Investigation génétique de NAFLD dans le diabète de type 2 via construction d’un modèle de prédiction de la maladie et par criblage du locus PNPLA3-SAMM50

La stéatose hépatique non-alcoolique (NAFLD) est une altération hépatique fréquente dans le diabète de type 2 (DT2) et est associée à diverses complications telles que la mortalité. L’établissement d’outils de prédiction non-invasifs de NAFLD est primordial. Mon projet de maîtrise avait pour objectif d’établir des marqueurs génétiques de NAFLD dans le DT2 via deux stratégies : 1) une sélection non-ciblée des marqueurs génétiques (SNPs) via la méthode LASSO et 2) une sélection ciblée de SNPs rapportés comme liés à la maladie ou à des altérations associées. Une population de 4098 patients avec DT2 d’origine caucasienne (ADVANCE) a été utilisée. Des données statistiques sommaires d’études pangénomiques ont été exploitées pour sélectionner, via LASSO, les marqueurs génétiques (SNPs) à inclure dans le score de risque polygénique (PRS). J’ai également développé un modèle de 3210 SNPs ajusté par des covariables capable de prédire les taux élevés de ALT (AUC=0,69) et la mortalité non-cardiovasculaire (AUC=0,66). Le criblage du locus candidat PNPLA3-SAMM50 a mis en avant une diversité des associations génétiques aux différentes altérations métaboliques comme les taux de ALT (substitut du diagnostic de NAFLD) (rs2294915, P = 1,83x10-7), à la mortalité non-cardiovasculaire (rs2294917, P = 3,9x10-4) et à l’efficacité de la thérapie intensive antidiabétique chez certains patients de la population (porteurs GG de rs16991236, P=0,007). Mes travaux ont permis de mieux comprendre le fond génétique de NAFLD dans le DT2 et laissent envisager l’établissement d’outils de diagnostic et de suivi de la maladie plus adéquats.Non-alcoholic fatty liver disease (NAFLD) is a liver disorder more frequent in type 2 diabetes (T2D) and is associated with complications such as mortality. For this reason, establishing non-invasive tools for predicting NAFLD is crucial. My master’s project aimed to establish genetic markers for NAFLD in T2D using two strategies: 1) a non-targeted selection of genetic markers (SNPs) by the LASSO method and 2) a targeted selection of SNPs reported as associated with the disease or its related abnormalities. A population involving 4098 patients with T2D and Caucasian ancestry was used. Summary statistics data of pangenomic studies were exploited for the selection of SNPs to be involved in the polygenic risk score (PRS). I also designed a model of 3210 SNPs adjusted by covariates and able to predict the high rates of ALT (AUC=0.69) and non-cardiovascular death (AUC=0.66). Mapping of the candidate locus PNPLA3-SAMM50 allowed the observation of diversity in terms of genetic association with the metabolic abnormalities such as ALT (surrogate of NAFLD) (rs2294915, P = 1.83x10-7), non-cardiovascular death (rs2294917, P = 3.9x10-4) and the efficiency of the intensive antidiabetic therapy within a subgroup in the population (individuals with GG of rs16991236, P = 0.007). My studies allowed for a better understanding of the genetic background of NAFLD in T2D and open perspectives for establishing more adequate tools for diagnosis and follow-up of the disease

Gęste mapowanie regionu VNTR genu insuliny w zespole policystycznych jajników w populacji kobiet z Europy Środkowej

Introduction: Insulin gene VNTR was associated with polycystic ovary syndrome (PCOS) in some studies but not in others. This couldb be due to the heterogeneity of the definition of PCOS and/or the use of inappropriate gene mapping strategies.Material and methods: In this investigation, the association of VNTR with PCOS was explored in a population of women from Central Europe (377 cases and 105 controls) in whom PCOS was diagnosed according to Rotterdam criteria. Seven SNPs: rs3842756 (G/A), rs3842755 (G/T), rs3842754 (C/T), rs3842753 (A/C), rs3842752 (C/T), rs3842748 (G/C), and rs689 (T/A) were genotyped in a portion of the population (160 cases and 95 controls) by sequencing or by SSO-PCR. Analysis of linkage disequilibrium (LD) pattern allowed selecting three tagSNPs (rs3842754, rs3842748, and rs689), which were genotyped in the rest of the population by KASPar.Results: Six haplotypes were reconstructed, among which three (h1, h2 and h6) were more frequent. Statistical analysis allowed observation of the association of the SNP rs3842748, through its GC genotype, with obesity in PCOS (P = 0.049; OR CI95% 1,59 [1.00–2.51]) and in classical PCOS (YPCOS) (P = 0.010), as well as the correlation of the SNP rs689 and the pair of haplotypes h1/h1 with higher levels of testosteronaemia in the PCOS group, although this was at the limit of significance (P = 0.054)Conclusion: These results are in accordance with some studies in literature and highlight the role of insulin gene VNTR in complex metabolic disorders. (Endokrynol Pol 2015; 66 (3): 198–206)Wstęp: W niektórych badaniach, zmienna liczba powtórzeń tandemowych (VNTR) genu insuliny była związana z zespołem policystycznych jajników (PCOS), lecz w innych taki związek nie występował. Mogło tak być z powodu heterogeniczności definicji PCOS i/lub stosowania nieprawidłowych strategii mapowania genów.Materiał i metody: W niniejszym badaniu, związek VNTR z PCOS zbadano w populacji kobiet pochodzących z Europy Środkowej (377 przypadków chorobowych oraz 105 osób kontrolnych), u których zdiagnozowano PCOS według kryteriów rotterdamskich. Siedem polimorfizmów pojedynczego nukleotydu (SNP): rs3842756 (G/A), rs3842755 (G/T), rs3842754 (C/T), rs3842753 (A/C), rs3842752 (C/T), rs3842748 (G/C), oraz rs689 (T/A) wytypowano w części populacji (160 przypadków chorobowych i 95 osób kontrolnych) poprzez sekwencjonowanie lub SSO-PCR. Analiza wzoru niezrównoważenia sprzężeń (LD) pozwoliła na selekcję trzech SNP znacznikowych (tagSNP) (rs3842754, rs3842748 i rs689), które wyselekcjonowano w pozostałej części populacji metodą KASPar.Wyniki: Sześć haplotypów odtworzono, z których 3 (h1, h2 i h6) występowały częściej. Analiza statystyczna pozwoliła na obserwację związku SNP rs3842748, poprzez genotyp GC, z otyłością w PCOS (P = 0,049; OR CI 95% 1,59 [1,00–2,51]) i klasycznym PCOS (YPCOS) (P = 0,010), jak również korelacji SNP rs689 i pary haplotypów h1/h1 z wyższym stężeniem testosteronemii w grupie PCOS, chociaż wynik ten znajdował się na granicy istotności (P = 0,054).Wnioski: Powyższe wyniki są zgodne z niektórymi badaniami w piśmiennictwie i podkreślają role VNTR genu insuliny w złożonych zaburzeniach metabolicznych. (Endokrynol Pol 2015; 66 (3): 198–206

Diversity of Y-chromosomal and mtDNA Markers Included in Mediscope Chip within Two Albanian Subpopulations from Croatia and Kosovo: Preliminary Data

The aim of this preliminary study is to analyze genetic specificity of Kosovo Albanians comparing with neighboring populations using new genetic tool - MEDISCOPE gene chip, to investigate the feasibility of this approach. We collected 37 DNA samples (9 Croats, 17 Albanians from Croatia and 11 Albanians from Kosovo) from unrelated males born in Croatia and Kosovo. Additionally, samples were expanded with female individuals and mtDNA analysis included a total of 61 samples (15 Croats, 23 Albanians from Croatia and 23 Albanians from Kosovo). This pilot study suggests that the usage of the MEDISCOPE chip could be recognized as an efficient tool within recognition of the population genetic specificity even within extremely small sample size

Déterminisme génétique de la résistance à l'insuline dans les maladies complexes (application des stratégies de criblage dense du génome basées sur les profils de déséquilibre de liaison dans la génétique du syndrome des ovaires polykystiques)

MONTPELLIER-BU Médecine UPM (341722108) / SudocMONTPELLIER-BU Médecine (341722104) / SudocSudocFranceF

Association of rs9939609 Polymorphism with Metabolic Parameters and FTO Risk Haplotype Among Tunisian Metabolic Syndrome

International audienceBackground: Variants in the fat mass and obesity-associated (FTO) gene are associated with obesity and type 2 diabetes mellitus.Aim of the study: This study aims to assess the association of the rs9939609 variant and haplotypes in FTO gene with metabolic syndrome (MetS) components in a Tunisian population sample.Methods: A total of 685 Tunisian subjects were genotyped for the rs9939609T>A using TaqMan allelic discrimination assay. Two variants rs1421085T>C and rs8057044A>G already genotyped in a previous study were used to test haplotype association of the FTO gene.Results: Genotype distribution of the variant rs9939609 was different between MetS and controls (P = 0.017). Individuals carrying TA genotypes had a significantly increased risk independently of body mass index or age (P = 0.009). The variant rs9939609 was also associated with impaired fasting glucose (IFG) (P = 0.002). Among the eight haplotypes in the population, the haplotype GCA was significantly associated with a higher risk of developing the MetS, higher systolic blood pressure, and higher levels of fasting glucose and triglycerides (TGs) in the total sample and females, separately. Separate analysis by gender revealed a protective haplotype TGT among women (P = 0.023).Conclusions:FTO haplotypes have a strong influence on blood pressures and TG and IFG levels. These findings provide evidence that FTO gene may play a critical role in leading to MetS in Tunisian population