1
|
Rahman A, Abu-Farha M, Channanath A, Hammad MM, Anoop E, Chandy B, Melhem M, Al-Mulla F, Thanaraj TA, Abubaker J. Single nucleotide polymorphisms in vitamin D binding protein and 25-hydroxylase genes affect vitamin D levels in adolescents of Arab ethnicity in Kuwait. Front Endocrinol (Lausanne) 2023; 14:1257051. [PMID: 37929021 PMCID: PMC10623322 DOI: 10.3389/fendo.2023.1257051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
Vitamin D deficiency (VDD) is widespread in the Arab world despite ample sunshine throughout the year. In our previous study, lifestyle and socio-demographic factors could explain only 45% of variability in vitamin D levels in Kuwaiti adolescents, suggesting that genetics might contribute to VDD in this region. Single nucleotide polymorphisms (SNP) in the 25-hydroxylase (CYP2R1) and the GC globulin (GC) genes have been reported to affect vitamin D levels in various ethnic groups in adults. In this study, we investigated the association of two SNPs from GC (rs4588 and rs7041) and three SNPs from CYP2R1 (rs10741657, rs11023374 and rs12794714) with vitamin D levels and VDD in a nationally representative sample of adolescents of Arab ethnicity from Kuwait. Multivariable linear regression, corrected for age, sex, parental education, governorate, body mass index, and exposure to sun, demonstrated that each of the 5 study variants showed significant associations with plasma 25(OH)D levels in one or more of the additive, recessive, and dominant genetic models - the rs10741657 under all the three models, rs12794714 under both the additive and recessive models, rs7041 under the recessive model; and rs4588 and rs11023374 under the dominant model. Minor alleles at rs4588 (T), rs7041 (A), rs11023374 (C), and rs12794714 (A) led to a decrease in plasma 25(OH)D levels - rs4588:[β (95%CI) = -4.522 (-8.66,-0.38); p=0.033]; rs7041:[β (95%CI) = -6.139 (-11.12,-1.15); p=0.016]; rs11023374:[β (95%CI) = -4.296 (-8.18,-0.40); p=0.031]; and rs12794714:[β (95%CI) = -3.498 (-6.27,-0.72); p=0.014]. Minor allele A at rs10741657 was associated with higher levels of plasma 25(OH)D levels [β (95%CI) = 4.844 (1.62,8.06); p=0.003)] and lower odds of vitamin D deficiency (OR 0.40; p=0.002). These results suggest that the CYP2R1 and GC SNP variants are partly responsible for the high prevalence of VDD in Kuwait. Genotyping these variants may be considered for the prognosis of VDD in Kuwait.
Collapse
Affiliation(s)
- Abdur Rahman
- Department of Food Science and Nutrition, College of Life Sciences, Kuwait University, Kuwait City, Kuwait
| | - Mohamed Abu-Farha
- Department of Biochemistry & Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Arshad Channanath
- Department of Genetics & Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Maha M. Hammad
- Department of Biochemistry & Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Emil Anoop
- Special Services Facilities, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Betty Chandy
- Special Services Facilities, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Motasem Melhem
- Special Services Facilities, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics & Bioinformatics, Dasman Diabetes Institute, Kuwait City, Kuwait
| | | | - Jehad Abubaker
- Department of Biochemistry & Molecular Biology, Dasman Diabetes Institute, Kuwait City, Kuwait
| |
Collapse
|
2
|
Jasper EA, Hellwege JN, Piekos JA, Jones SH, Hartmann KE, Mautz B, Aronoff DM, Edwards TL, Edwards DRV. Genetically-predicted placental gene expression is associated with birthweight and adult body mass index. Sci Rep 2023; 13:322. [PMID: 36609580 PMCID: PMC9822919 DOI: 10.1038/s41598-022-26572-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/16/2022] [Indexed: 01/09/2023] Open
Abstract
The placenta is critical to human growth and development and has been implicated in health outcomes. Understanding the mechanisms through which the placenta influences perinatal and later-life outcomes requires further investigation. We evaluated the relationships between birthweight and adult body mass index (BMI) and genetically-predicted gene expression in human placenta. Birthweight genome-wide association summary statistics were obtained from the Early Growth Genetics Consortium (N = 298,142). Adult BMI summary statistics were obtained from the GIANT consortium (N = 681,275). We used S-PrediXcan to evaluate associations between the outcomes and predicted gene expression in placental tissue and, to identify genes where placental expression was exclusively associated with the outcomes, compared to 48 other tissues (GTEx v7). We identified 24 genes where predicted placental expression was significantly associated with birthweight, 15 of which were not associated with birthweight in any other tissue. One of these genes has been previously linked to birthweight. Analyses identified 182 genes where placental expression was associated with adult BMI, 110 were not associated with BMI in any other tissue. Eleven genes that had placental gene expression levels exclusively associated with BMI have been previously associated with BMI. Expression of a single gene, PAX4, was associated with both outcomes exclusively in the placenta. Inter-individual variation of gene expression in placental tissue may contribute to observed variation in birthweight and adult BMI, supporting developmental origins hypothesis.
Collapse
Affiliation(s)
- Elizabeth A Jasper
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA.
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
| | - Jacklyn N Hellwege
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN, USA
| | | | - Sarah H Jones
- Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Katherine E Hartmann
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN, USA
- Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Brian Mautz
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
- Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN, USA
- Population Analytics, Analytics and Insights, Data Sciences, Janssen Research & Development, Spring House, PA, USA
| | - David M Aronoff
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Todd L Edwards
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
- Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA
- Division of Epidemiology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Digna R Velez Edwards
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA.
- Department of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, TN, USA.
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA.
- Institute for Medicine and Public Health, Vanderbilt University Medical Center, Nashville, TN, USA.
| |
Collapse
|
3
|
Joseph A, Thirupathamma M, Mathews E, Alagu M. Genetics of type 2 diabetes mellitus in Indian and Global Population: A Review. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022; 23:135. [PMID: 37192883 PMCID: PMC9438889 DOI: 10.1186/s43042-022-00346-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Non-communicable diseases such as cardiovascular diseases, respiratory diseases and diabetes contribute to the majority of deaths in India. Public health programmes on non-communicable diseases (NCD) prevention primarily target the behavioural risk factors of the population. Hereditary is known as a risk factor for most NCDs, specifically, type 2 diabetes mellitus (T2DM), and hence, understanding of the genetic markers of T2DM may facilitate prevention, early case detection and management. Main body We reviewed the studies that explored marker-trait association with type 2 diabetes mellitus globally, with emphasis on India. Globally, single nucleotide polymorphisms (SNPs) rs7903146 of Transcription Factor 7-like 2 (TCF7L2) gene was common, though there were alleles that were unique to specific populations. Within India, the state-wise data were also taken to foresee the distribution of risk/susceptible alleles. The findings from India showcased the common and unique alleles for each region. Conclusion Exploring the known and unknown genetic determinants might assist in risk prediction before the onset of behavioural risk factors and deploy prevention measures. Most studies were conducted in non-representative groups with inherent limitations such as smaller sample size or looking into only specific marker-trait associations. Genome-wide association studies using data from extensive prospective studies are required in highly prevalent regions worldwide. Further research is required to understand the singular effect and the interaction of genes in predicting diabetes mellitus and other comorbidities.
Collapse
Affiliation(s)
- Anjaly Joseph
- Department of Public Health and Community Medicine, Central University of Kerala, Kasaragod, Kerala 671320 India
| | - Maradana Thirupathamma
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala 671320 India
| | - Elezebeth Mathews
- Department of Public Health and Community Medicine, Central University of Kerala, Kasaragod, Kerala 671320 India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala 671320 India
| |
Collapse
|
4
|
Solstad A, Hogaboam O, Forero A, Hemann EA. RIG-I-like Receptor Regulation of Immune Cell Function and Therapeutic Implications. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:845-854. [PMID: 36130131 PMCID: PMC9512390 DOI: 10.4049/jimmunol.2200395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/30/2022] [Indexed: 01/04/2023]
Abstract
Retinoic acid-inducible gene I-like receptors (RLRs) are cytosolic RNA sensors critical for initiation of antiviral immunity. Activation of RLRs following RNA recognition leads to production of antiviral genes and IFNs for induction of broad antiviral immunity. Although the RLRs are ubiquitously expressed, much of our understanding of these molecules comes from their study in epithelial cells and fibroblasts. However, RLR activation is critical for induction of immune function and long-term protective immunity. Recent work has focused on the roles of RLRs in immune cells and their contribution to programming of effective immune responses. This new understanding of RLR function in immune cells and immune programming has led to the development of vaccines and therapeutics targeting the RLRs. This review covers recent advances in our understanding of the contribution of RLRs to immune cell function during infection and the emerging RLR-targeting strategies for induction of immunity against cancer and viral infection.
Collapse
Affiliation(s)
- Abigail Solstad
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH
| | - Octavia Hogaboam
- Biomedical Sciences Graduate Program, College of Medicine, The Ohio State University, Columbus, OH
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH
| | - Adriana Forero
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH
- Infectious Diseases Institute, The Ohio State University, Columbus, OH; and
| | - Emily A Hemann
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, OH;
- Infectious Diseases Institute, The Ohio State University, Columbus, OH; and
| |
Collapse
|
5
|
Pan J, Tong R, Deng Q, Tian Y, Wang N, Peng Y, Fei S, Zhang W, Cui J, Guo C, Yao J, Wei C, Xu J. The Effect of SOCS2 Polymorphisms on Type 2 Diabetes Mellitus Susceptibility and Diabetic Complications in the Chinese Han Population. Pharmgenomics Pers Med 2022; 15:65-79. [PMID: 35125882 PMCID: PMC8809519 DOI: 10.2147/pgpm.s347018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/23/2021] [Indexed: 12/07/2022] Open
Abstract
Background SOCS2 is downregulated in diabetes, which might be related to diabetes. We explored the effect of SOCS2 polymorphisms on the development of type 2 diabetes mellitus (T2DM) and diabetic complications. Methods The subjects consisted of 500 patients with T2DM and 501 healthy controls. Five variants in SOCS2 were genotyped by Agena MassARRAY system. RT-qPCR profiling was performed to detect the expression of SOCS2 mRNA. Logistic regression analysis was utilized to calculate odds ratio (OR) and 95% confidence intervals (95% CIs). Results Rs3825199 (OR = 1.44, p = 0.007), rs11107116 (OR = 1.39, p = 0.014) and rs10492321 (OR = 1.48, p = 0.004) had an increased T2DM risk of T2DM. Moreover, the contribution of SOCS2 polymorphisms to T2DM risk was associated with age, gender, smoking, drinking, and BMI. SOCS2 variants also had a reduced risk for T2DM patients with diabetic nephropathy, diabetic retinopathy and coronary heart disease. SOCS2 rs10492321 was the best single locus model. SOCS2 mRNA was downregulated in patients with T2DM compared to healthy controls (p = 0.029). Conclusion This study firstly reported that rs3825199, rs11107116 and rs10492321 in SOCS2 conferred to an increased risk for the occurrence of T2DM in the Chinese Han population. Moreover, SOCS2 mRNA was downregulated in patients with T2DM, suggesting that SOCS2 might have an important role in the occurrence of T2DM.
Collapse
Affiliation(s)
- Juan Pan
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
- Department of Endocrinology, Xianyang Central Hospital, Xianyang, 712000, Shaanxi, People’s Republic of China
| | - Rui Tong
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
| | - Qing Deng
- Department of Endocrinology, No. 215 Hospital of Shaanxi Nuclear Industry, Xianyang, 712000, Shaanxi, People’s Republic of China
| | - Yanni Tian
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
| | - Ning Wang
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
| | - Yanqi Peng
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
| | - Sijia Fei
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
| | - Wei Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
| | - Jiaqi Cui
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
| | - Chaoying Guo
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
| | - Juanchuan Yao
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
| | - Cui Wei
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
- Correspondence: Cui Wei; Jing Xu, Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, #277 West Yanta Road, Xi’an, 710061, Shaanxi, People’s Republic of China, Tel +86 18991232462; Tel +86 18991232462 Email ;
| | - Jing Xu
- Department of Geriatric Endocrinology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, People’s Republic of China
| |
Collapse
|
6
|
Identification of Maturity-Onset-Diabetes of the Young (MODY) mutations in a country where diabetes is endemic. Sci Rep 2021; 11:16060. [PMID: 34373539 PMCID: PMC8352960 DOI: 10.1038/s41598-021-95552-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/13/2021] [Indexed: 01/02/2023] Open
Abstract
Genetic variants responsible for Maturity-Onset-Diabetes of the Young (MODY) in Kuwait were investigated. A newly established a National Referral Clinic, the Dasman Diabetes Institute (DDI-NRC), assessed forty-five members from 31 suspected MODY families by whole exome sequencing. Thirty-three of the 45 samples were independently sequenced at the DDI-NRI, Exeter University, UK (https://www.diabetesgenes.org/) using targeted 21-gene panel approach. Pathogenic mutations in GCK, HNF1A, HNF1B, HNF4A, and PDX1 confirmed MODY in 7 families, giving an overall positivity rate of 22.6% in this cohort. Novel variants were identified in three families in PDX1, HNF1B, and HNF1B. In this cohort, Multiplex Ligation-dependent Probe Amplification assay did not add any value to MODY variant detection rate in sequencing negative cases. In highly selected familial autoantibody negative diabetes, known MODY genes represent a minority and 77.3% of the familial cases have yet to have a causal variant described.
Collapse
|
7
|
Cao C, Kwok D, Edie S, Li Q, Ding B, Kossinna P, Campbell S, Wu J, Greenberg M, Long Q. kTWAS: integrating kernel machine with transcriptome-wide association studies improves statistical power and reveals novel genes. Brief Bioinform 2021; 22:5985285. [PMID: 33200776 DOI: 10.1093/bib/bbaa270] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/31/2022] Open
Abstract
The power of genotype-phenotype association mapping studies increases greatly when contributions from multiple variants in a focal region are meaningfully aggregated. Currently, there are two popular categories of variant aggregation methods. Transcriptome-wide association studies (TWAS) represent a set of emerging methods that select variants based on their effect on gene expressions, providing pretrained linear combinations of variants for downstream association mapping. In contrast to this, kernel methods such as sequence kernel association test (SKAT) model genotypic and phenotypic variance use various kernel functions that capture genetic similarity between subjects, allowing nonlinear effects to be included. From the perspective of machine learning, these two methods cover two complementary aspects of feature engineering: feature selection/pruning and feature aggregation. Thus far, no thorough comparison has been made between these categories, and no methods exist which incorporate the advantages of TWAS- and kernel-based methods. In this work, we developed a novel method called kernel-based TWAS (kTWAS) that applies TWAS-like feature selection to a SKAT-like kernel association test, combining the strengths of both approaches. Through extensive simulations, we demonstrate that kTWAS has higher power than TWAS and multiple SKAT-based protocols, and we identify novel disease-associated genes in Wellcome Trust Case Control Consortium genotyping array data and MSSNG (Autism) sequence data. The source code for kTWAS and our simulations are available in our GitHub repository (https://github.com/theLongLab/kTWAS).
Collapse
Affiliation(s)
- Chen Cao
- Department of Biochemistry & Molecular Biology, University of Calgary
| | - Devin Kwok
- Department of Mathematics & Statistics, University of Calgary
| | | | - Qing Li
- Department of Biochemistry & Molecular Biology, University of Calgary
| | - Bowei Ding
- Department of Mathematics & Statistics, University of Calgary
| | - Pathum Kossinna
- Department of Biochemistry & Molecular Biology, University of Calgary
| | | | - Jingjing Wu
- Department of Mathematics & Statistics, University of Calgary
| | | | - Quan Long
- Departments of Biochemistry & Molecular Biology, Medical Genetics and Mathematics & Statistics
| |
Collapse
|
8
|
Taher I, Almaeen A, Ghazy A, Abu-Farha M, Mohamed Channanath A, Elsa John S, Hebbar P, Arefanian H, Abubaker J, Al-Mulla F, Alphonse Thanaraj T. Relevance Between COVID-19 and Host Genetics of Immune Response. Saudi J Biol Sci 2021; 28:6645-6652. [PMID: 34305429 PMCID: PMC8285220 DOI: 10.1016/j.sjbs.2021.07.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Revised: 07/08/2021] [Accepted: 07/11/2021] [Indexed: 12/09/2022] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) was caused by the newly emerged corona virus (2019-nCoV alias SARS-CoV-2) that resembles the severe acute respiratory syndrome virus (SARS-CoV). SARS-CoV-2, which was first identified in Wuhan (China) has spread globally, resulting in a high mortality worldwide reaching ~4 million deaths to date. As of first week of July 2021, ~181 million cases of COVID-19 have been reported. SARS-CoV-2 infection is mediated by the binding of virus spike protein to Angiotensin Converting Enzyme 2 (ACE2). ACE2 is expressed on many human tissues; however, the major entry point is probably pneumocytes, which are responsible for synthesis of alveolar surfactant in lungs. Viral infection of pneumocytes impairs immune responses and leads to, apart from severe hypoxia resulting from gas exchange, diseases with serious complications. During viral infection, gene products (e.g. ACE2) that mediate viral entry, antigen presentation, and cellular immunity are of crucial importance. Human leukocyte antigens (HLA) I and II present antigens to the CD8+ and CD4+ T lymphocytes, which are crucial for immune defence against pathogens including viruses. HLA gene variants affect the recognition and presentation of viral antigenic peptides to T-cells, and cytokine secretion. Additionally, endoplasmic reticulum aminopeptidases (ERAP) trim antigenic precursor peptides to fit into the binding groove of MHC class I molecules. Polymorphisms in ERAP genes leading to aberrations in ERAP’s can alter antigen presentation by HLA class I molecules resulting in aberrant T-cell responses, which may affect susceptibility to infection and/or activation of immune response. Polymorphisms from these genes are associated, in global genetic association studies, with various phenotype traits/disorders many of which are related to the pathogenesis and progression of COVID-19; polymorphisms from various genes are annotated in genotype-tissue expression data as regulating the expression of ACE2, HLA’s and ERAP’s. We review such polymorphisms and illustrate variations in their allele frequencies in global populations. These reported findings highlight the roles of genetic modulators (e.g. genotype changes in ACE2, HLA’s and ERAP’s leading to aberrations in the expressed gene products or genotype changes at other genes regulating the expression levels of these genes) in the pathogenesis of viral infection.
Collapse
Affiliation(s)
- Ibrahim Taher
- Department of Pathology, College of Medicine, Jouf University, Sakaka, Saudi Arabia
| | - Abdulrahman Almaeen
- Department of Pathology, College of Medicine, Jouf University, Sakaka, Saudi Arabia
| | - Amany Ghazy
- Department of Pathology, College of Medicine, Jouf University, Sakaka, Saudi Arabia.,Departments of Microbiology & Medical Immunology, Faculty of Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | | | - Sumi Elsa John
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Prashantha Hebbar
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Hossein Arefanian
- Department of Immunology and Microbiology, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | | |
Collapse
|
9
|
Ludwig-Słomczyńska AH, Seweryn MT, Kapusta P, Pitera E, Mantaj U, Cyganek K, Gutaj P, Dobrucka Ł, Wender-Ożegowska E, Małecki MT, Wołkow PP. The transcriptome-wide association search for genes and genetic variants which associate with BMI and gestational weight gain in women with type 1 diabetes. Mol Med 2021; 27:6. [PMID: 33472578 PMCID: PMC7818927 DOI: 10.1186/s10020-020-00266-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Clinical data suggest that BMI and gestational weight gain (GWG) are strongly interconnected phenotypes; however, the genetic basis of the latter is rather unclear. Here we aim to find genes and genetic variants which influence BMI and/or GWG. METHODS We have genotyped 316 type 1 diabetics using Illumina Infinium Omni Express Exome-8 v1.4 arrays. The GIANT, ARIC and T2D-GENES summary statistics were used for TWAS (performed with PrediXcan) in adipose tissue. Next, the analysis of association of imputed expression with BMI in the general and diabetic cohorts (Analysis 1 and 2) or GWG (Analysis 3 and 4) was performed, followed by variant association analysis (1 Mb around identified loci) with the mentioned phenotypes. RESULTS In Analysis 1 we have found 175 BMI associated genes and 19 variants (p < 10-4) which influenced GWG, with the strongest association for rs11465293 in CCL24 (p = 3.18E-06). Analysis 2, with diabetes included in the model, led to discovery of 1812 BMI associated loci and 207 variants (p < 10-4) influencing GWG, with the strongest association for rs9690213 in PODXL (p = 9.86E-07). In Analysis 3, among 648 GWG associated loci, 2091 variants were associated with BMI (FDR < 0.05). In Analysis 4, 7 variants in GWG associated loci influenced BMI in the ARIC cohort. CONCLUSIONS Here, we have shown that loci influencing BMI might have an impact on GWG and GWG associated loci might influence BMI, both in the general and T1DM cohorts. The results suggest that both phenotypes are related to insulin signaling, glucose homeostasis, mitochondrial metabolism, ubiquitinoylation and inflammatory responses.
Collapse
Affiliation(s)
| | - Michał T Seweryn
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Przemysław Kapusta
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
| | - Ewelina Pitera
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland
| | - Urszula Mantaj
- Department of Reproduction, Poznan University of Medical Sciences, Poznan, Poland
| | - Katarzyna Cyganek
- Department of Metabolic Diseases, University Hospital Kraków, Kraków, Poland
- Department of Metabolic Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Paweł Gutaj
- Department of Reproduction, Poznan University of Medical Sciences, Poznan, Poland
| | - Łucja Dobrucka
- Department of Metabolic Diseases, University Hospital Kraków, Kraków, Poland
| | - Ewa Wender-Ożegowska
- Department of Reproduction, Poznan University of Medical Sciences, Poznan, Poland
| | - Maciej T Małecki
- Department of Metabolic Diseases, University Hospital Kraków, Kraków, Poland
- Department of Metabolic Diseases, Jagiellonian University Medical College, Kraków, Poland
| | - Paweł P Wołkow
- Center for Medical Genomics OMICRON, Jagiellonian University Medical College, Kraków, Poland.
| |
Collapse
|
10
|
Abu-Farha M, Al-Sabah S, Hammad MM, Hebbar P, Channanath AM, John SE, Taher I, Almaeen A, Ghazy A, Mohammad A, Abubaker J, Arefanian H, Al-Mulla F, Thanaraj TA. Prognostic Genetic Markers for Thrombosis in COVID-19 Patients: A Focused Analysis on D-Dimer, Homocysteine and Thromboembolism. Front Pharmacol 2020; 11:587451. [PMID: 33362545 PMCID: PMC7756688 DOI: 10.3389/fphar.2020.587451] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 10/28/2020] [Indexed: 12/17/2022] Open
Abstract
COVID-19 is caused by Severe Acute Respiratory Syndrome Coronavirus-2, which has infected over thirty eight million individuals worldwide. Emerging evidence indicates that COVID-19 patients are at a high risk of developing coagulopathy and thrombosis, conditions that elevate levels of D-dimer. It is believed that homocysteine, an amino acid that plays a crucial role in coagulation, may also contribute to these conditions. At present, multiple genes are implicated in the development of these disorders. For example, single-nucleotide polymorphisms (SNPs) in FGG, FGA, and F5 mediate increases in D-dimer and SNPs in ABO, CBS, CPS1 and MTHFR mediate differences in homocysteine levels, and SNPs in TDAG8 associate with Heparin-induced Thrombocytopenia. In this study, we aimed to uncover the genetic basis of the above conditions by examining genome-wide associations and tissue-specific gene expression to build a molecular network. Based on gene ontology, we annotated various SNPs with five ancestral terms: pulmonary embolism, venous thromboembolism, vascular diseases, cerebrovascular disorders, and stroke. The gene-gene interaction network revealed three clusters that each contained hallmark genes for D-dimer/fibrinogen levels, homocysteine levels, and arterial/venous thromboembolism with F2 and F5 acting as connecting nodes. We propose that genotyping COVID-19 patients for SNPs examined in this study will help identify those at greatest risk of complications linked to thrombosis.
Collapse
Affiliation(s)
- Mohamed Abu-Farha
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Salman Al-Sabah
- Department of Surgery, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | - Maha M Hammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Prashantha Hebbar
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | | | - Sumi Elsa John
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | - Ibrahim Taher
- Department of Pathology, College of Medicine, Jouf University, Sakaka, Saudi Arabia
| | - Abdulrahman Almaeen
- Department of Pathology, College of Medicine, Jouf University, Sakaka, Saudi Arabia
| | - Amany Ghazy
- Department of Pathology, College of Medicine, Jouf University, Sakaka, Saudi Arabia.,Department of Microbiology & Medical Immunology, Faculty of Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Hossein Arefanian
- Department of Immunology and Microbiology, Dasman Diabetes Institute, Dasman, Kuwait
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman, Kuwait
| | | |
Collapse
|
11
|
Dysregulated expression of mRNA and SNP in pulmonary artery remodeling in ascites syndrome in broilers. Poult Sci 2020; 100:100877. [PMID: 33518352 PMCID: PMC7936122 DOI: 10.1016/j.psj.2020.11.054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/14/2020] [Accepted: 11/23/2020] [Indexed: 02/08/2023] Open
Abstract
Broiler ascites syndrome (AS), also called pulmonary artery hypertension, is a metabolic disorder that has been observed worldwide in fast-growing broilers. Pulmonary arterial remodeling is a key step in the development of AS. The precise relationship between mRNA and SNP of the pulmonary artery in regulating AS progression remains unclear. In this study, we obtained pulmonary artery tissues from broilers with AS to perform pathologic section and pathologic anatomic observation. SNP, InDel, and mRNA data analysis were carried out using GATK and ANNOVAR software to study the SNP loci of 985 previously reported genes (437 upregulated and 458 downregulated). The pathology results showed that there was a lot of yellow fluid in the abdominal cavity and pericardium, that the ascites cardiac index and hematocrit changed significantly, and that the pulmonary artery had remodeled and become thicker in the disease group. Myocardial sections showed vacuolar degeneration of myocytes and rupture of muscle fibers. In addition, ALDH7A1, IRG1, GGT5, IGSF1, DHX58, USP36, TREML2, SPAG1, CD34, and PLEKHA7 were found to be closely associated with the pathogenesis of pulmonary artery remodeling in AS progression. Taken together, our present study further illuminates the molecular mechanism of pulmonary artery remodeling underlying AS progression.
Collapse
|
12
|
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.
Collapse
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.
| | | |
Collapse
|