Cellular action potential is characterized by a particular sequence of depolarizing and repolarizing ion currents regulated by ion channels. Genetic mutations in these channels disrupt the essential movement of ions, such as Na+, Ca++, and K+, across the cell membrane, leading to dangerous arrhythmias and sudden cardiac death (SCD). Most cases of unexplained SCD are caused by pathogenic variants in genes linked to channelopathies and cardiomyopathy. Genetic investigations might aid in confirming the clinical diagnosis based solely on observations. Other advantages of genetic studies are clinical management of the patient, family screening, appropriate genetic counseling, and risk assessment for family members. This study was conducted to investigate the genetic cause of early-onset SCD in two Iranian families. Whole-exome sequencing was performed on the probands from each family, and the Illumina DRAGEN haplotype variant calling system was used to identify variants in each patient. Here, we identified rare heterozygous missense variants in the RYR2 and SCN5A genes, which are linked to cardiac channelopathies. Alignment studies reveal that the mutated residues are conserved across humans and primates, underscoring their crucial role in protein function. Previously reported associations between these mutations and channelopathy pathogenesis have been confirmed in the present study. This study provides valuable insights for genetic counseling of families with a history of sudden death.

Cardiovascular diseases (CVD) remain a major global health challenge. Early markers of disease initiation and progression are urgently needed. We, and others, have previously shown changes in the gut microbiome in association with metabolic and CVD. Here, we demonstrate that gut microbiome-related changes can be detected in association with subclinical variations in heart and kidney function. Markers related to gut microbial metabolism of aromatic amino acids, phenylalanine and tyrosine, associate with circulating pro-atrial natriuretic peptide and estimated glomerular filtration rate in a metabolically healthy European population. Observational and genetic evidence further identify microbiome-related metabolites as mediators of this gut microbiome-kidney axis, with their baseline levels associating with incident CVD in an external Canadian population. Altogether, our work suggests that the gut microbiome interacts with the cardiorenal axis and participates in an interorgan crosstalk affecting host physiology and risk of CVD.

BACKGROUND:The relationships between allergic diseases (AD) and IgE levels are complex. OBJECTIVE:We sought to identify genes associated with AD and IgE having close proximity in the interactome and to elucidate the associated biological mechanisms. METHODS:We integrated a comprehensive interactome with data from genome-wide (GWAS) and epigenome-wide (EWAS) association studies of AD and IgE levels, respectively. We used the SigMod algorithm to identify gene modules enriched in AD- and IgE-associated signals. We performed a connectivity analysis of these two modules to characterize direct cross-trait connections. Finally, we conducted an in-depth functional analysis of the directly-connected AD and IgE genes. RESULTS:We identified gene modules that were significantly associated with AD and IgE, respectively (P < 10-5). The connectivity analysis revealed that 139 AD- and IgE-associated genes had direct cross-trait connections in the interactome. Combinations of these genes were enriched (false discovery rate < 0.05) in pathways notably involved in type 2 and non-type 2 immune responses. These results were corroborated by cell-specific enrichment of gene expression. Of the 139 genes, 55% (77 genes) had not previously been associated with AD and/or IgE. These genes are implicated in biological processes including host defense against pathogens, ubiquitination, gene expression regulation, inflammation, and neuroimmune interactions. The 139 genes are enriched in drug targets (P = 7.7 × 10-7). CONCLUSIONS:This study sheds light on the biological mechanisms influenced by AD and IgE genes that are directly linked in the interactome. It emphasizes the role of IgE in both allergic and antiviral responses. This study also identifies new genes for further investigation.

Coronary artery disease (CAD) is a leading global cause of mortality, with genetic predisposition conferring a more than two-fold increased risk in individuals with a family history of premature disease. This study aimed to identify rare genetic variants underlying inherited premature CAD (PCAD) in familial cases. Fifty unrelated Iranian families with early-onset familial CAD/MI were recruited. Inclusion required at least two affected members with PCAD (≤ 45 years in men, ≤ 55 years in women) across generations. Whole-exome sequencing (WES) data analysis was performed using the Illumina DRAGEN Bio-IT platform for alignment and variant-calling, and Ilyome software for annotation. Sanger sequencing was used for co-segregation analysis in additional family members. The study identified novel candidate genes potentially associated with premature CAD, as well as rare variants in well-established CAD genes in familial premature CAD, in seven unrelated families. Among the potential candidates, PIKFYVE emerged as the most compelling primary candidate, supported by its established role in cardiac calcium homeostasis, platelet function, and vascular biology. Three additional genes (PKP2, CAPN5, OBSCN) represent secondary novel findings that warrant further investigation. These findings expand the genetic architecture of familial PCAD and highlight the value of WES in early-onset familial cases. GTEx expression data supported the biological relevance of candidate genes. Functional studies are warranted to confirm the pathogenicity of the identified variants.

Advances in sequencing technology have enabled population-level Whole Genome Sequencing (WGS) efforts to be undertaken in many countries. Often, this requires collaboration across a distributed network of sequencing centres to allow efficient use of existing resources. Previously we tested the robustness of short-read sequencing technology and analysis pipelines across three established sequencing centres located in Montreal, Toronto, and Vancouver, constituting CGEn, Canada's national platform for genome sequencing and analysis (www.cgen.ca). In this work, we extend the study to cover Oxford Nanopore Technologies (ONT) long read-based WGS technology which is increasingly being used for large-scale genomics studies. Thus, we performed ONT WGS of the HG002 cell line, a well-characterized standard obtained directly from the Coriell Institute, aiming for a minimum of 30× coverage using one R10.4 PromethION flowcell at each centre. The sequencing datasets were analyzed using commonly developed pipelines for SNVs, Indels, SV, and CpG methylation detection and then compared to the relevant publicly available GIAB benchmark datasets. As a result, we tested the robustness of the laboratory protocols as well as the effectiveness of the analytical pipelines for simultaneous analysis of genomic variation and CpG methylation. Key findings include: SNV detection with higher F1-scores in RefSeq Coding regions for the ONT datasets (99.1%-99.5%) compared to Illumina NovaSeqX data (96.5%); additionally, there was high correlation of CpG methylation across all the sequencing centres (R = 0.97), as well as with publicly available WGBS (R = 0.88) and EM-Seq (R = 0.93) data from the EpiQC study.

DFS amongst Leibovich risk groups stratified by genomic classifier

Brain regions drive multiple physiological functions through specific gene expression patterns that adapt to environmental influences, drug treatments and disease conditions. To generate a detailed atlas of the brain transcriptome in the context of diabetes, we carried out RNA sequencing in hypothalamus, hippocampus, brainstem and striatum of the Goto-Kakizaki (GK) rat model of spontaneous type 2 diabetes, which was applied to identify gene transcription adaptation to improved glycemic control following vertical sleeve gastrectomy (VSG) in the GK. Over 19,000 distinct transcripts were detected in the rat brain, including 2794 which were consistently expressed in the four brain regions. Region-specific gene expression was identified in hypothalamus (n = 477), hippocampus (n = 468), brainstem (n = 1173) and striatum (n = 791), resulting in differential regulation of biological processes between regions. Differentially expressed genes between VSG and sham operated rats were only found in the hypothalamus and were predominantly involved in the regulation of endothelium and extracellular matrix. These results provide a detailed atlas of regional gene expression in the diabetic rat brain and suggest that the long term effects of gastrectomy-promoted diabetes remission involve functional changes in the hypothalamus endothelium.

Somatic mutations detected in 12 interrogated genes for cohorts C1-C3

DFS by tumor stage stratified by genomic classifier

Supplementary Tables S3-S13

Metabolomics is a powerful molecular phenotyping technology which can be used in population studies to identify metabolites underlying disease conditions. To identify plasma biomarkers potentially predicting chronic diseases we applied 1H nuclear magnetic resonance (NMR) metabolomics using a 600 MHz spectrometer fitted with an In Vitro Diagnostics Research (IVDr) platform to test associations between 18 known metabolites and 111 lipoprotein constituents that could be quantified and passed our quality control procedure and 944 phenotypes determined in 302 healthy participants of the Japanese Nagahama Study. We identified 907 statistically significant associations (p < 4.11 × 10-7) between 34 phenotypes and at least one metabolite or lipoprotein. Eight metabolites and 109 lipoprotein (sub)classes showed evidence of associations with phenotypes predominantly related to lipid and cholesterol metabolism, liver function, fatness and hematology. We confirmed previously reported associations between plasma trimethylamine-N-oxide (TMAO) and cholesterol, and between the branched-chain amino acids leucine and valine and body mass index (BMI). BMI and fatness were positively associated with components of plasma LDL-4 and VLDL-1 and the ratios of apolipoproteins A1 to B100 and LDL to HDL cholesterol, whereas they were inversely associated with HDL-1 constituents. HDL-1 and LDL-4 subclasses systematically follow the patterns of association of HDL and LDL, respectively, and we propose that these can be examined to improve cardiometabolic risk evaluation. Results from our study exemplify the power of quantitative NMR-based metabolome profiling applied to even relatively small cohorts of healthy individuals extensively characterized for multiple phenotypes underlying unrelated clinical conditions to identify potentially disease-predicting metabolite biomarkers.

Cerebral small vessel disease (cSVD) is a leading cause of stroke and dementia with no specific treatment, of which molecular mechanisms remain poorly understood. To identify potential biomarkers and therapeutic targets, we applied Mendelian randomization to examine over 2,500 proteins measured in plasma and, uniquely, cerebrospinal fluid, in relation to magnetic resonance imaging (MRI) markers of cSVD in more than 40,000 individuals. Here we show that 49 proteins are associated with MRI markers of cSVD, most prominently in cerebrospinal fluid. We highlight associations that are consistent across platforms and ancestries, and supported by complementary observational analyses, and we explore differences between fluids. The proteins are enriched in pathways related to the extracellular matrix, immune response and microglial activity. Many also associate with stroke and dementia, and several correspond to existing drug targets. Together, these findings reveal a robust biological fingerprint of cSVD and highlight opportunities for biomarker and drug discovery and repositioning.

Bariatric surgery results in type 2 diabetes (T2D) improvement. To identify mechanisms associated with gastrectomy-promoted T2D remission in lean individuals, we performed pathophysiological, behavioural and molecular (liver transcriptome, metabolome and lipidome) investigations in the Goto-Kakizaki (GK) model of spontaneously-occurring non-obese T2D following vertical sleeve gastrectomy (VSG) or sham operation. VSG resulted in sustained reduction in hyperglycemia and changes in nycthemeral feeding patterns and activity. Liver transcriptome and lipidome profiling pointed to changes in the expression of genes involved in inflammation, PPAR signalling and fatty acid metabolism, and in the regulation of phosphatidylcholine and lysophosphatidylethanolamine classes. Deeper analysis revealed altered expression of genes involved in histone methylation and co-ordinately differential transcription of key regulators of the molecular clock (Clock, Arntl/Bmal1, Per1, Per2, Per3). In addition to previously reported changes in bile acid metabolism and gut microbiome in this model of VSG, our findings underline the multiple biological mechanisms associated with diabetes remission following VSG and suggest a contribution of chronobiology and epigenetic processes in the long-term therapeutic consequences of VSG in the context of polygenic non-obese T2D.

Background Asthma pathophysiology varies by age-of-onset and involves diverse immune processes reflected in white blood cell (WBC) subsets. To investigate the genetic architecture of asthma and potential endophenotypes, we analyzed the chr17q12-q21 locus, a robustly replicated asthma locus, across European (EUR), African (AFR), East Asian (EAS), and South Asian (SAS) ancestry groups from the UK Biobank (UKB) and Biobank Japan (BBJ). The largest EUR sample was further stratified by age-of-onset as a proxy for etiological heterogeneity. Results Eight independent asthma signals were identified in UKB-EUR, including two novel associations (Signal 2-rs72832915 and Signal 6-rs507671). Signal 4, corresponding to the originally identified pediatric signal, showed the strongest cross-ancestry evidence, with asthma risk and diminished lymphocyte count co-localizing in three populations. Signal 8 was distinguished by multiple lines of evidence converging on rs112401631 as a likely causal variant, including fine-mapping, colocalization with eosinophil and lymphocyte counts, and mediation of asthma risk through eosinophil count. Signal 6 implicated RARA expression, suggesting vitamin A metabolism impacts on late-onset asthma, the only associated stratum. Notably, integrating WBC traits and Bayesian fine-mapping enabled leveraging non-European ancestry groups to strengthen causal inference despite smaller sample sizes. Conclusion These findings illustrate how combining age-of-onset stratification, quantitative endophenotypes, and multi-ancestry analyses can reveal mechanistic heterogeneity and prioritize specific variants and pathways for functional validation. This framework is broadly applicable to complex diseases with measurable quantitative endophenotypes. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was financially supported by the Queen Elizabeth II Diamond Jubilee Scholarship program (QEII) and the McGill Genome Centre ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The data used in this study were accessed from the UK Biobank under approved application number 6728 I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors

Sickle cell trait is the quintessential example of the human evolutionary response to malaria, providing protection against severe disease, but leading to sickle cell disease (SCD) in the homozygous state. Fetal Hemoglobin (HbF) reduces the pathology of SCD and several mutations lead to the prolonged production of HbF into childhood and adult life. HbF has been suggested to contribute to protection against malaria. Two long-term cohorts were genotyped for three quantitative trait loci associated with HbF production and analyzed for HbF titers, malaria clinical episodes and the production of parasite stages infectious to mosquitoes, gametocytes, in asymptomatic infections. Plasmodium falciparum parasites were also grown in vitro in HbSS cells with measured levels of HbF. The genetic determinants of prolonged HbF production were associated with increased HbF titers and that increased HbF afforded protection from malaria disease but increased the production of gametocytes. The presence of HbF in sickled red cells was also shown in in vitro culture to enable parasite persistence in conditions otherwise deleterious for the parasite and enabled complete maturation of gametocytes. The beneficial personal effect of HbF, whether through protection against malaria or alleviating effects of SCD, is seemingly offset by increased parasite transmissibility and potential disease burden for the community. These individuals represent a potentially important reservoir of infection and could be targeted in elimination strategies.

Chronic hyperglycemia is a major risk factor for glomerular or retinal microangiopathy and cardiovascular complications of type 1 diabetes (T1D). At the interface of genetics and environment, dynamic epigenetic changes associated with hyperglycemia may unravel some of the mechanisms contributing to these T1D complications. In this study, blood samples were collected from 112 young patients at T1D diagnosis and 3 years later in average. Whole genome-wide bisulfite sequencing was used to measure blood DNA methylation changes of about 28 million CpGs at single base resolution over this time. Chronic hyperglycemia was estimated every 3–4 months by HbA1c measurement. Linear regressions with adjustment to age, sex, treatment duration, blood proportions and batch effects were employed to characterize the relationships between the dynamic changes of DNA methylation and average HbA1c levels. We identified that longitudinal DNA methylation changes at 815 CpGs (with suggestive p-value threshold of 1e-4) were associated with average HbA1c. Most of them (> 98%) were located outside of the promoter regions and were enriched in CpG island shores and multiple immune cell type specific accessible chromatin regions. Among the 36 more strongly associated loci (p-value < 5e-6), 16 were harbouring genes or non-coding sequences involved in angiogenesis regulation, glomerular and retinal vascularization or development, or coronary disease. Our findings support the identification of new genomic sites where CpG methylation associated with hyperglycemia may contribute to long-term complications of T1D, shedding light on potential mechanisms for further exploration.

Peak width of skeletonized mean diffusivity (PSMD) is an emerging automated diffusion imaging marker showing clinically relevant changes in cerebral small vessel disease (cSVD), a leading cause of stroke and dementia with no mechanism-based treatment. We conducted a genome-wide association study of PSMD in 58,403 participants from 24 population-based cohorts (89% European, 10% East-Asian, 1% African-American), identifying 31 independent common variant associations. Additionally, a whole-exome sequencing analysis in 32,957 participants yielded associations of PSMD with single and burden of rare coding variants in four novel genes. Mendelian randomization supported causal association of higher blood pressure with larger PSMD values, and of larger PSMD with an increased risk of stroke, especially intracerebral hemorrhage. Strikingly, genetic susceptibility to white matter hyperintensities, an established MRI-marker of cSVD, was associated with higher PSMD from early childhood to older age, with prominent lifespan effects for VCAN and SMG6. Leveraging unique brain single-cell sequencing resources we showed temporal changes in the cell-type specificity of these genes in the developing brain and overall enrichment of PSMD risk loci in genes expressed in fetal brain endothelial cells. Finally, through extensive integration with multi-omics resources, we provide precious leads for gene prioritization to accelerate drug discovery for cSVD.

Cerebral small vessel disease (cSVD) is a leading cause of stroke and dementia. Genetic risk loci for white matter hyperintensities (WMH), the most common MRI-marker of cSVD in older age, were recently shown to be significantly associated with white matter (WM) microstructure on diffusion tensor imaging (signal-based) in young adults. To provide new insights into these early changes in WM microstructure and their relation with cSVD, we sought to explore the genetic underpinnings of cutting-edge tissue-based diffusion imaging markers across the adult lifespan. We conducted a genome-wide association study of neurite orientation dispersion and density imaging (NODDI) markers in young adults (i-Share study: N = 1 758, (mean[range]) 22.1[18-35] years), with follow-up in young middle-aged (Rhineland Study: N = 714, 35.2[30-40] years) and late middle-aged to older individuals (UK Biobank: N = 33 224, 64.3[45-82] years). We identified 21 loci associated with NODDI markers across brain regions in young adults. The most robust association, replicated in both follow-up cohorts, was with Neurite Density Index (NDI) at chr5q14.3, a known WMH locus in VCAN. Two additional loci were replicated in UK Biobank, at chr17q21.2 with NDI, and chr19q13.12 with Orientation Dispersion Index (ODI). Transcriptome-wide association studies showed associations of STAT3 expression in arterial and adipose tissue (chr17q21.2) with NDI, and of several genes at chr19q13.12 with ODI. Genetic susceptibility to larger WMH volume, but not to vascular risk factors, was significantly associated with decreased NDI in young adults, especially in regions known to harbor WMH in older age. Individually, seven of 25 known WMH risk loci were associated with NDI in young adults. In conclusion, we identified multiple novel genetic risk loci associated with NODDI markers, particularly NDI, in early adulthood. These point to possible early-life mechanisms underlying cSVD and to processes involving remyelination, neurodevelopment and neurodegeneration, with a potential for novel approaches to prevention.