Lung IL-33 is involved in pathogen defense, barrier homeostasis, and development of allergic responses. We previously identified a 5 kb noncoding region within a GWAS-defined segment that regulates expression of human IL33 (hIL33) but is absent in the murine locus. To understand how this region affects IL-33 expression in vivo, we engineered 2 BAC-transgenic strains in which 166 kb of the human genome upstream of the hIL33 locus, along with a fluorescent reporter, was inserted into the murine genome, both with and without the 5 kb region. Comparison to a murine Il33 (mIl33) reporter strain revealed species-specific tropism; hIL33 reporter was mostly expressed in the endothelium, while mIl33 reporter was expressed in type 2 alveolar epithelium. hIL33 reporter expression in tracheal basal epithelium, submucosal glands, and lung microvasculature required the 5 kb region. Surprisingly, allergen and exogenous IL-33 downregulated hIL33 reporter in lung endothelium only when the 5 kb region was present. Similar IL-33-dependent downregulation of IL33 transcripts was observed in human endothelial cell lines, validating that our hIL33 reporter strain recapitulated human endothelial biology. Together, these data reveal the importance of the asthma-associated human 5 kb region in regulating human IL33 expression in a cell type-and context-dependent manner.

BACKGROUND:Cardiomyopathies frequently arise from rare, highly penetrant coding variants with variable clinical expressivity. Genome-wide association studies (GWAS) suggest significant polygenic contributions to cardiovascular diseases, including cardiomyopathy. Most GWAS loci map to poorly conserved noncoding regions, requiring human genome context for experimental validation. METHODS:We created engineered heart tissues (EHTs) from human induced pluripotent stem cell-derived cardiomyocytes and primary cardiac fibroblasts. We assayed single-cell gene expression and chromatin accessibility to generate comprehensive genome-wide regulatory maps. Open chromatin regions were integrated with chromatin contact information and used to fine-map cardiomyopathy GWAS single-nucleotide polymorphisms. Single-nucleotide polymorphisms and their associated open chromatin regions were assessed using reporter assays, genome editing, and expression profiling. RESULTS:EHT Single-cell RNA-seq recapitulated major cardiac cell types, with advanced cardiomyocyte maturation compared with monolayer human induced pluripotent stem cell cardiomyocytes. More than 400 000 open chromatin regions were resolved to cell types and assayed for transcription factor motifs. Functional fine-mapping of GWAS loci prioritized 5817 variants, and reporter assays validated allele-specific enhancer activity. We identified an intergenic chr3p25.1 locus harboring significant GWAS signals from both dilated cardiomyopathy and left ventricular ejection fraction. Several of these variants lie in open chromatin regions participating in long-range chromatin interactions with SLC6A6 and GRIP2. Haplotype-resolved and synthetic reporter assays confirmed enhancer activity and narrowed candidate single-nucleotide polymorphisms. CRISPR-deletion of this region reduced expression of both SLC6A6 and GRIP2, indicating the enhancer regulates the expression of multiple genes. EHTs with the enhancer deletion displayed markedly reduced contractile function, confirming that this enhancer region contributes to myocardial function. CONCLUSIONS:EHTs are an experimentally tractable platform for testing the function of noncoding variants as modifiers of cardiomyopathy. Variants fine-mapped from cardiomyopathies using EHT regulatory maps have functional consequences and provide a set of prioritized sites to advance the study of polygenic heart failure.

In response to hypoxic stress at high altitudes, variation at the EPAS1 locus has experienced strong selection in Tibetans. Functional dissection of the selection signals at this locus identified ENH5, an enhancer within the adaptive haplotype that has a blunted response to hypoxic stress in Tibetans. ENH5 was shown to be pleiotropic in several tissues related to hypoxia response, suggesting that a possible mechanism behind the strong selection signatures could be adaptive pleiotropy. Tibetans not only experience hypoxic conditions, but also cold temperatures due to the altitude and climate of the Tibetan Plateau. However, it is unclear whether cold temperatures affect ENH5 activity possibly contributing to the selective pressure at this locus. Here, we further characterized the role of ENH5 in subcutaneous white adipose tissue, an important tissue type that regulates body temperature in response to cold temperatures by releasing stored fat as heat through a process called thermogenesis. In this work, we investigated the role of ENH5 in adipocytes using ENH5 knockout mice (ENH5 KO), which phenocopy the reduced activity of the Tibetan allele. We show that ENH5 KO mice at normoxia and room temperature do not have significant differences in organismal phenotypes related to adiposity and metabolism compared to WT mice on a high fat diet. However, we detected effects of ENH5 conditional on thermogenic stimulation and hypoxia exposure, independently, in adipocytes cultured in vitro . Under either of these conditions, ENH5 KO has stronger differential expression of key genes involved in thermogenesis activity and adipocyte differentiation compared to WT. This differential response to thermogenic stimulation expands on the pleiotropic effects of the Tibetan ENH5 allele(s), in addition to those previously shown in well-established hypoxia-responsive tissues. Our results raise the possibility that pleiotropic effects of ENH5 may implicate unforeseen mechanisms, such as cellular energetics and thermogenesis, possibly contributing to the phenotypic adaptation to high altitude in Tibetans.

Genome-wide studies (GWAS) on asthma have identified nearly 200 genomic loci. However, the underlying mechanisms remain mostly elusive. While functional profiling of blood immune cell types has helped interpret asthma GWAS signals, high-resolution functional genomic data of lung immune cells, which differ from circulating immune cells, are lacking. We thus profiled single-cell multi-omics (RNA-seq and ATAC-seq) on lymphocytes of lung and spleen tissues from 9 donors. Cross-tissue comparison identified distinct transcriptomes for each immune cell type, but subtle differences in chromatin accessibility. We next assessed open chromatin regions (OCRs) of lung vs. blood, using a public dataset, for their enrichment of asthma risk. Strikingly, lung T cells showed unique contributions to heritability of adult-onset (AOA) and childhood-onset asthma (COA), beyond blood T cells. Using lung OCRs and previously fine-mapped variants for AOA and COA, we identified 43 cis-regulatory elements (CREs) likely contributing to asthma risk. By creating enhancer-gene maps from our single-cell data, we identified target genes for these CREs. We highlighted CCR4 and LRRC32 with their CREs displaying cell-type specific regulatory activities. Lastly, we built cell-type level gene regulatory networks (GRNs) to identify target genes of transcription factors (TFs). Lung GRNs not only shed light on the cell-type specific functions of several TFs that are known asthma risk genes but also allowed us to detect novel TFs such as STAT1 that may regulate asthma-related biological pathways in CD4 T cells. Our results demonstrate the utility of single-cell multiomics to identify asthma risk genes and understand their cell-type specific functions. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was funded by U19 AI62310 (C.O., M.A.N., A.I.S.). ### 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: Institutional Review Board (IRB) approval of the University of Chicago was waived because this research was not deemed to constitute human subject research. 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 publication

Genome-wide association studies of asthma have identified nearly 200 independent loci, yet the mechanisms through which individual loci influence asthma risk remain largely unknown. A growing array of computational and experimental tools has begun to fill these gaps by identifying causal variants and effector genes and characterizing their functions. In parallel, emerging studies are exploring the translational applications of genetic and multiomics data in asthma, including defining molecular endotypes and predicting disease risk. Here we review the strengths and limitations of current approaches for addressing the post-genome-wide association study challenges and discuss the next tier of questions and directions for the field.

Deciphering which genes are most important to disease etiology is a central challenge in human genetics. While genome-wide association studies have cataloged thousands of variants, it’s been proposed that most are indirect regulators of a limited, currently unidentified set of central disease-driving genes, defined here as disease-proximal genes (DPGs). Here, we introduce DANDELION, a mediation-inspired statistical framework that prioritizes DPGs by integrating trans-regulatory effects from disease-relevant tissues with gene-level burden from whole-exome sequencing. Applying DANDELION to asthma uncovers novel DPGs that escape detection by conventional methods. CRISPR screens in epithelial and T cells find that most DPGs regulate key asthma-related cellular phenotypes. We also demonstrate that loss of two DPGs, SLC27A3 and SCD, affects inflammation and airway remodeling in a mouse model of allergic asthma. Our study establishes DANDELION as a powerful framework for prioritizing novel, therapeutically actionable genes and pathways underlying disease pathogenesis.

Seminal plasma can have wide-ranging effects on reproductive fitness-from affecting sperm fertilization capacity and female reproductive physiology to influencing offspring viability and health. Seminal plasma can also change in response to environmental conditions including diet, which of itself is known to affect reproductive traits and fitness outcomes. However, an understanding of how paternal diet alters seminal plasma composition and how these effects relate to fetal development remains elusive. Here, we applied the geometric framework for nutrition to systematically manipulate dietary macronutrient balance in male mice and determine dietary effects on the seminal vesicle fluid (SVF; comprising much of the seminal plasma) proteome, as well as relate differences in the proteome to aspects of fetal development. We (i) identified the largest number of proteins in the mouse SVF proteome to date, (ii) determined a set of proteins that were significantly affected by dietary macronutrients, (iii) showed that differences in a protein related to lipid mobilization and metabolism (APOA4) were correlated with fetal development, and (iv) detected dietary effects on aspects of fetal development that were unrelated to SVF protein abundance. This study provides a comprehensive characterization of the male SVF proteome across nutritional space and highlights potential functional ways in which male diet and the seminal plasma may mediate fitness.

Dietary macronutrient composition in males influences brown adipose tissue (BAT) size and BAT size of daughters in C57BL/6J mice. However, the effects of macronutrients and paternal effects on BAT function have yet to be characterized. We investigated the effects of macronutrient composition on the BAT proteome in male mice and offspring. In fathers, >50% of the proteome was affected by macronutrients. We identified two clusters with inverse patterns that correlated with BAT mass. Notably, uncoupling protein 1 (UCP1) was reduced on low-fat diets that promoted increased BAT mass, while there were increased levels of proteins involved in protein turnover. The same diets also led to a reduction in proteins involved in purine biosynthesis (purines are often UCP1 inhibitors). We also found that paternal protein intake negatively affected basigin expression in daughters, a protein that regulates Ucp1 transcription. Our results show that macronutrients in males remodel the protein expression of BAT directly and in their daughters.

Consumption of ultra-processed food is associated with increased caloric intake and impaired health. Here, we conducted a nutrition trial (NCT05368194) with controlled, 2 × 2 crossover design and tested whether ultra-processed food impairs reproductive and metabolic fitness, with further aggravation by excess caloric intake. Comparing the response from an unprocessed to ultra-processed diet identified increased body weight and low-density lipoprotein (LDL):high-density lipoprotein (HDL) ratio, independent of caloric load. Several hormones involved in energy metabolism and spermatogenesis were affected, including decreased levels of growth/differentiation factor 15 and follicle-stimulating hormone. Sperm quality trended toward impairment, with a decrease in total motility. Differential accumulation of pollutants between the discordant diets were detected, such as decreased plasma lithium and a trend for increased levels of the phthalate mono(4-methyl-7-carboxyheptyl)phthalate (cxMINP) in serum, following the ultra-processed diet. Alteration in caloric load alone had distinct effects on the measured outcomes. This study provides evidence that consumption of ultra-processed food is detrimental for cardiometabolic and reproductive outcomes, regardless of excessive caloric intake.

A better understanding of gene regulation in metabolically unhealthy adipose tissue can provide insights into the mechanisms underlying adipose tissue dysfunction. We used RNA-seq data from a differentiation time course of lean individuals, individuals with obesity, and individuals with obesity and T2D to characterize alternative splicing in adipocyte function. Splicing was highly dynamic across adipocyte differentiation, and the dynamics of splicing were impacted by metabolic phenotype. There was little overlap between genes that were differentially spliced and those that were differentially expressed, positioning alternative splicing as an independent regulatory mechanism whose impact would be missed when looking at gene expression changes alone. We integrated our splicing results with GWAS for BMI and T2D, and found that T2D-associated variants were enriched in regions that were differentially spliced in early differentiation. These findings provide insight into the role of splicing in adipocyte differentiation and serve as a resource to guide variant-to-function studies.

Background:Genome-wide association studies (GWAS) have identified hundreds of loci underlying adult-onset asthma (AOA) and childhood-onset asthma (COA). However, the causal variants, regulatory elements, and effector genes at these loci are largely unknown. Methods:We performed heritability enrichment analysis to determine relevant cell types for AOA and COA, respectively. Next, we fine-mapped putative causal variants at AOA and COA loci. To improve the resolution of fine-mapping, we integrated ATAC-seq data in blood and lung cell types to annotate variants in candidate cis-regulatory elements (CREs). We then computationally prioritized candidate CREs underlying asthma risk, experimentally assessed their enhancer activity by massively parallel reporter assay (MPRA) in bronchial epithelial cells (BECs) and further validated a subset by luciferase assays. Combining chromatin interaction data and expression quantitative trait loci, we nominated genes targeted by candidate CREs and prioritized effector genes for AOA and COA. Results:Heritability enrichment analysis suggested a shared role of immune cells in the development of both AOA and COA while highlighting the distinct contribution of lung structural cells in COA. Functional fine-mapping uncovered 21 and 67 credible sets for AOA and COA, respectively, with only 16% shared between the two. Notably, one-third of the loci contained multiple credible sets. Our CRE prioritization strategy nominated 62 and 169 candidate CREs for AOA and COA, respectively. Over 60% of these candidate CREs showed open chromatin in multiple cell lineages, suggesting their potential pleiotropic effects in different cell types. Furthermore, COA candidate CREs were enriched for enhancers experimentally validated by MPRA in BECs. The prioritized effector genes included many genes involved in immune and inflammatory responses. Notably, multiple genes, including TNFSF4, a drug target undergoing clinical trials, were supported by two independent GWAS signals, indicating widespread allelic heterogeneity. Four out of six selected candidate CREs demonstrated allele-specific regulatory properties in luciferase assays in BECs. Conclusions:We present a comprehensive characterization of causal variants, regulatory elements, and effector genes underlying AOA and COA genetics. Our results supported a distinct genetic basis between AOA and COA and highlighted regulatory complexity at many GWAS loci marked by both extensive pleiotropy and allelic heterogeneity.

Background Inherited cardiomyopathies frequently arise from rare, highly penetrant coding variants with variable clinical expressivity. Recent biobank-scale genome-wide association studies (GWAS) suggest significant polygenic contributions to cardiovascular diseases, including cardiomyopathy. Most GWAS loci map to noncoding regions, which are poorly conserved across species, requiring a human genome context for experimental validation. Methods We created engineered heart tissues (EHTs) from human induced pluripotent stem cell (hiPSC)-derived cardiomyocytes and primary cardiac fibroblasts. We assayed single-cell gene expression and chromatin accessibility to generate comprehensive genome-wide regulatory maps. Open chromatin regions (OCRs) were integrated with chromatin contact information and used to functionally fine-map single nucleotide polymorphisms (SNPs) in cardiomyopathy GWAS. SNPs and their associated regulatory regions were assessed using reporter assays, genome editing, and expression profiling. Results Single-cell RNA-seq of EHTs confirmed populations recapitulating major cell types found in hearts, with advanced cardiomyocyte maturation compared to monolayer hiPSC-cardiomyocytes. More than 400,000 OCRs were resolved to cell type and assayed for canonical transcription factor footprints. Functional fine-mapping of GWAS loci prioritized 5817 variants, and reporter assays on select variants validated allele-specific enhancer activity. We identified a locus harboring significant GWAS signals from both dilated cardiomyopathy and left ventricle ejection fraction in an intergenic region at chr3p25.1. Several of these variants lie in OCRs participating in long range chromatin interactions with SLC6A6 and GRIP2. Haplotype-resolved and synthetic reporter assays confirmed enhancer activity and narrowed candidate SNPs. CRISPR-deletion of this region reduced expression of both SLC6A6 and GRIP2, indicating the enhancer regulates the expression of more than one gene. Conclusions EHTs derived from hiPSCs are an experimentally tractable platform for testing the function of noncoding variants as modifiers of cardiomyopathy. Variants fine-mapped from cardiomyopathies using EHT regulatory maps have functional consequences and provide a set of prioritized sites to advance the study of polygenic heart failure liability.

Cardiac ventricular arrhythmias can cause sudden death. Despite known genomic contributions, multigenic risk predictors are limited. The genetics of arrhythmias and cardiomyopathies overlap, with additional overlap with epilepsy. To improve genetic risk prediction, we assemble a cohort with non-ischemic ventricular arrhythmias and controls lacking cardiac diagnoses. Here, we integrate 18 polygenic scores; variants from clinical gene panels for coding regions of cardiomyopathy, arrhythmia, and epilepsy genes; and noncoding regulatory regions mapping to those genes. Polygenic scores alone hold prognostic value. Rare coding variants identify cumulative risk extending beyond known pathogenic/likely pathogenic variants. We also find enrichment of ultrarare regulatory variation. A risk predictor that combines all variant classes outperforms any single class or subset and replicates in a validation cohort. This combined genomic arrhythmia propensity score (GAPS) identifies high-risk individuals even among those who lack known primary pathogenic variants. This integrated approach serves as a model for other complex traits.

Asthma, allergic rhinitis, and atopic dermatitis are common, complex traits that are frequently co-morbid and have strong genetic correlation. However, the extent to which genome-wide genetic correlation between traits reflects shared causal variants or risk genes remains unclear. To address this question, we used functional fine-mapping. We generated genomic annotations from primary cells treated with immunomodulatory stimuli, then used these data to identify likely causal variants mediating genetic risk for allergic diseases including adult-onset asthma, childhood-onset asthma, allergic rhinitis, and atopic dermatitis. After identifying likely causal variants, we combined our functional annotations with expression quantitative trait loci and activity-by-contact modeling to predict effector genes. We confirmed a high degree of genetic correlation between GWAS loci for allergic diseases, but on the local level very few of the hundreds of likely causal variants identified by functional fine-mapping were shared between diseases. Instead, we found that each allergic disease was associated with a set of mostly unique variants. Nonetheless, nearly 40% of effector genes predicted to be the regulatory targets of these variants were shared between more than one allergic disease. When we tested candidate regulatory elements containing likely causal variants, we found that regulatory elements demonstrated variable allele-specific enhancer activity depending on the cell type in which they were tested. Overall, our findings suggest a highly pleiotropic gene regulatory network underlying allergic diseases, wherein disease-specific risk variants affect different regulatory elements that converge on the same set of target genes.

Vascular homeostasis and pathophysiology are tightly regulated by mechanical forces generated by hemodynamics. Vascular disorders such as atherosclerotic diseases largely occur at curvatures and bifurcations where disturbed blood flow activates endothelial cells while unidirectional flow at the straight part of vessels promotes endothelial health. Integrated analysis of the endothelial transcriptome, the 3D epigenome, and human genetics systematically identified the SNP-enriched cistrome in vascular endothelium subjected to well-defined atherosclerosis-prone disturbed flow or atherosclerosis-protective unidirectional flow. Our results characterized the endothelial typical- and super-enhancers and underscored the critical regulatory role of flow-sensitive endothelial super-enhancers. CRISPR interference and activation validated the function of a previously unrecognized unidirectional flow-induced super-enhancer that upregulates antioxidant genes NQO1, CYB5B, and WWP2, and a disturbed flow-induced super-enhancer in endothelium which drives prothrombotic genes EDN1 and HIVEP in vascular endothelium. Our results employing multiomics identify the cis-regulatory architecture of the flow-sensitive endothelial epigenome related to atherosclerosis and highlight the regulatory role of super-enhancers in mechanotransduction mechanisms.

Paternal diet can influence the phenotype of the next generation, yet, the dietary components inducing specific responses in the offspring are not identified. Here, we use the Nutritional Geometry Framework to determine the effects of pre-conception paternal dietary macronutrient balance on offspring metabolic and behavioral traits in mice. Ten isocaloric diets varying in the relative proportion of protein, fats, and carbohydrates are fed to male mice prior to mating. Dams and offspring are fed standard chow and never exposed to treatment diets. Body fat in female offspring is positively associated with the paternal consumption of fat, while in male offspring, an anxiety-like phenotype is associated to paternal diets low in protein and high in carbohydrates. Our study uncovers that the nature and the magnitude of paternal effects are driven by interactions between macronutrient balance and energy intake and are not solely the result of over- or undernutrition. The dietary factors causing varying intergenerational responses are not fully identified. Here, the authors show that the relative proportion of protein, fats, and carbohydrates in paternal diets before conception differentially influences the phenotype of the next-generation offspring on energy metabolism and behaviour.

Diet is a key lifestyle component that influences metabolic health through several factors, including total energy intake and macronutrient composition. While the impact of caloric intake on gene expression and physiological phenomena in various tissues is well described, the influence of dietary macronutrient composition on these parameters is less well studied. Here, we use the Nutritional Geometry framework to investigate the role of macronutrient composition on metabolic function and gene regulation in adipose tissue. Using ten isocaloric diets that vary systematically in their proportion of energy from fat, protein, and carbohydrates, we find that gene expression and splicing are highly responsive to macronutrient composition, with distinct sets of genes regulated by different macronutrient interactions. Specifically, the expression of many genes associated with Bardet-Biedl syndrome is responsive to dietary fat content. Splicing and expression changes occur in largely separate gene sets, highlighting distinct mechanisms by which dietary composition influences the transcriptome and emphasizing the importance of considering splicing changes to more fully capture the gene regulation response to environmental changes such as diet. Our study provides insight into the gene regulation plasticity of adipose tissue in response to macronutrient composition, beyond the already well-characterized response to caloric intake.

Abstract IL-33 is abundantly expressed in the human lung, where it is involved in pathogen defense, barrier homeostasis, and development of type 2 allergic responses. We recently identified a 5 kb region within a GWAS-defined segment that acts as an enhancer barrier element in vivo and in vitro. We showed that the asthma-associated SNP rs1888909, located within the 5 kb region, is associated with IL33 gene expression in human airway epithelial cells and IL-33 protein in human plasma. To study this human regulatory region in vivo, we engineered a novel IL33 reporter mouse containing the human 5kb regulatory element to reflect human IL33 expression. As expected, human and mouse IL33 reporters were primarily expressed in non-overlapping cell types: human IL33 reporter was mostly expressed in vascular and lymphatic endothelium, while mouse IL33 reporter was expressed in ATII epithelium. Interestingly, we demonstrate negative regulation of human IL33 in lung endothelium during house dust mite (HDM)-induced allergic airway inflammation, which was dependent on the human 5kb regulatory region. Similar downregulation of endothelium IL-33 was induced with only IL-33 treatment in vivo and in vitro. We found that this IL-33-induced negative feedback loop worked through the induction of cytoplasmic IL33 mRNA instability. Together, these data reveal the importance of the asthma-associated human 5kb enhancer element in regulating human IL33 expression in a cell type- and context-dependent manner.