Biology subjects

Rader, D. J.

Publications and source records attributed to Rader, D. J..

At least 19 recordsLinked to original sources

bioRxiv2025

Modeling Fibrosis with MASH Patient Liver-Derived Organoids.

Metabolic dysfunction-associated steatohepatitis (MASH) can lead to liver fibrosis and cirrhosis ultimately leading to liver transplantation or death. Therapeutic options for MASH-associated fibrosis are limited in part because of the lack of good model systems. To address this challenge, we developed a 3D MASH liver fibrosis model by using organoids derived from MASH patient liver co-cultured with human liver-derived hepatic stellate cells (HSC) and human peripheral blood monocytes (MC). Spontaneous self-assembly resulted in fibrotic scar-like 3D structures with senescent parenchymal cells, proliferating collagen secreting myofibroblasts (MFB) and proinflammatory TREM2+ scar-associated macrophages (MP). Single cell RNA sequencing suggested high similarity with MASH patient liver fibrotic scars. Lipid nanoparticles (LNPs) formulated with anti-YAP1siRNA could specifically and efficiently knockdown YAP1 in the MFBs, resulting in MFB senescence, a desirable therapeutic goal. This MASH patient liver-derived fibrosis model opens novel avenues towards testing treatments for MASH-associated liver fibrosis with reduced adverse effects.

bioengineering↗

bioRxiv2025

OxLDL-targeted Chimeric Antigen Receptor T Regulatory Cells Reduce Atherosclerotic Plaque Development

Cardiovascular disease caused by atherosclerosis is responsible for 18 million deaths annually, highlighting a significant need for new medical therapies, especially for patients ineligible for surgical interventions. Atherosclerosis is driven by the accumulation of low-density lipoprotein (LDL) and the formation of foam cells, accompanied by oxidative stress and the deposition of oxidized LDL (OxLDL), a pro-inflammatory molecule. Lowering LDL is the mainstay of current medical treatment in addition to blood pressure control and lifestyle changes, but to date, specifically targeting the inflammatory pathways contributing to plaque development without significant systemic side effects has not been feasible. Over the past decade, chimeric antigen receptor (CAR) T cells have treated cancer and restored immune imbalance in autoimmune diseases in patients and resolved cardiac fibrosis in preclinical models. Using an inducible T regulatory cell (Treg) platform, we created an anti-OxLDL-specific CAR Treg therapy that exerts cell- and cytokine-mediated immunosuppression to reduce macrophage-foam cell formation in vitro. Murine anti-OxLDL CAR Tregs inhibited 80% of atherosclerotic plaque formation in immunocompetent mouse models of hyperlipidemia and atherosclerosis. These studies illustrate the potential of anti-OxLDL CAR Tregs to mitigate the inflammation and plaque deposition associated with OxLDL, potentially offering a new therapeutic option for atherosclerosis.

synthetic biology↗

bioRxiv2024

Sleep and Activity Patterns in Autism Spectrum Disorder

BackgroundAutism spectrum disorder (ASD) is a highly heritable and heterogeneous neurodevelopmental disorder characterized by impaired social interactions, repetitive behaviors, and a wide range of comorbidities. Between 44-83% of autistic individuals report sleep disturbances, which may share an underlying neurodevelopmental basis with ASD. MethodsWe recruited 382 ASD individuals and 223 of their family members to obtain quantitative ASD-related traits and wearable device-based accelerometer data spanning three consecutive weeks. An unbiased approach identifying traits associated with ASD was achieved by applying the elastic net machine learning algorithm with five-fold cross-validation on 6,878 days of data. The relationship between sleep and physical activity traits was examined through linear mixed-effects regressions using each night of data. ResultsThis analysis yielded 59 out of 242 actimetry measures associated with ASD status in the training set, which were validated in a test set (AUC: 0.777). For several of these traits (e.g. total light physical activity), the day-to-day variability, in addition to the mean, was associated with ASD. Individuals with ASD were found to have a stronger correlation between physical activity and sleep, where less physical activity decreased their sleep more significantly than that of their non-ASD relatives. ConclusionsThe average duration of sleep/physical activity and the variation in the average duration of sleep/physical activity strongly predict ASD status. Physical activity measures were correlated with sleep quality, traits, and regularity, with ASD individuals having stronger correlations. Interventional studies are warranted to investigate whether improvements in both sleep and increased physical activity may improve the core symptoms of ASD.

neuroscience↗

bioRxiv2024

An aortic hemodynamic fingerprint reduced order modeling analysis reveals traits associated with vascular disease in a medical biobank

PurposeTo determine the clinical relevance of reduced order model (ROM) aortic hemodynamic imaging-derived phenotypes (IDPs) for a range of flow conditions applied to computed tomography (CT) scan data in the Penn Medicine Biobank (PMBB). MethodsThe human thoracic aorta was automatically segmented in 3,204 chest CT scans from patients in the Penn Medicine Biobank (PMBB) patients using deep learning. Thoracic aorta anatomic IDPs such as aortic diameter and length were computed. Resistance, and flow boundary conditions, were varied, resulting in 125,000 ROM simulations, producing a fingerprint of aortic hemodynamics IDPs for a range of flow conditions. To determine the clinical relevance of the aortic hemodynamic fingerprint, untargeted phenome wide association studies (PheWAS) for disease conditions were performed using aortic geometries and pulse pressure as IDPs. ResultsBy utilizing patient metadata from the PMBB, the human aortic radius for different age groups over a normalized radius was visualized, showing how the vessel deforms with age, as well as other characteristic geometric information. The average radius of the ascending thoracic aortic data set was 26.6 {+/-} 3.1 mm, with an average length of 310 {+/-} 37 mm. A combination of pathology codes (phecodes) and hemodynamic simulations were utilized to develop a relationship between them, showing a strong relationship between the resulting pulse pressure and diseases relating to aortic aneurysms and heart valve disorders. The average pulse pressure calculated by the model was 22.5 {+/-} 8.5 mmHg, with the maximum pressure modeled by the system being 201 mmHg, with the minimum being 63.6 mmHg. The pulse pressures of the most significant phecodes were examined for patients with and without the condition, showing a slight separation between the two cases. The pulse pressure was also slightly negatively correlated with the calculated tapering angle of the ascending thoracic aorta. ConclusionsROM hemodynamic simulations can be applied to aortic imaging traits from thoracic imaging data in a medical biobank. The derived hemodynamic fingerprint, describing the response of the aorta to a range of flow conditions, shows clinically relevant associations with disease.

bioengineering↗

bioRxiv2023

PPP1R3B is a metabolic switch that shifts hepatic energy storage from lipid to glycogen

Obesity is a growing worldwide epidemic that carries numerous metabolic complications including increased risk of type 2 diabetes (T2D), cardiovascular disease (CVD), and non-alcoholic fatty liver disease (NAFLD). Multiple genome-wide association studies (GWAS) have associated the PPP1R3B locus with cardiometabolic traits including fasting glucose and insulin levels (T2D traits), plasma lipids (CVD traits), and indications of hepatic steatosis and liver damage (NAFLD traits)1-5. The PPP1R3B gene encodes the glycogen regulatory protein PPP1R3B (also known as GL) which has an established role in liver glycogen metabolism and plasma glucose homeostasis6,7. The metabolic and NAFLD GWAS single nucleotide polymorphisms (SNPs) in this region, which are all in high linkage disequilibrium, result in increased liver PPP1R3B expression and hepatic glycogen accumulation, but have provided conflicting results on the impacts on hepatic steatosis and liver damage. Here we investigate the consequences of both Ppp1r3b overexpression and deletion in mouse and cell models and find that dysregulated Ppp1r3b expression in either direction promotes metabolic dysfunction and liver injury. Hepatocyte overexpression of Ppp1r3b increases hepatic glycogen storage, prolongs fasting blood glucose levels, and confers protection from hepatic steatosis, but increases plasma ALT in aged animals. Conversely, deletion of hepatocyte Ppp1r3b eliminates hepatic glycogen, causes impaired glucose disposal, and results in hepatic steatosis with age or high sucrose diet. We investigated the metabolic pathways contributing to steatosis and found that Ppp1r3b deletion and diminished glycogenesis diverts the storage of exogenous glucose to hepatic triglycerides (TG), and stored liver lipids are preferentially used for energy during fasting through lipid oxidation and ketogenesis. Further, we interrogated two large human biobank cohorts and found carriers of SNPs associated with increased PPP1R3B expression have increased plasma glucose, decreased hepatic fat, and lower plasma lipids, while putative loss-of-function (pLoF) variant carriers have increased hepatic fat and elevated plasma ketones and lipids, consistent with the results seen in our mouse models. These findings suggest hepatic PPP1R3B serves as a metabolic switch favoring hepatic energy storage as glycogen instead of TG.

molecular biology↗

bioRxiv2023

Prior vaccination enhances immune responses during SARS-CoV-2 breakthrough infection with early activation of memory T cells followed by production of potent neutralizing antibodies

SARS-CoV-2 infection of vaccinated individuals is increasingly common but rarely results in severe disease, likely due to the enhanced potency and accelerated kinetics of memory immune responses. However, there have been few opportunities to rigorously study early recall responses during human viral infection. To better understand human immune memory and identify potential mediators of lasting vaccine efficacy, we used high-dimensional flow cytometry and SARS-CoV-2 antigen probes to examine immune responses in longitudinal samples from vaccinated individuals infected during the Omicron wave. These studies revealed heightened Spike-specific responses during infection of vaccinated compared to unvaccinated individuals. Spike-specific CD4 T cells and plasmablasts expanded and CD8 T cells were robustly activated during the first week. In contrast, memory B cell activation, neutralizing antibody production, and primary responses to non-Spike antigens occurred during the second week. Collectively, these data demonstrate the functionality of vaccine-primed immune memory and highlight memory T cells as rapid responders during SARS-CoV-2 infection.

immunology↗

bioRxiv2020

Disrupting upstream translation in mRNAs leads to loss-of function associated with human disease

Ribosome-profiling has uncovered pervasive translation in 5UTRs, however the biological significance of this phenomenon remains unclear. Using genetic variation from 71,702 human genomes, we assess patterns of selection in translated upstream open reading frames (uORFs) in 5UTRs. We show that uORF variants introducing new stop codons, or strengthening existing stop codons, are under strong negative selection comparable to protein-coding missense variants. Using these variants, we map and validate new gene-disease associations in two independent biobanks containing exome sequencing from 10,900 and 32,268 individuals respectively, and demonstrate their impact on gene expression in human cells. Our results establish new mechanisms relating uORF variation to loss-of-function of downstream genes, and demonstrate that translated uORFs are genetically constrained regulatory elements in 40% of human genes.

genomics↗

bioRxiv2020

ApoC-III helical structure determines its ability to bind plasma lipoproteins and inhibit Lipoprotein Lipase-mediated triglyceride lipolysis.

In humans, apolipoprotein C-III (apoC-III) plasma levels have been associated with increased risk of cardiovascular disease. This association is in part explained by the effects of apoC-III on triglyceride (TG) metabolism; apoC-III raises plasma TG by increasing very low density lipoprotein (VLDL) secretion, inhibiting lipoprotein lipase (LPL)-mediated TG lipolysis, and impairing the removal of triglyceride-rich lipoprotein (TRL) remnants from the circulation. In this study, we explored the structure-function relationship the interaction of apoC-III with plasma lipoproteins and its ultimate impact on LPL activity. The structural and functional properties of wild-type (WT) apoC-III were compared with two missense variants previously associated with lower (A23T) and higher (Q38K) plasma TG. ApoC-III in the lipid-free state is unstructured but its helix content and stability increases when bound to lipid. Lipid-bound apoC-III contains two alpha helices spanning residues amino acids 11 - 38 (helix 1) and 44 – 64 (helix 2). Investigation of the structural and functional consequences of the A23T and Q38K variants showed that these amino acid substitutions within helix 1 do not significantly alter the stability of the helical structure but affect its hydrophilic-lipophilic properties. The A23T substitution impairs lipoprotein binding capacity, reduces LPL inhibition, and ultimately leads to lower plasma TG levels. Conversely, the Q to K substitution at position 38 enhances the lipid affinity of helix 1, increases TRL binding capacity and LPL inhibition, and is associated with hypertriglyceridemia. This study indicates that structural modifications that perturb the hydrophilic/lipophilic properties of the alpha helices can modulate the hypertriglyceridemic effects of apoC-III.Competing Interest StatementDJR is a a co-founder of Staten Biotechnology, he is a member of the Scientific Advisory Boards of Alnylam, Novartis, and Pfizer, and he was previously a consultant for Akcea. The other authors declare no competing financial interests.View Full Text

biochemistry↗

bioRxiv2019

Polygenic risk of psychiatric disorders exhibits cross-trait associations in electronic health record data

ObjectivePrediction of disease risk is a key component of precision medicine. Common, complex traits such as psychiatric disorders have a complex polygenic architecture making the identification of a single risk predictor difficult. Polygenic risk scores (PRS) denoting the sum of an individuals genetic liability for a disorder are a promising biomarker for psychiatric disorders, but require evaluation in a clinical setting. MethodsWe develop PRS for six psychiatric disorders (schizophrenia, bipolar disorder, major depressive disorder, cross disorder, attention-deficit/hyperactivity disorder, anorexia nervosa) and 17 non-psychiatric traits in over 10,000 individuals from the Penn Medicine Biobank with accompanying electronic health records. We perform phenome-wide association analyses to test their association across disease categories. ResultsFour of the six psychiatric PRS were associated with their primary phenotypes (odds ratios between 1.2-1.6). Individuals in the highest quintile of risk had between 1.4-2.9 times higher odds of the disorder than the remaining 80% of individuals. Cross-trait associations were identified both within the psychiatric domain and across trait domains. PRS for coronary artery disease and years of education were significantly associated with psychiatric disorders, largely driven by an association with tobacco use disorder. ConclusionsWe demonstrate that the genetic architecture of common psychiatric disorders identified in a clinical setting confirms that which has been derived from large consortia. Even though the risk associated is low in this context, these results suggest that as identification of genetic markers proceeds, PRS is a promising approach for prediction of psychiatric disorders and associated conditions in clinical registries.

genetics↗

bioRxiv2019

Exome-by-phenome-wide rare variant gene burden association with electronic health record phenotypes

BackgroundBy coupling large-scale DNA sequencing with electronic health records (EHR), \"genome-first\" approaches can enhance our understanding of the contribution of rare genetic variants to disease. Aggregating rare, loss-of-function variants in a candidate gene into a \"gene burden\" to test for association with EHR phenotypes can identify both known and novel clinical implications for the gene in human disease. However, this methodology has not yet been applied on both an exome-wide and phenome-wide scale, and the clinical ontologies of rare loss-of-function variants in many genes have yet to be described.\n\nMethodsWe leveraged whole exome sequencing (WES) data in participants (N=11,451) in the Penn Medicine Biobank (PMBB) to address on an exome-wide scale the association of a burden of rare loss-of-function variants in each gene with diverse EHR phenotypes using a phenome-wide association study (PheWAS) approach. For discovery, we collapsed rare (minor allele frequency (MAF) [≤] 0.1%) predicted loss-of-function (pLOF) variants (i.e. frameshift insertions/deletions, gain/loss of stop codon, or splice site disruption) per gene to perform a gene burden PheWAS. Subsequent evaluation of the significant gene burden associations was done by collapsing rare (MAF [≤] 0.1%) missense variants with Rare Exonic Variant Ensemble Learner (REVEL) scores [≥] 0.5 into corresponding yet distinct gene burdens, as well as interrogation of individual low-frequency to common (MAF > 0.1%) pLOF variants and missense variants with REVEL[≥] 0.5. We replicated our findings using the UK Biobanks (UKBB) whole exome sequence dataset (N=49,960).\n\nResultsFrom the pLOF-based discovery phase, we identified 106 gene burdens with phenotype associations at p<10-6 from our exome-by-phenome-wide association studies. Positive-control associations included TTN (cardiomyopathy, p=7.83E-13), MYBPC3 (hypertrophic cardiomyopathy, p=3.48E-15), CFTR (cystic fibrosis, p=1.05E-15), CYP2D6 (adverse effects due to opiates/narcotics, p=1.50E-09), and BRCA2 (breast cancer, p=1.36E-07). Of the 106 genes, 12 gene-phenotype relationships were also detected by REVEL-informed missense-based gene burdens and 19 by single-variant analyses, demonstrating the robustness of these gene-phenotype relationships. Three genes showed evidence of association using both additional methods (BRCA1, CFTR, TGM6), leading to a total of 28 robust gene-phenotype associations within PMBB. Furthermore, replication studies in UKBB validated 30 of 106 gene burden associations, of which 12 demonstrated robustness in PMBB.\n\nConclusionOur study presents 12 exome-by-phenome-wide robust gene-phenotype associations, which include three proof-of-concept associations and nine novel findings. We show the value of aggregating rare pLOF variants into gene burdens on an exome-wide scale for unbiased association with EHR phenotypes to identify novel clinical ontologies of human genes. Furthermore, we show the significance of evaluating gene burden associations through complementary, yet non-overlapping genetic association studies from the same dataset. Our results suggest that this approach applied to even larger cohorts of individuals with WES or whole-genome sequencing data linked to EHR phenotype data will yield many new insights into the relationship of genetic variation and disease phenotypes.

genomics↗

bioRxiv2019

NASH patient liver derived organoids exhibit patient specific NASH phenotypes and drug responses.

To determine if patient liver derived organoids can in principle be a useful experimental model for non alcoholic staetohepatitis (NASH), we derived to our knowledge for the first time bipotent ductal organoids from endstage NASH patient livers, and for comparison from normal donor livers. We found that all tested NASH liver derived organoids exhibited a profound failure to dedifferentiate from the hepatic state back to the biliary state, consistent with the known poor regenerative capacity of NASH livers. Indeed, RNAseq on all tested NASH organoid populations confirmed down regulation of multiple cell cycle pathways. NASH liver derived hepatically differentiated organoids can slowly expand as monolayers, significantly simplifying microscopic quantitation: The monolayers show variable, but overall significantly increased lipid droplet accumulation in response to free fatty acids. Transcriptome analysis of NASH organoids reveals strong upregulation of a wide variety of pro inflammatory pathways in a NASH patient specific manner. Surprisingly, NASH liver derived organoids are highly diverse not only regarding their cytochrome cytochrome p450 metabolism and inflammatory response, but also react differentially to known antisteatotic, anti inflammatory and antifibrotic drugs, raising the possibility of using NASH patient liver biopsy derived organoids for personalized drug screening and therapy.\n\nOne Sentence SummaryNASH patient liver derived organoids replicate NASH liver phenotypes in a patient specific manner and exhibit profound differences in their response to drugs that are currently used in NASH clinical trials.

cell biology↗

bioRxiv2019

Heterozygous ATP-binding Cassette Transporter G5 Gene Deficiency and Risk of Coronary Artery Disease

BackgroundFamilial sitosterolemia is a rare, recessive Mendelian disorder characterized by hyperabsorption and decreased biliary excretion of dietary sterols. Affected individuals typically have complete genetic deficiency - homozygous loss-of-function (LoF) variants -- in the ATP-binding cassette transporter G5 (ABCG5) or G8 (ABCG8) genes, and have substantially elevated plasma sitosterol and low-density lipoprotein cholesterol (LDL-C) levels. The impact of partial genetic deficiency of ABCG5 or ABCG8, as occurs in heterozygous carriers of LoF variants, on LDL-C and risk of coronary artery disease (CAD) has remained uncertain.\n\nMethodsWe first recruited nine sitosterolemia families, identified causative LoF variants in ABCG5 or ABCG8, and evaluated the associations of these ABCG5 or ABCG8 LoF variants with plasma phytosterols and lipid levels. We next assessed for LoF variants in ABCG5 or ABCG8 in CAD cases (n=29,361) versus controls (n=357,326). We tested the association of rare LoF variants in ABCG5 or ABCG8 with blood lipids and risk for CAD. Rare LoF variants were defined as protein-truncating variants with minor allele frequency less than 0.1% in ABCG5 or ABCG8.\n\nResultsIn sitosterolemia families, seven pedigrees harbored causative LoF variants in ABCG5 and two pedigrees in ABCG8. Homozygous LoF variants in either ABCG5 or ABCG8 led to marked elevations in sitosterol and LDL-C. Of those sitosterolemia families, heterozygous carriers of ABCG5 LoF variants exhibited increased sitosterol and LDL-C levels compared to non-carriers. Within the large-scale CAD case-control cohorts, prevalence of rare LoF variants in ABCG5 and in ABCG8 were approximately 0.1% each. ABCG5 heterozygous LoF variant carriers had significantly elevated LDL-C levels (24.7 mg/dL; 95% confidence interval [CI] 14 to 35; P=1.1x10-6), and were at two-fold increased risk of CAD (odds ratio 2.06, 95% CI 1.27 to 3.35; P=0.004). By contrast, ABCG8 heterozygous LoF carrier status was not associated with increased LDL-C or risk of CAD.\n\nConclusionsAlthough familial sitosterolemia is traditionally considered as a recessive disorder, we observed that heterozygous carriers of a LoF variant in ABCG5 had significantly increased sitosterol and LDL-C levels and a two-fold increase in risk of CAD.

genetics↗

bioRxiv2019

Polygenic Risk Scores for Cardio-renal-metabolic Diseases in the Penn Medicine Biobank

Cardio-renal-metabolic (CaReMe) conditions are common and the leading cause of mortality around the world. Genome-wide association studies have shown that these diseases are polygenic and share many genetic risk factors. Identifying individuals at high genetic risk will allow us to target prevention and treatment strategies. Polygenic risk scores (PRS) are aggregate weighted counts that can demonstrate an individuals genetic liability for disease. However, current PRS are often based on European ancestry individuals, limiting the implementation of precision medicine efforts in diverse populations. In this study, we develop PRS for six diseases and traits related to cardio-renal-metabolic disease in the Penn Medicine Biobank. We investigate their performance in both European and African ancestry individuals, and identify genetic and phenotypic overlap within these conditions. We find that genetic risk is associated with the primary phenotype in both ancestries, but this does not translate into a model of predictive value in African ancestry individuals. We conclude that future research should prioritize genetic studies in diverse ancestries in order to address this disparity.

genomics↗

bioRxiv2019

The role of lipoprotein subfractions in coronary artery disease: A Mendelian randomization study

Recent genetic data can offer important insights into the roles of lipoprotein subfractions and particle sizes in preventing coronary artery disease (CAD), as previous observational studies have often reported conflicting results. In this study, we first used the LD score regression to estimate the genetic correlation of 77 subfraction traits with traditional lipid profile and identified 27 traits that may involve distinct genetic mechanisms. We then used Mendelian randomization (MR) to estimate the causal effect of these traits on the risk of CAD. In univariable MR, the concentration and content of medium high-density lipoprotein (HDL) particles showed a protective effect against coronary artery disease. The effect was not attenuated in multivariable MR that adjusted for traditional lipid profile. The multivariable MR analyses also found that small HDL particles and smaller mean HDL particle diameter may have a protective effect. We identified four genetic markers for HDL particle size and CAD.

genetics↗

bioRxiv2019

Myeloid Tribbles 1 induces early atherosclerosis via enhanced foam cell expansion

Macrophages drive atherosclerotic plaque progression and rupture, hence attenuating their atherosclerosis-inducing properties holds promise for reducing coronary heart disease (CHD). Recent studies in mouse models have demonstrated that Tribbles 1 (Trib1) regulates macrophage phenotype and shows that Trib1 deficiency increases plasma cholesterol and triglyceride levels, suggesting that reduced TRIB1 expression mediates the strong genetic association between the TRIB1 locus and increased CHD risk in man. However, we report here that myeloid-specific Trib1 (mTrib1) deficiency reduces early atheroma formation and that mTrib1 transgene expression increases atherogenesis. Mechanistically, mTrib1 increased macrophage lipid accumulation and the expression of a critical receptor (OLR1), promoting oxidized low density lipoprotein uptake and the formation of lipid-laden foam cells. As TRIB1 and OLR1 RNA levels were also strongly correlated in human macrophages, we suggest that a conserved, TRIB1-mediated mechanism drives foam cell formation in atherosclerotic plaque and that inhibiting mTRIB1 could be used therapeutically to reduce CHD.

immunology↗

bioRxiv2019

Genome-wide Association Study of Alcohol Consumption and Use Disorder in Multiple Populations (N = 274,424)

Although alcohol consumption level and alcohol use disorder (AUD) diagnosis are both moderately heritable, their genetic risks and overlap are not well understood. We conducted genome-wide association studies of these traits using longitudinal Alcohol Use Disorder Identification Test-Consumption (AUDIT-C) scores (reflecting alcohol consumption) and AUD diagnoses from electronic health records (EHRs) in a single, large multi-ancestry Million Veteran Program sample. Meta-analysis across population groups (N = 274,424) identified 18 genome-wide significant loci, 5 of which were associated with both traits and 13 with either AUDIT-C (N = 8) or AUD (N = 5). A significant genetic correlation between the traits reflects this overlap. However, downstream analyses revealed biologically meaningful points of divergence. Cell-type group partitioning heritability enrichment analyses indicated that central nervous system was the most significant cell type for AUDIT-C and the only significant cell type for AUD. Polygenic risk scores (PRS) for both traits were associated with alcohol-related disorders in two independent samples. Genetic correlations for 188 non-alcohol-related traits were significantly different for the two traits, as were the phenotypes associated with the traits polygenic risk scores. We conclude that EHR-derived, longitudinal, repeated measures of alcohol consumption level and AUD diagnosis can facilitate genetic discovery and help to elucidate the relationship between drinking level and AUD risk. Finally, although heavy drinking is a key risk factor for AUD, it is not a sufficient cause of the disorder.

genetics↗

bioRxiv2018

Genetic And Epigenetic Fine Mapping Of Complex Trait Associated Loci In The Human Liver

Deciphering the impact of genetic variation on gene regulation is fundamental to understanding common, complex human diseases. Although histone modifications are important markers of gene regulatory regions of the genome, any specific histone modification has not been assayed in more than a few individuals in the human liver. As a result, the impacts of genetic variation that direct histone modification states in the liver are poorly understood. Here, we generate the most comprehensive genome-wide dataset of two epigenetic marks, H3K4me3 and H3K27ac, and annotate thousands of putative regulatory elements in the human liver. We integrate these findings with genome-wide gene expression data collected from the same human liver tissues and high-resolution promoter-focused chromatin interaction maps collected from human liver-derived HepG2 cells. We demonstrate widespread functional consequences of natural genetic variation on putative regulatory element activity and gene expression levels. Leveraging these extensive datasets, we fine-map a total of 77 GWAS loci that have been associated with at least one complex phenotype. Our results contribute to the repertoire of genes and regulatory mechanisms governing complex disease development and further the basic understanding of genetic and epigenetic regulation of gene expression in the human liver tissue.

genetics↗

bioRxiv2018

RNA-binding protein A1CF modulates plasma triglyceride levels through posttranscriptional regulation of stress-induced VLDL secretion

BackgroundA recent human exome-chip study on plasma lipids identified a missense mutation in the A1CF (APOBEC1 complementation factor) gene that is associated with elevated triglyceride (TG) levels, but how A1CF, an RNA binding protein, influences plasma TG is unknown.\n\nMethodsWe generated A1cf knockout (A1cf -/-) mice and knock-in mice homozygous for the TG-associated Gly398Ser mutation (A1cfGS/GS), determined lipid phenotypes, and assessed TG physiology through measurements of clearance and secretion. We further identified A1CFs RNA binding targets using enhanced cross-linking and immunoprecipitation sequencing of cultured HepG2 cells and investigated pathways enriched for these targets. Transcriptomic effects of A1CF deficiency were evaluated through RNA sequencing and analyses for differential expression, alternative splicing, and RNA editing.\n\nResultsBoth A1cf -/-and A1cfGS/GS mice exhibited increased fasting plasma TG, establishing that the TG phenotype is due to A1CF loss of function. In vivo TG secretion and clearance studies revealed increased TG secretion without changes in clearance in A1cf -/-mice. Increased VLDL-apoB secretion was also seen in A1cf -/-rat hepatoma cells, but no increase in apoB synthesis was observed. This phenotype was seen without significant shifts in apoB-100/apoB-48 in A1CF deficiency. To discover novel pathways for A1CFs role in TG metabolism, we identified A1CFs RNA binding targets, which were enriched for pathways related to proteasomal catabolism and endoplasmic reticulum (ER) stress. Indeed, proteasomal inhibition led to increased cellular stress in A1cf -/-cells, and higher expression of ER-stress protein GRP78 was observed in resting A1cf -/-cells. RNA-seq of whole livers from wild-type and A1cf -/-mice revealed that pro-inflammatory, not lipogenesis, genes were upregulated as a secondary effect of A1CF deficiency. Differential alternative splicing (AS) analysis and RNA editing analysis revealed that genes involved in cellular stress and metabolism underwent differential changes in A1CF deficiency, and top A1CF binding target proteins with relevance to intracellular stress were differentially expressed on the protein but not mRNA level, implicating multiple mechanisms by which A1CF influences TG secretion.\n\nConclusionsThese data suggest an important role for A1CF in mediating VLDL-TG secretion through regulating intracellular stress.

genomics↗