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1.
Nature ; 627(8003): 347-357, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38374256

RESUMEN

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes1,2 and molecular mechanisms that are often specific to cell type3,4. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P < 5 × 10-8) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores5 in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.


Asunto(s)
Diabetes Mellitus Tipo 2 , Progresión de la Enfermedad , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Humanos , Adipocitos/metabolismo , Cromatina/genética , Cromatina/metabolismo , Enfermedad de la Arteria Coronaria/complicaciones , Enfermedad de la Arteria Coronaria/genética , Diabetes Mellitus Tipo 2/clasificación , Diabetes Mellitus Tipo 2/complicaciones , Diabetes Mellitus Tipo 2/genética , Diabetes Mellitus Tipo 2/patología , Diabetes Mellitus Tipo 2/fisiopatología , Nefropatías Diabéticas/complicaciones , Nefropatías Diabéticas/genética , Células Endoteliales/metabolismo , Células Enteroendocrinas , Epigenómica , Predisposición Genética a la Enfermedad/genética , Islotes Pancreáticos/metabolismo , Herencia Multifactorial/genética , Enfermedad Arterial Periférica/complicaciones , Enfermedad Arterial Periférica/genética , Análisis de la Célula Individual
2.
medRxiv ; 2023 Mar 31.
Artículo en Inglés | MEDLINE | ID: mdl-37034649

RESUMEN

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes. To characterise the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study (GWAS) data from 2,535,601 individuals (39.7% non-European ancestry), including 428,452 T2D cases. We identify 1,289 independent association signals at genome-wide significance (P<5×10-8) that map to 611 loci, of which 145 loci are previously unreported. We define eight non-overlapping clusters of T2D signals characterised by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial, and enteroendocrine cells. We build cluster-specific partitioned genetic risk scores (GRS) in an additional 137,559 individuals of diverse ancestry, including 10,159 T2D cases, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned GRS are more strongly associated with coronary artery disease and end-stage diabetic nephropathy than an overall T2D GRS across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings demonstrate the value of integrating multi-ancestry GWAS with single-cell epigenomics to disentangle the aetiological heterogeneity driving the development and progression of T2D, which may offer a route to optimise global access to genetically-informed diabetes care.

3.
Nat Genet ; 54(5): 560-572, 2022 05.
Artículo en Inglés | MEDLINE | ID: mdl-35551307

RESUMEN

We assembled an ancestrally diverse collection of genome-wide association studies (GWAS) of type 2 diabetes (T2D) in 180,834 affected individuals and 1,159,055 controls (48.9% non-European descent) through the Diabetes Meta-Analysis of Trans-Ethnic association studies (DIAMANTE) Consortium. Multi-ancestry GWAS meta-analysis identified 237 loci attaining stringent genome-wide significance (P < 5 × 10-9), which were delineated to 338 distinct association signals. Fine-mapping of these signals was enhanced by the increased sample size and expanded population diversity of the multi-ancestry meta-analysis, which localized 54.4% of T2D associations to a single variant with >50% posterior probability. This improved fine-mapping enabled systematic assessment of candidate causal genes and molecular mechanisms through which T2D associations are mediated, laying the foundations for functional investigations. Multi-ancestry genetic risk scores enhanced transferability of T2D prediction across diverse populations. Our study provides a step toward more effective clinical translation of T2D GWAS to improve global health for all, irrespective of genetic background.


Asunto(s)
Diabetes Mellitus Tipo 2 , Estudio de Asociación del Genoma Completo , Diabetes Mellitus Tipo 2/epidemiología , Etnicidad , Predisposición Genética a la Enfermedad , Humanos , Polimorfismo de Nucleótido Simple/genética , Factores de Riesgo
4.
Nutrients ; 11(12)2019 Dec 13.
Artículo en Inglés | MEDLINE | ID: mdl-31847144

RESUMEN

The present study describes the geographically isolated Pomak population and its particular dietary patterns in relationship to cardiovascular risk factors. We collected a population-based cohort in a cross-sectional study, with detailed anthropometric, biochemical, clinical, and lifestyle parameter information. Dietary patterns were derived through principal component analysis based on a validated food-frequency questionnaire, administered to 1702 adult inhabitants of the Pomak villages on the Rhodope mountain range in Greece. A total of 69.9% of the participants were female with a population mean age of 44.9 years; 67% of the population were overweight or obese with a significantly different prevalence for obesity between men and women (17.5% vs. 37.5%, respectively, p < 0.001). Smoking was more prevalent in men (45.8% vs. 2.2%, p < 0.001), as 97.3% of women had never smoked. Four dietary patterns emerged as characteristic of the population, and were termed "high in sugars", "quick choices", "balanced", and "homemade". Higher adherence to the "high in sugars" dietary pattern was associated with increased glucose levels (p < 0.001) and increased risk of hypertension (OR (95% CI) 2.61 (1.55, 4.39), p < 0.001) and nominally associated with high blood glucose levels (OR (95% CI) 1.85 (1.11, 3.08), p = 0.018), compared to lower adherence. Overall, we characterize the dietary patterns of the Pomak population and describe associations with cardiovascular risk factors.


Asunto(s)
Enfermedades Cardiovasculares/epidemiología , Dieta/estadística & datos numéricos , Azúcares de la Dieta/análisis , Etnicidad/estadística & datos numéricos , Sobrepeso/epidemiología , Adulto , Bulgaria/epidemiología , Femenino , Grecia/epidemiología , Humanos , Hipertensión , Islamismo , Estilo de Vida , Masculino , Persona de Mediana Edad , Obesidad/epidemiología , Factores de Riesgo
5.
Nat Commun ; 9(1): 5460, 2018 12 19.
Artículo en Inglés | MEDLINE | ID: mdl-30568165

RESUMEN

The original version of this Article contained an error in Fig. 2. In panel a, the two legend items "rare" and "common" were inadvertently swapped. This has been corrected in both the PDF and HTML versions of the Article.

6.
Nat Commun ; 9(1): 4674, 2018 11 07.
Artículo en Inglés | MEDLINE | ID: mdl-30405126

RESUMEN

The role of rare variants in complex traits remains uncharted. Here, we conduct deep whole genome sequencing of 1457 individuals from an isolated population, and test for rare variant burdens across six cardiometabolic traits. We identify a role for rare regulatory variation, which has hitherto been missed. We find evidence of rare variant burdens that are independent of established common variant signals (ADIPOQ and adiponectin, P = 4.2 × 10-8; APOC3 and triglyceride levels, P = 1.5 × 10-26), and identify replicating evidence for a burden associated with triglyceride levels in FAM189B (P = 2.2 × 10-8), indicating a role for this gene in lipid metabolism.


Asunto(s)
Alelos , Carácter Cuantitativo Heredable , Secuenciación Completa del Genoma , Estudios de Cohortes , Frecuencia de los Genes/genética , Variación Genética , Humanos
7.
BMC Psychiatry ; 18(1): 249, 2018 08 02.
Artículo en Inglés | MEDLINE | ID: mdl-30071838

RESUMEN

BACKGROUND: Schizophrenia (SCZ) is associated with increased risk of type 2 diabetes (T2D). The potential diabetogenic effect of concomitant application of psychotropic treatment classes in patients with SCZ has not yet been evaluated. The overarching goal of the Genetic Overlap between Metabolic and Psychiatric disease (GOMAP) study is to assess the effect of pharmacological, anthropometric, lifestyle and clinical measurements, helping elucidate the mechanisms underlying the aetiology of T2D. METHODS: The GOMAP case-control study (Genetic Overlap between Metabolic and Psychiatric disease) includes hospitalized patients with SCZ, some of whom have T2D. We enrolled 1653 patients with SCZ; 611 with T2D and 1042 patients without T2D. This is the first study of SCZ and T2D comorbidity at this scale in the Greek population. We retrieved detailed information on first- and second-generation antipsychotics (FGA, SGA), antidepressants and mood stabilizers, applied as monotherapy, 2-drug combination, or as 3- or more drug combination. We assessed the effects of psychotropic medication, body mass index, duration of schizophrenia, number of hospitalizations and physical activity on risk of T2D. Using logistic regression, we calculated crude and adjusted odds ratios (OR) to identify associations between demographic factors and the psychiatric medications. RESULTS: Patients with SCZ on a combination of at least three different classes of psychiatric drugs had a higher risk of T2D [OR 1.81 (95% CI 1.22-2.69); p = 0.003] compared to FGA alone therapy, after adjustment for age, BMI, sex, duration of SCZ and number of hospitalizations. We did not find evidence for an association of SGA use or the combination of drugs belonging to two different classes of psychiatric medications with increased risk of T2D [1.27 (0.84-1.93), p = 0.259 and 0.98 (0.71-1.35), p = 0.885, respectively] compared to FGA use. CONCLUSIONS: We find an increased risk of T2D in patients with SCZ who take a combination of at least three different psychotropic medication classes compared to patients whose medication consists only of one or two classes of drugs.


Asunto(s)
Antipsicóticos/administración & dosificación , Índice de Masa Corporal , Diabetes Mellitus Tipo 2/inducido químicamente , Diabetes Mellitus Tipo 2/epidemiología , Esquizofrenia/tratamiento farmacológico , Esquizofrenia/epidemiología , Adulto , Anciano , Antipsicóticos/efectos adversos , Estudios de Casos y Controles , Terapia Combinada , Comorbilidad , Diabetes Mellitus Tipo 2/genética , Femenino , Grecia/epidemiología , Hospitalización/tendencias , Humanos , Masculino , Persona de Mediana Edad , Psicotrópicos/administración & dosificación , Psicotrópicos/efectos adversos , Factores de Riesgo , Esquizofrenia/genética
8.
Diabetes ; 66(11): 2888-2902, 2017 11.
Artículo en Inglés | MEDLINE | ID: mdl-28566273

RESUMEN

To characterize type 2 diabetes (T2D)-associated variation across the allele frequency spectrum, we conducted a meta-analysis of genome-wide association data from 26,676 T2D case and 132,532 control subjects of European ancestry after imputation using the 1000 Genomes multiethnic reference panel. Promising association signals were followed up in additional data sets (of 14,545 or 7,397 T2D case and 38,994 or 71,604 control subjects). We identified 13 novel T2D-associated loci (P < 5 × 10-8), including variants near the GLP2R, GIP, and HLA-DQA1 genes. Our analysis brought the total number of independent T2D associations to 128 distinct signals at 113 loci. Despite substantially increased sample size and more complete coverage of low-frequency variation, all novel associations were driven by common single nucleotide variants. Credible sets of potentially causal variants were generally larger than those based on imputation with earlier reference panels, consistent with resolution of causal signals to common risk haplotypes. Stratification of T2D-associated loci based on T2D-related quantitative trait associations revealed tissue-specific enrichment of regulatory annotations in pancreatic islet enhancers for loci influencing insulin secretion and in adipocytes, monocytes, and hepatocytes for insulin action-associated loci. These findings highlight the predominant role played by common variants of modest effect and the diversity of biological mechanisms influencing T2D pathophysiology.


Asunto(s)
Diabetes Mellitus Tipo 2/genética , Regulación de la Expresión Génica/fisiología , Estudio de Asociación del Genoma Completo , Población Blanca , Variación Genética , Humanos
9.
Nat Commun ; 8: 15606, 2017 05 26.
Artículo en Inglés | MEDLINE | ID: mdl-28548082

RESUMEN

Next-generation association studies can be empowered by sequence-based imputation and by studying founder populations. Here we report ∼9.5 million variants from whole-genome sequencing (WGS) of a Cretan-isolated population, and show enrichment of rare and low-frequency variants with predicted functional consequences. We use a WGS-based imputation approach utilizing 10,422 reference haplotypes to perform genome-wide association analyses and observe 17 genome-wide significant, independent signals, including replicating evidence for association at eight novel low-frequency variant signals. Two novel cardiometabolic associations are at lead variants unique to the founder population sequences: chr16:70790626 (high-density lipoprotein levels beta -1.71 (SE 0.25), P=1.57 × 10-11, effect allele frequency (EAF) 0.006); and rs145556679 (triglycerides levels beta -1.13 (SE 0.17), P=2.53 × 10-11, EAF 0.013). Our findings add empirical support to the contribution of low-frequency variants in complex traits, demonstrate the advantage of including population-specific sequences in imputation panels and exemplify the power gains afforded by population isolates.


Asunto(s)
Frecuencia de los Genes/genética , Genoma Humano/genética , Estudio de Asociación del Genoma Completo/métodos , Población Blanca/genética , Adulto , Anciano , Femenino , Variación Genética , Grecia , Haplotipos , Humanos , Masculino , Persona de Mediana Edad , Fenotipo , Polimorfismo de Nucleótido Simple , Secuenciación Completa del Genoma/métodos
10.
Am J Hum Genet ; 100(6): 865-884, 2017 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-28552196

RESUMEN

Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole-genome sequencing (WGS) and deep imputation approach to examine the broader allelic architecture of 12 anthropometric traits associated with height, body mass, and fat distribution in up to 267,616 individuals. We report 106 genome-wide significant signals that have not been previously identified, including 9 low-frequency variants pointing to functional candidates. Of the 106 signals, 6 are in genomic regions that have not been implicated with related traits before, 28 are independent signals at previously reported regions, and 72 represent previously reported signals for a different anthropometric trait. 71% of signals reside within genes and fine mapping resolves 23 signals to one or two likely causal variants. We confirm genetic overlap between human monogenic and polygenic anthropometric traits and find signal enrichment in cis expression QTLs in relevant tissues. Our results highlight the potential of WGS strategies to enhance biologically relevant discoveries across the frequency spectrum.


Asunto(s)
Antropometría , Genoma Humano , Estudio de Asociación del Genoma Completo , Sitios de Carácter Cuantitativo/genética , Análisis de Secuencia de ADN/métodos , Estatura/genética , Estudios de Cohortes , Metilación de ADN/genética , Bases de Datos Genéticas , Femenino , Variación Genética , Humanos , Lipodistrofia/genética , Masculino , Metaanálisis como Asunto , Obesidad/genética , Mapeo Físico de Cromosoma , Caracteres Sexuales , Síndrome , Reino Unido
11.
Hum Mol Genet ; 25(18): 4094-4106, 2016 09 15.
Artículo en Inglés | MEDLINE | ID: mdl-27466198

RESUMEN

It has been hypothesized that low frequency (1-5% minor allele frequency (MAF)) and rare (<1% MAF) variants with large effect sizes may contribute to the missing heritability in complex traits. Here, we report an association analysis of lipid traits (total cholesterol, LDL-cholesterol, HDL-cholesterol triglycerides) in up to 27 312 individuals with a comprehensive set of low frequency coding variants (ExomeChip), combined with conditional analysis in the known lipid loci. No new locus reached genome-wide significance. However, we found a new lead variant in 26 known lipid association regions of which 16 were >1000-fold more significant than the previous sentinel variant and not in close LD (six had MAF <5%). Furthermore, conditional analysis revealed multiple independent signals (ranging from 1 to 5) in a third of the 98 lipid loci tested, including rare variants. Addition of our novel associations resulted in between 1.5- and 2.5-fold increase in the proportion of heritability explained for the different lipid traits. Our findings suggest that rare coding variants contribute to the genetic architecture of lipid traits.


Asunto(s)
HDL-Colesterol/genética , LDL-Colesterol/genética , Metabolismo de los Lípidos/genética , Lípidos/genética , Adolescente , Adulto , Anciano , Niño , HDL-Colesterol/sangre , LDL-Colesterol/sangre , Exoma/genética , Frecuencia de los Genes , Estudio de Asociación del Genoma Completo , Humanos , Lípidos/sangre , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , Triglicéridos/sangre , Triglicéridos/genética , Población Blanca
12.
Nat Commun ; 5: 5345, 2014 Nov 06.
Artículo en Inglés | MEDLINE | ID: mdl-25373335

RESUMEN

Isolated populations are emerging as a powerful study design in the search for low-frequency and rare variant associations with complex phenotypes. Here we genotype 2,296 samples from two isolated Greek populations, the Pomak villages (HELIC-Pomak) in the North of Greece and the Mylopotamos villages (HELIC-MANOLIS) in Crete. We compare their genomic characteristics to the general Greek population and establish them as genetic isolates. In the MANOLIS cohort, we observe an enrichment of missense variants among the variants that have drifted up in frequency by more than fivefold. In the Pomak cohort, we find novel associations at variants on chr11p15.4 showing large allele frequency increases (from 0.2% in the general Greek population to 4.6% in the isolate) with haematological traits, for example, with mean corpuscular volume (rs7116019, P=2.3 × 10(-26)). We replicate this association in a second set of Pomak samples (combined P=2.0 × 10(-36)). We demonstrate significant power gains in detecting medical trait associations.


Asunto(s)
Flujo Genético , Variación Genética/genética , Genética de Población , Genotipo , Mutación Missense/genética , Población/genética , Adolescente , Células Sanguíneas/citología , Tamaño de la Célula , Estudios de Cohortes , Frecuencia de los Genes/genética , Estudio de Asociación del Genoma Completo , Grecia , Haplotipos/genética , Humanos , Fenotipo , Aislamiento Social
13.
PLoS One ; 9(1): e87335, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24498077

RESUMEN

INTRODUCTION: Polycystic Ovary Syndrome (PCOS) has a strong genetic background and the majority of patients with PCOS have elevated BMI levels. The aim of this study was to determine to which extent BMI-increasing alleles contribute to risk of PCOS when contemporaneous BMI is taken into consideration. METHODS: Patients with PCOS and controls were recruited from the United Kingdom (563 cases and 791 controls) and The Netherlands (510 cases and 2720 controls). Cases and controls were of similar BMI. SNPs mapping to 12 BMI-associated loci which have been extensively replicated across different ethnicities, i.e., BDNF, FAIM2, ETV5, FTO, GNPDA2, KCTD15, MC4R, MTCH2, NEGR1, SEC16B, SH2B1, and TMEM18, were studied in association with PCOS within each cohort using the additive genetic model followed by a combined analysis. A genetic allelic count risk score model was used to determine the risk of PCOS for individuals carrying increasing numbers of BMI-increasing alleles. RESULTS: None of the genetic variants, including FTO and MC4R, was associated with PCOS independently of BMI in the meta-analysis. Moreover, no differences were observed between cases and controls in the number of BMI-risk alleles present and no overall trend across the risk score groups was observed. CONCLUSION: In this combined analysis of over 4,000 BMI-matched individuals from the United Kingdom and the Netherlands, we observed no association of BMI risk alleles with PCOS independent of BMI.


Asunto(s)
Índice de Masa Corporal , Predisposición Genética a la Enfermedad/genética , Síndrome del Ovario Poliquístico/genética , Polimorfismo de Nucleótido Simple , Alelos , Peso Corporal/genética , Estudios de Casos y Controles , Femenino , Frecuencia de los Genes , Genotipo , Humanos , Países Bajos , Obesidad/genética , Sobrepeso/genética , Medición de Riesgo/métodos , Medición de Riesgo/estadística & datos numéricos , Factores de Riesgo , Reino Unido
14.
Nat Commun ; 4: 2872, 2013.
Artículo en Inglés | MEDLINE | ID: mdl-24343240

RESUMEN

Isolated populations can empower the identification of rare variation associated with complex traits through next generation association studies, but the generalizability of such findings remains unknown. Here we genotype 1,267 individuals from a Greek population isolate on the Illumina HumanExome Beadchip, in search of functional coding variants associated with lipids traits. We find genome-wide significant evidence for association between R19X, a functional variant in APOC3, with increased high-density lipoprotein and decreased triglycerides levels. Approximately 3.8% of individuals are heterozygous for this cardioprotective variant, which was previously thought to be private to the Amish founder population. R19X is rare (<0.05% frequency) in outbred European populations. The increased frequency of R19X enables discovery of this lipid traits signal at genome-wide significance in a small sample size. This work exemplifies the value of isolated populations in successfully detecting transferable rare variant associations of high medical relevance.


Asunto(s)
Apolipoproteína C-III/genética , Enfermedades Cardiovasculares/genética , Enfermedades Cardiovasculares/prevención & control , Variación Genética , Población Blanca/genética , Adulto , Anciano , Anciano de 80 o más Años , Apolipoproteína C-III/metabolismo , Enfermedades Cardiovasculares/metabolismo , Femenino , Frecuencia de los Genes , Estudio de Asociación del Genoma Completo , Grecia , Haplotipos , Humanos , Lipoproteínas HDL/metabolismo , Masculino , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , Triglicéridos/metabolismo
15.
J Lipid Res ; 54(11): 3170-6, 2013 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-24023261

RESUMEN

Although numerous genes are known to regulate serum lipid traits, identified variants explain only a small proportion of the expected heritability. We intended to identify further genetic variants associated with lipid phenotypes in a self-contained population of Sorbs in Germany. We performed a genome-wide association study (GWAS) on LDL-cholesterol, HDL-cholesterol (HDL-C), and triglyceride (TG) levels in 839 Sorbs. All single-nucleotide polymorphisms with a P value <0.01 were subjected to a meta-analysis, including an independent Swedish cohort (Diabetes Genetics Initiative; n = ∼3,100). Novel association signals with the strongest effects were subjected to replication studies in an additional German cohort (Berlin, n = 2,031). In the initial GWAS in the Sorbs, we identified 14 loci associated with lipid phenotypes reaching P values <10⁻5 and confirmed significant effects for 18 previously reported loci. The combined meta-analysis of the three study cohorts (n(HDL) = 6041; n(LDL) = 5,995; n(TG) = 6,087) revealed a novel association for a variant in THOC5 (rs8135828) with serum HDL-C levels (P = 1.78 × 10⁻7; Z-score = -5.221). Consistently, the variant was also associated with circulating APOA1 levels in Sorbs. The small interfering RNA-mediated mRNA silencing of THOC5 in HepG2 cells resulted in lower mRNA levels of APOA1, SCARB1, and ABCG8 (all P < 0.05). We propose THOC5 to be a novel gene involved in the regulation of serum HDL-C levels.


Asunto(s)
HDL-Colesterol/metabolismo , Proteínas Nucleares/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Estudios de Cohortes , Femenino , Estudio de Asociación del Genoma Completo , Alemania/etnología , Células Hep G2 , Humanos , Masculino , Metaanálisis como Asunto , Persona de Mediana Edad , Polimorfismo de Nucleótido Simple , ARN Mensajero/genética , ARN Mensajero/metabolismo , Adulto Joven
16.
Ann Rheum Dis ; 72(1): 136-9, 2013 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-22984172

RESUMEN

OBJECTIVES: Osteoarthritis (OA) has a complex aetiology with a strong genetic component. Genome-wide association studies implicate several nuclear genes in the aetiology, but a major component of the heritability has yet to be defined at the molecular level. Initial studies implicate maternally inherited variants of mitochondrial DNA (mtDNA) in subgroups of patients with OA based on gender and specific joint involvement, but these findings have not been replicated. METHODS: The authors studied 138 maternally inherited mtDNA variants genotyped in a two cohort genetic association study across a total of 7393 OA cases from the arcOGEN consortium and 5122 controls genotyped in the Wellcome Trust Case Control consortium 2 study. RESULTS: Following data quality control we examined 48 mtDNA variants that were common in cohort 1 and cohort 2, and found no association with OA. None of the phenotypic subgroups previously associated with mtDNA haplogroups were associated in this study. CONCLUSIONS: We were not able to replicate previously published findings in the largest mtDNA association study to date. The evidence linking OA to mtDNA is not compelling at present.


Asunto(s)
ADN Mitocondrial/genética , Osteoartritis/genética , Femenino , Predisposición Genética a la Enfermedad , Variación Genética , Estudio de Asociación del Genoma Completo , Genotipo , Haplotipos , Humanos , Masculino , Análisis de Componente Principal
17.
Lancet ; 380(9844): 815-23, 2012 Sep 01.
Artículo en Inglés | MEDLINE | ID: mdl-22763110

RESUMEN

BACKGROUND: Osteoarthritis is the most common form of arthritis worldwide and is a major cause of pain and disability in elderly people. The health economic burden of osteoarthritis is increasing commensurate with obesity prevalence and longevity. Osteoarthritis has a strong genetic component but the success of previous genetic studies has been restricted due to insufficient sample sizes and phenotype heterogeneity. METHODS: We undertook a large genome-wide association study (GWAS) in 7410 unrelated and retrospectively and prospectively selected patients with severe osteoarthritis in the arcOGEN study, 80% of whom had undergone total joint replacement, and 11,009 unrelated controls from the UK. We replicated the most promising signals in an independent set of up to 7473 cases and 42,938 controls, from studies in Iceland, Estonia, the Netherlands, and the UK. All patients and controls were of European descent. FINDINGS: We identified five genome-wide significant loci (binomial test p≤5·0×10(-8)) for association with osteoarthritis and three loci just below this threshold. The strongest association was on chromosome 3 with rs6976 (odds ratio 1·12 [95% CI 1·08-1·16]; p=7·24×10(-11)), which is in perfect linkage disequilibrium with rs11177. This SNP encodes a missense polymorphism within the nucleostemin-encoding gene GNL3. Levels of nucleostemin were raised in chondrocytes from patients with osteoarthritis in functional studies. Other significant loci were on chromosome 9 close to ASTN2, chromosome 6 between FILIP1 and SENP6, chromosome 12 close to KLHDC5 and PTHLH, and in another region of chromosome 12 close to CHST11. One of the signals close to genome-wide significance was within the FTO gene, which is involved in regulation of bodyweight-a strong risk factor for osteoarthritis. All risk variants were common in frequency and exerted small effects. INTERPRETATION: Our findings provide insight into the genetics of arthritis and identify new pathways that might be amenable to future therapeutic intervention. FUNDING: arcOGEN was funded by a special purpose grant from Arthritis Research UK.


Asunto(s)
Osteoartritis/genética , Artroplastia de Reemplazo , Estudios de Casos y Controles , Femenino , Predisposición Genética a la Enfermedad , Estudio de Asociación del Genoma Completo , Humanos , Desequilibrio de Ligamiento , Masculino , Osteoartritis/cirugía , Osteoartritis de la Cadera/genética , Osteoartritis de la Cadera/cirugía , Osteoartritis de la Rodilla/genética , Osteoartritis de la Rodilla/cirugía , Polimorfismo de Nucleótido Simple
18.
PLoS Genet ; 8(2): e1002505, 2012.
Artículo en Inglés | MEDLINE | ID: mdl-22383892

RESUMEN

Metabolic Syndrome (MetS) is highly prevalent and has considerable public health impact, but its underlying genetic factors remain elusive. To identify gene networks involved in MetS, we conducted whole-genome expression and genotype profiling on abdominal (ABD) and gluteal (GLU) adipose tissue, and whole blood (WB), from 29 MetS cases and 44 controls. Co-expression network analysis for each tissue independently identified nine, six, and zero MetS-associated modules of coexpressed genes in ABD, GLU, and WB, respectively. Of 8,992 probesets expressed in ABD or GLU, 685 (7.6%) were expressed in ABD and 51 (0.6%) in GLU only. Differential eigengene network analysis of 8,256 shared probesets detected 22 shared modules with high preservation across adipose depots (D(ABD-GLU) = 0.89), seven of which were associated with MetS (FDR P<0.01). The strongest associated module, significantly enriched for immune response-related processes, contained 94/620 (15%) genes with inter-depot differences. In an independent cohort of 145/141 twins with ABD and WB longitudinal expression data, median variability in ABD due to familiality was greater for MetS-associated versus un-associated modules (ABD: 0.48 versus 0.18, P = 0.08; GLU: 0.54 versus 0.20, P = 7.8×10(-4)). Cis-eQTL analysis of probesets associated with MetS (FDR P<0.01) and/or inter-depot differences (FDR P<0.01) provided evidence for 32 eQTLs. Corresponding eSNPs were tested for association with MetS-related phenotypes in two GWAS of >100,000 individuals; rs10282458, affecting expression of RARRES2 (encoding chemerin), was associated with body mass index (BMI) (P = 6.0×10(-4)); and rs2395185, affecting inter-depot differences of HLA-DRB1 expression, was associated with high-density lipoprotein (P = 8.7×10(-4)) and BMI-adjusted waist-to-hip ratio (P = 2.4×10(-4)). Since many genes and their interactions influence complex traits such as MetS, integrated analysis of genotypes and coexpression networks across multiple tissues relevant to clinical traits is an efficient strategy to identify novel associations.


Asunto(s)
Tejido Adiposo/metabolismo , Perfilación de la Expresión Génica , Redes Reguladoras de Genes , Síndrome Metabólico/genética , Índice de Masa Corporal , Quimiocinas/genética , Femenino , Sitios Genéticos , Estudio de Asociación del Genoma Completo , Cadenas HLA-DRB1/genética , Humanos , Péptidos y Proteínas de Señalización Intercelular , Síndrome Metabólico/patología , Especificidad de Órganos , Fenotipo , Sitios de Carácter Cuantitativo
19.
PLoS One ; 6(11): e27338, 2011.
Artículo en Inglés | MEDLINE | ID: mdl-22102887

RESUMEN

To understand how miRNAs contribute to the molecular phenotype of adipose tissues and related traits, we performed global miRNA expression profiling in subcutaneous abdominal and gluteal adipose tissue of 70 human subjects and characterised which miRNAs were differentially expressed between these tissues. We found that 12% of the miRNAs were significantly differentially expressed between abdominal and gluteal adipose tissue (FDR adjusted p<0.05) in the primary study, of which 59 replicated in a follow-up study of 40 additional subjects. Further, 14 miRNAs were found to be associated with metabolic syndrome case-control status in abdominal tissue and three of these replicated (primary study: FDR adjusted p<0.05, replication: p<0.05 and directionally consistent effect). Genome-wide genotyping was performed in the 70 subjects to enable miRNA expression quantitative trait loci (eQTL) analysis. Candidate miRNA eQTLs were followed-up in the additional 40 subjects and six significant, independent cis-located miRNA eQTLs (primary study: p<0.001; replication: p<0.05 and directionally consistent effect) were identified. Finally, global mRNA expression profiling was performed in both tissues to enable association analysis between miRNA and target mRNA expression levels. We find 22% miRNAs in abdominal and 9% miRNAs in gluteal adipose tissue with expression levels significantly associated with the expression of corresponding target mRNAs (FDR adjusted p<0.05). Taken together, our results indicate a clear difference in the miRNA molecular phenotypic profile of abdominal and gluteal adipose tissue, that the expressions of some miRNAs are influenced by cis-located genetic variants and that miRNAs are associated with expression levels of their predicted mRNA targets.


Asunto(s)
Grasa Abdominal/fisiología , Biomarcadores/metabolismo , Nalgas/fisiología , MicroARNs/genética , Sitios de Carácter Cuantitativo , ARN Mensajero/genética , Adulto , Estudios de Casos y Controles , Femenino , Estudios de Seguimiento , Perfilación de la Expresión Génica , Estudio de Asociación del Genoma Completo , Genotipo , Humanos , Masculino , Síndrome Metabólico/genética , Análisis de Secuencia por Matrices de Oligonucleótidos , Polimorfismo de Nucleótido Simple/genética
20.
Am J Hum Genet ; 89(3): 446-50, 2011 Sep 09.
Artículo en Inglés | MEDLINE | ID: mdl-21871595

RESUMEN

Osteoarthritis (OA) is a prevalent, heritable degenerative joint disease with a substantial public health impact. We used a 1000-Genomes-Project-based imputation in a genome-wide association scan for osteoarthritis (3177 OA cases and 4894 controls) to detect a previously unidentified risk locus. We discovered a small disease-associated set of variants on chromosome 13. Through large-scale replication, we establish a robust association with SNPs in MCF2L (rs11842874, combined odds ratio [95% confidence interval] 1.17 [1.11-1.23], p = 2.1 × 10(-8)) across a total of 19,041 OA cases and 24,504 controls of European descent. This risk locus represents the third established signal for OA overall. MCF2L regulates a nerve growth factor (NGF), and treatment with a humanized monoclonal antibody against NGF is associated with reduction in pain and improvement in function for knee OA patients.


Asunto(s)
Cromosomas Humanos Par 13/genética , Predisposición Genética a la Enfermedad/genética , Factores de Intercambio de Guanina Nucleótido/genética , Osteoartritis/genética , Anticuerpos Monoclonales/uso terapéutico , Estudio de Asociación del Genoma Completo , Factores de Intercambio de Guanina Nucleótido/metabolismo , Humanos , Factor de Crecimiento Nervioso/inmunología , Factor de Crecimiento Nervioso/metabolismo , Oportunidad Relativa , Osteoartritis/inmunología , Polimorfismo de Nucleótido Simple/genética , Factores de Intercambio de Guanina Nucleótido Rho , Población Blanca/genética
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