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Al Hageh C, O'Sullivan S, Henschel A, Chacar S, Hantouche M, Nader M, Zalloua PA. Assessment of genetic and clinical factors in T2D susceptibility among patients with hypertension. Acta Diabetol 2024:10.1007/s00592-024-02279-0. [PMID: 38767674 DOI: 10.1007/s00592-024-02279-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/19/2024] [Indexed: 05/22/2024]
Abstract
AIMS Hypertension (HTN) and Type 2 Diabetes (T2D) often coexist, therefore understanding the relationship between both diseases is imperative to guide targeted prevention/therapy. This study aims to explore the relationship between HTN and T2D using genome-wide association study (GWAS) analysis and biochemical data to understand the implication of both clinical and genetic factors in these pathologies. METHODS A total of 2,876 patients were enrolled. Using GWAS and biochemical data, patients with both T2D and HTN were compared to patients with only HTN. Specificity was confirmed by testing the detected genetic variants for associations with HTN development in T2D patients, or with HTN in healthy subjects. Regression models were applied to examine the association of T2D in patients with HTN with cardiovascular risk factors. Replication was performed using UK Biobank dataset with 31,170 subjects. RESULTS Data showed that females with HTN are at higher risk of developing T2D due to dyslipidemia, while males faced higher risk due to high BMI (body mass index) and family history of T2D. GWAS identified Single Nucleotide Polymorphisms (SNPs) linked to T2D in patients with HTN. Notably, rs7865889, rs7756992, and rs10896290 were positively associated with T2D, whereas rs12737517 yielded negative association. Three SNPs were replicated in the UK Biobank (rs10896290, rs7865889, and rs7756992). CONCLUSION Incorporating clinical and genetic screening into risk assessment is important for the detection and prevention of T2D in patients with HTN. The detected SNPs (rs7865889, rs12737517, and rs10896290), especially the protective SNP (rs12737517), provide an opportunity for better diagnosis, prevention, and therapy of patients with T2D and HTN.
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Affiliation(s)
- Cynthia Al Hageh
- Department of Public Health and Epidemiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Siobhán O'Sullivan
- Department of Biological Sciences, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Andreas Henschel
- Department of Electrical Engineering and Computer, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Stephanie Chacar
- Department of Medical Sciences, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Mireille Hantouche
- Department of Public Health and Epidemiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Moni Nader
- Department of Medical Sciences, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
| | - Pierre A Zalloua
- Department of Public Health and Epidemiology, College of Medicine and Health Sciences, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates.
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Elashi AA, Toor SM, Umlai UKI, Al-Sarraj YA, Taheri S, Suhre K, Abou-Samra AB, Albagha OME. Genome-wide association study and trans-ethnic meta-analysis identify novel susceptibility loci for type 2 diabetes mellitus. BMC Med Genomics 2024; 17:115. [PMID: 38685053 PMCID: PMC11059680 DOI: 10.1186/s12920-024-01855-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND The genetic basis of type 2 diabetes (T2D) is under-investigated in the Middle East, despite the rapidly growing disease prevalence. We aimed to define the genetic determinants of T2D in Qatar. METHODS Using whole genome sequencing of 11,436 participants (2765 T2D cases and 8671 controls) from the population-based Qatar Biobank (QBB), we conducted a genome-wide association study (GWAS) of T2D with and without body mass index (BMI) adjustment. RESULTS We replicated 93 known T2D-associated loci in a BMI-unadjusted model, while 96 known loci were replicated in a BMI-adjusted model. The effect sizes and allele frequencies of replicated SNPs in the Qatari population generally concurred with those from European populations. We identified a locus specific to our cohort located between the APOBEC3H and CBX7 genes in the BMI-unadjusted model. Also, we performed a transethnic meta-analysis of our cohort with a previous GWAS on T2D in multi-ancestry individuals (180,834 T2D cases and 1,159,055 controls). One locus in DYNC2H1 gene reached genome-wide significance in the meta-analysis. Assessing polygenic risk scores derived from European- and multi-ancestries in the Qatari population showed higher predictive performance of the multi-ancestry panel compared to the European panel. CONCLUSION Our study provides new insights into the genetic architecture of T2D in a Middle Eastern population and identifies genes that may be explored further for their involvement in T2D pathogenesis.
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Affiliation(s)
- Asma A Elashi
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Education City, Doha, P.O. Box 34110, Qatar
| | - Salman M Toor
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Education City, Doha, P.O. Box 34110, Qatar
| | - Umm-Kulthum Ismail Umlai
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Education City, Doha, P.O. Box 34110, Qatar
| | - Yasser A Al-Sarraj
- Qatar Genome Program (QGP), Qatar Foundation Research, Development and Innovation, Qatar Foundation (QF), Doha, P.O. Box 5825, Qatar
| | - Shahrad Taheri
- Qatar Metabolic Institute, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, P.O. Box 24144, Qatar
- Department of Biophysics and Physiology, Weill Cornell Medicine, 510065, New York, USA
| | | | - Omar M E Albagha
- College of Health and Life Sciences (CHLS), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Education City, Doha, P.O. Box 34110, Qatar.
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, EH4 2XU, Edinburgh, UK.
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Sullivan SO', Al Hageh C, Henschel A, Chacar S, Abchee A, Zalloua P, Nader M. HDL levels modulate the impact of type 2 diabetes susceptibility alleles in older adults. Lipids Health Dis 2024; 23:56. [PMID: 38389069 PMCID: PMC10882764 DOI: 10.1186/s12944-024-02039-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 02/02/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Type 2 Diabetes (T2D) is influenced by genetic, environmental, and ageing factors. Ageing pathways exacerbate metabolic diseases. This study aimed to examine both clinical and genetic factors of T2D in older adults. METHODS A total of 2,909 genotyped patients were enrolled in this study. Genome Wide Association Study was conducted, comparing T2D patients to non-diabetic older adults aged ≥ 60, ≥ 65, or ≥ 70 years, respectively. Binomial logistic regressions were applied to examine the association between T2D and various risk factors. Stepwise logistic regression was conducted to explore the impact of low HDL (HDL < 40 mg/dl) on the relationship between the genetic variants and T2D. A further validation step using data from the UK Biobank with 53,779 subjects was performed. RESULTS The association of T2D with both low HDL and family history of T2D increased with the age of control groups. T2D susceptibility variants (rs7756992, rs4712523 and rs10946403) were associated with T2D, more significantly with increased age of the control group. These variants had stronger effects on T2D risk when combined with low HDL cholesterol levels, especially in older control groups. CONCLUSIONS The findings highlight a critical role of age, genetic predisposition, and HDL levels in T2D risk. The findings suggest that individuals over 70 years who have high HDL levels without the T2D susceptibility alleles may be at the lowest risk of developing T2D. These insights can inform tailored preventive strategies for older adults, enhancing personalized T2D risk assessments and interventions.
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Affiliation(s)
- Siobhán O ' Sullivan
- Department of Biological Sciences, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Cynthia Al Hageh
- Department of Public Health and Epidemiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Andreas Henschel
- Department of Computer Science, College of Engineering, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Stephanie Chacar
- Department of Medical Sciences, College of Medicine and Health Sciences, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates
| | - Antoine Abchee
- Faculty of Medicine, University of Balamand, Balamand, Lebanon
| | - Pierre Zalloua
- Faculty of Medicine, University of Balamand, Balamand, Lebanon.
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Public Health and Epidemiology, College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates.
| | - Moni Nader
- Department of Medical Sciences, College of Medicine and Health Sciences, Khalifa University, PO Box 127788, Abu Dhabi, United Arab Emirates.
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Mohamed SA, Fernadez-Tajes J, Franks PW, Bennet L. GWAS in people of Middle Eastern descent reveals a locus protective of kidney function-a cross-sectional study. BMC Med 2022; 20:76. [PMID: 35227251 PMCID: PMC8886846 DOI: 10.1186/s12916-022-02267-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/18/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Type 2 diabetes is one of the leading causes of chronic kidney failure, which increases globally and represents a significant threat to public health. People from the Middle East represent one of the largest immigrant groups in Europe today. Despite poor glucose regulation and high risk for early-onset insulin-deficient type 2 diabetes, they have better kidney function and lower rates of all-cause and cardiovascular-specific mortality compared with people of European ancestry. Here, we assessed the genetic basis of estimated glomerular filtration rate (eGFR) and other metabolic traits in people of Iraqi ancestry living in southern Sweden. METHODS Genome-wide association study (GWAS) analyses were performed in 1201 Iraqi-born residents of the city of Malmö for eGFR and ten other metabolic traits using linear mixed-models to account for family structure. RESULTS The strongest association signal was detected for eGFR in CST9 (rs13037490; P value = 2.4 × 10-13), a locus previously associated with cystatin C-based eGFR; importantly, the effect (major) allele here contrasts the effect (minor) allele in other populations, suggesting favorable selection at this locus. Additional novel genome-wide significant loci for eGFR (ERBB4), fasting glucose (CAMTA1, NDUFA10, TRIO, WWC1, TRAPPC9, SH3GL2, ABCC11), quantitative insulin-sensitivity check index (METTL16), and HbA1C (CAMTA1, ME1, PAK1, RORA) were identified. CONCLUSIONS The genetic effects discovered here may help explain why people from the Middle East have better kidney function than those of European descent. Genetic predisposition to preserved kidney function may also underlie the observed survival benefits in Middle Eastern immigrants with type 2 diabetes.
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Affiliation(s)
- Siham A Mohamed
- Lund University Diabetes Center, Lund University, Malmö, Sweden.,Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Juan Fernadez-Tajes
- Lund University Diabetes Center, Lund University, Malmö, Sweden.,Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Paul W Franks
- Lund University Diabetes Center, Lund University, Malmö, Sweden. .,Department of Clinical Sciences, Lund University, Malmö, Sweden.
| | - Louise Bennet
- Department of Clinical Sciences, Lund University, Malmö, Sweden. .,Clinical Research and Trial Center, Lund University Hospital, Lund, Sweden.
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El-Kebbi IM, Bidikian NH, Hneiny L, Nasrallah MP. Epidemiology of type 2 diabetes in the Middle East and North Africa: Challenges and call for action. World J Diabetes 2021; 12:1401-1425. [PMID: 34630897 PMCID: PMC8472500 DOI: 10.4239/wjd.v12.i9.1401] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/21/2021] [Accepted: 08/02/2021] [Indexed: 02/06/2023] Open
Abstract
Type 2 diabetes continues to be a serious and highly prevalent public health problem worldwide. In 2019, the highest prevalence of diabetes in the world at 12.2%, with its associated morbidity and mortality, was found in the Middle East and North Africa region. In addition to a genetic predisposition in its population, evidence suggests that obesity, physical inactivity, urbanization, and poor nutritional habits have contributed to the high prevalence of diabetes and prediabetes in the region. These risk factors have also led to an earlier onset of type 2 diabetes among children and adolescents, negatively affecting the productive years of the youth and their quality of life. Furthermore, efforts to control the rising prevalence of diabetes and its complications have been challenged and complicated by the political instability and armed conflict in some countries of the region and the recent coronavirus disease 2019. Broad strategies, coupled with targeted interventions at the regional, national, and community levels are needed to address and curb the spread of this public health crisis.
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Affiliation(s)
- Imad M El-Kebbi
- Department of Internal Medicine, Division of Endocrinology, American University of Beirut Medical Center, Faculty of Medicine, Beirut 11072020, Lebanon
- Department of Internal Medicine, Sheikh Shakhbout Medical City, Abou Dhabi 11001, United Arab Emirates
| | - Nayda H Bidikian
- School of Medicine, American University of Beirut, Faculty of Medicine, Beirut 11072020, Lebanon
| | - Layal Hneiny
- University Libraries, Saab Medical Library, American University of Beirut, Beirut 11072020, Lebanon
| | - Mona Philippe Nasrallah
- Department of Internal Medicine, Division of Endocrinology, American University of Beirut Medical Center, Faculty of Medicine, Beirut 11072020, Lebanon
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Abstract
The Middle East and North Africa regions, including Lebanon, have recently witnessed rapid urbanization and modernization over the last couple of decades that has led to a dramatic transformation affecting lifestyle and diet. The World Health Organization reports that the leading cause of death in Lebanon is due to cardiovascular disease (CVD) at 47% of all-cause mortality. Over the last 30 years, especially the last 10, the population of Lebanon has changed dramatically due to the effect of wars in the region and refugees seeking asylum. With a population of around 4.5 million and a relatively high rate of consanguinity in Lebanon, a variety of novel mutations have been discovered explaining several familial causes of hypercholesterolemia, diabetes mellitus, congenital heart disease, and cardiomyopathies. Due to the Syrian civil war, 1.5 million Syrian refugees now reside in Lebanon in either low-income housing or tented settlements. A National Institutes of Health study is examining diabetes and CVD in Syrian refugees in comparison to native Lebanese. We provide the first review of CVD in Lebanon in its metabolic component including coronary artery disease and its risk factors, mainly hyperlipidemia and diabetes mellitus, and its structural component, including congenital heart disease, valvular heart disease, cardiomyopathies, and heart failure. The knowledge in this review has been compiled to guide clinicians and assist researchers in efforts to recognize risk factors for disease, improve delivery of health care, and prevent and treat CVDs in Lebanon, both for the native Lebanese and Syrian refugees.
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7
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Hebbar P, Abubaker JA, Abu-Farha M, Alsmadi O, Elkum N, Alkayal F, John SE, Channanath A, Iqbal R, Pitkaniemi J, Tuomilehto J, Sladek R, Al-Mulla F, Thanaraj TA. Genome-wide landscape establishes novel association signals for metabolic traits in the Arab population. Hum Genet 2020; 140:505-528. [PMID: 32902719 PMCID: PMC7889551 DOI: 10.1007/s00439-020-02222-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 09/01/2020] [Indexed: 02/07/2023]
Abstract
While the Arabian population has a high prevalence of metabolic disorders, it has not been included in global studies that identify genetic risk loci for metabolic traits. Determining the transferability of such largely Euro-centric established risk loci is essential to transfer the research tools/resources, and drug targets generated by global studies to a broad range of ethnic populations. Further, consideration of populations such as Arabs, that are characterized by consanguinity and a high level of inbreeding, can lead to identification of novel risk loci. We imputed published GWAS data from two Kuwaiti Arab cohorts (n = 1434 and 1298) to the 1000 Genomes Project haplotypes and performed meta-analysis for associations with 13 metabolic traits. We compared the observed association signals with those established for metabolic traits. Our study highlighted 70 variants from 9 different genes, some of which have established links to metabolic disorders. By relaxing the genome-wide significance threshold, we identified ‘novel’ risk variants from 11 genes for metabolic traits. Many novel risk variant association signals were observed at or borderline to genome-wide significance. Furthermore, 349 previously established variants from 187 genes were validated in our study. Pleiotropic effect of risk variants on multiple metabolic traits were observed. Fine-mapping illuminated rs7838666/CSMD1 rs1864163/CETP and rs112861901/[INTS10,LPL] as candidate causal variants influencing fasting plasma glucose and high-density lipoprotein levels. Computational functional analysis identified a variety of gene regulatory signals around several variants. This study enlarges the population ancestry diversity of available GWAS and elucidates new variants in an ethnic group burdened with metabolic disorders.
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Affiliation(s)
- Prashantha Hebbar
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait.,Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | | | | | - Naser Elkum
- Sidra Medical and Research Center, Doha, Qatar
| | - Fadi Alkayal
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait
| | - Sumi Elsa John
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait
| | | | - Rasheeba Iqbal
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait
| | - Janne Pitkaniemi
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Jaakko Tuomilehto
- Department of Public Health, University of Helsinki, Helsinki, Finland.,Department of Public Health Solutions, National Institute for Health and Welfare, Helsinki, Finland
| | - Robert Sladek
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
| | - Fahd Al-Mulla
- Dasman Diabetes Institute, P.O. Box 1180, 15462, Dasman, Kuwait.
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Dou J, Wu D, Ding L, Wang K, Jiang M, Chai X, Reilly DF, Tai ES, Liu J, Sim X, Cheng S, Wang C. Using off-target data from whole-exome sequencing to improve genotyping accuracy, association analysis and polygenic risk prediction. Brief Bioinform 2020; 22:5857014. [PMID: 32591784 DOI: 10.1093/bib/bbaa084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 04/09/2020] [Accepted: 04/21/2020] [Indexed: 12/12/2022] Open
Abstract
Whole-exome sequencing (WES) has been widely used to study the role of protein-coding variants in genetic diseases. Non-coding regions, typically covered by sparse off-target data, are often discarded by conventional WES analyses. Here, we develop a genotype calling pipeline named WEScall to analyse both target and off-target data. We leverage linkage disequilibrium shared within study samples and from an external reference panel to improve genotyping accuracy. In an application to WES of 2527 Chinese and Malays, WEScall can reduce the genotype discordance rate from 0.26% (SE= 6.4 × 10-6) to 0.08% (SE = 3.6 × 10-6) across 1.1 million single nucleotide polymorphisms (SNPs) in the deeply sequenced target regions. Furthermore, we obtain genotypes at 0.70% (SE = 3.0 × 10-6) discordance rate across 5.2 million off-target SNPs, which had ~1.2× mean sequencing depth. Using this dataset, we perform genome-wide association studies of 10 metabolic traits. Despite of our small sample size, we identify 10 loci at genome-wide significance (P < 5 × 10-8), including eight well-established loci. The two novel loci, both associated with glycated haemoglobin levels, are GPATCH8-SLC4A1 (rs369762319, P = 2.56 × 10-12) and ROR2 (rs1201042, P = 3.24 × 10-8). Finally, using summary statistics from UK Biobank and Biobank Japan, we show that polygenic risk prediction can be significantly improved for six out of nine traits by incorporating off-target data (P < 0.01). These results demonstrate WEScall as a useful tool to facilitate WES studies with decent amounts of off-target data.
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Affiliation(s)
- Jinzhuang Dou
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Degang Wu
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lin Ding
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Wang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Minghui Jiang
- School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | | | | | - E Shyong Tai
- Saw Swee Hock School of Public Health, Duke-NUS Medical School, and Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore and a professor at Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xueling Sim
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Shanshan Cheng
- Ministry of Education Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaolong Wang
- Ministry of Education Key Laboratory for Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Genome-wide association study identifies novel risk variants from RPS6KA1, CADPS, VARS, and DHX58 for fasting plasma glucose in Arab population. Sci Rep 2020; 10:152. [PMID: 31932636 PMCID: PMC6957513 DOI: 10.1038/s41598-019-57072-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 12/20/2019] [Indexed: 12/14/2022] Open
Abstract
Consanguineous populations of the Arabian Peninsula, which has seen an uncontrolled rise in type 2 diabetes incidence, are underrepresented in global studies on diabetes genetics. We performed a genome-wide association study on the quantitative trait of fasting plasma glucose (FPG) in unrelated Arab individuals from Kuwait (discovery-cohort:n = 1,353; replication-cohort:n = 1,196). Genome-wide genotyping in discovery phase was performed for 632,375 markers from Illumina HumanOmniExpress Beadchip; and top-associating markers were replicated using candidate genotyping. Genetic models based on additive and recessive transmission modes were used in statistical tests for associations in discovery phase, replication phase, and meta-analysis that combines data from both the phases. A genome-wide significant association with high FPG was found at rs1002487 (RPS6KA1) (p-discovery = 1.64E-08, p-replication = 3.71E-04, p-combined = 5.72E-11; β-discovery = 8.315; β-replication = 3.442; β-combined = 6.551). Further, three suggestive associations (p-values < 8.2E-06) with high FPG were observed at rs487321 (CADPS), rs707927 (VARS and 2Kb upstream of VWA7), and rs12600570 (DHX58); the first two markers reached genome-wide significance in the combined analysis (p-combined = 1.83E-12 and 3.07E-09, respectively). Significant interactions of diabetes traits (serum triglycerides, FPG, and glycated hemoglobin) with homeostatic model assessment of insulin resistance were identified for genotypes heterozygous or homozygous for the risk allele. Literature reports support the involvement of these gene loci in type 2 diabetes etiology.
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Al Ali M, El hajj Chehadeh S, Osman W, Almansoori K, Abdulrahman M, Tay G, Alsafar H. Investigating the association of rs7903146 of TCF7L2 gene, rs5219 of KCNJ11 gene, rs10946398 of CDKAL1 gene, and rs9939609 of FTO gene with type 2 diabetes mellitus in Emirati population. Meta Gene 2019. [DOI: 10.1016/j.mgene.2019.100600] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Abstract
BACKGROUND As Genome-Wide Association Studies (GWAS) have been increasingly used with data from various populations, it has been observed that data from different populations reveal different sets of Single Nucleotide Polymorphisms (SNPs) that are associated with the same disease. Using Type II Diabetes (T2D) as a test case, we develop measures and methods to characterize the functional overlap of SNPs associated with the same disease across populations. RESULTS We introduce the notion of an Overlap Matrix as a general means of characterizing the functional overlap between different SNP sets at different genomic and functional granularities. Using SNP-to-gene mapping, functional annotation databases, and functional association networks, we assess the degree of functional overlap across nine populations from Asian and European ethnic origins. We further assess the generalizability of the method by applying it to a dataset for another complex disease - Prostate Cancer. Our results show that more overlap is captured as more functional data is incorporated as we go through the pipeline, starting from SNPs and ending at network overlap analyses. We hypothesize that these observed differences in the functional mechanisms of T2D across populations can also explain the common use of different prescription drugs in different populations. We show that this hypothesis is concordant with the literature on the functional mechanisms of prescription drugs. CONCLUSION Our results show that although the etiology of a complex disease can be associated with distinct processes that are affected in different populations, network-based annotations can capture more functional overlap across populations. These results support the notion that it can be useful to take ethnicity into account in making personalized treatment decisions for complex diseases.
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Affiliation(s)
- Dalia Elmansy
- Department of Electrical Engineering and Computer Science, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106 USA
| | - Mehmet Koyutürk
- Department of Electrical Engineering and Computer Science, Center for Proteomics and Bioinformatics, Case Western Reserve University, 10900 Euclid Ave, Cleveland, OH 44106 USA
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Ghassibe-Sabbagh M, Mehanna Z, Farraj LA, Salloum AK, Zalloua PA. Gestational diabetes mellitus and macrosomia predispose to diabetes in the Lebanese population. J Clin Transl Endocrinol 2019; 16:100185. [PMID: 30899673 PMCID: PMC6406007 DOI: 10.1016/j.jcte.2019.100185] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/17/2019] [Accepted: 02/18/2019] [Indexed: 01/06/2023] Open
Abstract
AIMS The Middle East has the fastest rising rate of Type 2 Diabetes Mellitus (T2DM) worldwide, with Lebanon having 15.8% of its population affected. This study aims at studying Polycystic Ovarian Syndrome (PCOS), Gestational Diabetes Mellitus (GDM), and macrosomia as risk factors of T2DM in Lebanon. Such epidemiological and statistical study has never been conducted before in the Middle East region and would be useful for clinical diagnosis. METHODS Our cohort is comprised of 1453 Lebanese individuals, with 897 controls and 556 patients. We tested the correlation between T2DM and the covariates GDM, PCOS, and macrosomia independently. We conducted multinomial logistic regression and cross tabulations with T2DM as an outcome. RESULTS The results showed a significant association of the independent factors GDM and macrosomia with T2DM. The risk of having T2DM was increased by 4.192 times with the GDM, and by 2.315 times with macrosomia respectively. CONCLUSION In conclusion, GDM and macrosomia, but not PCOS, are significant risk factors for T2DM in our Lebanese cohort. Our results, reported for the first time in the Middle East, present insights into risk factors management and disease prevention.
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Affiliation(s)
- Michella Ghassibe-Sabbagh
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | - Zeina Mehanna
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | - Layal Abi Farraj
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | | | - Pierre A. Zalloua
- School of Medicine, Lebanese American University, Beirut, Lebanon
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
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13
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Abuhendi N, Qush A, Naji F, Abunada H, Al Buainain R, Shi Z, Zayed H. Genetic polymorphisms associated with type 2 diabetes in the Arab world: A systematic review and meta-analysis. Diabetes Res Clin Pract 2019; 151:198-208. [PMID: 30954515 DOI: 10.1016/j.diabres.2019.03.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/27/2019] [Indexed: 02/07/2023]
Abstract
AIMS T2DM reach epidemic levels in the Arab countries. In this study, we aimed to perform a systematic review and meta-analysis to underline the susceptibility genetic profile of Arab patients with T2DM that result from SNPs. METHODS We searched four literature databases (PubMed, Scopus, Science Direct and Web of Science) through January 2019. We included all SNPs in candidate genes with an OR > 1 that were associated with T2DM among Arab patients with T2DM. Statistical programs such as software Review Manager (Version 5.02) and STATA (Version 15.1) were used. The pooled odds ratios (ORs) and 95% confidence intervals (CIs) were calculated with a random effects model or a fixed effect model depending on the heterogeneity among studies. I2 statistics and Egger's tests were performed to assess heterogeneity and publication bias. RESULTS Out of 2245 studies, 47 were used for meta-analysis. We captured 31,307 cases and 26,464 controls in which we collected 71 SNPs in 32 genes. A pooled meta-analysis demonstrated 24-69% increase in T2DM risk. Among the 57 SNPs (in 32 genes) that were not included in the meta-analysis, the OR for diabetes ranged from 1.02 to 5.10, with a median of 1.38 (interquartile range 1.33-2.09). Ten studies examined the association between the TCF7L2 polymorphism rs7903146 and T2DM, leading to an aggregated OR of 1.34 (95%CI 1.27-1.41). CONCLUSION The genetic profile that confer susceptibility to T2DM in Arab patients is diverse. This study may serve as a platform for designing a gene panel for testing the susceptibility to T2DM.
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Affiliation(s)
- Najat Abuhendi
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Abeer Qush
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Fozieh Naji
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Hanan Abunada
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Reeham Al Buainain
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar
| | - Zumin Shi
- Department of Nutrition, College of Health Sciences, Qatar University, Doha, Qatar
| | - Hatem Zayed
- Department of Biomedical Sciences, College of Health Sciences, Qatar University, Doha, Qatar.
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14
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Zhou Z, Sun B, Huang S, Jia W, Yu D. The tRNA-associated dysregulation in diabetes mellitus. Metabolism 2019; 94:9-17. [PMID: 30711570 DOI: 10.1016/j.metabol.2019.01.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/26/2019] [Accepted: 01/30/2019] [Indexed: 12/26/2022]
Abstract
Diabetes mellitus (DM) is a complex endocrine and metabolic disorder for human health and well-being. Deregulated glucose and lipid metabolism are the primary underlying manifestations associated with this disease. Transfer RNAs (tRNAs) are considered to mainly participate in protein translation and may contribute to complex human pathologies. Although the molecular mechanisms remain, for the most part, unknown, accumulating evidence indicates that tRNAs play a vital role in the pathogenesis of DM. This paper reviews different aspects of tRNA-associated dysregulation in DM, such as tRNA mutations, tRNA modifications, tRNA aminoacylation and tRNA derivatives, aiming at a better understanding of the pathogenesis of DM and providing new ideas for the personalized treatment of this metabolism-associated disease.
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Affiliation(s)
- Zheng Zhou
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Bao Sun
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410000, China; Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410000, China
| | - Shiqiong Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410000, China; Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha 410000, China
| | - Wenrui Jia
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China.
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15
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Hebbar P, Abubaker JA, Abu-Farha M, Tuomilehto J, Al-Mulla F, Thanaraj TA. A Perception on Genome-Wide Genetic Analysis of Metabolic Traits in Arab Populations. Front Endocrinol (Lausanne) 2019; 10:8. [PMID: 30761081 PMCID: PMC6362414 DOI: 10.3389/fendo.2019.00008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/09/2019] [Indexed: 12/16/2022] Open
Abstract
Despite dedicated nation-wide efforts to raise awareness against the harmful effects of fast-food consumption and sedentary lifestyle, the Arab population continues to struggle with an increased risk for metabolic disorders. Unlike the European population, the Arab population lacks well-established genetic risk determinants for metabolic disorders, and the transferability of established risk loci to this population has not been satisfactorily demonstrated. The most recent findings have identified over 240 genetic risk loci (with ~400 independent association signals) for type 2 diabetes, but thus far only 25 risk loci (ADAMTS9, ALX4, BCL11A, CDKAL1, CDKN2A/B, COL8A1, DUSP9, FTO, GCK, GNPDA2, HMG20A, HNF1A, HNF1B, HNF4A, IGF2BP2, JAZF1, KCNJ11, KCNQ1, MC4R, PPARγ, SLC30A8, TCF7L2, TFAP2B, TP53INP1, and WFS1) have been replicated in Arab populations. To our knowledge, large-scale population- or family-based association studies are non-existent in this region. Recently, we conducted genome-wide association studies on Arab individuals from Kuwait to delineate the genetic determinants for quantitative traits associated with anthropometry, lipid profile, insulin resistance, and blood pressure levels. Although these studies led to the identification of novel recessive variants, they failed to reproduce the established loci. However, they provided insights into the genetic architecture of the population, the applicability of genetic models based on recessive mode of inheritance, the presence of genetic signatures of inbreeding due to the practice of consanguinity, and the pleiotropic effects of rare disorders on complex metabolic disorders. This perspective presents analysis strategies and study designs for identifying genetic risk variants associated with diabetes and related traits in Arab populations.
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Affiliation(s)
- Prashantha Hebbar
- Genetics and Bioinformatics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
- Doctoral Program in Population Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jehad Ahmed Abubaker
- Genetics and Bioinformatics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Mohamed Abu-Farha
- Genetics and Bioinformatics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Jaakko Tuomilehto
- Genetics and Bioinformatics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Genetics and Bioinformatics Unit, Dasman Diabetes Institute, Kuwait City, Kuwait
- *Correspondence: Fahd Al-Mulla
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16
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Hebbar P, Nizam R, Melhem M, Alkayal F, Elkum N, John SE, Tuomilehto J, Alsmadi O, Thanaraj TA. Genome-wide association study identifies novel recessive genetic variants for high TGs in an Arab population. J Lipid Res 2018; 59:1951-1966. [PMID: 30108155 DOI: 10.1194/jlr.p080218] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 07/23/2018] [Indexed: 12/12/2022] Open
Abstract
Abnormal blood lipid levels are influenced by genetic and lifestyle/dietary factors. Although many genetic variants associated with blood lipid traits have been identified in Europeans, similar data in Middle Eastern populations are limited. We performed a genome-wide association study with Arab individuals (discovery cohort: 1,353; replication cohort: 1,176) from Kuwait to identify possible associations of genetic variants with high lipid levels. We used Illumina HumanOmniExpress BeadChip and candidate SNP genotyping in the discovery and replication phases, respectively. For association tests, we used genetic models that were based on additive and recessive modes of inheritance. High triglycerides (TGs) were recessively associated with six risk variants (rs1002487/RPS6KA1, rs11805972/LAD1) rs7761746/Or5v1, rs39745/CTTNBP2-LSM8, rs2934952/PGAP3, and rs9626773/RP11-191L9.4-CERK) at genome-wide significance (P 6.12E-09), and another six variants (rs10873925/ST6GALNAC5, rs4663379/SPP2-ARL4C, rs10033119/NPY1R, rs17709449/LINC00911-FLRT2, rs11654954/CDK12-NEUROD2, and rs9972882/STARD3) were associated at borderline significance (P 5.0E-08). High TG was also additively associated with rs11654954. All of the 12 identified markers are novel and are harbored in runs of homozygosity. Literature evidence supports the involvement of these gene loci in lipid-related processes. This study in an Arab population augments international efforts to identify genetic regulation of lipid traits.
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Affiliation(s)
- Prashantha Hebbar
- Dasman Diabetes Institute, Dasman 15462, Kuwait.,Faculty of Medicine, Univerisity of Helsinki, Helsinki, Finland
| | | | | | | | - Naser Elkum
- Dasman Diabetes Institute, Dasman 15462, Kuwait
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17
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Dajani R, Li J, Wei Z, March ME, Xia Q, Khader Y, Hakooz N, Fatahallah R, El-Khateeb M, Arafat A, Saleh T, Dajani AR, Al-Abbadi Z, Abdul Qader M, Shiyab AH, Bateiha A, Ajlouni K, Hakonarson H. Genome-wide association study identifies novel type II diabetes risk loci in Jordan subpopulations. PeerJ 2017; 5:e3618. [PMID: 28828242 PMCID: PMC5563445 DOI: 10.7717/peerj.3618] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 07/06/2017] [Indexed: 12/14/2022] Open
Abstract
The prevalence of Type II Diabetes (T2D) has been increasing and has become a disease of significant public health burden in Jordan. None of the previous genome-wide association studies (GWAS) have specifically investigated the Middle East populations. The Circassian and Chechen communities in Jordan represent unique populations that are genetically distinct from the Arab population and other populations in the Caucasus. Prevalence of T2D is very high in both the Circassian and Chechen communities in Jordan despite low obesity prevalence. We conducted GWAS on T2D in these two populations and further performed meta-analysis of the results. We identified a novel T2D locus at chr20p12.2 at genome-wide significance (rs6134031, P = 1.12 × 10−8) and we replicated the results in the Wellcome Trust Case Control Consortium (WTCCC) dataset. Another locus at chr12q24.31 is associated with T2D at suggestive significance level (top SNP rs4758690, P = 4.20 × 10−5) and it is a robust eQTL for the gene, MLXIP (P = 1.10 × 10−14), and is significantly associated with methylation level in MLXIP, the functions of which involves cellular glucose response. Therefore, in this first GWAS of T2D in Jordan subpopulations, we identified novel and unique susceptibility loci which may help inform the genetic underpinnings of T2D in other populations.
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Affiliation(s)
- Rana Dajani
- Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan
| | - Jin Li
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States of America.,Department of Cell Biology, Tianjin Medical University, Tianjin, China
| | - Zhi Wei
- Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, United States of America
| | - Michael E March
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Qianghua Xia
- Department of Cell Biology, Tianjin Medical University, Tianjin, China.,Divisions of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States of America
| | - Yousef Khader
- Department of Community Medicine, Public Health and Family Medicine, Faculty of Medicine, Jordan University for Science and Technology, Irbid, Jordan
| | - Nancy Hakooz
- Department of Biopharmaceutics and Clinical Pharmacy, School of Pharmacy, University of Jordan, Amman, Jordan
| | - Raja Fatahallah
- National Center for Diabetes, Endocrinology and Genetics, Amman, Jordan
| | | | - Ala Arafat
- National Center for Diabetes, Endocrinology and Genetics, Amman, Jordan
| | - Tareq Saleh
- Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan
| | - Abdel Rahman Dajani
- Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan
| | - Zaid Al-Abbadi
- Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan
| | - Mohamed Abdul Qader
- Department of Biology and Biotechnology, Hashemite University, Zarqa, Jordan
| | | | - Anwar Bateiha
- Department of Community Medicine, Public Health and Family Medicine, Faculty of Medicine, Jordan University for Science and Technology, Irbid, Jordan
| | - Kamel Ajlouni
- National Center for Diabetes, Endocrinology and Genetics, Amman, Jordan
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States of America.,Divisions of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, PA, United States of America.,The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States of America
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18
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Haber M, Doumet-Serhal C, Scheib C, Xue Y, Danecek P, Mezzavilla M, Youhanna S, Martiniano R, Prado-Martinez J, Szpak M, Matisoo-Smith E, Schutkowski H, Mikulski R, Zalloua P, Kivisild T, Tyler-Smith C. Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences. Am J Hum Genet 2017; 101:274-282. [PMID: 28757201 PMCID: PMC5544389 DOI: 10.1016/j.ajhg.2017.06.013] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 06/27/2017] [Indexed: 12/11/2022] Open
Abstract
The Canaanites inhabited the Levant region during the Bronze Age and established a culture that became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole genomes from ∼3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalog modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600–3,550 years ago, coinciding with recorded massive population movements in Mesopotamia during the mid-Holocene. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate that this Eurasian ancestry arrived in the Levant around 3,750–2,170 years ago during a period of successive conquests by distant populations.
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19
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Ju H, Lin R, Yuan Z, Sun Y, Zeng L, Su Z, Jin L. No association detected between seven common variants in the CDKAL1 gene and gestational glycemic traits. Mol Cell Probes 2017; 34:64-67. [PMID: 28502787 DOI: 10.1016/j.mcp.2017.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 01/12/2023]
Abstract
Elevated plasma glucose levels in pregnancy increase adverse pregnancy outcomes. Cyclin-dependent kinase 5 regulatory subunit-associated protein 1-like 1 (CDKAL1) has been shown to be involved in insulin secretion in pancreatic β cells. In this study, we investigated the impact of genetic variants in CDKAL1 on plasma glucose, insulin values, β cell function and insulin resistance in the fasted state as well as plasma glucose 1 h after the consumption of a 50-g oral glucose load between 24 and 28 weeks of pregnancy among 929 unrelated pregnant Han Chinese women. Seven common variants previously reported to associate with diabetes were genotyped. Insulin resistance and β cell function were assessed by homeostasis model assessment. The genetic impacts were analyzed using analysis of variance and analysis of covariance. The results showed that there was no significant association between any of the seven variants and those gestational glycemic traits. Therefore, this study suggests that the seven common variants in CDKAL1 are not significant factors for the variations of several gestational glycemic traits in the Han Chinese population. However, further well-designed studies with larger sample size, more ethnic groups and more CDKAL1 variants are required to validate the association between CDKAL1 and gestational glycemic traits.
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Affiliation(s)
- Hongfang Ju
- Department of Gynaecology and Obstetrics, Taizhou People's Hospital, Taizhou, Jiangsu, China
| | - Rong Lin
- Department of Biology, Hainan Medical College, Haikou, Hainan, China.
| | - Ziyu Yuan
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China; Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China
| | - Yuantian Sun
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Liangliang Zeng
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Zhenyu Su
- Department of Biology, Hainan Medical College, Haikou, Hainan, China
| | - Li Jin
- Ministry of Education Key Laboratory of Contemporary Anthropology and State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China; Fudan-Taizhou Institute of Health Sciences, Taizhou, Jiangsu, China; CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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20
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Hebbar P, Elkum N, Alkayal F, John SE, Thanaraj TA, Alsmadi O. Genetic risk variants for metabolic traits in Arab populations. Sci Rep 2017; 7:40988. [PMID: 28106113 PMCID: PMC5247683 DOI: 10.1038/srep40988] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 12/14/2016] [Indexed: 12/11/2022] Open
Abstract
Despite a high prevalence of metabolic trait related diseases in Arabian Peninsula, there is a lack of convincingly identified genetic determinants for metabolic traits in this population. Arab populations are underrepresented in global genome-wide association studies. We genotyped 1965 unrelated Arab individuals from Kuwait using Cardio-MetaboChip, and tested SNP associations with 13 metabolic traits. Models based on recessive mode of inheritance identified Chr15:40531386-rs12440118/ZNF106/W->R as a risk variant associated with glycated-hemoglobin at close to ‘genome-wide significant’ p-value and five other risk variants ‘nominally’ associated (p-value ≤ 5.45E-07) with fasting plasma glucose (rs7144734/[OTX2-AS1,RPL3P3]) and triglyceride (rs17501809/PLGRKT; rs11143005/LOC105376072; rs900543/[THSD4,NR2E3]; and Chr12:101494770/IGF1). Furthermore, we identified 33 associations (30 SNPs with 12 traits) with ‘suggestive’ evidence of association (p-value < 1.0E-05); 20 of these operate under recessive mode of inheritance. Two of these ‘suggestive’ associations (rs1800775-CETP/HDL; and rs9326246-BUD13/TGL) showed evidence at genome-wide significance in previous studies on Euro-centric populations. Involvement of many of the identified loci in mediating metabolic traits was supported by literature evidences. The identified loci participate in critical metabolic pathways (such as Ceramide signaling, and Mitogen-Activated Protein Kinase/Extracellular Signal Regulated Kinase signaling). Data from Genotype-Tissue Expression database affirmed that 7 of the identified variants differentially regulate the up/downstream genes that mediate metabolic traits.
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Affiliation(s)
| | - Naser Elkum
- Dasman Diabetes Institute, P.O. Box 1180, Dasman 15462, Kuwait
| | - Fadi Alkayal
- Dasman Diabetes Institute, P.O. Box 1180, Dasman 15462, Kuwait
| | - Sumi Elsa John
- Dasman Diabetes Institute, P.O. Box 1180, Dasman 15462, Kuwait
| | | | - Osama Alsmadi
- Dasman Diabetes Institute, P.O. Box 1180, Dasman 15462, Kuwait
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Type 2 Diabetes Susceptibility in the Greek-Cypriot Population: Replication of Associations with TCF7L2, FTO, HHEX, SLC30A8 and IGF2BP2 Polymorphisms. Genes (Basel) 2017; 8:genes8010016. [PMID: 28067832 PMCID: PMC5295011 DOI: 10.3390/genes8010016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/13/2016] [Accepted: 12/30/2016] [Indexed: 01/17/2023] Open
Abstract
Type 2 diabetes (T2D) has been the subject of numerous genetic studies in recent years which revealed associations of the disease with a large number of susceptibility loci. We hereby initiate the evaluation of T2D susceptibility loci in the Greek-Cypriot population by performing a replication case-control study. One thousand and eighteen individuals (528 T2D patients, 490 controls) were genotyped at 21 T2D susceptibility loci, using the allelic discrimination method. Statistically significant associations of T2D with five of the tested single nucleotide polymorphisms (SNPs) (TCF7L2 rs7901695, FTO rs8050136, HHEX rs5015480, SLC30A8 rs13266634 and IGF2BP2 rs4402960) were observed in this study population. Furthermore, 14 of the tested SNPs had odds ratios (ORs) in the same direction as the previously published studies, suggesting that these variants can potentially be used in the Greek-Cypriot population for predictive testing of T2D. In conclusion, our findings expand the genetic assessment of T2D susceptibility loci and reconfirm five of the worldwide established loci in a distinct, relatively small, newly investigated population.
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22
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Liu NJ, Xiong Q, Wu HH, Li YL, Yang Z, Tao XM, Du YP, Lu B, Hu RM, Wang XC, Wen J. The association analysis polymorphism of CDKAL1 and diabetic retinopathy in Chinese Han population. Int J Ophthalmol 2016; 9:707-12. [PMID: 27275426 DOI: 10.18240/ijo.2016.05.12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/27/2015] [Indexed: 01/12/2023] Open
Abstract
AIM To identify the contribution of CDKAL1 to the development of diabetic retinopathy (DR) in Chinese population. METHODS A case-control study was performed to investigate the genetic association between DR and polymorphic variants of CDKAL1 in Chinese Han population with type 2 diabetes mellitus (T2DM). A well-defined population with T2DM, consisting of 475 controls and 105 DR patients, was recruited. All subjects were genotyped for the genetic variant (rs10946398) of CDKAL1. Genotyping was performed by iPLEX technology. The association between rs10946398 and T2DM was assessed by univariate and multivariate logistic regression (MLR) analysis. RESULTS There were significant differences in C allele frequencies of rs10946398 (CDKAL1) between control and DR groups (45.06% versus 55.00%, P<0.05). The rs10946398 of CDKAL1 was found to be associated with the increased risk of DR among patients with diabetes. CONCLUSION Our findings suggest that rs10946398 of CDKAL1 is independently associated with DR in a Chinese Han population.
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Affiliation(s)
- Nai-Jia Liu
- Department of Endocrinology and Metabolism, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Qian Xiong
- Department of Endocrinology and Metabolism, Jing'an District Center Hospital of Shanghai, Shanghai 200040, China
| | - Hui-Hui Wu
- Department of Endocrinology and Metabolism, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Yan-Liang Li
- Department of Endocrinology and Metabolism, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Zhen Yang
- Department of Endocrinology and Metabolism, Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200020, China
| | - Xiao-Ming Tao
- Department of Endocrinology and Metabolism, Hua Dong Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Yan-Ping Du
- Department of Endocrinology and Metabolism, Hua Dong Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Bin Lu
- Department of Endocrinology and Metabolism, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Ren-Ming Hu
- Department of Endocrinology and Metabolism, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Xuan-Chun Wang
- Department of Endocrinology and Metabolism, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, China
| | - Jie Wen
- Department of Endocrinology and Metabolism, Huashan Hospital Affiliated to Fudan University, Shanghai 200040, China
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Detecting Genetic Associations between ATG5 and Lupus Nephritis by trans-eQTL. J Immunol Res 2015; 2015:153132. [PMID: 26509176 PMCID: PMC4609853 DOI: 10.1155/2015/153132] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 05/26/2015] [Accepted: 05/28/2015] [Indexed: 11/17/2022] Open
Abstract
Objectives. Numerous loci were identified to perturb gene expression in trans. As elevated ATG5 expression was observed in systemic lupus erythematosus (SLE), the study was conducted to analyze the genome-wide genetic regulatory mechanisms associated with ATG5 expression in a Chinese population with lupus nephritis (LN). Methods. The online expression quantitative trait loci database was searched for trans-expression single nucleotide polymorphisms (trans-eSNPs) of ATG5. Tagging trans-eSNPs were genotyped by a custom-made genotyping chip in 280 patients and 199 controls. For positive findings, clinical information and bioinformation analyses were performed. Results. Four trans-eSNPs were observed to be associated with susceptibility to LN (P < 0.05), including ANKRD50 rs17008504, AGA rs2271100, PAK7 rs6056923, and TET2 rs1391441, while seven other trans-eSNPs showed marginal significant associations (0.05 < P < 0.1). Correlations between the trans-eSNPs and ATG5 expression and different expression levels of ATG5 in SLE patients and controls were validated, and their regulatory effects were annotated. However, no significant associations were observed between different genotypes of trans-eSNPs and severity or outcome of the patients. Conclusion. Using the new systemic genetics approach, we identified 10 loci associated with susceptibility to LN potentially, which may be complementary to future pathway based genetic studies.
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