriers, we searched in constitutional WES of nine carriers for potential modifying rare variants and identified three in platelet-derived growth factor receptor (PDGFRA) gene. Molecular modelling showed that two never-described variants could impact the PDGFRA extracellular domain structure. CONCLUSION Germline mutations in CDKN2A/P16INK4A, a gene known to predispose to hereditary melanoma, pancreatic cancer and tobacco-related cancers, account also for a subset of hereditary sarcoma. In addition, we identified PDGFRA as a candidate modifier gene.
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Affiliation(s)
- Fanélie Jouenne
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- INSERM, U1186, Université Paris-Saclay, Villejuif, France
| | | | - Emeline Bollaert
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Marie-Françoise Avril
- Department of Dermatology, Assistance Publique-Hopitaux de Paris, Hopital Cochin Tarnier, Paris, France
- Faculté de Médecine, Paris 5 Descartes, Paris, France
| | - Olivier Caron
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | | | - Axel Lecesne
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Patrick Benusiglio
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Philippe Terrier
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Vincent Caumette
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Daniel Pissaloux
- Department of Pathology, Centre Leon Bérard, Lyon, Rhône-Alpes, France
| | | | - Odile Cabaret
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Birama N'Diaye
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Amélie Velghe
- De Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Gaelle Bougeard
- Faculty of Medicine, INSERM U1079, Normandy University, Rouen, France
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and personalized Medicine, Rouen, Haute-Normandie, France
| | - Graham J Mann
- Centre for Cancer Research, Weastmead Institute for Medical Research and Melanoma Institute, Sydney, New South Wales, Australia
| | - Serge Koscielny
- Service de Biostatistiques et d'Epidemiologie, Gustave Roussy, Villejuif, France
- INSERM U1018, CESP, Université Paris-Sud, Université Paris-Saclay, Villejuif, France
| | - Jennifer H Barrett
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Mark Harland
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Julia Newton-Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Cancer and Pathology, University of Leeds, Leeds, UK
| | - Nelleke Gruis
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Remco Van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Gaelle Pierron
- Institut Curie Hospital Group, Service de Génétique, Paris, France
| | | | - Isabelle Coupier
- Hopital Arnaud de Villeneuve, Service de Génétique Médicale et Oncogénétique, CHU de Montpellier, Montpellier, France
- CRCM Val d'Aurellle, INSERM U896, Montpellier, France
| | | | - Capucine Delnatte
- Unité d'Oncogénétique, Centre René Gauducheau, Nantes Saint Herblain, France
| | - Jean-Yves Scoazec
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Alexander M Eggermont
- INSERM U1015 and Faculté de médecine, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Jean Feunteun
- CNRS UMR8200, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Luba Tchertanov
- Centre de Mathématiques et de leurs applications, Ecole Normale Supérieure de Cachan, Université Paris-Saclay, Cachan, France
| | | | - Thierry Frebourg
- Faculty of Medicine, INSERM U1079, Normandy University, Rouen, France
- Department of Genetics, Rouen University Hospital, Normandy Centre for Genomic and personalized Medicine, Rouen, Haute-Normandie, France
| | - Brigitte Bressac-de Paillerets
- Département de Biologie et Pathologie Médicales, Gustave Roussy, Université Paris-Saclay, Villejuif, France
- INSERM, U1186, Université Paris-Saclay, Villejuif, France
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12
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Mossman K, Nebesio N, Vidal SM. Discovery of Variants Underlying Host Susceptibility to Virus Infection Using Whole-Exome Sequencing. Methods Mol Biol 2017; 1656:209-227. [PMID: 28808973 PMCID: PMC7120756 DOI: 10.1007/978-1-4939-7237-1_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
The clinical course of any viral infection greatly differs in individuals. This variation results from various viral, host, and environmental factors. The identification of host genetic factors influencing inter-individual variation in susceptibility to several pathogenic viruses has tremendously increased our understanding of the mechanisms and pathways required for immunity. Next-generation sequencing of whole exomes represents a powerful tool in biomedical research. In this chapter, we briefly introduce whole-exome sequencing in the context of genetic approaches to identify host susceptibility genes to viral infections. We then describe general aspects of the workflow for whole-exome sequence analysis together with the tools and online resources that can be used to identify and annotate variant calls, and then prioritize them for their potential association to phenotypes of interest.
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Affiliation(s)
- Karen Mossman
- grid.25073.330000 0004 1936 8227Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Nestor Nebesio
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University Research Center on Complex Traits, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Silvia M Vidal
- Department of Human Genetics, McGill University, Montreal, QC, Canada. .,McGill University Research Center on Complex Traits, Montreal, QC, Canada. .,Department of Medicine, McGill University, Montreal, QC, Canada.
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13
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Ku CS, Cooper DN, Patrinos GP. The Rise and Rise of Exome Sequencing. Public Health Genomics 2016; 19:315-324. [DOI: 10.1159/000450991] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/23/2016] [Indexed: 12/19/2022] Open
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14
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Nicolas E, Arora S, Zhou Y, Serebriiskii IG, Andrake MD, Handorf ED, Bodian DL, Vockley JG, Dunbrack RL, Ross EA, Egleston BL, Hall MJ, Golemis EA, Giri VN, Daly MB. Systematic evaluation of underlying defects in DNA repair as an approach to case-only assessment of familial prostate cancer. Oncotarget 2015; 6:39614-33. [PMID: 26485759 PMCID: PMC4741850 DOI: 10.18632/oncotarget.5554] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/02/2015] [Indexed: 01/03/2023] Open
Abstract
Risk assessment for prostate cancer is challenging due to its genetic heterogeneity. In this study, our goal was to develop an operational framework to select and evaluate gene variants that may contribute to familial prostate cancer risk. Drawing on orthogonal sources, we developed a candidate list of genes relevant to prostate cancer, then analyzed germline exomes from 12 case-only prostate cancer patients from high-risk families to identify patterns of protein-damaging gene variants. We described an average of 5 potentially disruptive variants in each individual and annotated them in the context of public databases representing human variation. Novel damaging variants were found in several genes of relevance to prostate cancer. Almost all patients had variants associated with defects in DNA damage response. Many also had variants linked to androgen signaling. Treatment of primary T-lymphocytes from these prostate cancer patients versus controls with DNA damaging agents showed elevated levels of the DNA double strand break (DSB) marker γH2AX (p < 0.05), supporting the idea of an underlying defect in DNA repair. This work suggests the value of focusing on underlying defects in DNA damage in familial prostate cancer risk assessment and demonstrates an operational framework for exome sequencing in case-only prostate cancer genetic evaluation.
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Affiliation(s)
| | - Sanjeevani Arora
- Programs in Molecular Therapeutics Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Yan Zhou
- Programs in Biostatistics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ilya G. Serebriiskii
- Programs in Molecular Therapeutics Fox Chase Cancer Center, Philadelphia, PA, USA
- Kazan Federal University, Kazan, Russia
| | - Mark D. Andrake
- Programs in Molecular Therapeutics Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | - Dale L. Bodian
- Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA
| | - Joseph G. Vockley
- Inova Translational Medicine Institute, Inova Health System, Falls Church, VA, USA
| | - Roland L. Dunbrack
- Programs in Molecular Therapeutics Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Eric A. Ross
- Programs in Biostatistics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Brian L. Egleston
- Programs in Biostatistics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Michael J. Hall
- Cancer Prevention and Control, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Erica A. Golemis
- Programs in Molecular Therapeutics Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Veda N. Giri
- Sidney Kimmel Cancer Center at Thomas Jefferson University, Philadelphia, PA, USA
| | - Mary B. Daly
- Cancer Prevention and Control, Fox Chase Cancer Center, Philadelphia, PA, USA
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15
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Sokolenko AP, Suspitsin EN, Kuligina ES, Bizin IV, Frishman D, Imyanitov EN. Identification of novel hereditary cancer genes by whole exome sequencing. Cancer Lett 2015; 369:274-88. [PMID: 26427841 DOI: 10.1016/j.canlet.2015.09.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 09/23/2015] [Accepted: 09/23/2015] [Indexed: 02/09/2023]
Abstract
Whole exome sequencing (WES) provides a powerful tool for medical genetic research. Several dozens of WES studies involving patients with hereditary cancer syndromes have already been reported. WES led to breakthrough in understanding of the genetic basis of some exceptionally rare syndromes; for example, identification of germ-line SMARCA4 mutations in patients with ovarian hypercalcemic small cell carcinomas indeed explains a noticeable share of familial aggregation of this disease. However, studies on common cancer types turned out to be more difficult. In particular, there is almost a dozen of reports describing WES analysis of breast cancer patients, but none of them yet succeeded to reveal a gene responsible for the significant share of missing heritability. Virtually all components of WES studies require substantial improvement, e.g. technical performance of WES, interpretation of WES results, mode of patient selection, etc. Most of contemporary investigations focus on genes with autosomal dominant mechanism of inheritance; however, recessive and oligogenic models of transmission of cancer susceptibility also need to be considered. It is expected that the list of medically relevant tumor-predisposing genes will be rapidly expanding in the next few years.
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Affiliation(s)
- Anna P Sokolenko
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Evgeny N Suspitsin
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia
| | - Ekatherina Sh Kuligina
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia
| | - Ilya V Bizin
- Laboratory of Bioinformatics, RASA Research Center, St.-Petersburg State Polytechnical University, St.-Petersburg 195251, Russia
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, TU Muenchen, Freising 85354, Germany; Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Neuherberg 85764, Germany
| | - Evgeny N Imyanitov
- Department of Tumor Growth Biology, N.N. Petrov Institute of Oncology, St.-Petersburg 197758, Russia; Department of Medical Genetics, St.-Petersburg Pediatric Medical University, St.-Petersburg 194100, Russia; Department of Oncology, I.I. Mechnikov North-Western Medical University, St.-Petersburg 191015, Russia; Department of Oncology, St.-Petersburg State University, St.-Petersburg 199034, Russia.
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16
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Pharmacologic Therapy of Diabetes and Overall Cancer Risk and Mortality: A Meta-Analysis of 265 Studies. Sci Rep 2015; 5:10147. [PMID: 26076034 PMCID: PMC4467243 DOI: 10.1038/srep10147] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/31/2015] [Indexed: 12/14/2022] Open
Abstract
Different anti-diabetic medications (ADMs) may modify cancer risk and mortality in patients with diabetes. We conducted a systematic review and meta-analysis to estimate the magnitude of association and quality of supporting evidence for each ADM. A total of 265 studies (44 cohort studies, 39 case-control studies, and 182 randomized controlled trials (RCT)) were identified, involving approximately 7.6 million and 137,540 patients with diabetes for observational studies and RCTs, respectively. The risk of bias overall was moderate. Meta-analysis demonstrated that the use of metformin or thiazolidinediones was associated with a lower risk of cancer incidence (RR = 0.86, 95% CI 0.83-0.90, I2 = 88.61%; RR = 0.93, 95% CI 0.91-0.96, I2 = 0.00% respectively). On the other hand, insulin, sulfonylureas and alpha glucosidase inhibitor use was associated with an increased risk of cancer incidence (RR = 1.21, 95% CI 1.08-1.36, I2 = 96.31%; RR = 1.20, 95% CI 1.13-1.27, I2 = 95.02%; RR = 1.10, 95% CI 1.05-1.15, I2 = 0.00% respectively). Use of other types of ADMs was not significantly associated with cancer risk. This study indicates that some ADMs may modify the risk of cancer in individuals with diabetes. Knowledge of this risk may affect the choice of ADM in individuals concerned about cancer or at increased risk for cancer.
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17
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Oussalah A, Bosco P, Anello G, Spada R, Guéant-Rodriguez RM, Chery C, Rouyer P, Josse T, Romano A, Elia M, Bronowicki JP, Guéant JL. Exome-Wide Association Study Identifies New Low-Frequency and Rare UGT1A1 Coding Variants and UGT1A6 Coding Variants Influencing Serum Bilirubin in Elderly Subjects: A Strobe Compliant Article. Medicine (Baltimore) 2015; 94:e925. [PMID: 26039129 PMCID: PMC4616369 DOI: 10.1097/md.0000000000000925] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Genome-wide association studies (GWASs) have identified loci contributing to total serum bilirubin level. However, no exome-wide approaches have been performed to address this question. Using exome-wide approach, we assessed the influence of protein-coding variants on unconjugated, conjugated, and total serum bilirubin levels in a well-characterized cohort of 773 ambulatory elderly subjects from Italy. Coding variants were replicated in 227 elderly subjects from the same area. We identified 4 missense rare (minor allele frequency, MAF < 0.5%) and low-frequency (MAF, 0.5%-5%) coding variants located in the first exon of the UGT1A1 gene, which encodes for the substrate-binding domain (rs4148323 [MAF = 0.06%; p.Gly71Arg], rs144398951 [MAF = 0.06%; p.Ile215Val], rs35003977 [MAF = 0.78%; p.Val225Gly], and rs57307513 [MAF = 0.06%; p.Ser250Pro]). These variants were in strong linkage disequilibrium with 3 intronic UGT1A1 variants (rs887829, rs4148325, rs6742078), which were significantly associated with total bilirubin level (P = 2.34 × 10(-34), P = 7.02 × 10(-34), and P = 8.27 × 10(-34)), as well as unconjugated, and conjugated bilirubin levels. We also identified UGT1A6 variants in association with total (rs6759892, p.Ser7Ala, P = 1.98 × 10(-26); rs2070959, p.Thr181Ala, P = 2.87 × 10(-27); and rs1105879, p.Arg184Ser, P = 3.27 × 10(-29)), unconjugated, and conjugated bilirubin levels. All UGT1A1 intronic variants (rs887829, rs6742078, and rs4148325) and UGT1A6 coding variants (rs6759892, rs2070959, and rs1105879) were significantly associated with gallstone-related cholecystectomy risk. The UGT1A6 variant rs2070959 (p.Thr181Ala) was associated with the highest risk of gallstone-related cholecystectomy (OR, 4.58; 95% CI, 1.58-13.28; P = 3.21 × 10(-3)). Using an exome-wide approach we identified coding variants on UGT1A1 and UGT1A6 genes in association with serum bilirubin level and hyperbilirubinemia risk in elderly subjects. UGT1A1 intronic single-nucleotide polymorphisms (SNPs) (rs6742078, rs887829, rs4148324) serve as proxy markers for the low-frequency and rare UGT1A1 variants, thereby providing mechanistic explanation to the relationship between UGT1A1 intronic SNPs and the UGT1A1 enzyme activity. UGT1A1 and UGT1A6 variants might be potentially associated with gallstone-related cholecystectomy risk.
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Affiliation(s)
- Abderrahim Oussalah
- From the Inserm, NGERE - Nutrition, Genetics, and Environmental Risk Exposure (AO, R-MG-R, CC, PR, J-PB, J-LG); Faculty of Medicine of Nancy, University of Lorraine (AO, R-MG-R, CC, J-PB, J-LG); University Hospital of Nancy, Department of Molecular Medicine and Personalized Therapeutics, Department of Biochemistry, Molecular Biology, Nutrition, and Metabolism (AO, R-MG-R, CC, TJ, J-LG); Reference Centre for Inherited Metabolic Diseases (ORPHA67872), Vandoeuvre-lès-Nancy, France (AO, R-MG-R, CC, TJ, J-LG); IRCCS, Oasi Maria SS-Institute for Research on Mental Retardation, Troina (PB, GA, RS, AR, ME); Department of Internal Medicine and Geriatrics, UCSC, CI Columbus, Roma, Italy (AR); and Department of Gastroenterology and Hepatology, University Hospital of Nancy, Vandoeuvre-lès-Nancy, France (J-PB)
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18
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Wu L, Chaffee KG, Parker AS, Sicotte H, Petersen GM. Zinc transporter genes and urological cancers: integrated analysis suggests a role for ZIP11 in bladder cancer. Tumour Biol 2015; 36:7431-7. [PMID: 25900876 DOI: 10.1007/s13277-015-3459-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 04/13/2015] [Indexed: 01/01/2023] Open
Abstract
Although zinc transporters were shown to play roles in the development of prostate, bladder, and renal cancer, no study has evaluated the genetic variants in zinc transporter genes with risk of urological cancers. A candidate gene association study using genome-wide association study (GWAS) datasets was conducted for variants in 24 zinc transporter genes. Genotypes were analyzed using logistic regression models adjusted for covariates. The function of identified variants was assessed by using the Encyclopedia of DNA Elements (ENCODE). We further evaluated tumors for somatic change of the implicated gene(s) and the associations between identified variants and patient survival from data in The Cancer Genome Atlas (TCGA). A ZIP11 variant, rs8081059, was significantly associated with increased risk of renal cell carcinoma (odds ratios (OR) = 1.28, 95 % confidence intervals (CI) (1.13-1.45), p = 0.049). No zinc transporter variants were associated with prostate cancer risk. Four variants within ZIP11 were significantly associated with bladder cancer risk: rs11871756 (OR = 1.43, 95 % CI (1.24-1.63), p = 0.0002), rs11077654 (OR = 0.76, 95 % CI (0.68-0.85), p = 0.001), rs9913017 (OR = 0.76, 95 % CI (0.68-0.85), p = 0.002), and rs4969054 (OR = 0.78, 95 % CI (0.69-0.88), p = 0.02); the three protective variants were co-located and highly correlated. These variants were located within predicted transcribed or enhancer regions. Among the 253 bladder cancer patients in TCGA, two had tumors that contained deleterious missense mutations in ZIP11. Moreover, rs11077654 was significantly associated with survival of bladder cancer patients (p = 0.046). In conclusion, zinc transporter gene, ZIP11, may play an important role in bladder cancer. Further studies of the gene are warranted.
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Affiliation(s)
- Lang Wu
- Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA.,Center for Clinical and Translational Science, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA.,Mayo Graduate School, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Kari G Chaffee
- Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Alexander S Parker
- Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road, Jacksonville, FL, 32224, USA
| | - Hugues Sicotte
- Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA.
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