Identification of novel loci affecting human disorders of iron homeostasis and their effect on lipid metabolism

2013/2014Il ferro è un elemento fondamentale per molti processi di cellule e tessuti ma è potenzialmente tossico e un eccesso può danneggiare diversi componenti cellulari. A livello fisiologico il ferro circolante è regolato da segnali da pathway che lo consumano e da cellule che lo forniscono. Il principale ormone regolatore epcidina agisce insieme al recettore cellulare ferroportina nel controllare l’assorbimento con la dieta, l’immagazzinamento e la distribuzione del ferro nel flusso sanguigno. Disturbi genetici che colpiscono i componenti del pathway così altamente regolato possono causare serie malattie nell’uomo come l’emocromatosi ereditaria e l’anemia sideropenia refrattaria al ferro (IRIDA) principalmente causate da mutazioni note nei geni HFE e TMPRSS6. Gli studi descritti in questa tesi hanno lo scopo di evidenziare varianti nuove e causative che hanno un ruolo nella regolazione del pathway di ecpidina-ferroportina per spiegare l’effetto delle variazioni di ferro e le basi molecolari dell’insorgenza dei disturbi genetici del ferro nell’uomo. Studi di associazione sull’intero genoma (GWAS) sono stati condotti sui valori quantitativi di epcidina, parametri del ferro e tratti eritroidi misurati nell’ampia popolazione della Val Borbera che include 1785 individui genotipizzati da un isolato genetico italiano. Il principale risultato mostra che l’associazione di HFE e TMPRRS6 ai tratti eritroidi dipendono in maggior parte dal totale di ferro disponibile e non da un effetto diretto di HFE e TMPRSS6. I livelli di epcidina sono stati associati alle variazioni in HFE e TMPRSS6 e una prima ampia meta-analisi condotta su circa 6,000 individui VBI e olandesi ha evidenziato 2 nuovi loci associati significativamente (p<5x10-8) all’epcidina: il primo sul cromosoma 10 vicino al gene FOXI2 e il secondo sul cromosoma 2 nel gene EML6 e vicino a SPTBN1 (alias ELF). SPTBN1 è un gene interessante in quanto essenziale nel signaling TGF-β mediante le proteine SMAD, una delle quali svolge un ruolo anche nella regolazione della trascrizione dell’epcidina. Per identificare ulteriori loci che hanno un ruolo nell’omeostasi del ferro è stata condotta un’ampia meta-analisi sui marcatori clinici dello stato del ferro su 48,000 individui di origine europea in collaborazione con il consorzio australiano per lo studio genetico del ferro (GIS): lo studio mostra associazioni più significative ed effetto pleiotropico dei geni noti del ferro HFE, TF, TFR2 and TMPRSS6 e cinque nuovi geni associati a livello Bonferroni (ABO, ARNTL, FADS2, NAT2, TEX14). In particolare la trasferrina è associata a NAT2 precedentemente associato a disturbi dei lipidi e a rischio cardiovascolare e FADS2 le cui variazioni hanno un effetto su diversi fenotipi come gli acidi grassi, il glucosio nel sangue e gli enzimi del fegato. I risultati mostrano una forte correlazione tra omeostasi del ferro e metabolismo dei lipidi nell’uomo e quindi il ferro potrebbe avere un ruolo nell’insorgenza dei disturbi cardiovascolari. I risultati confermano che l’isolato della Val Borbera ha costituito un modello della popolazione generale adatto a studi genetici su malattie comuni. Per aumentare la possiblità di trovare varianti rare e causative sfruttando i vantaggi e le caratteristiche delle popolazioni isolate, la coorte della Val Borbera e gli altri isolati genetici italiani si sono riuniti in un progetto che utilizza le tecniche innovative di sequenziamento dell’intero genoma allo scopo di creare un pannello di riferimento ricco di sequenze italiane rare e di altà qualità per ulteriori studi genetici sul ferro, epcidina e altri tratti di rischio.Iron is a key element for cellular and tissue processes. It is also potentially toxic and excess iron can damage various cellular components. At physiological levels circulating iron is regulated by signals from pathways that use iron and from cells that supply iron. The main iron-regulatory hormone hepcidin and its receptor iron channel ferroportin play a critical role controlling the dietary absorption, storage, and tissue distribution of iron through the bloodstream. Genetic disorders that affect the components of the tightly regulated hepcidin-ferroportin pathway could cause severe pathologies in humans as hereditary hemocromatosis and iron-refractory iron-deficiency anemia or IRIDA mainly caused respectively by mutation in two known loci, HFE and TMPRSS6. The studies described in this thesis aimed at highlighting novel and causative variants in loci that have a role in the regulation of hepcidin-iron pathway to explain the effect of unbalanced iron in humans and the molecular basis of the onset of genetic iron disorders. First, genome-wide association studies (GWAS) have been carried out on quantitative hepcidin, iron parameters and erythrocyte traits measured in the population of Val Borbera (VBI) that includes 1785 genotyped individuals from an Italian genetic isolate. The main result showed that association of HFE and TMPRSS6 to erythroid traits is mostly dependent on the amount of iron available and not a direct effect of HFE and TMPRSS6 variants. Hepcidin levels have been associated to HFE and TMPRSS6 variations and a first large meta-analysis, performed on 6,000 VBI and Dutch individuals, revealed two novel loci associated to hepcidin at genome-wide significance (p<5x10-8): the first on chromosome 10, near the gene FOXI2 and the second signal on chromosome 2 in the EML6 gene and near SPTBN1 (alias ELF). SPTBN1 is an interesting gene as it is essential in TGF-β signaling by SMAD proteins and one of the SMADs is involved in hepcidin transcription regulation. To identify additional loci affecting iron homeostasis, a large international meta-analysis on the serum biomarkers commonly used to determine the clinical iron status has been carried out in 48,000 European ancestry individuals in collaboration with Australian Genetic Iron Status (GIS) Consortium: the study showed more significant associations and pleiotropic effect for known loci as HFE, TF, TFR2 and TMPRSS6 and five novel associated loci at significant levels (ABO, ARNTL, FADS2, NAT2, TEX14). In particular, transferrin is associated to NAT2, previously associated to lipids affections and cardiovascular risk, and to FADS2 that affects several phenotypes as lipids fatty acids, fasting glucose and liver enzyme. The results highlighted a strong correlation between iron homeostasis and lipid metabolism in humans that could have implication on the onset of cardiovascular disorders. The Val Borbera genetic isolate has represented a suitable model for genetic study on common disease. To increase the power of detection of rare and causative variants and to take advantage of the characteristics of genetic isolates, VBI and other Italian isolated populations are now involved in an innovative whole-genome sequencing (WGS) project with the aim to create an Italian specific panel enriched in lower-frequency high-quality variants to be used in further genetic analysis on iron parameters, hepcidin and other traits.XXVII Ciclo198

Prenatal Serum Concentrations of Brominated Flame Retardants and Autism Spectrum Disorder and Intellectual Disability in the Early Markers of Autism Study: A Population-Based Case-Control Study in California.

BackgroundPrior studies suggest neurodevelopmental impacts of polybrominated diphenyl ethers (PBDEs), but few have examined diagnosed developmental disorders.ObjectivesOur aim was to determine whether prenatal exposure to brominated flame retardants (BFRs) is associated with autism spectrum disorder (ASD) or intellectual disability without autism (ID).MethodsWe conducted a population-based case-control study including children with ASD (n=545) and ID (n=181) identified from the California Department of Developmental Services and general population (GP) controls (n=418) from state birth certificates. ASD cases were matched to controls by sex, birth month, and birth year. Concentrations of 10 BFRs were measured in maternal second trimester serum samples stored from routine screening. Logistic regression was used to calculate crude and adjusted odds ratios (AOR) for associations with ASD, and separately for ID, compared with GP controls, by quartiles of analyte concentrations in primary analyses.ResultsGeometric mean concentrations of five of the six congeners with ≥55% of samples above the limit of detection were lower in mothers of children with ASD or ID than in controls. In adjusted analyses, inverse associations with several congeners were found for ASD relative to GP (e.g., quartile 4 vs. 1, BDE-153: AOR=0.56, 95% CI: 0.38, 0.84). When stratified by child sex (including 99 females with ASD, 77 with ID, and 73 with GP), estimates were consistent with overall analyses in boys, but in the opposite direction among girls, particularly for BDE-28 and -47 (AOR=2.58, 95% CI: 0.86, 7.79 and AOR=2.64, 95% CI: 0.97, 7.19, respectively). Similar patterns overall and by sex were observed for ID.ConclusionsContrary to expectation, higher PBDE concentrations were associated with decreased odds of ASD and ID, though not in girls. These findings require confirmation but suggest potential sexual dimorphism in associations with prenatal exposure to BFRs. https://doi.org/10.1289/EHP1079

Cross-genetic determination of maternal and neonatal immune mediators during pregnancy.

BACKGROUND:The immune system plays a fundamental role in development during pregnancy and early life. Alterations in circulating maternal and neonatal immune mediators have been associated with pregnancy complications as well as susceptibility to autoimmune and neurodevelopmental conditions in later life. Evidence suggests that the immune system in adults not only responds to environmental stimulation but is also under strong genetic control. METHODS:This is the first genetic study of &gt; 700 mother-infant pairs to analyse the circulating levels of 22 maternal mid-gestational serum-derived and 42 neonatal bloodspot-derived immune mediators (cytokines/chemokines) in the context of maternal and fetal genotype. We first estimated the maternal and fetal genome-wide SNP-based heritability (h2g) for each immune molecule and then performed genome-wide association studies (GWAS) to identify specific loci contributing to individual immune mediators. Finally, we assessed the relationship between genetic immune determinants and ASD outcome. RESULTS:We show maternal and neonatal cytokines/chemokines displaying genetic regulation using independent methodologies. We demonstrate that novel fetal loci for immune function independently affect the physiological levels of maternal immune mediators and vice versa. The cross-associated loci are in distinct genomic regions compared with individual-specific immune mediator loci. Finally, we observed an interaction between increased IL-8 levels at birth, autism spectrum disorder (ASD) status, and a specific maternal genotype. CONCLUSIONS:Our results suggest that maternal and fetal genetic variation influences the immune system during pregnancy and at birth via distinct mechanisms and that a better understanding of immune factor determinants in early development may shed light on risk factors for developmental disorders

Heritability and Demographic Analyses in the Large Isolated Population of Val Borbera Suggest Advantages in Mapping Complex Traits Genes

Isolated populations are a useful resource for mapping complex traits due to shared stable environment, reduced genetic complexity and extended Linkage Disequilibrium (LD) compared to the general population. Here we describe a large genetic isolate from the North West Apennines, the mountain range that runs through Italy from the North West Alps to the South.The study involved 1,803 people living in 7 villages of the upper Borbera Valley. For this large population cohort, data from genealogy reconstruction, medical questionnaires, blood, anthropometric and bone status QUS parameters were evaluated. Demographic and epidemiological analyses indicated a substantial genetic component contributing to each trait variation as well as overlapping genetic determinants and family clustering for some traits.The data provide evidence for significant heritability of medical relevant traits that will be important in mapping quantitative traits. We suggest that this population isolate is suitable to identify rare variants associated with complex phenotypes that may be difficult to study in larger but more heterogeneous populations

Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis

Variation in body iron is associated with or causes diseases, including anaemia and iron overload. Here, we analyse genetic association data on biochemical markers of iron status from 11 European-population studies, with replication in eight additional cohorts (total up to 48,972 subjects). We find 11 genome-wide-significant (

A genome-wide association study of early menopause and the combined impact of identified variants

Early menopause (EM) affects up to 10% of the female population, reducing reproductive lifespan considerably. Currently, it constitutes the leading cause of infertility in the western world, affecting mainly those women who postpone their first pregnancy beyond the age of 30 years. The genetic aetiology of EM is largely unknown in the majority of cases. We have undertaken a meta-analysis of genome-wide association studies (GWASs) in 3493 EM cases and 13 598 controls from 10 independent studies. No novel genetic variants were discovered, but the 17 variants previously associated with normal age at natural menopause as a quantitative trait (QT) were also associated with EM and primary ovarian insufficiency (POI). Thus, EM has a genetic aetiology which overlaps variation in normal age at menopause and is at least partly explained by the additive effects of the same polygenic variants. The combined effect of the common variants captured by the single nucleotide polymorphism arrays was estimated to account for ∼30% of the variance in EM. The association between the combined 17 variants and the risk of EM was greater than the best validated non-genetic risk factor, smokin

Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis.

Variation in body iron is associated with or causes diseases, including anaemia and iron overload. Here, we analyse genetic association data on biochemical markers of iron status from 11 European-population studies, with replication in eight additional cohorts (total up to 48,972 subjects). We find 11 genome-wide-significant (P<5 × 10(-8)) loci, some including known iron-related genes (HFE, SLC40A1, TF, TFR2, TFRC, TMPRSS6) and others novel (ABO, ARNTL, FADS2, NAT2, TEX14). SNPs at ARNTL, TF, and TFR2 affect iron markers in HFE C282Y homozygotes at risk for hemochromatosis. There is substantial overlap between our iron loci and loci affecting erythrocyte and lipid phenotypes. These results will facilitate investigation of the roles of iron in disease

Rare coding variants and X-linked loci associated with age at menarche.

More than 100 loci have been identified for age at menarche by genome-wide association studies; however, collectively these explain only ∼3% of the trait variance. Here we test two overlooked sources of variation in 192,974 European ancestry women: low-frequency protein-coding variants and X-chromosome variants. Five missense/nonsense variants (in ALMS1/LAMB2/TNRC6A/TACR3/PRKAG1) are associated with age at menarche (minor allele frequencies 0.08-4.6%; effect sizes 0.08-1.25 years per allele; P<5 × 10(-8)). In addition, we identify common X-chromosome loci at IGSF1 (rs762080, P=9.4 × 10(-13)) and FAAH2 (rs5914101, P=4.9 × 10(-10)). Highlighted genes implicate cellular energy homeostasis, post-transcriptional gene silencing and fatty-acid amide signalling. A frequently reported mutation in TACR3 for idiopathic hypogonatrophic hypogonadism (p.W275X) is associated with 1.25-year-later menarche (P=2.8 × 10(-11)), illustrating the utility of population studies to estimate the penetrance of reportedly pathogenic mutations. Collectively, these novel variants explain ∼0.5% variance, indicating that these overlooked sources of variation do not substantially explain the 'missing heritability' of this complex trait.UK sponsors (see article for overseas ones): This work made use of data and samples generated by the 1958 Birth Cohort (NCDS). Access to these resources was enabled via the 58READIE Project funded by Wellcome Trust and Medical Research Council (grant numbers WT095219MA and G1001799). A full list of the financial, institutional and personal contributions to the development of the 1958 Birth Cohort Biomedical resource is available at http://www2.le.ac.uk/projects/birthcohort. Genotyping was undertaken as part of the Wellcome Trust Case-Control Consortium (WTCCC) under Wellcome Trust award 076113, and a full list of the investigators who contributed to the generation of the data is available at www.wtccc.org.uk ... The Fenland Study is funded by the Wellcome Trust and the Medical Research Council, as well as by the Support for Science Funding programme and CamStrad. ... SIBS - CRUK ref: C1287/A8459 SEARCH - CRUK ref: A490/A10124 EMBRACE is supported by Cancer Research UK Grants C1287/A10118, C1287/A16563 and C1287/A17523. Genotyping was supported by Cancer Research - UK grant C12292/A11174D and C8197/A16565. Gareth Evans and Fiona Lalloo are supported by an NIHR grant to the Biomedical Research Centre, Manchester. The Investigators at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust are supported by an NIHR grant to the Biomedical Research Centre at The Institute of Cancer Research and The Royal Marsden NHS Foundation Trust. Ros Eeles and Elizabeth Bancroft are supported by Cancer Research UK Grant C5047/A8385. ... Generation Scotland - Scottish Executive Health Department, Chief Scientist Office, grant number CZD/16/6. Exome array genotyping for GS:SFHS was funded by the Medical Research Council UK. 23andMe - This work was supported in part by NIH Award 2R44HG006981-02 from the National Human Genome Research Institute.This is the final version of the article. It first appeared from NPG via http://dx.doi.org/10.1038/ncomms875

Large-scale genomic analyses link reproductive ageing to hypothalamic signaling, breast cancer susceptibility and BRCA1-mediated DNA repair

John Perry and colleagues report the results of a large genome-wide association study meta-analysis to identify variants influencing age at natural menopause. They identify 54 independent signals and find enrichment near genes involved in delayed puberty and DNA damage response