1
|
Kheriji N, Dallali H, Gouiza I, Hechmi M, Mahjoub F, Mrad M, Krir A, Soltani M, Trabelsi H, Hamdi W, Bahlous A, Ben Ahmed M, Jamoussi H, Kefi R. Whole-exome sequencing reveals novel variants of monogenic diabetes in Tunisia: impact on diagnosis and healthcare management. Front Genet 2023; 14:1224284. [PMID: 38162681 PMCID: PMC10757615 DOI: 10.3389/fgene.2023.1224284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: Monogenic diabetes (MD) accounts for 3%-6% of all cases of diabetes. This prevalence is underestimated due to its overlapping clinical features with type 1 and type 2 diabetes. Hence, genetic testing is the most appropriate tool for obtaining an accurate diagnosis. In Tunisia, few cohorts of MD have been investigated until now. The aim of this study is to search for pathogenic variants among 11 patients suspected of having MD in Tunisia using whole-exome sequencing (WES). Materials and methods: WES was performed in 11 diabetic patients recruited from a collaborating medical center. The pathogenicity of genetic variation was assessed using combined filtering and bioinformatics prediction tools. The online ORVAL tool was used to predict the likelihood of combinations of pathogenic variations. Then, Sanger sequencing was carried out to confirm likely pathogenic predicted variants among patients and to check for familial segregation. Finally, for some variants, we performed structural modeling to study their impact on protein function. Results: We identified novel variants related to MD in Tunisia. Pathogenic variants are located in several MODY and non-MODY genes. We highlighted the presence of syndromic forms of diabetes, including the Bardet-Biedl syndrome, Alström syndrome, and severe insulin resistance, as well as the presence of isolated diabetes with significantly reduced penetrance for Wolfram syndrome-related features. Idiopathic type 1 diabetes was also identified in one patient. Conclusion: In this study, we emphasized the importance of genetic screening for MD in patients with a familial history of diabetes, mainly among admixed and under-represented populations living in low- and middle-income countries. An accurate diagnosis with molecular investigation of MD may improve the therapeutic choice for better management of patients and their families. Additional research and rigorous investigations are required to better understand the physiopathological mechanisms of MD and implement efficient therapies that take into account genomic context and other related factors.
Collapse
Affiliation(s)
- Nadia Kheriji
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
| | - Hamza Dallali
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Ismail Gouiza
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- MitoLab Team, Unité MitoVasc, UMR CNRS 6015, Institut national de la santé et de la recherche médicale U1083, SFR ICAT, University of Angers, Angers, France
| | - Meriem Hechmi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Faten Mahjoub
- University of Tunis El Manar, Tunis, Tunisia
- Faculté de Médecine de Tunis, Research Unit UR18ES01 on “Obesity”, Tunis, Tunisia
- National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Mehdi Mrad
- University of Tunis El Manar, Tunis, Tunisia
- Faculty of Medicine of Tunis, Tunis, Tunisia
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Asma Krir
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Manel Soltani
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Hajer Trabelsi
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Walid Hamdi
- Laboratory of Clinical Immunology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Afef Bahlous
- University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Clinical Biochemistry and Hormonology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Melika Ben Ahmed
- University of Tunis El Manar, Tunis, Tunisia
- Laboratory of Clinical Immunology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Henda Jamoussi
- University of Tunis El Manar, Tunis, Tunisia
- Faculté de Médecine de Tunis, Research Unit UR18ES01 on “Obesity”, Tunis, Tunisia
- National Institute of Nutrition and Food Technology, Tunis, Tunisia
| | - Rym Kefi
- Laboratory of Biomedical Genomics and Oncogenetics, Institut Pasteur de Tunis, Tunis, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| |
Collapse
|
2
|
Schroeder P, Mandla R, Huerta-Chagoya A, Alkanak A, Nagy D, Szczerbinski L, Madsen JGS, Cole JB, Porneala B, Westerman K, Li JH, Pollin TI, Florez JC, Gloyn AL, Cebola I, Manning A, Leong A, Udler M, Mercader JM. Rare variant association analysis in 51,256 type 2 diabetes cases and 370,487 controls informs the spectrum of pathogenicity of monogenic diabetes genes. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.28.23296244. [PMID: 37808701 PMCID: PMC10557807 DOI: 10.1101/2023.09.28.23296244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
We meta-analyzed array data imputed with the TOPMed reference panel and whole-genome sequence (WGS) datasets and performed the largest, rare variant (minor allele frequency as low as 5×10-5) GWAS meta-analysis of type 2 diabetes (T2D) comprising 51,256 cases and 370,487 controls. We identified 52 novel variants at genome-wide significance (p<5 × 10-8), including 8 novel variants that were either rare or ancestry-specific. Among them, we identified a rare missense variant in HNF4A p.Arg114Trp (OR=8.2, 95% confidence interval [CI]=4.6-14.0, p = 1.08×10-13), previously reported as a variant implicated in Maturity Onset Diabetes of the Young (MODY) with incomplete penetrance. We demonstrated that the diabetes risk in carriers of this variant was modulated by a T2D common variant polygenic risk score (cvPRS) (carriers in the top PRS tertile [OR=18.3, 95%CI=7.2-46.9, p=1.2×10-9] vs carriers in the bottom PRS tertile [OR=2.6, 95% CI=0.97-7.09, p = 0.06]. Association results identified eight variants of intermediate penetrance (OR>5) in monogenic diabetes (MD), which in aggregate as a rare variant PRS were associated with T2D in an independent WGS dataset (OR=4.7, 95% CI=1.86-11.77], p = 0.001). Our data also provided support evidence for 21% of the variants reported in ClinVar in these MD genes as benign based on lack of association with T2D. Our work provides a framework for using rare variant imputation and WGS analyses in large-scale population-based association studies to identify large-effect rare variants and provide evidence for informing variant pathogenicity.
Collapse
Affiliation(s)
- Philip Schroeder
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Ravi Mandla
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine and Cardiovascular Research Institute, Cardiology Division, University of California, San Francisco, CA, USA
| | - Alicia Huerta-Chagoya
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ahmed Alkanak
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Dorka Nagy
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- National Heart and Lung Institute, Faculty of Medicine, London, UK
| | - Lukasz Szczerbinski
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, Bialystok, 15-276, Poland
- Clinical Research Centre, Medical University of Bialystok, Bialystok, 15-276, Poland
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Jesper G S Madsen
- Institute of Mathematics and Computer Science, University of Southern Denmark, Odense M, 5230, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Joanne B Cole
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Bianca Porneala
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Kenneth Westerman
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Josephine H Li
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Toni I Pollin
- Emory University, Atlanta, Georgia, USA., Atlanta, GA, USA
| | - Jose C Florez
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Endocrine Division, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Anna L Gloyn
- Department of Pediatrics, Division of Endocrinology, Stanford School of Medicine, Stanford, CA, USA
| | - Inês Cebola
- Section of Genetics and Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Alisa Manning
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Aaron Leong
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Endocrine Division, Massachusetts General Hospital, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Miriam Udler
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Josep M Mercader
- Programs in Metabolism and Medical & Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
4
|
Younis H, Ha SE, Jorgensen BG, Verma A, Ro S. Maturity-Onset Diabetes of the Young: Mutations, Physiological Consequences, and Treatment Options. J Pers Med 2022; 12:jpm12111762. [PMID: 36573710 PMCID: PMC9697644 DOI: 10.3390/jpm12111762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/18/2022] [Indexed: 02/01/2023] Open
Abstract
Maturity-Onset Diabetes of the Young (MODY) is a rare form of diabetes which affects between 1% and 5% of diagnosed diabetes cases. Clinical characterizations of MODY include onset of diabetes at an early age (before the age of 30), autosomal dominant inheritance pattern, impaired glucose-induced secretion of insulin, and hyperglycemia. Presently, 14 MODY subtypes have been identified. Within these subtypes are several mutations which contribute to the different MODY phenotypes. Despite the identification of these 14 subtypes, MODY is often misdiagnosed as type 1 or type 2 diabetes mellitus due to an overlap in clinical features, high cost and limited availability of genetic testing, and unfamiliarity with MODY outside of the medical profession. The primary aim of this review is to investigate the genetic characterization of the MODY subtypes. Additionally, this review will elucidate the link between the genetics, function, and clinical manifestations of MODY in each of the 14 subtypes. In providing this knowledge, we hope to assist in the accurate diagnosis of MODY patients and, subsequently, in ensuring they receive appropriate treatment.
Collapse
Affiliation(s)
- Hazar Younis
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV 89557, USA
| | - Se Eun Ha
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV 89557, USA
| | - Brian G. Jorgensen
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV 89557, USA
| | - Arushi Verma
- Department of Pediatrics, Division of Pediatric Endocrinology, University of Nevada School of Medicine, Reno, NV 89557, USA
| | - Seungil Ro
- Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, NV 89557, USA
- RosVivo Therapeutics, Applied Research Facility, Reno, NV 89557, USA
- Correspondence:
| |
Collapse
|