1
|
Alkhidir S, El-Akouri K, Al-Dewik N, Khodjet-El-Khil H, Okashah S, Islam N, Ben-Omran T, Al-Shafai M. The genetic basis and the diagnostic yield of genetic testing related to nonsyndromic hearing loss in Qatar. Sci Rep 2024; 14:4202. [PMID: 38378725 PMCID: PMC10879212 DOI: 10.1038/s41598-024-52784-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Hearing loss is the most predominant sensory defect occurring in pediatrics, of which, 66% cases are attributed to genetic factors. The prevalence of hereditary hearing loss increases in consanguineous populations, and the prevalence of hearing loss in Qatar is 5.2%. We aimed to investigate the genetic basis of nonsyndromic hearing loss (NSHL) in Qatar and to evaluate the diagnostic yield of different genetic tests available. A retrospective chart review was conducted for 59 pediatric patients with NSHL referred to the Department of Adult and Pediatric Medical Genetics at Hamad Medical Corporation in Qatar, and who underwent at least one genetic test. Out of the 59 patients, 39 were solved cases due to 19 variants in 11 genes and two copy number variants that explained the NSHL phenotype. Of them 2 cases were initially uncertain and were reclassified using familial segregation. Around 36.8% of the single variants were in GJB2 gene and c.35delG was the most common recurrent variant seen in solved cases. We detected the c.283C > T variant in FGF3 that was seen in a Qatari patient and found to be associated with NSHL for the first time. The overall diagnostic yield was 30.7%, and the diagnostic yield was significantly associated with genetic testing using GJB2 sequencing and using the hearing loss (HL) gene panel. The diagnostic yield for targeted familial testing was 60% (n = 3 patients) and for gene panel was 50% (n = 5). Thus, we recommend using GJB2 gene sequencing as a first-tier genetic test and HL gene panel as a second-tier genetic test for NSHL. Our work provided new insights into the genetic pool of NSHL among Arabs and highlights its unique diversity, this is believed to help further in the diagnostic and management options for NSHL Arab patients.
Collapse
Affiliation(s)
- Shaza Alkhidir
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
| | - Karen El-Akouri
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
- Division of Genetic and Genomic Medicine, Sidra Medicine, Doha, Qatar
| | - Nader Al-Dewik
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
| | - Houssein Khodjet-El-Khil
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Sarah Okashah
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar
- Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Nazmul Islam
- Department of Public Health, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
| | - Tawfeg Ben-Omran
- Department of Adult and Pediatric Medical Genetics, Hamad Medical Corporation, Doha, Qatar.
- Division of Genetic and Genomic Medicine, Sidra Medicine, Doha, Qatar.
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar.
- Biomedical Research Center, Qatar University, Doha, Qatar.
| |
Collapse
|
2
|
Abbas A, Hammad AS, Al-Shafai M. The role of genetic and epigenetic GNAS alterations in the development of early-onset obesity. Mutat Res Rev Mutat Res 2023; 793:108487. [PMID: 38103632 DOI: 10.1016/j.mrrev.2023.108487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND GNAS (guanine nucleotide-binding protein, alpha stimulating) is an imprinted gene that encodes Gsα, the α subunit of the heterotrimeric stimulatory G protein. This subunit mediates the signalling of a diverse array of G protein-coupled receptors (GPCRs), including the melanocortin 4 receptor (MC4R) that serves a pivotal role in regulating food intake, energy homoeostasis, and body weight. Genetic or epigenetic alterations in GNAS are known to cause pseudohypoparathyroidism in its different subtypes and have been recently associated with isolated, early-onset, severe obesity. Given the diverse biological functions that Gsα serves, multiple molecular mechanisms involving various GPCRs, such as MC4R, β2- and β3-adrenoceptors, and corticotropin-releasing hormone receptor, have been implicated in the pathophysiology of severe, early-onset obesity that results from genetic or epigenetic GNAS changes. SCOPE OF REVIEW This review examines the structure and function of GNAS and provides an overview of the disorders that are caused by defects in this gene and may feature early-onset obesity. Moreover, it elucidates the potential molecular mechanisms underlying Gsα deficiency-induced early-onset obesity, highlighting some of their implications for the diagnosis, management, and treatment of this complex condition. MAJOR CONCLUSIONS Gsα deficiency is an underappreciated cause of early-onset, severe obesity. Therefore, screening children with unexplained, severe obesity for GNAS defects is recommended, to enhance the molecular diagnosis and management of this condition.
Collapse
Affiliation(s)
- Alaa Abbas
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Ayat S Hammad
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar; Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, P.O. Box 2713, Doha, Qatar; Biomedical Research Center, Qatar University, P.O. Box 2713, Doha, Qatar.
| |
Collapse
|
3
|
Mohammed I, Haris B, Al-Barazenji T, Vasudeva D, Tomei S, Al Azwani I, Dauleh H, Shehzad S, Chirayath S, Mohamadsalih G, Petrovski G, Khalifa A, Love DR, Al-Shafai M, Hussain K. Understanding the Genetics of Early-Onset Obesity in a Cohort of Children From Qatar. J Clin Endocrinol Metab 2023; 108:3201-3213. [PMID: 37329217 PMCID: PMC10655519 DOI: 10.1210/clinem/dgad366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/10/2023] [Accepted: 06/14/2023] [Indexed: 06/18/2023]
Abstract
CONTEXT Monogenic obesity is a rare form of obesity due to pathogenic variants in genes implicated in the leptin-melanocortin signaling pathway and accounts for around 5% of severe early-onset obesity. Mutations in the genes encoding the MC4R, leptin, and leptin receptor are commonly reported in various populations to cause monogenic obesity. Determining the genetic cause has important clinical benefits as novel therapeutic interventions are now available for some forms of monogenic obesity. OBJECTIVE To unravel the genetic causes of early-onset obesity in the population of Qatar. METHODS In total, 243 patients with early-onset obesity (above the 95% percentile) and age of onset below 10 years were screened for monogenic obesity variants using a targeted gene panel, consisting of 52 obesity-related genes. RESULTS Thirty rare variants potentially associated with obesity were identified in 36 of 243 (14.8%) probands in 15 candidate genes (LEP, LEPR, POMC, MC3R, MC4R, MRAP2, SH2B1, BDNF, NTRK2, DYRK1B, SIM1, GNAS, ADCY3, RAI1, and BBS2). Twenty-three of the variants identified were novel to this study and the rest, 7 variants, were previously reported in literature. Variants in MC4R were the most common cause of obesity in our cohort (19%) and the c.485C>T p.T162I variant was the most frequent MC4R variant seen in 5 patients. CONCLUSION We identified likely pathogenic/pathogenic variants that seem to explain the phenotype of around 14.8% of our cases. Variants in the MC4R gene are the commonest cause of early-onset obesity in our population. Our study represents the largest monogenic obesity cohort in the Middle East and revealed novel obesity variants in this understudied population. Functional studies will be required to elucidate the molecular mechanism of their pathogenicity.
Collapse
Affiliation(s)
- Idris Mohammed
- College of Health & Life Sciences, Hamad Bin Khalifa University, PO Box 34110, Doha, Qatar
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Basma Haris
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Tara Al-Barazenji
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, PO Box 2713, Doha, Qatar
| | - Dhanya Vasudeva
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Sara Tomei
- Omics Core, Integrated Genomic Services, Research Branch, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Iman Al Azwani
- Omics Core, Integrated Genomic Services, Research Branch, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Hajar Dauleh
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Saira Shehzad
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Shiga Chirayath
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Ghassan Mohamadsalih
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Goran Petrovski
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Amel Khalifa
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Donald R Love
- Division of Genetic Pathology, Department of Pathology, Sidra Medicine, PO Box 26999, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, PO Box 2713, Doha, Qatar
- Biomedical Research Center, Qatar University, PO Box 2713, Doha, Qatar
| | - Khalid Hussain
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, PO Box 26999, Doha, Qatar
| |
Collapse
|
4
|
Mohammed I, Selvaraj S, Ahmed WS, Al-Barazenji T, Hammad AS, Dauleh H, Saraiva LR, Al-Shafai M, Hussain K. Functional Characterization of Novel MC4R Variants Identified in Two Unrelated Patients with Morbid Obesity in Qatar. Int J Mol Sci 2023; 24:16361. [PMID: 38003551 PMCID: PMC10671262 DOI: 10.3390/ijms242216361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
The leptin-melanocortin pathway is pivotal in appetite and energy homeostasis. Pathogenic variants in genes involved in this pathway lead to severe early-onset monogenic obesity (MO). The MC4R gene plays a central role in leptin-melanocortin signaling, and heterozygous variants in this gene are the most common cause of MO. A targeted gene panel consisting of 52 obesity-related genes was used to screen for variants associated with obesity. Variants were analyzed and filtered to identify potential disease-causing activity and validated using Sanger sequencing. We identified two novel heterozygous variants, c.253A>G p.Ser85Gly and c.802T>C p.Tyr268His, in the MC4R gene in two unrelated patients with morbid obesity and evaluated the functional impact of these variants. The impact of the variants on the MC4R gene was assessed using in silico prediction tools and molecular dynamics simulation. To further study the pathogenicity of the identified variants, GT1-7 cells were transfected with plasmid DNA encoding either wild-type or mutant MC4R variants. The effects of allelic variations in the MC4R gene on cAMP synthesis, MC4R protein level, and activation of PKA, ERB, and CREB signaling pathways in both stimulated and unstimulated ɑ-MSH paradigms were determined for their functional implications. In silico analysis suggested that the variants destabilized the MC4R structure and affected the overall dynamics of the MC4R protein, possibly leading to intracellular receptor retention. In vitro analysis of the functional impact of these variants showed a significant reduction in cell surface receptor expression and impaired extracellular ligand binding activity, leading to reduced cAMP production. Our analysis shows that the variants do not affect total protein expression; however, they are predicted to affect the post-translational localization of the MC4R protein to the cell surface and impair downstream signaling cascades such as PKA, ERK, and CREB signaling pathways. This finding might help our patients to benefit from the novel therapeutic advances for monogenic forms of obesity.
Collapse
Affiliation(s)
- Idris Mohammed
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar; (I.M.); (W.S.A.); (L.R.S.)
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar;
| | - Senthil Selvaraj
- Department of Disease Modeling and Therapeutics, Sidra Medicine, Doha P.O. Box 26999, Qatar;
| | - Wesam S. Ahmed
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar; (I.M.); (W.S.A.); (L.R.S.)
| | - Tara Al-Barazenji
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (T.A.-B.); (A.S.H.)
| | - Ayat S Hammad
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (T.A.-B.); (A.S.H.)
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
| | - Hajar Dauleh
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar;
| | - Luis R. Saraiva
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha P.O. Box 34110, Qatar; (I.M.); (W.S.A.); (L.R.S.)
- Department of Disease Modeling and Therapeutics, Sidra Medicine, Doha P.O. Box 26999, Qatar;
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (T.A.-B.); (A.S.H.)
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
| | - Khalid Hussain
- Division of Endocrinology, Department of Pediatric Medicine, Sidra Medicine, Doha P.O. Box 26999, Qatar;
| |
Collapse
|
5
|
Almaghrbi H, Al-Shafai M, Al-Asmakh M, Bawadi H. Association of Vitamin D Genetic Risk Score with Noncommunicable Diseases: A Systematic Review. Nutrients 2023; 15:4040. [PMID: 37764823 PMCID: PMC10537716 DOI: 10.3390/nu15184040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
Background and Aims: The genetic risk score (GRS) is an important tool for estimating the total genetic contribution or susceptibility to a certain outcome of interest in an individual, taking into account their genetic risk alleles. This study aims to systematically review the association between the GRS of low vitamin D with different noncommunicable diseases/markers. Methods: The article was first registered in PROSPERO CRD42023406929. PubMed and Embase were searched from the time of inception until March 2023 to capture all the literature related to the vitamin D genetic risk score (vD-GRS) in association with noncommunicable diseases. This was performed using comprehensive search terms including "Genetic Risk Score" OR "Genetics risk assessment" OR "Genome-wide risk score" AND "Vitamin D" OR 25(HO)D OR "25-hydroxyvitamin D". Results: Eleven eligible studies were included in this study. Three studies reported a significant association between vD-GRS and metabolic parameters, including body fat percentage, body mass index, glycated hemoglobin, and fasting blood glucose. Moreover, colorectal cancer overall mortality and the risk of developing arterial fibrillation were also found to be associated with genetically deprived vitamin D levels. Conclusions: This systematic review highlights the genetic contribution of low-vitamin-D-risk single nucleotides polymorphisms (SNPs) as an accumulative factor associated with different non-communicable diseases/markers, including cancer mortality and the risk of developing obesity, type 2 diabetes, and cardiovascular diseases such as arterial fibrillation.
Collapse
Affiliation(s)
- Heba Almaghrbi
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.); (M.A.-S.); (M.A.-A.)
| | - Mashael Al-Shafai
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.); (M.A.-S.); (M.A.-A.)
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
| | - Maha Al-Asmakh
- Department of Biomedical Science, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar; (H.A.); (M.A.-S.); (M.A.-A.)
- Biomedical Research Center, Qatar University, Doha P.O. Box 2713, Qatar
| | - Hiba Bawadi
- Department of Human Nutrition, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar
| |
Collapse
|
6
|
Patrinos D, Ghaly M, Al-Shafai M, Zawati MH. Legal approaches to risk of harm in genetic counseling: perspectives from Quebec and Qatar. Front Genet 2023; 14:1190421. [PMID: 37576562 PMCID: PMC10416622 DOI: 10.3389/fgene.2023.1190421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/21/2023] [Indexed: 08/15/2023] Open
Abstract
Genetic counseling is a fast-growing profession worldwide, with genetic counselors taking on increasingly comprehensive and autonomous roles in the healthcare sector. However, the absence of appropriate legal frameworks could potentially create risks of harm to the public. Legal recognition serves to protect the public from risk of harm by regulating the safe and competent practice of healthcare professionals. Genetic counseling is not legally recognized in most world jurisdictions. Examination of the legal status of genetic counseling in different jurisdictions and whether existing legal mechanisms are adequate to address potential risks of harm is therefore timely. This paper examines the different roles of genetic counselors in the Canadian province of Quebec and the state of Qatar, the authors' respective jurisdictions. It considers the types of harms that may be created where appropriate legal mechanisms are lacking, considering the socio-political and legal differences between the two jurisdictions. Moreover, it examines the legal status of genetic counseling in Quebec and Qatar to determine whether these statuses appropriately address the identified risks of harm. The authors argue that existing legal frameworks are inadequate to address these risks and recommend that additional regulatory mechanisms be implemented to properly protect the public from risks of harm.
Collapse
Affiliation(s)
- Dimitri Patrinos
- Centre of Genomics and Policy, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| | - Mohammed Ghaly
- Research Center for Islamic Legislation and Ethics, College of Islamic Studies, Hamad Bin Khalifa University, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Ma’n H. Zawati
- Centre of Genomics and Policy, School of Biomedical Sciences, Faculty of Medicine and Health Sciences, McGill University, Montreal, QC, Canada
| |
Collapse
|
7
|
Kohil A, Abdallah AM, Hussain K, Al-Shafai M. Genetic epidemiology of Woodhouse-Sakati Syndrome in the Greater Middle East region and beyond: a systematic review. Orphanet J Rare Dis 2023; 18:22. [PMID: 36721231 PMCID: PMC9887781 DOI: 10.1186/s13023-023-02614-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 01/15/2023] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Woodhouse-Sakati syndrome (WSS) is a rare, autosomal recessive genetic disorder with variable clinical manifestations mainly affecting the endocrine and nervous systems. The aim of this study was to systematically review the genetic basis of WSS and report the genetic variants and clinical phenotypes associated with the disease. METHODS PubMed, Science Direct, Scopus, and Web of Science databases were searched from the time of inception until June 2022. Broad search terms were used to capture the literature describing all genetic variants associated with WSS. The search keywords used are "Woodhouse Sakati" along with the term "mutation" OR "gene" OR "variant" OR "polymorphism". RESULTS Twenty-five eligible studies were included in this study. One hundred and eighty-five patients in 97 families from 12 different countries were diagnosed with WSS. In patients from the Greater Middle East (GME) region, consanguineous marriages were common (67%). Thirteen different DCAF17 variants were associated with WSS development (including 8 identified in the GME region). The most frequent variant was a frameshift deletion variant (c.436delC, p.Ala147Hisfs*9) unique to Arabs that was reported in 11 cases from Tunisia, Kuwait, Qatar, Bahrain, and Saudi Arabia. There were no clear genotype-phenotype correlations for the different variants. CONCLUSIONS This systematic review highlights the molecular basis and clinical manifestations of WSS globally, including the GME region, where the disease is prevalent due to consanguinity. Additional studies are now needed to understand the genotype-phenotype correlation for different DCAF17 variants and their impact on the phenotypic heterogeneity observed in WSS patients.
Collapse
Affiliation(s)
- Amira Kohil
- grid.412603.20000 0004 0634 1084Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713 Doha, Qatar
| | - Atiyeh M. Abdallah
- grid.412603.20000 0004 0634 1084Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713 Doha, Qatar
| | - Khalid Hussain
- grid.467063.00000 0004 0397 4222Department of Pediatrics, Division of Endocrinology, Sidra Medicine, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, 2713, Doha, Qatar.
| |
Collapse
|
8
|
AbouHashem N, Al-Shafai K, Al-Shafai M. The genetic elucidation of monogenic obesity in the Arab world: a systematic review. J Pediatr Endocrinol Metab 2022; 35:699-707. [PMID: 35437977 DOI: 10.1515/jpem-2021-0710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/21/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Investigation of monogenic obesity (MO), a rare condition caused by a single gene variant(s), especially in consanguineous populations, is a powerful approach for obtaining novel insights into the genetic alterations involved. Here, we present a systematic review of the genetics of MO in the 22 Arab countries and apply protein modeling in silico to the missense variants reported. METHODS We searched four literature databases (PubMed, Web of Science, Science Direct and Scopus) from the time of their first creation until December 2020, utilizing broad search terms to capture all genetic studies related to MO in the Arab countries. Only articles published in peer-reviewed journals involving subjects from at least one of the 22 Arab countries and dealing with genetic variants related to MO were included. Protein modelling of the variants identified was performed using PyMOL. RESULTS The 30 cases with severe early-onset obesity identified in 13 studies carried 14 variants in five genes (LEP, LEPR, POMC, MC4R and CPE). All of these variants were pathogenic, homozygous and carried by members of consanguineous families. CONCLUSION Despite the elevated presence of consanguinity in the Arab countries, the genetic origins of MO remain largely unexplained and require additional studies, both of a genetic and functional character.
Collapse
Affiliation(s)
- Nadien AbouHashem
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | | | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| |
Collapse
|
9
|
Jithesh PV, Abuhaliqa M, Syed N, Ahmed I, El Anbari M, Bastaki K, Sherif S, Umlai UK, Jan Z, Gandhi G, Manickam C, Selvaraj S, George C, Bangarusamy D, Abdel-Latif R, Al-Shafai M, Tatari-Calderone Z, Estivill X, Pirmohamed M. A population study of clinically actionable genetic variation affecting drug response from the Middle East. NPJ Genom Med 2022; 7:10. [PMID: 35169154 PMCID: PMC8847489 DOI: 10.1038/s41525-022-00281-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/22/2021] [Indexed: 02/08/2023] Open
Abstract
Clinical implementation of pharmacogenomics will help in personalizing drug prescriptions and alleviate the personal and financial burden due to inefficacy and adverse reactions to drugs. However, such implementation is lagging in many parts of the world, including the Middle East, mainly due to the lack of data on the distribution of actionable pharmacogenomic variation in these ethnicities. We analyzed 6,045 whole genomes from the Qatari population for the distribution of allele frequencies of 2,629 variants in 1,026 genes known to affect 559 drugs or classes of drugs. We also performed a focused analysis of genotypes or diplotypes of 15 genes affecting 46 drugs, which have guidelines for clinical implementation and predicted their phenotypic impact. The allele frequencies of 1,320 variants in 703 genes affecting 299 drugs or class of drugs were significantly different between the Qatari population and other world populations. On average, Qataris carry 3.6 actionable genotypes/diplotypes, affecting 13 drugs with guidelines for clinical implementation, and 99.5% of the individuals had at least one clinically actionable genotype/diplotype. Increased risk of simvastatin-induced myopathy could be predicted in ~32% of Qataris from the diplotypes of SLCO1B1, which is higher compared to many other populations, while fewer Qataris may need tacrolimus dosage adjustments for achieving immunosuppression based on the CYP3A5 diplotypes compared to other world populations. Distinct distribution of actionable pharmacogenomic variation was also observed among the Qatari subpopulations. Our comprehensive study of the distribution of actionable genetic variation affecting drugs in a Middle Eastern population has potential implications for preemptive pharmacogenomic implementation in the region and beyond.
Collapse
Affiliation(s)
| | | | - Najeeb Syed
- Research Branch, Sidra Medicine, Doha, Qatar
| | | | | | - Kholoud Bastaki
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.,Hamad Medical Corporation, Doha, Qatar
| | - Shimaa Sherif
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Umm-Kulthum Umlai
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Zainab Jan
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Geethanjali Gandhi
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.,Research Branch, Sidra Medicine, Doha, Qatar
| | | | | | | | - Dhinoth Bangarusamy
- College of Health & Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Rania Abdel-Latif
- Qatar Genome Program, Qatar Foundation Research Development and Innovation, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | | | - Xavier Estivill
- Quantitative Genomics Laboratories, Barcelona, Catalonia, Spain
| | - Munir Pirmohamed
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | | |
Collapse
|
10
|
AbouHashem N, Zaied RE, Al-Shafai K, Nofal M, Syed N, Al-Shafai M. The Spectrum of Genetic Variants Associated with the Development of Monogenic Obesity in Qatar. Obes Facts 2022; 15:357-365. [PMID: 35026759 PMCID: PMC9210005 DOI: 10.1159/000521851] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Accepted: 01/06/2022] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Monogenic obesity (MO) is a rare genetic disease characterized by severe early-onset obesity in affected individuals. Previous genetic studies revealed 8 definitive genes for monogenic non-syndromic obesity; many were discovered in consanguineous populations. Here, we examined MO in the Qatari population, whose population is largely consanguineous (54%) and characterized by extensive obesity (45%). METHODS Whole genome sequencing data of Qatar Biobank samples from 250 subjects with obesity and 250 subjects with normal weight, obtained in association with the Qatar Genome Programme, were searched for genetic variants in the genes known to be associated with MO (i.e., LEP, LEPR, POMC, PCSK1, MC3R, MC4R, MRAP2, and ADCY3). The impact of the variants identified was investigated utilizing in silico tools for prediction in combination with protein visualization by PyMOL. RESULTS We identified potential MO variants in more than 5% of the cases in our cohort. We revealed 11 rare variants in 6 of the genes targeted, including two disease-causing variants in MC4R and MRAP2, all of which were heterozygous. Moreover, enrichment of a heterozygous ADCY3 variant (c.1658C>T; p.A553V) appeared to cause severe obesity in an autosomal dominant manner. CONCLUSION These findings highlight the importance of implementing routine testing for genetic variants that predispose for MO in Qatar. Clearly, additional studies of this nature on populations not yet examined are required. At the same time, functional investigations, both in vitro and in vivo, are necessary in order to better understand the role of the variants identified in the pathogenesis of obesity.
Collapse
Affiliation(s)
- Nadien AbouHashem
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar,
| | - Roan E Zaied
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- Institute of Infection, Immunity and Inflammation, MVLS, University of Glasgow, Glasgow, United Kingdom
| | | | - Mariam Nofal
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Najeeb Syed
- Applied Bioinformatics Core, Sidra Medicine, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| |
Collapse
|
11
|
Kohil A, Al-Asmakh M, Al-Shafai M, Terranegra A. The Interplay Between Diet and the Epigenome in the Pathogenesis of Type-1 Diabetes. Front Nutr 2021; 7:612115. [PMID: 33585535 PMCID: PMC7876257 DOI: 10.3389/fnut.2020.612115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022] Open
Abstract
The autoimmune disease, Type 1 Diabetes Mellitus (T1DM), results in the destruction of pancreatic β-cells, and the International Diabetes Federation reports that its incidence is increasing worldwide. T1DM is a complex disease due to the interaction between genetic and environmental factors. Certain dietary patterns and nutrients are known to cause epigenetic modifications in physiological conditions and diseases. However, the interplay between diet and epigenetics is not yet well-understood in the context of T1DM. Several studies have described epigenetic mechanisms involved in the autoimmune reactions that destroy the β-cells, but few explored diet components as potential triggers for epigenetic modifications. Clarifying the link between diet and epigenome can provide new insights into the pathogenesis of T1DM, potentially leading to new diagnostic and therapeutic approaches. In this mini review, we shed light on the influence of the diet-epigenome axis on the pathophysiology of T1DM.
Collapse
Affiliation(s)
- Amira Kohil
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | - Maha Al-Asmakh
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar.,Biomedical Research Center, Qatar University, Doha, Qatar.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
| | - Mashael Al-Shafai
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha, Qatar.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, Doha, Qatar
| | | |
Collapse
|
12
|
Visconti A, Al-Shafai M, Al Muftah WA, Zaghlool SB, Mangino M, Suhre K, Falchi M. PopPAnTe: population and pedigree association testing for quantitative data. BMC Genomics 2017; 18:150. [PMID: 28187711 PMCID: PMC5303218 DOI: 10.1186/s12864-017-3527-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/31/2017] [Indexed: 11/13/2022] Open
Abstract
Background Family-based designs, from twin studies to isolated populations with their complex genealogical data, are a valuable resource for genetic studies of heritable molecular biomarkers. Existing software for family-based studies have mainly focused on facilitating association between response phenotypes and genetic markers, and no user-friendly tools are at present available to straightforwardly extend association studies in related samples to large datasets of generic quantitative data, as those generated by current -omics technologies. Results We developed PopPAnTe, a user-friendly Java program, which evaluates the association of quantitative data in related samples. Additionally, PopPAnTe implements data pre and post processing, region based testing, and empirical assessment of associations. Conclusions PopPAnTe is an integrated and flexible framework for pairwise association testing in related samples with a large number of predictors and response variables. It works either with family data of any size and complexity, or, when the genealogical information is unknown, it uses genetic similarity information between individuals as those inferred from genome-wide genetic data. It can therefore be particularly useful in facilitating usage of biobank data collections from population isolates when extensive genealogical information is missing.
Collapse
Affiliation(s)
- Alessia Visconti
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Mashael Al-Shafai
- Department of Genomics of Common Diseases, Imperial College London, London, UK.,Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar.,Research Division, Qatar Science Leadership Program, Qatar Foundation, Doha, Qatar.,Department of Biomedical Sciences, College of Health Sciences at Qatar University, Doha, Qatar
| | - Wadha A Al Muftah
- Department of Genomics of Common Diseases, Imperial College London, London, UK.,Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar.,Research Division, Qatar Science Leadership Program, Qatar Foundation, Doha, Qatar
| | - Shaza B Zaghlool
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.,NIHR Biomedical Research Centre at Guy's and St Thomas' Foundation Trust, London, UK
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Mario Falchi
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| |
Collapse
|
13
|
Zaghlool SB, Al-Shafai M, Al Muftah WA, Kumar P, Gieger C, Waldenberger M, Falchi M, Suhre K. Mendelian inheritance of trimodal CpG methylation sites suggests distal cis-acting genetic effects. Clin Epigenetics 2016; 8:124. [PMID: 27895808 PMCID: PMC5120560 DOI: 10.1186/s13148-016-0295-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/15/2016] [Indexed: 11/17/2022] Open
Abstract
Background Environmentally influenced phenotypes, such as obesity and insulin resistance, can be transmitted over multiple generations. Epigenetic modifications, such as methylation of DNA cytosine-guanine (CpG) pairs, may be carriers of inherited information. At the population level, the methylation state of such “heritable” CpG sites is expected to follow a trimodal distribution, and their mode of inheritance should be Mendelian. Methods Using the Illumina Infinium 450 K DNA methylation array, we determined DNA CpG-methylation in blood cells from a family cohort 123 individuals of Arab ethnicity, including 18 elementary father-mother-child trios, we asked whether Mendelian inheritance of CpG methylation is observed, and most importantly, whether it is independent of any genetic signals. Using 40× whole genome sequencing, we therefore excluded all CpG sites with possibly confounding genetic variants (SNP) within the binding regions of the Illumina probes. Results We identified a total of 955 CpG sites that displayed a trimodal distribution and confirmed trimodality in a study of 1805 unrelated Caucasians. Of 955 CpG sites, 99.9% observed a strict Mendelian pattern of inheritance and had no SNP within +/−110 nucleotides of the CpG site by design. However, in 97% of these cases a distal cis-acting SNP within a +/−1 Mbp window was found that explained the observed CpG distribution, excluding the hypothesis of epigenetic inheritance for these clear-cut trimodal sites. Using power analysis, we showed that in 46% of all cases, the closest CpG-associated SNP was located more than 1000 bp from the CpG site. Conclusions Our findings suggest that CpG methylation is maintained over larger genomic distances. Furthermore, nearly half of the SNPs associated with these trimodal sites were also associated with the expression of nearby genes (P = 4.08 × 10−6), implying a regulatory effect of these trimodal CpG sites. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0295-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shaza B Zaghlool
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, PO Box 24144, Doha, Qatar ; Computer Engineering Department, Virginia Tech, Blacksburg, VA 24060 USA
| | - Mashael Al-Shafai
- Department of Genomics of Common Disease, Imperial College London, London, UK ; Research Division, Qatar Science Leadership Program, Qatar Foundation, Doha, Qatar ; Department of Biomedical Sciences, College of Health Sciences at Qatar University, Doha, Qatar
| | - Wadha A Al Muftah
- Department of Genomics of Common Disease, Imperial College London, London, UK ; Research Division, Qatar Science Leadership Program, Qatar Foundation, Doha, Qatar
| | - Pankaj Kumar
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Christian Gieger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany ; Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mario Falchi
- Department of Twin Research & Genetic Epidemiology, King's College London, London, SE1 7EH UK
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medical College in Qatar, Education City, PO Box 24144, Doha, Qatar
| |
Collapse
|
14
|
Zaghlool SB, Al-Shafai M, Al Muftah WA, Kumar P, Falchi M, Suhre K. Association of DNA methylation with age, gender, and smoking in an Arab population. Clin Epigenetics 2015; 7:6. [PMID: 25663950 PMCID: PMC4320840 DOI: 10.1186/s13148-014-0040-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 12/22/2014] [Indexed: 11/17/2022] Open
Abstract
Background Modification of DNA by methylation of cytosines at CpG dinucleotides is a widespread phenomenon that leads to changes in gene expression, thereby influencing and regulating many biological processes. Recent technical advances in the genome-wide determination of single-base DNA-methylation enabled epigenome-wide association studies (EWASs). Early EWASs established robust associations between age and gender with the degree of CpG methylation at specific sites. Other studies uncovered associations with cigarette smoking. However, so far these studies were mainly conducted in Caucasians, raising the question of whether these findings can also be extrapolated to other populations. Results Here, we present an EWAS with age, gender, and smoking status in a family study of 123 individuals of Arab descent. We determined DNA methylation at over 450,000 CpG sites using the Illumina Infinium HumanMethylation450 BeadChip, applied state-of-the-art data processing protocols, including correction for blood cell type heterogeneity and hidden confounders, and eliminated probes containing SNPs at the targeted CpG site using 40× whole-genome sequencing data. Using this approach, we could replicate the leading published EWAS associations with age, gender and smoking, and recovered hallmarks of gender-specific epigenetic changes. Interestingly, we could even replicate the recently reported precise prediction of chronological age based on the methylation of only a few selected CpG sites. Conclusion Our study supports the view that when applied with state-of-the art protocols to account for all potential confounders, DNA methylation arrays represent powerful tools for EWAS with more complex phenotypes that can also be successfully applied to non-Caucasian populations. Electronic supplementary material The online version of this article (doi:10.1186/s13148-014-0040-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Shaza B Zaghlool
- Bioinformatics Core, Weill Cornell Medical College in Qatar, Education City, PO Box 24144, Doha, Qatar ; Computer Engineering Department, Virginia Tech, Blacksburg, VA 24060 USA
| | - Mashael Al-Shafai
- Bioinformatics Core, Weill Cornell Medical College in Qatar, Education City, PO Box 24144, Doha, Qatar ; Department of Genomics of Common Disease, Imperial College London, London, UK ; Research Division, Qatar Science Leadership Program, Qatar Foundation, Doha, Qatar
| | - Wadha A Al Muftah
- Bioinformatics Core, Weill Cornell Medical College in Qatar, Education City, PO Box 24144, Doha, Qatar ; Department of Genomics of Common Disease, Imperial College London, London, UK ; Research Division, Qatar Science Leadership Program, Qatar Foundation, Doha, Qatar
| | - Pankaj Kumar
- Bioinformatics Core, Weill Cornell Medical College in Qatar, Education City, PO Box 24144, Doha, Qatar
| | - Mario Falchi
- Department of Genomics of Common Disease, Imperial College London, London, UK
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medical College in Qatar, Education City, PO Box 24144, Doha, Qatar ; Helmholtz Zentrum München, Germany, Research Center for Environmental Health, 85764 Neuherberg, Germany
| |
Collapse
|
15
|
Kumar P, Al-Shafai M, Al Muftah WA, Chalhoub N, Elsaid MF, Aleem AA, Suhre K. Evaluation of SNP calling using single and multiple-sample calling algorithms by validation against array base genotyping and Mendelian inheritance. BMC Res Notes 2014; 7:747. [PMID: 25339461 PMCID: PMC4216909 DOI: 10.1186/1756-0500-7-747] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Accepted: 10/03/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND With diminishing costs of next generation sequencing (NGS), whole genome analysis becomes a standard tool for identifying genetic causes of inherited diseases. Commercial NGS service providers in general not only provide raw genomic reads, but further deliver SNP calls to their clients. However, the question for the user arises whether to use the SNP data as is, or process the raw sequencing data further through more sophisticated SNP calling pipelines with more advanced algorithms. RESULTS Here we report a detailed comparison of SNPs called using the popular GATK multiple-sample calling protocol to SNPs delivered as part of a 40x whole genome sequencing project by Illumina Inc of 171 human genomes of Arab descent (108 unrelated Qatari genomes, 19 trios, and 2 families with rare diseases) and compare them to variants provided by the Illumina CASAVA pipeline. GATK multi-sample calling identifies more variants than the CASAVA pipeline. The additional variants from GATK are robust for Mendelian consistencies but weak in terms of statistical parameters such as TsTv ratio. However, these additional variants do not make a difference in detecting the causative variants in the studied phenotype. CONCLUSION Both pipelines, GATK multi-sample calling and Illumina CASAVA single sample calling, have highly similar performance in SNP calling at the level of putatively causative variants.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Karsten Suhre
- Weill Cornell Medical College in Qatar, Education City, Doha, Qatar.
| |
Collapse
|