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Mustafa R, Ghanbari M, Karhunen V, Evangelou M, Dehghan A. Phenome-wide association study on miRNA-related sequence variants: the UK Biobank. Hum Genomics 2023; 17:104. [PMID: 37996941 PMCID: PMC10668386 DOI: 10.1186/s40246-023-00553-w] [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: 08/17/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Genetic variants in the coding region could directly affect the structure and expression levels of genes and proteins. However, the importance of variants in the non-coding region, such as microRNAs (miRNAs), remain to be elucidated. Genetic variants in miRNA-related sequences could affect their biogenesis or functionality and ultimately affect disease risk. Yet, their implications and pleiotropic effects on many clinical conditions remain unknown. METHODS Here, we utilised genotyping and hospital records data in the UK Biobank (N = 423,419) to investigate associations between 346 genetic variants in miRNA-related sequences and a wide range of clinical diagnoses through phenome-wide association studies. Further, we tested whether changes in blood miRNA expression levels could affect disease risk through colocalisation and Mendelian randomisation analysis. RESULTS We identified 122 associations for six variants in the seed region of miRNAs, nine variants in the mature region of miRNAs, and 27 variants in the precursor miRNAs. These included associations with hypertension, dyslipidaemia, immune-related disorders, and others. Nineteen miRNAs were associated with multiple diagnoses, with six of them associated with multiple disease categories. The strongest association was reported between rs4285314 in the precursor of miR-3135b and celiac disease risk (odds ratio (OR) per effect allele increase = 0.37, P = 1.8 × 10-162). Colocalisation and Mendelian randomisation analysis highlighted potential causal role of miR-6891-3p in dyslipidaemia. CONCLUSIONS Our study demonstrates the pleiotropic effect of miRNAs and offers insights to their possible clinical importance.
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Affiliation(s)
- Rima Mustafa
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- UK Dementia Research Institute, Imperial College London, London, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ville Karhunen
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | | | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.
- UK Dementia Research Institute, Imperial College London, London, UK.
- MRC Centre for Environment and Health, Imperial College London, London, UK.
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2
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Toste CC, O’Donovan MC, Bray NJ. Mapping microRNA expression quantitative trait loci in the prenatal human brain implicates miR-1908-5p expression in bipolar disorder and other brain-related traits. Hum Mol Genet 2023; 32:2941-2949. [PMID: 37471622 PMCID: PMC10549788 DOI: 10.1093/hmg/ddad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023] Open
Abstract
MicroRNA (miRNA) are small non-coding RNA involved in post-transcriptional gene regulation. Given their known involvement in early neurodevelopment processes, we here sought to identify common genetic variants associated with altered miRNA expression in the prenatal human brain. We performed small RNA sequencing on brain tissue from 112 genome-wide genotyped fetuses from the second trimester of gestation, identifying high-confidence (false discovery rate < 0.05) expression quantitative trait loci for 30 mature miRNA. Integrating our findings with genome-wide association study data for brain-related disorders, we implicate increased prenatal expression of miR-1908-5p as a risk mechanism for bipolar disorder and find that predicted mRNA targets of miR-1908-5p that are expressed in the fetal brain are enriched for common variant genetic association with the condition. Extending these analyses to other brain-related traits, we find that common genetic variation associated with increased miR-1908-5p expression in fetal brain is additionally associated with depressive symptoms, irritability, increased right cerebellum exterior volume and increased sleep duration in the general population. Our findings provide support to the view that altered miRNA expression can influence susceptibility to neuropsychiatric illness and suggest an early neurodevelopmental risk mechanism for bipolar disorder.
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Affiliation(s)
- Carolina C Toste
- Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Cardiff CF10 4HQ, United Kingdom
| | - Michael C O’Donovan
- Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Cardiff CF10 4HQ, United Kingdom
| | - Nicholas J Bray
- Centre for Neuropsychiatric Genetics & Genomics, Division of Psychological Medicine & Clinical Neurosciences, Cardiff University, Cardiff CF10 4HQ, United Kingdom
- Neuroscience & Mental Health Innovation Institute, Cardiff University, Cardiff CF24 4HQ, United Kingdom
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3
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Velle A, Pesenti C, Grassi T, Beltrame L, Martini P, Jaconi M, Agostinis F, Calura E, Katsaros D, Borella F, Fruscio R, D'Incalci M, Marchini S, Romualdi C. A comprehensive investigation of histotype-specific microRNA and their variants in Stage I epithelial ovarian cancers. Int J Cancer 2023; 152:1989-2001. [PMID: 36541726 DOI: 10.1002/ijc.34408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/23/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
isomiRs, the sequence-variants of microRNA, are known to be tissue and cell type specific but their physiological role is largely unknown. In our study, we explored for the first time the expression of isomiRs across different Stage I epithelial ovarian cancer (EOC) histological subtypes, in order to shed new light on their biological role in tumor growth and progression. In a multicentric retrospective cohort of tumor biopsies (n = 215) we sequenced small RNAs finding 971 expressed miRNAs, 64% of which are isomiRs. Among them, 42 isomiRs showed a clear histotype specific pattern, confirming our previously identified miRNA markers (miR192/194 and miR30a-3p/5p for mucinous and clear cell subtypes, respectively) and uncovering new biomarkers for all the five subtypes. Using integrative models, we found that the 38% of these miRNA expression alterations is the result of copy number variations while the 17% of differential transcriptional activities. Our work represents the first attempt to characterize isomiRs expression in Stage I EOC within and across subtypes and to contextualize their alterations in the framework of the large genomic heterogeneity of this tumor.
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Affiliation(s)
- Angelo Velle
- Department of Biology, University of Padova, Padova, Italy
| | - Chiara Pesenti
- Department of Oncology, Mario Negri Institute for Pharmacological Research, Milan, Italy.,Medical Genetics Unit, ASST Santi Paolo e Carlo, Milan, Italy
| | - Tommaso Grassi
- Department of Obstetrics and Gynaecology, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Luca Beltrame
- IRCCS Humanitas Research Hospital, Molecular Pharmacology Lab, Rozzano, Italy
| | - Paolo Martini
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Marta Jaconi
- Department of Pathology, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | | | - Enrica Calura
- Department of Biology, University of Padova, Padova, Italy
| | - Dionyssios Katsaros
- Azienda Ospedaliero-Universitaria Città della Salute, Presidio S Anna and Department of Surgical Science, Gynecology, University of Torino, Torino, Italy
| | - Fulvio Borella
- Gynaecology and Obstetrics 1, Department of Surgical Sciences, St Anna Hospital and University of Torino, Turin, Italy
| | - Robert Fruscio
- Department of Obstetrics and Gynaecology, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Maurizio D'Incalci
- Cancer Pharmacology, IRCCS Humanitas Research Hospital, Italy.,Department of Biomedical Sciences, Humanitas University, Italy
| | - Sergio Marchini
- IRCCS Humanitas Research Hospital, Molecular Pharmacology Lab, Rozzano, Italy
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Plasma circulating microRNAs associated with obesity, body fat distribution, and fat mass: the Rotterdam Study. Int J Obes (Lond) 2022; 46:2137-2144. [PMID: 36216908 DOI: 10.1038/s41366-022-01227-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) represent a class of small non-coding RNAs that regulate gene expression post-transcriptionally and are implicated in the pathogenesis of different diseases. Limited studies have investigated the association of circulating miRNAs with obesity and body fat distribution and their link to obesity-related diseases using population-based data. METHODS We conducted a genome-wide profile of circulating miRNAs in plasma, collected between 2002 and 2005, in 1208 participants from the population-based Rotterdam Study cohort. Obesity and body fat distribution were measured as body mass index (BMI), waist-to-hip ratio (WHR), android-fat to gynoid-fat ratio (AGR), and fat mass index (FMI) measured by anthropometrics and Dual X-ray Absorptiometry. Multivariable linear regression models were used to assess the association of 591 miRNAs well-expressed in plasma with these traits adjusted for potential covariates. We further sought for the association of identified miRNAs with cardiovascular and metabolic diseases in the Rotterdam study and previous publications. RESULTS Plasma levels of 65 miRNAs were associated with BMI, 40 miRNAs with WHR, 65 miRNAs with FMI, and 15 miRNAs with AGR surpassing the Bonferroni-corrected P < 8.46 × 10-5. Of these, 12 miRNAs were significantly associated with all traits, while four miRNAs were associated only with WHR, three miRNAs only with FMI, and miR-378i was associated only with AGR. The most significant association among the overlapping miRNAs was with miR-193a-5p, which was shown to be associated with type 2 diabetes and hepatic steatosis in the Rotterdam Study. Moreover, five of the obesity-associated miRNAs and two of the body fat distribution miRNAs have been correlated previously to cardiovascular disease. CONCLUSIONS This study indicates that plasma levels of several miRNAs are associated with obesity and body fat distribution which could help to better understand the underlying mechanisms and may have the biomarker potential for obesity-related diseases.
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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Mir M, Mir R, Alghamdi M, Wani J, Elfaki I, Sabah Z, Alhujaily M, Jeelani M, Marakala V, Alharthi M, Al‑Shahrani A. Potential impact of GCK, MIR-196A-2 and MIR-423 gene abnormalities on the development and progression of type 2 diabetes mellitus in Asir and Tabuk regions of Saudi Arabia. Mol Med Rep 2022; 25:162. [PMID: 35293603 PMCID: PMC8941532 DOI: 10.3892/mmr.2022.12675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/28/2022] [Indexed: 11/17/2022] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a metabolic disorder characterized by persistent hyperglycemia and is associated with serious complications. The risk factors for T2DM include both genetic and lifestyle factors. Genome-wide association studies have indicated the association of genetic variations with many diseases, including T2DM. Glucokinase (GCK) plays a key role in the regulation of insulin release in the pancreas and catalyzes the first step in glycolysis in the liver. Genetic alterations in the GCK gene have been implicated in both hyperglycemia and hypoglycemia. MicroRNAs (miRNAs/miRs) are small non-coding RNA molecules that are involved in the important physiological processes including glucose metabolism. In the present study, the association of the single nucleotide polymorphisms (SNPs) in the GCK, MIR-196A-2 and MIR-423 genes with susceptibility to T2DM in patients from two regions of Saudi Arabia were examined, using the tetra-primer amplification refractory mutation system. The results showed that the AA genotype and the A allele of GCK rs1799884 were associated with T2DM [odds ratio (OR)=2.25, P=0.032 and OR=1.55, P=0.021, respectively]. Likewise, the CT genotype and T allele of MIR-196A-2 rs11614913 were associated with an increased risk of T2DM (OR=2.36, P=0.0059 and OR=1.74, P=0.023, respectively). In addition, the CA genotype of MIR-423 rs6505162 C>A was found to be linked with T2DM (OR=2.12 and P=0.021). It was concluded in the present research study that gene variations in GCK, MIR-196A-2 and MIR-423 are potentially associated with an increased risk of T2DM. These results, in the future, may help in the identification and stratification of individuals susceptible to T2DM. Future longitudinal studies with larger sample sizes and in different ethnic populations are recommended to validate these findings.
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Affiliation(s)
- Mohammad Mir
- Department of Basic Medical Sciences, College of Medicine, University of Bisha, Bisha 61922, Kingdom of Saudi Arabia
| | - Rashid Mir
- Prince Fahd Bin Sultan Research Chair, Department of Medical Laboratory Technology (MLT), Faculty of Applied Medical Sciences, University of Tabuk, Tabuk 71491, Kingdom of Saudi Arabia
| | - Mushabab Alghamdi
- Department of Internal Medicine, College of Medicine, University of Bisha, Bisha 61922, Kingdom of Saudi Arabia
| | - Javed Wani
- Department of Internal Medicine College of Medicine, King Khalid University, Abha 61421, Kingdom of Saudi Arabia
| | - Imadeldin Elfaki
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk 71491, Kingdom of Saudi Arabia
| | - Zia Sabah
- Department of Internal Medicine College of Medicine, King Khalid University, Abha 61421, Kingdom of Saudi Arabia
| | - Muhanad Alhujaily
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, Bisha 61922, Kingdom of Saudi Arabia
| | - Mohammed Jeelani
- Department of Basic Medical Sciences, College of Medicine, University of Bisha, Bisha 61922, Kingdom of Saudi Arabia
| | - Vijaya Marakala
- Department of Basic Medical Sciences, College of Medicine, University of Bisha, Bisha 61922, Kingdom of Saudi Arabia
| | - Muffarah Alharthi
- Department of Family Medicine, College of Medicine, University of Bisha, Bisha 61922, Kingdom of Saudi Arabia
| | - Abdullah Al‑Shahrani
- Department of Family Medicine, College of Medicine, University of Bisha, Bisha 61922, Kingdom of Saudi Arabia
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7
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Zhang X, Li TY, Xiao HM, Ehrlich KC, Shen H, Deng HW, Ehrlich M. Epigenomic and Transcriptomic Prioritization of Candidate Obesity-Risk Regulatory GWAS SNPs. Int J Mol Sci 2022; 23:1271. [PMID: 35163195 PMCID: PMC8836216 DOI: 10.3390/ijms23031271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/19/2022] [Indexed: 02/06/2023] Open
Abstract
Concern about rising rates of obesity has prompted searches for obesity-related single nucleotide polymorphisms (SNPs) in genome-wide association studies (GWAS). Identifying plausible regulatory SNPs is very difficult partially because of linkage disequilibrium. We used an unusual epigenomic and transcriptomic analysis of obesity GWAS-derived SNPs in adipose versus heterologous tissues. From 50 GWAS and 121,064 expanded SNPs, we prioritized 47 potential causal regulatory SNPs (Tier-1 SNPs) for 14 gene loci. A detailed examination of seven loci revealed that four (CABLES1, PC, PEMT, and FAM13A) had Tier-1 SNPs positioned so that they could regulate use of alternative transcription start sites, resulting in different polypeptides being generated or different amounts of an intronic microRNA gene being expressed. HOXA11 and long noncoding RNA gene RP11-392O17.1 had Tier-1 SNPs in their 3' or promoter region, respectively, and strong preferences for expression in subcutaneous versus visceral adipose tissue. ZBED3-AS1 had two intragenic Tier-1 SNPs, each of which could contribute to mediating obesity risk through modulating long-distance chromatin interactions. Our approach not only revealed especially credible novel regulatory SNPs, but also helped evaluate previously highlighted obesity GWAS SNPs that were candidates for transcription regulation.
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Affiliation(s)
- Xiao Zhang
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (X.Z.); (K.C.E.); (H.S.)
| | - Tian-Ying Li
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China; (T.-Y.L.); (H.-M.X.)
| | - Hong-Mei Xiao
- Center for System Biology, Data Sciences, and Reproductive Health, School of Basic Medical Science, Central South University, Changsha 410013, China; (T.-Y.L.); (H.-M.X.)
| | - Kenneth C. Ehrlich
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (X.Z.); (K.C.E.); (H.S.)
| | - Hui Shen
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (X.Z.); (K.C.E.); (H.S.)
| | - Hong-Wen Deng
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (X.Z.); (K.C.E.); (H.S.)
| | - Melanie Ehrlich
- Tulane Center for Biomedical Informatics and Genomics, Division of Biomedical Informatics and Genomics, Deming Department of Medicine, School of Medicine, Tulane University, New Orleans, LA 70112, USA; (X.Z.); (K.C.E.); (H.S.)
- Tulane Cancer Center and Hayward Genetics Center, Tulane University, New Orleans, LA 70112, USA
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Huang Q, Chen H, Xu F, Liu C, Wang Y, Tang W, Chen L. Relationship of microRNA locus with type 2 diabetes mellitus: a case-control study. Endocr Connect 2021; 10:1393-1402. [PMID: 34596578 PMCID: PMC8630770 DOI: 10.1530/ec-21-0261] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 09/30/2021] [Indexed: 12/11/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is considered as a metabolic disease with hyperglycemia. Accumulating investigations have explored the important role of hereditary factors for T2DM occurrence. Some functional microRNA (miR) polymorphisms may affect their interactions with target mRNAs and result in an aberrant expression. Thus, miR variants might be considered as a biomarker of the susceptibility of T2DM. In this study, we recruited 502 T2DM cases and 782 healthy subjects. We selected miR-146a rs2910164 C>G, miR-196a2 rs11614913 T>C and miR-499 rs3746444 A>G loci and carried out an investigation to identify whether these miR loci could influence T2DM occurrence. In this investigation, a Bonferroni correction was harnessed. After adjustment, we found that rs2910164 SNP was a protective factor for T2DM (GG vs CC/CG: adjusted P = 0.010), especially in never drinking (GG vs CC/CG: adjusted P = 0.001) and BMI ≥24 kg/m2 (GG vs CC/CG: adjusted P = 0.002) subgroups. We also identified that rs11614913 SNP was a protective factor for T2DM in smoking subjects (CC/TC vs TT: adjusted P = 0.002). When we analyzed an interaction of SNP-SNP with the susceptibility tof T2DM, rs11614913/rs3746444, rs2910164/rs3746444 and rs11614913/rs2910164 combinations were not associated with the risk of T2DM. In summary, this study highlights that rs2910164 SNP decreases the susceptibility of T2DM, especially in BMI ≥24 kg/m2 and never drinking subgroups. In addition, we also identify that rs11614913 C allele decreases the susceptibility of T2DM significantly in smoking subgroup.
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Affiliation(s)
- Qiuyu Huang
- Department of Cardiovascular Surgery, Union Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
- Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian Province, China
| | - Hanshen Chen
- Department of Anesthesiology, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian Province, China
- Correspondence should be addressed to W Tang or L Chen: or
| | - Fan Xu
- Department of Cardiovascular Surgery, Union Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
- Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian Province, China
| | - Chao Liu
- Department of Cardiothoracic Surgery, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Yafeng Wang
- Department of Cardiology, The People’s Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, Yunnan Province, China
| | - Weifeng Tang
- Department of Cardiothoracic Surgery, Nanjing Drum Tower Hospital, Nanjing University Medical School, Jiangsu Province, China
- Correspondence should be addressed to W Tang or L Chen: or
| | - Liangwan Chen
- Department of Cardiovascular Surgery, Union Hospital, Fujian Medical University, Fuzhou, Fujian Province, China
- Key Laboratory of Cardio-Thoracic Surgery (Fujian Medical University), Fujian Province University, Fuzhou, Fujian Province, China
- Correspondence should be addressed to W Tang or L Chen: or
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9
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Beehler K, Nikpay M, Lau P, Dang AT, Lagace TA, Soubeyrand S, McPherson R. A Common Polymorphism in the FADS1 Locus Links miR1908 to Low-Density Lipoprotein Cholesterol Through BMP1. Arterioscler Thromb Vasc Biol 2021; 41:2252-2262. [PMID: 34134519 DOI: 10.1161/atvbaha.121.316473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Kaitlyn Beehler
- Atherogenomics Laboratory (K.B., M.N., P.L., A.-T.D., S.S., R.M.), University of Ottawa Heart Institute, Canada
| | - Majid Nikpay
- Atherogenomics Laboratory (K.B., M.N., P.L., A.-T.D., S.S., R.M.), University of Ottawa Heart Institute, Canada
| | - Paulina Lau
- Atherogenomics Laboratory (K.B., M.N., P.L., A.-T.D., S.S., R.M.), University of Ottawa Heart Institute, Canada
| | - Anh-Thu Dang
- Atherogenomics Laboratory (K.B., M.N., P.L., A.-T.D., S.S., R.M.), University of Ottawa Heart Institute, Canada
| | - Thomas A Lagace
- Lipoprotein Receptor Biology Laboratory (T.A.L.), University of Ottawa Heart Institute, Canada
| | - Sébastien Soubeyrand
- Atherogenomics Laboratory (K.B., M.N., P.L., A.-T.D., S.S., R.M.), University of Ottawa Heart Institute, Canada
| | - Ruth McPherson
- Atherogenomics Laboratory (K.B., M.N., P.L., A.-T.D., S.S., R.M.), University of Ottawa Heart Institute, Canada
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10
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Moschos MM, Dettoraki M, Karekla A, Lamprinakis I, Damaskos C, Gouliopoulos N, Tibilis M, Gazouli M. Polymorphism analysis of miR182 and CDKN2B genes in Greek patients with primary open angle glaucoma. PLoS One 2020; 15:e0233692. [PMID: 32492046 PMCID: PMC7269255 DOI: 10.1371/journal.pone.0233692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/10/2020] [Indexed: 12/28/2022] Open
Abstract
Glaucoma is a progressive optic neuropathy resulting from retinal ganglion cells death; it represents one of the leading causes of irreversible blindness worldwide. Although, primary open angle glaucoma (POAG) is the most common type of the disease, the pathogenesis of POAG and the genetic factors contributing to disease development remain poorly understood. The aim of this study was to investigate whether the polymorphisms rs76481776 in miR182 gene and rs3217992 in cyclin-dependent kinase inhibitor-2B (CDKN2B) gene are risk factors for POAG in a series of patients of Greek origin. A case-control study was conducted including 120 patients with POAG and 113 unaffected healthy controls of Greek origin, surveyed for polymorphisms with potential correlation to POAG. DNA from each individual was tested for the miR182 rs76481776 and CDKN2B rs3217992 polymorphisms. Regarding the miR182 rs76481776 polymorphism, the T allele occurred with significantly higher frequency in POAG patients compared to controls (OR: 2.62, 95% CI: 1.56-4.39; p = 0.0002). The CDKN2B rs3217992 A allele frequency was found significantly increased in POAG patients compared to healthy individuals (OR: 1.72, 95% CI: 1.18-2.49; p = 0.005). Therefore, both rs76481776 polymorphism in miR182 gene and rs3217992 polymorphism in CDKN2B gene seem to be associated with the development of POAG in a Greek population. The carriers of the T allele of rs76481776 in miR182 and the carriers of the A allele of rs3217992 in CDKN2B have an increased risk of developing POAG.
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Affiliation(s)
- Marilita M. Moschos
- 1st Department of Ophthalmology, "G. Gennimatas" General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
- * E-mail:
| | - Maria Dettoraki
- 1st Department of Ophthalmology, "G. Gennimatas" General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Aggela Karekla
- Department of Ophthalmology, “Evangelismos” General Hospital, Athens, Greece
| | - Ioannis Lamprinakis
- Department of Ophthalmology, “Evangelismos” General Hospital, Athens, Greece
| | - Christos Damaskos
- Second Department of Propedeutic Surgery, “Laiko” General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Nikolaos Gouliopoulos
- 1st Department of Ophthalmology, "G. Gennimatas" General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Marios Tibilis
- 1st Department of Ophthalmology, "G. Gennimatas" General Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens, Greece
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11
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Mens MMJ, Maas SCE, Klap J, Weverling GJ, Klatser P, Brakenhoff JPJ, van Meurs JBJ, Uitterlinden AG, Ikram MA, Kavousi M, Ghanbari M. Multi-Omics Analysis Reveals MicroRNAs Associated With Cardiometabolic Traits. Front Genet 2020; 11:110. [PMID: 32174972 PMCID: PMC7056871 DOI: 10.3389/fgene.2020.00110] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 01/30/2020] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are non-coding RNA molecules that regulate gene expression. Extensive research has explored the role of miRNAs in the risk for type 2 diabetes (T2D) and coronary heart disease (CHD) using single-omics data, but much less by leveraging population-based omics data. Here we aimed to conduct a multi-omics analysis to identify miRNAs associated with cardiometabolic risk factors and diseases. First, we used publicly available summary statistics from large-scale genome-wide association studies to find genetic variants in miRNA-related sequences associated with various cardiometabolic traits, including lipid and obesity-related traits, glycemic indices, blood pressure, and disease prevalence of T2D and CHD. Then, we used DNA methylation and miRNA expression data from participants of the Rotterdam Study to further investigate the link between associated miRNAs and cardiometabolic traits. After correcting for multiple testing, 180 genetic variants annotated to 67 independent miRNAs were associated with the studied traits. Alterations in DNA methylation levels of CpG sites annotated to 38 of these miRNAs were associated with the same trait(s). Moreover, we found that plasma expression levels of 8 of the 67 identified miRNAs were also associated with the same trait. Integrating the results of different omics data showed miR-10b-5p, miR-148a-3p, miR-125b-5p, and miR-100-5p to be strongly linked to lipid traits. Collectively, our multi-omics analysis revealed multiple miRNAs that could be considered as potential biomarkers for early diagnosis and progression of cardiometabolic diseases.
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Affiliation(s)
- Michelle M J Mens
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Silvana C E Maas
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Jaco Klap
- World Without Disease Accelerator, Data Sciences & Prevention Biomarkers, Johnson & Johnson, Leiden, Netherlands
| | - Gerrit Jan Weverling
- World Without Disease Accelerator, Data Sciences & Prevention Biomarkers, Johnson & Johnson, Leiden, Netherlands
| | - Paul Klatser
- World Without Disease Accelerator, Data Sciences & Prevention Biomarkers, Johnson & Johnson, Leiden, Netherlands
| | - Just P J Brakenhoff
- World Without Disease Accelerator, Data Sciences & Prevention Biomarkers, Johnson & Johnson, Leiden, Netherlands
| | - Joyce B J van Meurs
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Maryam Kavousi
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
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12
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Zhong Y, Zhu F, Ding Y. Differential microRNA expression profile in the plasma of preeclampsia and normal pregnancies. Exp Ther Med 2019; 18:826-832. [PMID: 31281456 DOI: 10.3892/etm.2019.7637] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 03/10/2017] [Indexed: 12/15/2022] Open
Abstract
Preeclampsia is a common disease in pregnant women that can only be diagnosed from 20 weeks after fertilization. Developing early diagnosis markers is urgent and would be helpful in selecting appropriate treatment strategies. The present study aimed to identify the differential expression profiles of microRNAs in the plasma between patients with preeclampsia and normal pregnancies using microarray methods. Using quantitative polymerase chain reaction (qPCR), the differentially expressed microRNAs (miRNAs or miRs) identified from the microarray analysis were validated. A total of 3 miRNAs, including hsa-miR-1304-5p, hsa-miR-320a and hsa-miR-5002-5p, were upregulated in the plasma of patients with preeclampsia pregnancies. Examination of the functions of these miRNAs demonstrated that they were involved in cell proliferation, indicating that preeclampsia affected this pathway. In addition, 26 downregulated miRNAs were identified by microarray methods. The functions of these miRNAs included immune regulation, vascular development, cancer pathology and pathology of other disease (tuberculosis, oligozoospermia, psoriasis and Alzheimer's disease). Using qPCR, the most differentially expressed miRNAs were confirmed to be hsa-miR-1304-5p, hsa-miR-320a and hsa-miR-5002-5p, which were upregulated, as well as hsa-miR-188-3p, hsa-miR-211-5p, hiv1-miR-TAR-3p, hsa-miR-4432 and hsa-miR-4498 that were significantly downregulated in the plasma of preeclampsia patients. The present findings may be useful in the development of early diagnosis markers and treatment targets for preeclampsia.
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Affiliation(s)
- Yan Zhong
- Department of Gynaecology and Obstetrics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Fufan Zhu
- Department of Gynaecology and Obstetrics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
| | - Yiling Ding
- Department of Gynaecology and Obstetrics, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410011, P.R. China
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13
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Nikpay M, Beehler K, Valsesia A, Hager J, Harper ME, Dent R, McPherson R. Genome-wide identification of circulating-miRNA expression quantitative trait loci reveals the role of several miRNAs in the regulation of cardiometabolic phenotypes. Cardiovasc Res 2019; 115:1629-1645. [DOI: 10.1093/cvr/cvz030] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/18/2018] [Accepted: 01/29/2019] [Indexed: 11/13/2022] Open
Abstract
Abstract
Aims
To identify genetic variants that have a regulatory impact on circulating microRNAs (miRNAs) and to connect genetic risk to blood traits/biomarkers through the circulating miRNAs.
Methods and results
Leveraging miRNA-Seq data and the 1000 Genomes imputed genotypes, we carried out genome-wide association analysis for SNPs that regulate the expression of circulating miRNAs in a sample of 710 unrelated subjects of European ancestry. Wherever possible, we used data from the Framingham and the Geuvadis studies to replicate our findings. We found at least one genome-wide significant (P < 5e−8) miRNA-eQTL (mirQTL) for 143 circulating miRNAs. Overall each mirQTL explained a small portion (<1%) of variation in miRNA levels; however, we identified a few mirQTLs that explained 4% to 20% of variation in miRNA levels in plasma. Unlike trans-mirQTLs (P = 0.7), cis-mirQTLs tend to be also associated with their counterpart mature miRNAs (P < 0.0001), this suggests trans-mirQTLs exert their effect through processes that affect the stability of mature miRNAs; whereas, cis-mirQTLs mainly regulate the expression of primary-miRNAs. Next, we used the identified mirQTLs to investigate the links between circulating miRNAs with blood traits/biomarkers through Mendelian randomization analysis. We found miR-1908-5p plays an important role in regulating low-density lipoprotein (LDL), total cholesterol (TC), fasting glucose, HbA1c, and several lipid-metabolites in blood, whereas, miR-10b-5p mediates the trans-regulatory effect of the ABO locus on several blood proteins, coronary artery disease, and TC. Moreover, we demonstrated that a higher plasma level of miR-199a is causally associated with lower levels of LDL and TC. Finally, we found miR-143-3p and miR-145-5p are functionally related and mediate the effect of ZFPM2 on a number of its protein targets in blood including VEGFA, SERPINE1, and PDGFs.
Conclusions
This study identifies SNPs that have a regulatory impact on circulating miRNAs, and underlines the role of several circulating miRNAs in mediating the effect of a number of GWAS loci on cardiometabolic phenotypes.
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Affiliation(s)
- Majid Nikpay
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, 40 Ruskin St – H4208, Ottawa, Canada
| | - Kaitlyn Beehler
- Atherogenomics Laboratory, University of Ottawa Heart Institute, 40 Ruskin St – H4203, Ottawa, Canada
| | - Armand Valsesia
- Nestle Institute of Health Sciences, EPFL Innovation Park, 1015 Lausanne, Switzerland
| | - Jorg Hager
- Nestle Institute of Health Sciences, EPFL Innovation Park, 1015 Lausanne, Switzerland
| | - Mary-Ellen Harper
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Roger Guindon Hall, Room 4220, Ottawa, Canada
| | - Robert Dent
- Ottawa Hospital Weight Management Clinic, 1053 Carling Avenue, Ottawa, Canada
| | - Ruth McPherson
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, 40 Ruskin St – H4208, Ottawa, Canada
- Atherogenomics Laboratory, University of Ottawa Heart Institute, 40 Ruskin St – H4203, Ottawa, Canada
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14
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A systematic analysis highlights multiple long non-coding RNAs associated with cardiometabolic disorders. J Hum Genet 2018; 63:431-446. [PMID: 29382920 DOI: 10.1038/s10038-017-0403-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/04/2017] [Accepted: 12/05/2017] [Indexed: 12/19/2022]
Abstract
Genome-wide association studies (GWAS) have identified many susceptibility loci for cardiometabolic disorders. Most of the associated variants reside in non-coding regions of the genome including long non-coding RNAs (lncRNAs), which are thought to play critical roles in diverse biological processes. Here, we leveraged data from the available GWAS meta-analyses on lipid and obesity-related traits, blood pressure, type 2 diabetes, and coronary artery disease and identified 179 associated single-nucleotide polymorphisms (SNPs) in 102 lncRNAs (p-value < 2.3 × 10-7). Of these, 55 SNPs, either the lead SNP or in strong linkage disequilibrium with the lead SNP in the related loci, were selected for further investigations. Our in silico predictions and functional annotations of the SNPs as well as expression and DNA methylation analysis of their lncRNAs demonstrated several lncRNAs that fulfilled predefined criteria for being potential functional targets. In particular, we found evidence suggesting that LOC157273 (at 8p23.1) is involved in regulating serum lipid-cholesterol. Our results showed that rs4841132 in the second exon and cg17371580 in the promoter region of LOC157273 are associated with lipids; the lncRNA is expressed in liver and associates with the expression of its nearby coding gene, PPP1R3B. Collectively, we highlight a number of loci associated with cardiometabolic disorders for which the association may act through lncRNAs.
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15
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Genetic Polymorphism of miR-196a-2 is Associated with Bone Mineral Density (BMD). Int J Mol Sci 2017; 18:ijms18122529. [PMID: 29186852 PMCID: PMC5751132 DOI: 10.3390/ijms18122529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 11/22/2017] [Accepted: 11/23/2017] [Indexed: 12/27/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that post-transcriptionally regulate the translation of messenger RNAs. Given the crucial role of miRNAs in gene expression, genetic variants within miRNA-related sequences may affect miRNA function and contribute to disease risk. Osteoporosis is characterized by reduced bone mass, and bone mineral density (BMD) is a major diagnostic proxy to assess osteoporosis risk. Here, we aimed to identify miRNAs that are involved in BMD using data from recent genome-wide association studies (GWAS) on femoral neck, lumbar spine and forearm BMD. Of 242 miRNA-variants available in the GWAS data, we found rs11614913:C > T in the precursor miR-196a-2 to be significantly associated with femoral neck-BMD (p-value = 9.9 × 10−7, β = −0.038) and lumbar spine-BMD (p-value = 3.2 × 10−11, β = −0.061). Furthermore, our sensitivity analyses using the Rotterdam study data showed a sex-specific association of rs11614913 with BMD only in women. Subsequently, we highlighted a number of miR-196a-2 target genes, expressed in bone and associated with BMD, that may mediate the miRNA function in BMD. Collectively, our results suggest that miR-196a-2 may contribute to variations in BMD level. Further biological investigations will give more insights into the mechanisms by which miR-196a-2 control expression of BMD-related genes.
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16
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Ghanbari M, Iglesias AI, Springelkamp H, van Duijn CM, Ikram MA, Dehghan A, Erkeland SJ, Klaver CCW, Meester-Smoor MA. A Genome-Wide Scan for MicroRNA-Related Genetic Variants Associated With Primary Open-Angle Glaucoma. Invest Ophthalmol Vis Sci 2017; 58:5368-5377. [PMID: 29049738 PMCID: PMC6110129 DOI: 10.1167/iovs.17-22410] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To identify microRNAs (miRNAs) involved in primary open-angle glaucoma (POAG), using genetic data. MiRNAs are small noncoding RNAs that posttranscriptionally regulate gene expression. Genetic variants in miRNAs or miRNA-binding sites within gene 3'-untranslated regions (3'UTRs) are expected to affect miRNA function and contribute to disease risk. Methods Data from the recent genome-wide association studies on intraocular pressure, vertical cup-to-disc ratio (VCDR), cupa area and disc area were used to investigate the association of miRNAs with POAG endophenotypes. Putative targets of the associated miRNAs were studied according to their association with POAG and tested in cell line by transfection experiments for regulation by the miRNAs. Results Of 411 miRNA variants, rs12803915:A/G in the terminal loop of pre-miR-612 and rs2273626:A/C in the seed sequence of miR-4707 were significantly associated with VCDR and cup area (P values < 1.2 × 10-4). The first variant is demonstrated to increase the miR-612 expression. We showed that the second variant does not affect the miR-4707 biogenesis, but reduces the binding of miR-4707-3p to CARD10, a gene known to be involved in glaucoma. Moreover, of 72,052 miRNA-binding-site variants, 47 were significantly associated with four POAG endophenotypes (P value < 6.9 × 10-6). Of these, we highlighted 10 variants that are more likely to affect miRNA-mediated gene regulation in POAG. These include rs3217992 and rs1063192, which have been shown experimentally to affect miR-138-3p- and miR-323b-5p-mediated regulation of CDKN2B. Conclusions We identified a number of miRNAs that are associated with POAG endophenotypes. The identified miRNAs and their target genes are candidates for future studies on miRNA-related therapies for POAG.
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Affiliation(s)
- Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Genetics, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Adriana I Iglesias
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Henriët Springelkamp
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Neurology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Abbas Dehghan
- Department of Epidemiology & Biostatistics, Imperial College London, London, United Kingdom
| | - Stefan J Erkeland
- Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Radbound University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Magda A Meester-Smoor
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Center, Rotterdam, The Netherlands
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17
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Ikram MA, Brusselle GGO, Murad SD, van Duijn CM, Franco OH, Goedegebure A, Klaver CCW, Nijsten TEC, Peeters RP, Stricker BH, Tiemeier H, Uitterlinden AG, Vernooij MW, Hofman A. The Rotterdam Study: 2018 update on objectives, design and main results. Eur J Epidemiol 2017; 32:807-850. [PMID: 29064009 PMCID: PMC5662692 DOI: 10.1007/s10654-017-0321-4] [Citation(s) in RCA: 338] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/06/2017] [Indexed: 02/07/2023]
Abstract
The Rotterdam Study is a prospective cohort study ongoing since 1990 in the city of Rotterdam in The Netherlands. The study targets cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, otolaryngological, locomotor, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. Since 2016, the cohort is being expanded by persons aged 40 years and over. The findings of the Rotterdam Study have been presented in over 1500 research articles and reports (see www.erasmus-epidemiology.nl/rotterdamstudy ). This article gives the rationale of the study and its design. It also presents a summary of the major findings and an update of the objectives and methods.
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Affiliation(s)
- M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
- Department of Neurology, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Guy G O Brusselle
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Sarwa Darwish Murad
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Gastro-Enterology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Cardiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - André Goedegebure
- Department of Otolaryngology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Tamar E C Nijsten
- Department of Dermatology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Robin P Peeters
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Henning Tiemeier
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Psychiatry, Erasmus Medical Center, Rotterdam, The Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, PO Box 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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18
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Abstract
microRNAs (miRNAs) are a small RNA species without protein-coding potential. However, they are key modulators of protein translation. Many studies have linked miRNAs with cancer initiation, progression, diagnosis, and prognosis, and recent studies have also linked them with cancer etiology and susceptibility, especially through single-nucleotide polymorphisms (SNPs). This review discusses some of the recent advances in miRNA-SNP literature-including SNPs in miRNA genes, miRNA target sites, and the processing machinery. In addition, we highlight some emerging areas of interest, including isomiRs and non-3'UTR focused miRNA-binding mechanisms that could provide further novel insight into the relationship between miR-SNPs and cancer. Finally, we note that additional epidemiological and experimental research is needed to close the gap in our understanding of the genotype-phenotype relationship between miRNA-SNPs and cancer.
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Affiliation(s)
- Bríd M Ryan
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, Bethesda, MD, United States.
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19
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Teng C, Zheng H. Low expression of microRNA-1908 predicts a poor prognosis for patients with ovarian cancer. Oncol Lett 2017; 14:4277-4281. [PMID: 28943939 DOI: 10.3892/ol.2017.6714] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/23/2017] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRs) serve important roles in cancer genesis and progression. The expression of miR-1908 has been reported in a number of types of cancer; however, the clinical significance of miR-1908 in human ovarian cancer (OC) remains unclear. A total of 491 patients with OC from The Cancer Genome Atlas project cohort were selected and divided into two groups according to the median expression level of miR-1908. Univariate and multivariate analyses, using the Kaplan-Meier method and Cox regression, were performed to identify the characteristics that predict OC prognosis. Bioinformatics tools were used to identify potential targets of miR-1908. It was identified that the low expression of miR-1908 is associated with a poor prognosis for OC (P<0.05). The potential target genes of miR-1908 included podocan-like 1, JunB AP-1 transcription factor subunit, homeobox B8, SET binding factor 1 and sirtuin 2; high expression of these five genes additionally predicted a poor prognosis. These results suggest that miR-1908 may be a suitable target for the development of novel approaches in OC diagnosis and therapy in the future.
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Affiliation(s)
- Changcai Teng
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Hong Zheng
- Department of Epidemiology and Biostatistics, Tianjin Medical University Cancer Hospital and Institute, National Clinical Research Center of Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
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20
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Banach E, Dmitrzak-Weglarz M, Pawlak J, Kapelski P, Szczepankiewicz A, Rajewska-Rager A, Slopien A, Skibinska M, Czerski P, Hauser J. Dysregulation of miR-499, miR-708 and miR-1908 during a depression episode in bipolar disorders. Neurosci Lett 2017. [PMID: 28647289 DOI: 10.1016/j.neulet.2017.06.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Affective disorders include unipolar disorder (UP) (depression episodes) and bipolar disorder (BP) (depression and mania episodes). Currently, no biological markers are known that can help to differentiate these disorders. However, recent studies have suggested that psychiatric disorders can be connected with small, non-coding RNA, like microRNA. The objective of this study was to analyse the expression level of three microRNAs (miR-499, miR-708, miR-1908) in bipolar and unipolar disorder during depression episodes and after entering the remission state. The group consisted of adult women only, 17 UP (age: 50±17) and 15 BP (age: 33±13) patients. The expression level of miRNAs was investigated by RT-qPCR with the TaqMan assay. Our study has shown a lower expression level of miR-499 (p=0.008), miR-708 (p=0.02) and miR-1908 (p=0.004) in depression episodes of the bipolar disorder patients in comparison to remission state. We have not found similar differences in unipolar disorder and between those types in acute phase of depression and during remission. Obtained results indicate that miRNAs: miR-499, miR-708 and miR-1908 are the most promising candidates for biomarkers of depression episodes of bipolar disorder.
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Affiliation(s)
- Ewa Banach
- Psychiatric Genetics Unit, Department of Psychiatry, Poznan University of Medical Sciences, Poland.
| | - Monika Dmitrzak-Weglarz
- Psychiatric Genetics Unit, Department of Psychiatry, Poznan University of Medical Sciences, Poland
| | - Joanna Pawlak
- Psychiatric Genetics Unit, Department of Psychiatry, Poznan University of Medical Sciences, Poland
| | - Pawel Kapelski
- Psychiatric Genetics Unit, Department of Psychiatry, Poznan University of Medical Sciences, Poland; Department of Adult Psychiatry, Poznan University of Medical Sciences, Poland
| | - Aleksandra Szczepankiewicz
- Psychiatric Genetics Unit, Department of Psychiatry, Poznan University of Medical Sciences, Poland; Laboratory of Molecular and Cell Biology, Department of Pulmonology, Pediatric Allergy and Clinical Immunology, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Agnieszka Slopien
- Department of Children and Adolescents' Psychiatry, Poznan University of Medical Sciences, Poland
| | - Maria Skibinska
- Psychiatric Genetics Unit, Department of Psychiatry, Poznan University of Medical Sciences, Poland
| | - Piotr Czerski
- Psychiatric Genetics Unit, Department of Psychiatry, Poznan University of Medical Sciences, Poland
| | - Joanna Hauser
- Psychiatric Genetics Unit, Department of Psychiatry, Poznan University of Medical Sciences, Poland
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21
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Kim YR, Hong SH. Associations of MicroRNA Polymorphisms (miR-146a, miR-196a2, and miR-499) with the Risk of Hypertension in the Korean Population. Genet Test Mol Biomarkers 2016; 20:420-6. [PMID: 27379568 DOI: 10.1089/gtmb.2016.0039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AIMS Polymorphisms in microRNA (miR) genes are thought to be associated with various cancers and vascular diseases. To date, however, the effects of the miR gene polymorphisms on susceptibility to hypertension have rarely been investigated. In this study, we investigated the associations of three miR gene polymorphisms (miR-146aC>G/rs2910164, miR-196a2T>C/rs11614913, and miR-499A>G/rs3746444) with the risk of hypertension in Korean patients. METHODS A total of 855 study subjects (340 patients with hypertension and 515 healthy normotensive subjects) were included in this study. Genotyping of the three miR gene polymorphisms was accomplished by polymerase chain reaction-restriction fragment length polymorphism analyses. RESULTS Significant differences were observed in the genotype distributions of the miR-146aC>G polymorphism between the hypertensive patients and controls with the GG genotype, in both model-independent analyses, as well as in dominant (CC vs. CG+GG) and recessive (CC+CG vs. GG) models, being highly significantly associated with disease (AOR = 2.293, 95% CI: 1.466-3.586, p = 0.001; AOR = 1.727, 95% CI: 1.182-2.522, p = 0.015; AOR = 1.782, 95% CI: 1.267-2.506, p = 0.001, respectively). Neither the miR-196a2T>C nor the miR-499A>G polymorphisms were distributed significantly differently between hypertensive patients and control subjects. Several allelic combinations of the three miR polymorphisms were also associated with susceptibility to hypertension. Stratified analysis revealed that the miR-146aC>G and miR-499A>G polymorphisms are associated with a greater risk of hypertension. CONCLUSION This study suggests that the variant of miR-146aC>G polymorphism and allelic combinations, at least in Koreans, affect susceptibility to hypertension.
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Affiliation(s)
- Young Ree Kim
- 1 Department of Laboratory Medicine, School of Medicine, Jeju National University , Jeju, Republic of Korea
| | - Seung-Ho Hong
- 2 Department of Science Education, Teachers College, Jeju National University , Jeju, Republic of Korea
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Genome-wide identification of microRNA-related variants associated with risk of Alzheimer's disease. Sci Rep 2016; 6:28387. [PMID: 27328823 PMCID: PMC4916596 DOI: 10.1038/srep28387] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 06/03/2016] [Indexed: 01/16/2023] Open
Abstract
MicroRNAs (miRNAs) serve as key post-transcriptional regulators of gene expression. Genetic variation in miRNAs and miRNA-binding sites may affect miRNA function and contribute to disease risk. Here, we investigated the extent to which variants within miRNA-related sequences could constitute a part of the functional variants involved in developing Alzheimer’s disease (AD), using the largest available genome-wide association study of AD. First, among 237 variants in miRNAs, we found rs2291418 in the miR-1229 precursor to be significantly associated with AD (p-value = 6.8 × 10−5, OR = 1.2). Our in-silico analysis and in-vitro miRNA expression experiments demonstrated that the variant’s mutant allele enhances the production of miR-1229-3p. Next, we found miR-1229-3p target genes that are associated with AD and might mediate the miRNA function. We demonstrated that miR-1229-3p directly controls the expression of its top AD-associated target gene (SORL1) using luciferase reporter assays. Additionally, we showed that miR-1229-3p and SORL1 are both expressed in the human brain. Second, among 42,855 variants in miRNA-binding sites, we identified 10 variants (in the 3′ UTR of 9 genes) that are significantly associated with AD, including rs6857 that increases the miR-320e-mediated regulation of PVRL2. Collectively, this study shows that miRNA-related variants are associated with AD and suggests miRNA-dependent regulation of several AD genes.
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23
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de Vries PS, Chasman DI, Sabater-Lleal M, Chen MH, Huffman JE, Steri M, Tang W, Teumer A, Marioni RE, Grossmann V, Hottenga JJ, Trompet S, Müller-Nurasyid M, Zhao JH, Brody JA, Kleber ME, Guo X, Wang JJ, Auer PL, Attia JR, Yanek LR, Ahluwalia TS, Lahti J, Venturini C, Tanaka T, Bielak LF, Joshi PK, Rocanin-Arjo A, Kolcic I, Navarro P, Rose LM, Oldmeadow C, Riess H, Mazur J, Basu S, Goel A, Yang Q, Ghanbari M, Willemsen G, Rumley A, Fiorillo E, de Craen AJM, Grotevendt A, Scott R, Taylor KD, Delgado GE, Yao J, Kifley A, Kooperberg C, Qayyum R, Lopez LM, Berentzen TL, Räikkönen K, Mangino M, Bandinelli S, Peyser PA, Wild S, Trégouët DA, Wright AF, Marten J, Zemunik T, Morrison AC, Sennblad B, Tofler G, de Maat MPM, de Geus EJC, Lowe GD, Zoledziewska M, Sattar N, Binder H, Völker U, Waldenberger M, Khaw KT, Mcknight B, Huang J, Jenny NS, Holliday EG, Qi L, Mcevoy MG, Becker DM, Starr JM, Sarin AP, Hysi PG, Hernandez DG, Jhun MA, Campbell H, Hamsten A, Rivadeneira F, Mcardle WL, Slagboom PE, Zeller T, Koenig W, Psaty BM, Haritunians T, Liu J, Palotie A, Uitterlinden AG, Stott DJ, Hofman A, Franco OH, Polasek O, Rudan I, Morange PE, Wilson JF, Kardia SLR, Ferrucci L, Spector TD, Eriksson JG, Hansen T, Deary IJ, Becker LC, Scott RJ, Mitchell P, März W, Wareham NJ, Peters A, Greinacher A, Wild PS, Jukema JW, Boomsma DI, Hayward C, Cucca F, Tracy R, Watkins H, Reiner AP, Folsom AR, Ridker PM, O'Donnell CJ, Smith NL, Strachan DP, Dehghan A. A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration. Hum Mol Genet 2015; 25:358-70. [PMID: 26561523 DOI: 10.1093/hmg/ddv454] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/27/2015] [Indexed: 12/11/2022] Open
Abstract
Genome-wide association studies have previously identified 23 genetic loci associated with circulating fibrinogen concentration. These studies used HapMap imputation and did not examine the X-chromosome. 1000 Genomes imputation provides better coverage of uncommon variants, and includes indels. We conducted a genome-wide association analysis of 34 studies imputed to the 1000 Genomes Project reference panel and including ∼120 000 participants of European ancestry (95 806 participants with data on the X-chromosome). Approximately 10.7 million single-nucleotide polymorphisms and 1.2 million indels were examined. We identified 41 genome-wide significant fibrinogen loci; of which, 18 were newly identified. There were no genome-wide significant signals on the X-chromosome. The lead variants of five significant loci were indels. We further identified six additional independent signals, including three rare variants, at two previously characterized loci: FGB and IRF1. Together the 41 loci explain 3% of the variance in plasma fibrinogen concentration.
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Affiliation(s)
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA, Harvard Medical School, Boston, MA, USA
| | - Maria Sabater-Lleal
- Department of Medicine, Cardiovascular Genetics and Genomics Group, Atherosclerosis Research Unit and
| | - Ming-Huei Chen
- Department of Neurology, Boston University School of Medicine, Boston, MA, USA, Framingham Heart Study, Population Sciences Branch, Division of Intramural Research National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, USA
| | - Jennifer E Huffman
- Framingham Heart Study, Population Sciences Branch, Division of Intramural Research National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, USA, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionaledelle Ricerche, Monserrato, Cagliari, Italy
| | - Weihong Tang
- Division of Epidemiology and Community Health and
| | | | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, Centre for Genomic and Experimental Medicine, Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | | | - Jouke J Hottenga
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands
| | - Stella Trompet
- Department of Cardiology, Department of Gerontology and Geriatrics and
| | - Martina Müller-Nurasyid
- Institute of Genetic Epidemiology, Department of Medicine I, Ludwig-Maximilians-University Munich, Munich, Germany, DZHK (German Centre for Cardiovascular Research) and
| | - Jing Hua Zhao
- MRC Epidemiology Unit, School of Clinical Medicine and
| | | | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences and Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor/UCLA Medical Center, Torrance, CA, USA
| | - Jie Jin Wang
- Department of Ophthalmology, Centre for Vision Research, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - John R Attia
- Public Health Stream and School of Medicine and Public Health and
| | - Lisa R Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tarunveer S Ahluwalia
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences and Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark, The Danish Pediatric Asthma Center, Gentofte Hospital, The Capital Region, Copenhagen, Denmark
| | - Jari Lahti
- Institute of Behavioural Sciences, Folkhälsan Research Centre, Helsinki, Finland
| | - Cristina Venturini
- Institute of Opthalmology, UCL, London, UK, Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Lawrence F Bielak
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Peter K Joshi
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and Informatics, Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics
| | - Ares Rocanin-Arjo
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Paris F-75013, France, Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris F-75013, France, Institute for Cardiometabolism and Nutrition (ICAN), Paris F-75013, France
| | - Ivana Kolcic
- Department of Public Health, Faculty of Medicine
| | - Pau Navarro
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | | | - Johanna Mazur
- Institute of Medical Biostatistics, Epidemiology and Informatics and
| | - Saonli Basu
- Division of Biostatistics, University of Minnesota, Minneapolis, MN, USA
| | - Anuj Goel
- Cardiovascular Medicine Department/Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Qiong Yang
- Framingham Heart Study, Population Sciences Branch, Division of Intramural Research National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, USA, Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Mohsen Ghanbari
- Department of Epidemiology, Department of Genetics, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gonneke Willemsen
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands
| | - Ann Rumley
- Institute of Cardiovascular and Medical Sciences and
| | - Edoardo Fiorillo
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionaledelle Ricerche, Monserrato, Cagliari, Italy
| | | | | | - Robert Scott
- MRC Epidemiology Unit, School of Clinical Medicine and
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences and
| | - Graciela E Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences and
| | - Annette Kifley
- Department of Ophthalmology, Centre for Vision Research, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, Australia
| | | | - Rehan Qayyum
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lorna M Lopez
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychiatry, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, Dublin, Ireland, University College Dublin, UCD Conway Institute, Centre for Proteome Research, UCD, Belfield, Dublin, Ireland
| | - Tina L Berentzen
- Institute of Preventive Medicine, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
| | | | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | | | - Patricia A Peyser
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Sarah Wild
- Centre for Population Health Sciences, Usher Institute of Population Health Sciences and Informatics
| | - David-Alexandre Trégouët
- Institut National pour la Santé et la Recherche Médicale (INSERM), Unité Mixte de Recherche en Santé (UMR_S) 1166, Paris F-75013, France, Sorbonne Universités, Université Pierre et Marie Curie (UPMC Univ Paris 06), UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, Paris F-75013, France, Institute for Cardiometabolism and Nutrition (ICAN), Paris F-75013, France
| | - Alan F Wright
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine
| | - Jonathan Marten
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine
| | | | - Alanna C Morrison
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Bengt Sennblad
- Department of Medicine, Cardiovascular Genetics and Genomics Group, Atherosclerosis Research Unit and Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Geoffrey Tofler
- Royal North Shore Hospital, Sydney University, Sydney, Australia
| | | | - Eco J C de Geus
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands, EMGO+ institute, VU University & VU Medical Center, Amsterdam
| | - Gordon D Lowe
- Institute of Cardiovascular and Medical Sciences and
| | - Magdalena Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionaledelle Ricerche, Monserrato, Cagliari, Italy
| | - Naveed Sattar
- Faculty of Medicine, BHF Glasgow Cardiovascular Research Centre, Glasgow, UK
| | - Harald Binder
- Institute of Medical Biostatistics, Epidemiology and Informatics and
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics and
| | - Melanie Waldenberger
- Institute of Epidemiology II and Research Unit of Molecular Epidemiology, Helmholtz ZentrumMünchen - German Research Center for Environmental Health, Neuherberg, Germany
| | - Kay-Tee Khaw
- Clinical Gerontology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Jie Huang
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | | | - Elizabeth G Holliday
- Public Health Stream, Hunter Medical Research Institute, School of Medicine and Public Health and
| | - Lihong Qi
- Division of Biostatistics, Department of Public Health Sciences, UC Davis, Davis, CA, USA
| | - Mark G Mcevoy
- School of Medicine and Public Health, University of Newcastle, Newcastle, Australia
| | - Diane M Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, Alzheimer Scotland Dementia Research Centre and
| | - Antti-Pekka Sarin
- Institute for Molecular Medicine Finland (FIMM) and Public Health Genomics Unit, National Institute for Health and Welfare, Helsinki, Finland
| | - Pirro G Hysi
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Min A Jhun
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics
| | - Anders Hamsten
- Department of Medicine, Cardiovascular Genetics and Genomics Group, Atherosclerosis Research Unit and
| | - Fernando Rivadeneira
- Department of Epidemiology, Department of Internal Medicine, Erasmus MC, Wytemaweg 80, Rotterdam, The Netherlands
| | - Wendy L Mcardle
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tanja Zeller
- Department of General and Interventional Cardiology, University Heart Centre, University Medical Center Hamburg-Eppendorf, Hamburg, Germany, German Center for Cardiovascular Research (DZHK), Partner Site Hamburg, Lübeck, Kiel, Hamburg, Germany
| | - Wolfgang Koenig
- German Centre for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany, Department of Internal Medicine II - Cardiology, University of Ulm Medical Centre, Ulm, Germany, Deutsches Herzzentrum München, Technische Universität München, Munich, Germany
| | - Bruce M Psaty
- Department of Medicine, Epidemiology, and Health Services and Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | - Talin Haritunians
- Inflammatory Bowel & Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jingmin Liu
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - André G Uitterlinden
- Department of Epidemiology, Department of Internal Medicine, Erasmus MC, Wytemaweg 80, Rotterdam, The Netherlands
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, Faculty of Medicine, University of Glasgow, Glasgow, UK
| | | | | | - Ozren Polasek
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, Department of Public Health, Faculty of Medicine, Centre for Global Health, University of Split, Split, Croatia
| | - Igor Rudan
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics
| | - Pierre-Emmanuel Morange
- Laboratory of Haematology, La Timone Hospital, Marseille F-13385, France, INSERM, UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, Marseille F-13385, France, Aix-Marseille University, UMR_S 1062, Nutrition Obesity and Risk of Thrombosis, Marseille F-13385, France
| | - James F Wilson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics
| | - Sharon L R Kardia
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD, USA
| | - Tim D Spector
- Department of Twin Research and Genetic Epidemiology, Kings College London, London, UK
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki, Helsinki, Finland, Folkhälsan Research Centre, Helsinki, Finland, National Institute for Health and Welfare, Helsinki, Finland, Unit of General Practice, Helsinki University Central Hospital, Helsinki, Finland
| | - Torben Hansen
- Novo Nordisk Foundation Centre for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences and
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Lewis C Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rodney J Scott
- Information based Medicine Program, Hunter Medical Research Institute, New Lambton Heights, Australia, School of Biomedical Sciences and Pharmacy, University of Newcastle, New Lambton Heights, Australia
| | - Paul Mitchell
- Department of Ophthalmology, Centre for Vision Research, Westmead Millennium Institute for Medical Research, University of Sydney, Sydney, Australia
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany, Synlab Academy, Synlab Services LLC, Mannheim, Germany, Clinical Institute of Medical, Chemical Laboratory Diagnostics, Medical University of Graz, Graz, Austria
| | | | - Annette Peters
- Institute of Epidemiology II and DZHK (German Centre for Cardiovascular Research) and
| | - Andreas Greinacher
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Philipp S Wild
- Center for Thrombosis and Hemostasis (CTH), Preventive Cardiology and Preventive Medicine, Department of Medicine 2, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany, German Center for Cardiovascular Research (DZHK), Partner Site RheinMain, Mainz, Germany
| | - J Wouter Jukema
- Department of Cardiology, Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands, Interuniversity Cardiology Institute of The Netherlands, Utrecht, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, VU University, Amsterdam, The Netherlands
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionaledelle Ricerche, Monserrato, Cagliari, Italy
| | - Russell Tracy
- Department of Pathology and Laboratory Medicine, Center for Clinical and Translational Sciences, University of Vermont College of Medicine, Colchester, VT, USA
| | - Hugh Watkins
- Cardiovascular Medicine Department/Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alex P Reiner
- Fred Hutchinson Cancer Research Center, Seattle, WA, USA, University of Washington, Seattle, WA, USA
| | | | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA, USA, Harvard Medical School, Boston, MA, USA
| | - Christopher J O'Donnell
- Framingham Heart Study, Population Sciences Branch, Division of Intramural Research National Heart Lung and Blood Institute, National Institutes of Health, Framingham, MA, USA, National Heart, Lung and Blood Institute, Division of Intramural Research, Cardiology Division, Massachusetts General Hospital, Boston, MA, USA
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle, WA, USA, Institute of Cardiovascular and Medical Sciences, Faculty of Medicine, University of Glasgow, Glasgow, UK, Department of Veterans Affairs, Office of Research and Development, Seattle Epidemiologic Research and Information Center, Seattle, WA, USA and
| | - David P Strachan
- Population Health Research Institute, St George's University of London, London, UK
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Abstract
The Rotterdam Study is a prospective cohort study ongoing since 1990 in the city of Rotterdam in The Netherlands. The study targets cardiovascular, endocrine, hepatic, neurological, ophthalmic, psychiatric, dermatological, otolaryngological, locomotor, and respiratory diseases. As of 2008, 14,926 subjects aged 45 years or over comprise the Rotterdam Study cohort. The findings of the Rotterdam Study have been presented in over 1200 research articles and reports (see www.erasmus-epidemiology.nl/rotterdamstudy ). This article gives the rationale of the study and its design. It also presents a summary of the major findings and an update of the objectives and methods.
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25
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Kruzliak P, Haley AP, Starcevic JN, Gaspar L, Petrovic D. Polymorphisms of the peroxisome proliferator-activated receptor-γ (rs1801282) and its coactivator-1 (rs8192673) are associated with obesity indexes in subjects with type 2 diabetes mellitus. Cardiovasc Diabetol 2015; 14:42. [PMID: 25928419 PMCID: PMC4450508 DOI: 10.1186/s12933-015-0197-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/20/2015] [Indexed: 12/19/2022] Open
Abstract
ᅟ The aim of this study was to clarify whether common single nucleotide polymorphisms (SNPs) of the Peroxisome Proliferator-Activated Receptor-γ (PPAR-γ) gene (rs1801282) and the Peroxisome Proliferator-Activated Receptor-γ Coactivator-1 (PGC-1α) gene (rs8192673) are associated with obesity indexes (BMI, waist circumference) in subjects with type 2 diabetes mellitus (T2DM) in Caucasian population. The second aim was to find an association of both polymorphisms with T2DM. Methods Two exonic SNPs of both genes rs1801282 of the PPAR-γ gene and rs8192673 of the PGC-1α gene) were genotyped in 881 unrelated Slovene subjects (Caucasians) with T2DM and in 348 subjects without T2DM (control subjects). Results Female homozygotes with the CC genotype of the rs8192673 had higher waist circumference in comparison with subjects with other genotypes. Homozygotes (females, males) with wild allele (Pro) of the rs1801282 (Pro12Ala polymorphism) had higher waist circumference in comparison with subjects with other genotypes. In the study, there were no differences in the distributions of the rs8192673 and the rs1801282 genotypes between patients with T2DM and controls. Linear regression analyses for both polymorphisms were performed and demonstrated an independent effect of the rs1801282 of the PPAR-γ on waist circumference in subjects with T2DM, whereas an independent effect on waist circumference was not demonstrated for the rs8192673 of the PGC-1α gene. Conclusions In a large sample of the Caucasians the rs8192673 of the PGC-1α gene and the rs1801282 of the PPAR-γ gene were associated with waist circumference in subjects with T2DM.
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Affiliation(s)
- Peter Kruzliak
- Department of Cardiovascular Diseases, International Clinical Research Center, St Anne's University Hospital and Masaryk University, Brno, Czech Republic.
| | - Andreana P Haley
- Department of Psychology, The University of Texas, Austin, TX, USA. .,University of Texas Imaging Research Center, Austin, TX, USA.
| | | | - Ludovit Gaspar
- 2nd Department of Internal Medicine, University Hospital and Comenius University, Bratislava, Slovak Republic.
| | - Daniel Petrovic
- Institute of Histology and Embryology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
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