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Background Non-coding RNA 886 (nc886) is coded from a maternally inherited metastable epiallele. We set out to investigate the determinants and dynamics of the methylation pattern at the nc886 epiallele and how this methylation status associates with nc886 RNA expression. Furthermore, we investigated the associations between the nc886 methylation status or the levels of nc886 RNAs and metabolic traits in the YFS and KORA cohorts. The association between nc886 epiallele methylation and RNA expression was also validated in induced pluripotent stem cell (iPSC) lines. Results We confirm that the methylation status of the nc886 epiallele is mostly binomial, with individuals displaying either a non- or hemi-methylated status, but we also describe intermediately and close to fully methylated individuals. We show that an individual’s methylation status is associated with the mother’s age and socioeconomic status, but not with the individual’s own genetics. Once established, the methylation status of the nc886 epiallele remains stable for at least 25 years. This methylation status is strongly associated with the levels of nc886 non-coding RNAs in serum, blood, and iPSC lines. In addition, nc886 methylation status associates with glucose and insulin levels during adolescence but not with the indicators of glucose metabolism or the incidence of type 2 diabetes in adulthood. However, the nc886-3p RNA levels also associate with glucose metabolism in adulthood. Conclusions These results indicate that nc886 metastable epiallele methylation is tuned by the periconceptional conditions and it associates with glucose metabolism through the expression of the ncRNAs coded in the epiallele region. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01132-3.

Preterm birth (PTB) is associated with increased risk of type 2 diabetes and neurocognitive impairment later in life. We analyzed for the first time the associations of PTB with blood miRNA levels in adulthood. We also investigated the relationship of PTB associated miRNAs and adulthood phenotypes previously linked with premature birth. Blood MicroRNA profiling, genome-wide gene expression analysis, computer-based cognitive testing battery (CANTAB) and serum NMR metabolomics were performed for Young Finns Study subjects (aged 34–49 years, full-term n = 682, preterm n = 84). Preterm birth (vs. full-term) was associated with adulthood levels of hsa-miR-29b-3p in a fully adjusted regression model (p = 1.90 × 10–4, FDR = 0.046). The levels of hsa-miR-29b-3p were down-regulated in subjects with PTB with appropriate birthweight for gestational age (p = 0.002, fold change [FC] = − 1.20) and specifically in PTB subjects with small birthweight for gestational age (p = 0.095, FC = − 1.39) in comparison to individuals born full term. Hsa-miR-29b-3p levels correlated with the expressions of its target-mRNAs BCL11A and CS and the gene set analysis results indicated a target-mRNA driven association between hsa-miR-29b-3p levels and Alzheimer's disease, Parkinson's disease, Insulin signaling and Regulation of Actin Cytoskeleton pathway expression. The level of hsa-miR-29b-3p was directly associated with visual processing and sustained attention in CANTAB test and inversely associated with serum levels of VLDL subclass component and triglyceride levels. In conlcusion, adult blood levels of hsa-miR-29b-3p were lower in subjects born preterm. Hsa-miR-29b-3p associated with cognitive function and may be linked with adulthood morbidities in subjects born preterm, possibly through regulation of gene sets related to neurodegenerative diseases and insulin signaling as well as VLDL and triglyceride metabolism. publishedVersion

Additional file 1. Supplementary tables and figures.

Additional file 1. Supplementary Figures S1-6, Supplementary Tables S1-3 and S11-13 and Supplementary materials and methods.

The research focuses on the co-morbidity study of atherosclerosis and osteoporosis.

INTRODUCTION: Asymptomatic carotid artery stenosis (ACAS) may cause future stroke and therefore patients with ACAS require best medical treatment. Patients at high risk for stroke may opt for additional revascularization (either surgery or stenting) but the future stroke risk should outweigh the risk for peri/post-operative stroke/death. Current risk stratification for patients with ACAS is largely based on outdated randomized-controlled trials that lack the integration of improved medical therapies and risk factor control. Furthermore, recent circulating and imaging biomarkers for stroke have never been included in a risk stratification model. The TAXINOMISIS Project aims to develop a new risk stratification model for cerebrovascular complications in patients with ACAS and this will be tested through a prospective observational multicentre clinical trial performed in six major European vascular surgery centres. METHODS AND ANALYSIS: The risk stratification model will compromise clinical, circulating, plaque and imaging biomarkers. The prospective multicentre observational study will include 300 patients with 50%-99% ACAS. The primary endpoint is the three-year incidence of cerebrovascular complications. Biomarkers will be retrieved from plasma samples, brain MRI, carotid MRA and duplex ultrasound. The TAXINOMISIS Project will serve as a platform for the development of new computer tools that assess plaque progression based on radiology images and a lab-on-chip with genetic variants that could predict medication response in individual patients. CONCLUSION: Results from the TAXINOMISIS study could potentially improve future risk stratification in patients with ACAS to assist personalized evidence-based treatment decision-making. publishedVersion

Smoking as a major risk factor for morbidity affects numerous regulatory systems of the human body including DNA methylation. Most of the previous studies with genome-wide methylation data are based on conventional association analysis and earliest threshold-based gene set analysis that lacks sensitivity to be able to reveal all the relevant effects of smoking. The aim of the present study was to investigate the impact of active smoking on DNA methylation at three biological levels: 5'-C-phosphate-G-3' (CpG) sites, genes and functionally related genes (gene sets). Gene set analysis was done with mGSZ, a modern threshold-free method previously developed by us that utilizes all the genes in the experiment and their differential methylation scores. Application of such method in DNA methylation study is novel. Epigenome-wide methylation levels were profiled from Young Finns Study (YFS) participants' whole blood from 2011 follow-up using Illumina Infinium Hu-manMethylation450 BeadChips. We identified three novel smoking related CpG sites and replicated 57 of the previously identified ones. We found that smoking is associated with hypomethylation in shore (genomic regions 0-2 kilobases from CpG island). We identified smoking related methylation changes in 13 gene sets with false discovery rate (FDR)

BioMed Central open access

Platelet production, maintenance, and clearance are tightly controlled processes indicative of platelets' important roles in hemostasis and thrombosis. Platelets are common targets for primary and secondary prevention of several conditions. They are monitored clinically by complete blood counts, specifically with measurements of platelet count (PLT) and mean platelet volume (MPV). Identifying genetic effects on PLT and MPV can provide mechanistic insights into platelet biology and their role in disease. Therefore, we formed the Blood Cell Consortium (BCX) to perform a large-scale meta-analysis of Exomechip association results for PLT and MPV in 157,293 and 57,617 individuals, respectively. Using the low-frequency/rare coding variant-enriched Exomechip genotyping array, we sought to identify genetic variants associated with PLT and MPV. In addition to confirming 47 known PLT and 20 known MPV associations, we identified 32 PLT and 18 MPV associations not previously observed in the literature across the allele frequency spectrum, including rare large effect (FCER1A), low-frequency (IQGAP2, MAP1A, LY75), and common (ZMIZ2, SMG6, PEAR1, ARFGAP3/PACSIN2) variants. Several variants associated with PLT/MPV (PEAR1, MRVI1, PTGES3) were also associated with platelet reactivity. In concurrent BCX analyses, there was overlap of platelet-associated variants with red (MAP1A, TMPRSS6, ZMIZ2) and white (PEAR1, ZMIZ2, LY75) blood cell traits, suggesting common regulatory pathways with shared genetic architecture among these hematopoietic lineages. Our large-scale Exomechip analyses identified previously undocumented associations with platelet traits and further indicate that several complex quantitative hematological, lipid, and cardiovascular traits share genetic factors.

Red blood cell (RBC) traits are important heritable clinical biomarkers and modifiers of disease severity. To identify coding genetic variants associated with these traits, we conducted meta-analyses of seven RBC phenotypes in 130,273 multi-ethnic individuals fromstudies genotyped on an exome array. After conditional analyses and replication in 27,480 independent individuals, we identified 16 new RBC variants. We found low-frequency missense variants in MAP1A (rs55707100, minor allele frequency [MAF] = 3.3%, p = 2×10(-10) for hemoglobin [HGB]) and HNF4A (rs1800961, MAF = 2.4%, p < 3× 10(-8) for hematocrit [HCT] and HGB). In African Americans, we identified a nonsense variant in CD36 associated with higher RBC distribution width (rs3211938, MAF = 8.7%, p = 7× 10(-11)) and showed that it is associated with lower CD36 expression and strong allelic imbalance in exvivo differentiated human erythroblasts. We also identified a rare missense variant in ALAS2 (rs201062903, MAF = 0.2%) associated with lower mean corpuscular volume and mean corpuscular hemoglobin (p < 8× 10(-9)). Mendelian mutations in ALAS2 are a cause of sideroblastic anemia and erythropoietic protoporphyria. Gene-based testing highlighted three rare missense variants in PKLR, a gene mutated in Mendelian non-spherocytic hemolytic anemia, associated with HGB and HCT (SKAT p < 8× 10(-7)). These rare, low-frequency, and common RBC variants showed pleiotropy, being also associated with platelet, white blood cell, and lipid traits. Our association results and functional annotation suggest the involvement of new genes in human erythropoiesis. We also confirm that rare and low-frequency variants play a role in the architecture of complex human traits, although their phenotypic effect is generally smaller than originally anticipated.

Genome-wide association studies (GWAS) have begun to identify the common genetic component to ischaemic stroke (IS). However, IS has considerable phenotypic heterogeneity. Where clinical covariates explain a large fraction of disease risk, covariate informed designs can increase power to detect associations. As prevalence rates in IS are markedly affected by age, and younger onset cases may have higher genetic predisposition, we investigated whether an age-at-onset informed approach could detect novel associations with IS and its subtypes; cardioembolic (CE), large artery atherosclerosis (LAA) and small vessel disease (SVD) in 6,778 cases of European ancestry and 12,095 ancestry-matched controls. Regression analysis to identify SNP associations was performed on posterior liabilities after conditioning on age-at-onset and affection status. We sought further evidence of an association with LAA in 1,881 cases and 50,817 controls, and examined mRNA expression levels of the nearby genes in atherosclerotic carotid artery plaques. Secondly, we performed permutation analyses to evaluate the extent to which age-at-onset informed analysis improves significance for novel loci. We identified a novel association with an MMP12 locus in LAA (rs660599; p = 2.5×10⁻⁷), with independent replication in a second population (p = 0.0048, OR(95% CI) = 1.18(1.05-1.32); meta-analysis p = 2.6×10⁻⁸). The nearby gene, MMP12, was significantly overexpressed in carotid plaques compared to atherosclerosis-free control arteries (p = 1.2×10⁻¹⁵; fold change = 335.6). Permutation analyses demonstrated improved significance for associations when accounting for age-at-onset in all four stroke phenotypes (p

Genome-wide association studies (GWAS) have begun to identify the common genetic component to ischaemic stroke (IS). However, IS has considerable phenotypic heterogeneity. Where clinical covariates explain a large fraction of disease risk, covariate informed designs can increase power to detect associations. As prevalence rates in IS are markedly affected by age, and younger onset cases may have higher genetic predisposition, we investigated whether an age-at-onset informed approach could detect novel associations with IS and its subtypes; cardioembolic (CE), large artery atherosclerosis (LAA) and small vessel disease (SVD) in 6,778 cases of European ancestry and 12,095 ancestry-matched controls. Regression analysis to identify SNP associations was performed on posterior liabilities after conditioning on age-at-onset and affection status. We sought further evidence of an association with LAA in 1,881 cases and 50,817 controls, and examined mRNA expression levels of the nearby genes in atherosclerotic carotid artery plaques. Secondly, we performed permutation analyses to evaluate the extent to which age-at-onset informed analysis improves significance for novel loci. We identified a novel association with an MMP12 locus in LAA (rs660599; p = 2.5×10−7), with independent replication in a second population (p = 0.0048, OR(95% CI) = 1.18(1.05–1.32); meta-analysis p = 2.6×10−8). The nearby gene, MMP12, was significantly overexpressed in carotid plaques compared to atherosclerosis-free control arteries (p = 1.2×10−15; fold change = 335.6). Permutation analyses demonstrated improved significance for associations when accounting for age-at-onset in all four stroke phenotypes (p, Author Summary Ischaemic stroke places an enormous burden on global healthcare. However, the disease processes that lead to stroke are not fully understood. Genome-wide association studies have recently established that common genetic variants can increase risk of ischaemic stroke and its subtypes. In this study, we aimed to identify novel genetic associations with ischaemic stroke and its subtypes by addressing the fact that younger onset cases may have a stronger genetic component, and using this information in our analyses. We identify a novel genetic variant on chromosome 11 (rs660599), which is associated with increased risk of large artery stroke. We also show that mRNA expression of the nearest gene (MMP12) is higher in arteries with the disease process underlying large artery stroke (atherosclerosis). Finally, we evaluate our novel analysis approach, and show that our method is likely to identify further associations with ischaemic stroke.

Upstream transcription factor 1 (USF1) allelic variants significantly influence future risk of cardiovascular disease and overall mortality in females. We investigated sex-specific effects of USF1 gene allelic variants on serum indices of lipoprotein metabolism, early markers of asymptomatic atherosclerosis and their changes during six years of follow-up. In addition, we investigated the cis-regulatory role of these USF1 variants in artery wall tissues in Caucasians. In the Cardiovascular Risk in Young Finns Study, 1,608 participants (56% women, aged 31.9 ± 4.9) with lipids and cIMT data were included. For functional study, whole genome mRNA expression profiling was performed in 91 histologically classified atherosclerotic samples. In females, serum total, LDL cholesterol and apoB levels increased gradually according to USF1 rs2516839 genotypes TT < CT < CC and rs1556259 AA < AG < GG as well as according to USF1 H3 (GCCCGG) copy number 0 < 1 < 2. Furthermore, the carriers of minor alleles of rs2516839 (C) and rs1556259 (G) of USF1 gene had decreased USF1 expression in atherosclerotic plaques (P = 0.028 and 0.08, respectively) as compared to non-carriers. The genetic variation in USF1 influence USF1 transcript expression in advanced atherosclerosis and regulates levels and metabolism of circulating apoB and apoB-containing lipoprotein particles in sex-dependent manner, but is not a major determinant of early markers of atherosclerosis.

Mikro-RNA:t valtimokovettumataudissa Filosofian maisteri Emma Raitoharjun väitöstutkimuksessa todettiin mikro-RNA:iden, eli miRNA:iden, liittyvät niin sydän- ja verisuonitautien riskitekijöihin kuin taudin patologiaan. Veren miRNA-profiilin muutosten näytettiin liittyvän riskitekijöistä erityisesti diabetesta edeltäviin sokeriaineenvaihdunnan muutoksiin. Sydän ja verisuonitauteihin liittyvän ateroskleroottisen vaurion muodostumisen todettiin myös muuttavan suonen seinämän mikro-RNA:iden ilmentymistä ja näiden muutosten vaikuttavan moniin ateroskleroosiin liitettyihin biologisiin tapahtumiin. Mikro-RNA:t geeni-ilmentymisen säätelijöinä Mikro-RNA:t ovat lyhyitä, proteiinia koodaamattomia RNA-molekyylejä, jotka osallistuvat geenien ilmentymisen eli proteiinituotannon säätelyyn solulimassa. 2000-luvun alussa miRNA:t löydettiin myös ihmiseltä ja tämän jälkeen niiden ilmentyminen on liitetty niin yksilön normaaliin kehitykseen, fysiologiaan ja moniin tautitiloihin. Tarkimmin tunnetaan mikro-RNA:iden tehtävät geeni-ilmentymisen hiljentäjinä transkription jälkeen. Tässä prosessissa miRNA:t sitoutuvat valikoituihin lähetti-RNA:ihin, estäen niiden translaation ja näin myös proteiinien tuottamisen. Yksittäiset miRNA:t voivat sitoutua useisiin eri lähetti-RNA:ihin ja yksittäiseen lähetti-RNA:n translaatioon voi vaikuttaa monta mikro-RNA:ta. Näin miRNA:t luovat kokonaisia säätelyverkkoja, jotka vaikuttavat solujen toimintaan laaja-alaisesti. Mikro-RNA:t voivat kulkeutua solulta toiselle ja myös kudoksien välillä esimerkiksi verenkierrossa. Väitöskirjassa tarkasteltiin mikro-RNA:iden ilmentymisen muutoksia valtimokovettumataudin aiheuttamissa suonenseinämän vaurioissa (ateroskleroottisessa plakissa), sekä liittyen sydän- ja verisuonitautien riskitekijöihin. Sydän- ja verisuonitaudit, joiden taustalla on usein valtimokovettumatauti, ovat suomalaisten yleisin kuolinsyy. Taudin kehitykseen liittyy monia aineenvaihdunnan muutoksia, mutta myös valtimokovettumataudin vaikutukset suonen rakenteeseen ja toimintaan ovat monimutkaisia. Tämän vuoksi tutkimuksessa selvitettiin valtimokovettumatautiin ja sen riskitekijöihin liittyviä miRNA-ilmentymisen muutoksia, sekä niitä biologisia prosesseja, joita nämä miRNA:t säätelevät. Osana väitöskirjatutkimusta tehtiin myös ensimmäinen miRNA -profilointi (>700 miRNA:n ilmentymistason määritys), jossa verrattiin ihmisen ateroskleroottisen plakin ja terveen valtimon miRNA-ilmentymistä. Työssä arvioitiin myös miRNA- ja lähetti-RNA – tasojen määritykseen käytettyjen menetelmien tarkkuutta. Mikro-RNA:t vaikuttavat sydän- ja verisuonitautien riskitekijöihin Tutkimuksessa löydettiin 9 mikro-RNA:ta, joiden ilmentyminen tutkimushenkilöiden veressä liittyi sydän- ja verisuonitautien riskitekijöiden merkkiaineisiin, kuten verensokeriin, kolesteroliarvoihin, sekä vyötärölihavuuteen liitettyihin glyserolitasoihin. Esimerkiksi miR-1207-5p:n tasot korreloivat pitkäaikaista verensokeritasoa kuvaavan sokerihemoglobiinin kanssa ja jatkotutkimukset paljastivat tämän miRNA:n, sekä glyserolitasojen kanssa korreloivan miR-129-2-3p:n voivan osallistua sokeriaineenvaihdunnan säätelyyn. Mikro-RNA:t siis voivat välittää yksittäisten riskitekijöiden seurauksia kudoksissa, mutta mahdollisesti myös koota useiden riskitekijöiden vaikutuksia suonenseinämään. Näiden mikro-RNA:iden toiminnan tarkempia tunteminen voisi tuoda lisäselvyyttä riskitekijöiden osuudesta sydän- ja verisuonitautien etenemisessä. Mikro-RNA – ilmentyminen muuttuu valtimokovettumataudin aiheuttaman vaurion kehittyessä Valtimokovettumataudin edetessä suonen seinämään kertyy kolesterolia, sekä tulehdussoluja ja myös valtimon omien endoteeli- ja sileälihassolujen toiminta häiriintyy. Seinämään eritetään sidekudosmaista soluväliainetta ja seinämässä voi esiintyä myös luunmuodostusta muistuttavaa kalkkeutumista. Verrattaessa tällaisen ateroskleroottisen plakin miRNA-ilmentymistä ihmisen terveen valtimon miRNA ilmentymiseen, todettiin miRNA-säätelyn häiriintyvän vaurion edetessä. Mikro-RNA:iden miR-21-5p, -34a-5p, -146a-5p, -146b-5p ja -210-3p ilmentyminen erosi eniten terveen ja sairaan valtimon välillä. Kaikkien näiden miRNA:iden ilmentymistasot olivat koholla sairaissa verisuonissa. Jatkotutkimusten mukaan valtimon vauriossa nämä miRNA:t osallistuisivat esimerkiksi sileälihassolujen supistelun, tulehdusreaktion, sekä ohjelmoidun solukuoleman säätelyyn. Väitöskirjassa sairaan ja terveen valtimon mikro-RNA -profiileja verrattiin laajasti aikaisempaan kirjallisuuteen. Eroja ilmentymisessä löytyi laajemmin niillä mikro-RNA:illa, joiden on havaittu vaikuttavan valtimon seinämän tulehdukseen ja sileälihassolujen ilmiasuun. Samansuuntaisia mikro-RNA:n ilmentymisen muutoksia on havaittu aikaisemmin solu- ja eläinkokeissa. Väitöskirjatyö varmentaa siis myös näiden mikro-RNA:iden osuutta ihmisen sydän- ja verisuonitaudeissa. Valtimokovettumatautipotilailla myös veren miRNA -ilmentyminen on muuttunut. Nämä muutokset ovat suurelta osalta samansuuntaisia kuin nyt löydetyt suonenseinämän muutokset. Suonenseinämän miRNA-ilmentymismuutokset näyttävät välittyvän myös vereen ja veren välittämät muutokset myös takaisin suonen seinämään. Veressä kiertävät miRNA:t näyttävät muodostavan eri kudosten välisen hormonien kaltaisen signalointisäätelyjärjestelmän, joka vaikuttaa osaltaan myös sydän- ja verisuoniterveyteen. Väitöskirjatutkimuksen tulokset osoittavat, että miRNA:t liittyvät läheisesti niin sydän- ja verisuonitautien patologiaan kuin riskitekijöihinkin. Tutkimustiedon lisääntyessä yksittäisiä mikro-RNA:ita tai laajempia miRNA-profiileja voidaan mahdollisesti käyttää diagnostisina tai taudin kulkua ennustavina merkkiaineina tai ehkäistä sydän- ja verisuonitautien etenemistä muuttamalla mikro-RNA:iden ilmentymistä. Background: Cardiovascular diseases (CVDs), often of atherosclerosic origin, are the leading cause of death worldwide. Death is typically due to a rupture of the atherosclerotic plaque and the ischemia caused by the formed thrombus in the vital arteries of the heart or the brain. There are many known risk factors of atherosclerosis (such as smoking, male gender, age, etc.) but the rise in the prevalence of CVDs is thought to be caused by the increase in population age and the incidence of metabolic syndrome (MetS) consisting of dyslipidemia, hypertension, insulin resistance and obesity. MicroRNAs (miRNAs) are small non-coding RNAs. They regulate gene expression primarily at the post-transcriptional level via inhibition of mRNA translation or by guiding their target mRNA into degradation. The miRNA system forms a novel genomic regulatory level that combines tens or hundreds of target genes and pathways under the regulation of one miRNA. Humans have been predicted to have 2579 mature miRNAs, which have been shown to exert a crucial role in the normal development and function of the individual but also in many pathological states. MicroRNA expression profiles have also been shown to be connected to processes associated with the risk and progression of CVDs. Aims of study: To a) profile the miRNA expression of advanced atherosclerotic plaque in comparison to a healthy artery b) investigate the association between peripheral blood miRNA expression and metabolites associated to MetS and c) study and pinpoint the biological pathways that these miRNAs may regulate, by analyzing their target mRNA expressions and d) validate the accuracy of the cDNA based expression microarrays used. Materials and Methods: Tampere Vascular study arterial tissue sample collection was used in the original communication I-III to investigate atherosclerotic plaques. Blood samples from the Cardiovascular Riksk in Young Finns Study were used in the original communication IV to investigate the association between miRNAs and metabolites associated with MetS (IV). RNA was isolated with appropriate commercial kits, and the quality and integrity of the RNA was closely examined. MicroRNA profiling was done with Agilent´s Human microRNA Microarrays and genome wide gene expression analysis with Illumina´s HumanHT-12 Expression BeadChips. Validations of the expression array results were completed with RT-qPCR. Statistical analyses were performed with SPSS/PASW, Chipster, R language, and Gene Set Enrichment Analysis tools. Other web-based bioinformatics tools and databases were also used. Results and conclusions: In the original communication (I) we found that the results obtained with expression arrays were validated with high accuracy by RT-qPCR. The miRNA expression profile of advanced atherosclerotic plaques was shown to differ significantly in comparison to healthy control arteries: hsa-miR-21-5p,-210-3p, -34a-5p, -146a-5p and -146b-5p being the most up-regulated miRNAs in atherosclerotic plaques. Messenger RNA target analysis revealed that these differentially expressed miRNAs may affect processes known to be connected with atherosclerosis, such as apoptosis and vascular smooth muscle cell proliferation. Our study also further validated previous results by showing that many of the miRNAs shown to have altered expression profiles in the blood fractions of individuals with CVD are also dysregulated in the atherosclerotic artery wall and several miRNAs connected to atherosclerosis in cell culture studies are expressed in the plaque in the same fashion as these experiments have predicted (II-III). In the blood hsa-miR-129-1-3p, -129-2-3p, -144-5p, -331-3p, -484, 625-3p, -1207-5p, 1237-3p and 1288-3p expression were associated with metabolites connected to MetS or its components. Target mRNA analysis revealed that hsa-miR-129-2-3p and -1207-5p may regulate pathways important for glucose and insulin metabolism (IV). Our results demonstrate that miRNAs function as important gene regulators in normal and atherosclerotic artery wall as well as in pheripheral blood. However, the miRNAs that have a role in the development of advanced atherosclerotic plaque partly differ from those associated with risk factors of CVDs.

Genome-wide association studies (GWAS) have begun to identify the common genetic component to ischaemic stroke (IS). However, IS has considerable phenotypic heterogeneity. Where clinical covariates explain a large fraction of disease risk, covariate informed designs can increase power to detect associations. As prevalence rates in IS are markedly affected by age, and younger onset cases may have higher genetic predisposition, we investigated whether an age-at-onset informed approach could detect novel associations with IS and its subtypes; cardioembolic (CE), large artery atherosclerosis (LAA) and small vessel disease (SVD) in 6,778 cases of European ancestry and 12,095 ancestry-matched controls. Regression analysis to identify SNP associations was performed on posterior liabilities after conditioning on age-at-onset and affection status. We sought further evidence of an association with LAA in 1,881 cases and 50,817 controls, and examined mRNA expression levels of the nearby genes in atherosclerotic carotid artery plaques. Secondly, we performed permutation analyses to evaluate the extent to which age-at-onset informed analysis improves significance for novel loci. We identified a novel association with an MMP12 locus in LAA (rs660599; p = 2.5×10−7), with independent replication in a second population (p = 0.0048, OR(95% CI) = 1.18(1.05–1.32); meta-analysis p = 2.6×10−8). The nearby gene, MMP12, was significantly overexpressed in carotid plaques compared to atherosclerosis-free control arteries (p = 1.2×10−15; fold change = 335.6). Permutation analyses demonstrated improved significance for associations when accounting for age-at-onset in all four stroke phenotypes (p

Red blood cell (RBC) traits are important heritable clinical biomarkers and modifiers of disease severity. To identify coding genetic variants associated with these traits, we conducted meta-analys ...

Cytokines are essential regulatory components of the immune system, and their aberrant levels have been linked to many disease states. Despite increasing evidence that cytokines operate in concert, many of the physiological interactions between cytokines, and the shared genetic architecture that underlies them, remain unknown. Here, we aimed to identify and characterize genetic variants with pleiotropic effects on cytokines. Using three population-based cohorts (n = 9,263), we performed multivariate genome-wide association studies (GWAS) for a correlation network of 11 circulating cytokines, then combined our results in meta-analysis. We identified a total of eight loci significantly associated with the cytokine network, of which two (PDGFRB and ABO) had not been detected previously. In addition, conditional analyses revealed a further four secondary signals at three known cytokine loci. Integration, through the use of Bayesian colocalization analysis, of publicly available GWAS summary statistics with the cytokine network associations revealed shared causal variants between the eight cytokine loci and other traits; in particular, cytokine network variants at the ABO, SERPINE2, and ZFPM2 loci showed pleiotropic effects on the production of immune-related proteins, on metabolic traits such as lipoprotein and lipid levels, on blood-cell-related traits such as platelet count, and on disease traits such as coronary artery disease and type 2 diabetes.

We analysed whole blood genome-wide expression data to identify gene co-expression modules shared by early traits of osteoporosis and atherosclerosis. Gene expression was profiled for the Young Finns Study participants. Bone mineral density and content were measured as early traits of osteoporosis. Carotid and bulbus intima media thickness were measured as early traits of atherosclerosis. Joint association of the modules, identified with weighted co-expression analysis, with early traits of the diseases was tested with multivariate analysis. Among the six modules significantly correlated with early traits of both the diseases, two had significant (adjusted p-values (p.adj) < 0.05) and another two had suggestively significant (p.adj < 0.25) joint association with the two diseases after adjusting for age, sex, body mass index, smoking habit, alcohol consumption, and physical activity. The three most significant member genes from the significant modules were NOSIP, GXYLT2, and TRIM63 (p.adj ≤ 0.18). Genes in the modules were enriched with biological processes that have separately been found to be involved in either bone metabolism or atherosclerosis. The gene modules and their most significant member genes identified in this study support the osteoporosis-atherosclerosis comorbidity hypothesis and can provide new joint biomarkers for both diseases and their dual prevention. publishedVersion

All Supplementary methods and Figures S1–S7. (DOCX 2445 kb)

Low-end normal hemoglobin levels, which carry less oxygen, are associated with lower body weight and healthier metabolism., Activation of the hypoxia-inducible factor (HIF) pathway reprograms energy metabolism. Hemoglobin (Hb) is the main carrier of oxygen. Using its normal variation as a surrogate measure for hypoxia, we explored whether lower Hb levels could lead to healthier metabolic profiles in mice and humans (n = 7175) and used Mendelian randomization (MR) to evaluate potential causality (n = 173,480). The results showed evidence for lower Hb levels being associated with lower body mass index, better glucose tolerance and other metabolic profiles, lower inflammatory load, and blood pressure. Expression of the key HIF target genes SLC2A4 and Slc2a1 in skeletal muscle and adipose tissue, respectively, associated with systolic blood pressure in MR analyses and body weight, liver weight, and adiposity in mice. Last, manipulation of murine Hb levels mediated changes to key metabolic parameters. In conclusion, low-end normal Hb levels may be favorable for metabolic health involving mild chronic activation of the HIF response.

All Supplementary methods and Figures S1–S7. (DOCX 2445 kb)