Risk factors affecting polygenic score performance across diverse cohorts

Apart from ancestry, personal or environmental covariates may contribute to differences in polygenic score (PGS) performance. We analyzed effects of covariate stratification and interaction on body mass index (BMI) PGS (PGS BMI ) across four cohorts of European (N=491,111) and African (N=21,612) ancestry. Stratifying on binary covariates and quintiles for continuous covariates, 18/62 covariates had significant and replicable R 2 differences among strata. Covariates with the largest differences included age, sex, blood lipids, physical activity, and alcohol consumption, with R 2 being nearly double between best and worst performing quintiles for certain covariates. 28 covariates had significant PGS BMI -covariate interaction effects, modifying PGS BMI effects by nearly 20% per standard deviation change. We observed overlap between covariates that had significant R 2 differences among strata and interaction effects - across all covariates, their main effects on BMI were correlated with their maximum R 2 differences and interaction effects (0.56 and 0.58, respectively), suggesting high-PGS BMI individuals have highest R 2 and increase in PGS effect. Using quantile regression, we show the effect of PGS BMI increases as BMI itself increases, and that these differences in effects are directly related to differences in R 2 when stratifying by different covariates. Given significant and replicable evidence for context-specific PGS BMI performance and effects, we investigated ways to increase model performance taking into account non-linear effects. Machine learning models (neural networks) increased relative model R 2 (mean 23%) across datasets. Finally, creating PGS BMI directly from GxAge GWAS effects increased relative R 2 by 7.8%. These results demonstrate that certain covariates, especially those most associated with BMI, significantly affect both PGS BMI performance and effects across diverse cohorts and ancestries, and we provide avenues to improve model performance that consider these effects.

Genome-wide association analyses define pathogenic signaling pathways and prioritize drug targets for IgA nephropathy

IgA nephropathy (IgAN) is a progressive form of kidney disease defined by glomerular deposition of IgA. Here we performed a genome-wide association study of 10,146 kidney-biopsy-diagnosed IgAN cases and 28,751 controls across 17 international cohorts. We defined 30 genome-wide significant risk loci explaining 11% of disease risk. A total of 16 loci were new, including TNFSF4/TNFSF18, REL, CD28, PF4V1, LY86, LYN, ANXA3, TNFSF8/TNFSF15, REEP3, ZMIZ1, OVOL1/RELA, ETS1, IGH, IRF8, TNFRSF13B and FCAR. The risk loci were enriched in gene orthologs causing abnormal IgA levels when genetically manipulated in mice. We also observed a positive genetic correlation between IgAN and serum IgA levels. High polygenic score for IgAN was associated with earlier onset of kidney failure. In a comprehensive functional annotation analysis of candidate causal genes, we observed convergence of biological candidates on a common set of inflammatory signaling pathways and cytokine ligand-receptor pairs, prioritizing potential new drug targets.

Genome-wide admixture and association analysis identifies African ancestry-specific risk loci of eosinophilic esophagitis in African Americans

BACKGROUND

Eosinophilic esophagitis (EoE), a chronic allergic inflammatory disease, is linked to multiple genetic risk factors, but studies have focused on populations of European ancestry. Few studies have assessed Black or African American (AA) populations for loci involved in EoE susceptibility.

OBJECTIVE

We performed admixture mapping (AM) and genome-wide association study (GWAS) of EoE using participants from AA populations.

METHODS

We conducted AM and GWAS of EoE using 137 EoE cases and 1465 healthy controls from the AA population. Samples were genotyped using molecular evolutionary genetics analysis (MEGA). Genotype imputation was carried out with the Consortium on Asthma Among African-Ancestry Populations in the Americas (CAAPA) reference panel using the Michigan Imputation Server. Global and local ancestry inference was carried out, followed by fine mapping and RNA sequencing. After quality control filtering, over 6,000,000 variants were tested by logistic regression adjusted for sex, age, and global ancestry.

RESULTS

The global African ancestry proportion was found to be significantly lower among cases than controls (0.751 vs 0.786, P = .012). Case-only AM identified 3 significant loci (9p13.3, 12q24.22-23, and 15q11.2) associated with EoE, of which 12q24.22-23 and 9p13.3 were further replicated in the case-control analysis, with associations observed with African ancestry. Fine mapping and multiomic functional annotations prioritized the variants rs11068264 (FBXW8) and rs7307331 (VSIG10) at 12q24.23 and rs2297879 (ARHGEF39) at 9p13.3. GWAS identified 1 genome-wide significant locus at chromosome 1p22.3 (rs17131726, DDAH1) and 10 other suggestive loci. Most GWAS variants were low-frequency African ancestry-specific variants. RNA sequencing revealed that esophageal DDAH1 and VSIG10 were downregulated and ARHGEF39 upregulated among EoE cases.

CONCLUSIONS

GWAS and AM for EoE in AA revealed that African ancestry-specific genetic susceptibility loci exist at 1p22.3, 9p13.3, and 12q24.23, providing evidence of ancestry-specific inheritance of EoE. More independent genetic studies of different ancestries for EoE are needed.

Returning integrated genomic risk and clinical recommendations: The eMERGE study

PURPOSE

Assessing the risk of common, complex diseases requires consideration of clinical risk factors as well as monogenic and polygenic risks, which in turn may be reflected in family history. Returning risks to individuals and providers may influence preventive care or use of prophylactic therapies for those individuals at high genetic risk.

METHODS

To enable integrated genetic risk assessment, the eMERGE (electronic MEdical Records and GEnomics) network is enrolling 25,000 diverse individuals in a prospective cohort study across 10 sites. The network developed methods to return cross-ancestry polygenic risk scores, monogenic risks, family history, and clinical risk assessments via a genome-informed risk assessment (GIRA) report and will assess uptake of care recommendations after return of results.

RESULTS

GIRAs include summary care recommendations for 11 conditions, education pages, and clinical laboratory reports. The return of high-risk GIRA to individuals and providers includes guidelines for care and lifestyle recommendations. Assembling the GIRA required infrastructure and workflows for ingesting and presenting content from multiple sources. Recruitment began in February 2022.

CONCLUSION

Return of a novel report for communicating monogenic, polygenic, and family history-based risk factors will inform the benefits of integrated genetic risk assessment for routine health care.

A DNA tumor virus globally reprograms host 3D genome architecture to achieve immortal growth

Epstein-Barr virus (EBV) immortalization of resting B lymphocytes (RBLs) to lymphoblastoid cell lines (LCLs) models human DNA tumor virus oncogenesis. RBL and LCL chromatin interaction maps are compared to identify the spatial and temporal genome architectural changes during EBV B cell transformation. EBV induces global genome reorganization where contact domains frequently merge or subdivide during transformation. Repressed B compartments in RBLs frequently switch to active A compartments in LCLs. LCLs gain 40% new contact domain boundaries. Newly gained LCL boundaries have strong CTCF binding at their borders while in RBLs, the same sites have much less CTCF binding. Some LCL CTCF sites also have EBV nuclear antigen (EBNA) leader protein EBNALP binding. LCLs have more local interactions than RBLs at LCL dependency factors and super-enhancer targets. RNA Pol II HiChIP and FISH of RBL and LCL further validate the Hi-C results. EBNA3A inactivation globally alters LCL genome interactions. EBNA3A inactivation reduces CTCF and RAD21 DNA binding. EBNA3C inactivation rewires the looping at the CDKN2A/B and AICDA loci. Disruption of a CTCF site at AICDA locus increases AICDA expression. These data suggest that EBV controls lymphocyte growth by globally reorganizing host genome architecture to facilitate the expression of key oncogenes.

Inference of Causal Relationships Between Genetic Risk Factors for Cardiometabolic Phenotypes and Female-Specific Health Conditions

Background Cardiometabolic diseases are highly comorbid, but their relationship with female-specific or overwhelmingly female-predominant health conditions (breast cancer, endometriosis, pregnancy complications) is understudied. This study aimed to estimate the cross-trait genetic overlap and influence of genetic burden of cardiometabolic traits on health conditions unique to women. Methods and Results Using electronic health record data from 71 008 ancestrally diverse women, we examined relationships between 23 obstetrical/gynecological conditions and 4 cardiometabolic phenotypes (body mass index, coronary artery disease, type 2 diabetes, and hypertension) by performing 4 analyses: (1) cross-trait genetic correlation analyses to compare genetic architecture, (2) polygenic risk score-based association tests to characterize shared genetic effects on disease risk, (3) Mendelian randomization for significant associations to assess cross-trait causal relationships, and (4) chronology analyses to visualize the timeline of events unique to groups of women with high and low genetic burden for cardiometabolic traits and highlight the disease prevalence in risk groups by age. We observed 27 significant associations between cardiometabolic polygenic scores and obstetrical/gynecological conditions (body mass index and endometrial cancer, body mass index and polycystic ovarian syndrome, type 2 diabetes and gestational diabetes, type 2 diabetes and polycystic ovarian syndrome). Mendelian randomization analysis provided additional evidence of independent causal effects. We also identified an inverse association between coronary artery disease and breast cancer. High cardiometabolic polygenic scores were associated with early development of polycystic ovarian syndrome and gestational hypertension. Conclusions We conclude that polygenic susceptibility to cardiometabolic traits is associated with elevated risk of certain female-specific health conditions.

B cell repertoire in children with skin barrier dysfunction supports altered IgE maturation associated with allergic food sensitization

The skin is a major immune organ and skin barrier dysfunction is a major risk factor for the development of the inappropriate immune response seen in allergic disease. Skin barrier disruption alters the landscape of antigens experienced by the immune system and the downstream impacts on the antibody repertoire remain poorly characterized, particularly for the IgE isotype responsible for allergic specificity and in early life, when allergic disease is developing. In this study, we sequenced antibody gene repertoires from a large and well-characterized cohort of children with atopic dermatitis and found that food sensitization was associated with lower mutation frequencies in the IgE compartment. This trend was abrogated in children living with pets during the first year of life. These results elucidate potential molecular mechanisms underlying the protective effects of pet ownership and non-antiseptic environs reported for allergic disease, and the hygiene hypothesis more broadly. We also observed increased IgE diversity and increased isotype-switching to the IgE isotype, suggesting that B cell development, particularly isotype-switching, is heavily altered in the those with food allergen sensitizations relative to those without food allergen sensitizations. Unlike for food antigens, aeroallergen sensitization exhibited no effect on IgE mutation or diversity. Consistent patterns of antibody rearrangement were associated with food allergen sensitization in subjects with atopic dermatitis. Thus, we propose the Immune Repertoire in Atopic Disease (IRAD) score, to quantify this repertoire shift and to aid clinically in patient diagnosis and risk stratification.

Quantifying factors that affect polygenic risk score performance across diverse ancestries and age groups for body mass index

Polygenic risk scores (PRS) have led to enthusiasm for precision medicine. However, it is well documented that PRS do not generalize across groups differing in ancestry or sample characteristics e.g., age. Quantifying performance of PRS across different groups of study participants, using genome-wide association study (GWAS) summary statistics from multiple ancestry groups and sample sizes, and using different linkage disequilibrium (LD) reference panels may clarify which factors are limiting PRS transferability. To evaluate these factors in the PRS generation process, we generated body mass index (BMI) PRS (PRSBMI) in the Electronic Medical Records and Genomics (eMERGE) network (N=75,661). Analyses were conducted in two ancestry groups (European and African) and three age ranges (adult, teenagers, and children). For PRSBMI calculations, we evaluated five LD reference panels and three sets of GWAS summary statistics of varying sample size and ancestry. PRSBMI performance increased for both African and European ancestry individuals using cross-ancestry GWAS summary statistics compared to European-only summary statistics (6.3% and 3.7% relative R2 increase, respectively, pAfrican=0.038, pEuropean=6.26x10-4). The effects of LD reference panels were more pronounced in African ancestry study datasets. PRSBMI performance degraded in children; R2 was less than half of teenagers or adults. The effect of GWAS summary statistics sample size was small when modeled with the other factors. Additionally, the potential of using a PRS generated for one trait to predict risk for comorbid diseases is not well understood especially in the context of cross-ancestry analyses - we explored clinical comorbidities from the electronic health record associated with PRSBMI and identified significant associations with type 2 diabetes and coronary atherosclerosis. In summary, this study quantifies the effects that ancestry, GWAS summary statistic sample size, and LD reference panel have on PRS performance, especially in cross-ancestry and age-specific analyses.

Multiancestral polygenic risk score for pediatric asthma

BACKGROUND

Asthma is the most common chronic condition in children and the third leading cause of hospitalization in pediatrics. The genome-wide association study catalog reports 140 studies with genome-wide significance. A polygenic risk score (PRS) with predictive value across ancestries has not been evaluated for this important trait.

OBJECTIVES

This study aimed to train and validate a PRS relying on genetic determinants for asthma to provide predictions for disease occurrence in pediatric cohorts of diverse ancestries.

METHODS

This study applied a Bayesian regression framework method using the Trans-National Asthma Genetic Consortium genome-wide association study summary statistics to derive a multiancestral PRS score, used one Electronic Medical Records and Genomics (eMERGE) cohort as a training set, used a second independent eMERGE cohort to validate the score, and used the UK Biobank data to replicate the findings. A phenome-wide association study was performed using the PRS to identify shared genetic etiology with other phenotypes.

RESULTS

The multiancestral asthma PRS was associated with asthma in the 2 pediatric validation datasets. Overall, the multiancestral asthma PRS has an area under the curve (AUC) of 0.70 (95% CI, 0.69-0.72) in the pediatric validation 1 and AUC of 0.66 (0.65-0.66) in the pediatric validation 2 datasets. We found significant discrimination across pediatric subcohorts of European (AUC, 95% CI, 0.60 and 0.66), African (AUC, 95% CI, 0.61 and 0.66), admixed American (AUC, 0.64 and 0.70), Southeast Asian (AUC, 0.65), and East Asian (AUC, 0.73) ancestry. Pediatric participants with the top 5% PRS had 2.80 to 5.82 increased odds of asthma compared to the bottom 5% across the training, validation 1, and validation 2 cohorts when adjusted for ancestry. Phenome-wide association study analysis confirmed the strong association of the identified PRS with asthma (odds ratio, 2.71, PFDR = 3.71 × 10-65) and related phenotypes.

CONCLUSIONS

A multiancestral PRS for asthma based on Bayesian posterior genomic effect sizes identifies increased odds of pediatric asthma.

Frontotemporal degeneration genetic risk loci and transcription regulation as a possible mechanistic link to disease risk

The etiology of Frontotemporal Degeneration (FTD) is not well understood. Genetic studies have established common genetic variants (GVs) that are associated with increased FTD risk. We review previous genome wide association studies (GWAS) of FTD and nominate specific transcriptional regulators as potential key players in the etiology of this disease. A list of GVs associated with FTD was compiled from published GWAS. The regulatory element locus intersection (RELI) tool was used to calculate the enrichment of the overlap between disease risk GVs and the genomic coordinates of data from a collection of >10,000 chromatin immunoprecipitation (ChIP-seq) experiments. After linkage disequilibrium expansion of the previously reported tag associated GVs, we identified 914 GV at 47 independent risk loci. Using the RELI algorithm, we identified several transcriptional regulators with enriched binding at FTD risk loci (0.05 < corrected P value <1.18 × 10-27), including Tripartite motif-containing 28 (TRIM28) and Chromodomain-Helicase DNA-binding 1 (CHD1) which have previously observed roles in FTD. FTD is a complex disease, and immune dysregulation has been previously implicated as a potential underlying cause. This assessment of established FTD risk loci and analysis of possible function implicates transcriptional dysregulation, and specifically particular transcriptional regulators with known roles in the immune response as important in the genetic etiology of FTD.

Development and validation of a trans-ancestry polygenic risk score for type 2 diabetes in diverse populations

BACKGROUND

Type 2 diabetes (T2D) is a worldwide scourge caused by both genetic and environmental risk factors that disproportionately afflicts communities of color. Leveraging existing large-scale genome-wide association studies (GWAS), polygenic risk scores (PRS) have shown promise to complement established clinical risk factors and intervention paradigms, and improve early diagnosis and prevention of T2D. However, to date, T2D PRS have been most widely developed and validated in individuals of European descent. Comprehensive assessment of T2D PRS in non-European populations is critical for equitable deployment of PRS to clinical practice that benefits global populations.

METHODS

We integrated T2D GWAS in European, African, and East Asian populations to construct a trans-ancestry T2D PRS using a newly developed Bayesian polygenic modeling method, and assessed the prediction accuracy of the PRS in the multi-ethnic Electronic Medical Records and Genomics (eMERGE) study (11,945 cases; 57,694 controls), four Black cohorts (5137 cases; 9657 controls), and the Taiwan Biobank (4570 cases; 84,996 controls). We additionally evaluated a post hoc ancestry adjustment method that can express the polygenic risk on the same scale across ancestrally diverse individuals and facilitate the clinical implementation of the PRS in prospective cohorts.

RESULTS

The trans-ancestry PRS was significantly associated with T2D status across the ancestral groups examined. The top 2% of the PRS distribution can identify individuals with an approximately 2.5-4.5-fold of increase in T2D risk, which corresponds to the increased risk of T2D for first-degree relatives. The post hoc ancestry adjustment method eliminated major distributional differences in the PRS across ancestries without compromising its predictive performance.

CONCLUSIONS

By integrating T2D GWAS from multiple populations, we developed and validated a trans-ancestry PRS, and demonstrated its potential as a meaningful index of risk among diverse patients in clinical settings. Our efforts represent the first step towards the implementation of the T2D PRS into routine healthcare.

Enrichment of Epstein Barr Virus in patients with Multiple Sclerosis

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system affecting more than 2 million people worldwide and has been linked with Epstein-Barr Virus (EBV) infection. Previous studies by the Kottyan and Weirauch labs show that the EBNA2 protein of both EBV type 1 and 2 binds unique MS risk loci potentially causing changes at the transcriptional level contributing to MS disease progress. We hypothesize that type 1 and type 2 EBV will be detectable in the MS patient samples, and we aim to quantify EBV enrichment and identify EBV type in MS patient-derived blood samples. Analysis by qPCR showed that 30% of the control population (n=10) and 66% of the MS patient population (n=41) had detectable levels of EBV whereas the MS patients had a significantly higher frequency of EBV presence (X2 test p=0.0389). Of the samples that tested positive for EBV, 66% showed presence of type 1 EBV while 33% were unknown without a significant difference between MS patients and control group (X2 test p&gt;0.9999). Due to issues with the limit of detection, droplet digital PCR was assessed for higher sensitivity compared to qPCR, but was found to have a comparable limit of detection to qPCR. To overcome the challenge of detecting low copy number viruses, we look toward targeted DNA capture and next generation sequencing to improve the sensitivity of EBV detection and specificity of EBV typing. Understanding the distribution of EBV types among MS patients would elucidate the precise role of EBV in MS development, potentially leading to improved treatment and prevention methods.

Supported by grants from NIH grants R01 HG010730, R01 NS099068, R01 GM055479, and U01 AI130830 to MTW; R01 DK107502, R01 AI148276, U19 AI070235, U01 HG011172, and P30 AR070549 to LCK; R01 AR073228, R01 AI024717, and CCHMC ARC Award 53632 to MTW and LCK.

A Lupus-Associated Variant in IRF7 amplifies IFN-α Production in response to TLR stimulation

Systemic Lupus Erythematosus (SLE) is an autoimmune disease characterized by chronic immune activation, loss of self-tolerance and organ destruction. More than 90 genetic risk loci are implicated in the etiology of SLE, yet the mechanisms connecting these loci to disease risk are not well understood. We focus on a SLE-associated coding variant (rs1131665) at the IRF7 risk locus that results in an arginine (R, non-risk) to glutamine (Q, risk) amino acid change in the auto inhibitory domain of interferon regulatory factor-7 (IRF7), a key transcriptional regulator of the expression of and response to type I interferon (IFN). The majority of SLE patients exhibit elevated levels of circulating IFN, a feature that correlates with disease activity. We generated cell lines expressing the risk and non-risk variants of IRF7 and isolated plasmacytoid dendritic cells from mice with CRISPR-mediated introduction of a mouse homologue of the risk variant of IRF7. In both experimental systems, the rs1131665 lupus risk variant drives increased toll like receptor-7 (TLR-7) ligand-induced IFN-α expression at both the mRNA and protein levels compared to the non-risk variant of IRF7. Additionally, we performed a covariance analysis that predicts that amino acid residues at the 84, 140, 142 positions interact with the variant position in the three-dimensional structure of IRF7. Mutation of the amino acid at the 84 position from a glutamic acid (E) residue to a threonine (T) residue results in amplified IFN production in response to TLR-7 stimulation. Our findings suggest a genotype-dependent mechanism for lupus risk variants in IRF7 in promoting exaggerated IFN production in SLE.

These experiments would not have been possible with out NIH NIAMS R01 AR073228. 

Comprehensive Review of Steroid-Sensitive Nephrotic Syndrome Genetic Risk Loci and Transcriptional Regulation as a Possible Mechanistic Link to Disease Risk

Introduction

The etiology of steroid-sensitive nephrotic syndrome (SSNS) is not well understood. Genetic studies have established common single nucleotide polymorphisms (SNPs) that are associated with increased SSNS disease risk. We review previous genetic association studies of SSNS and nominate particular transcriptional regulators and immune cells as potential key players in the etiology of this disease.

Methods

A list of SNPs associated with SSNS was compiled from published genome wide association and candidate gene studies. The Regulatory Element Locus Intersection (RELI) tool was used to calculate the enrichment of the overlap between disease risk SNPs and the genomic coordinates of data from a collection of >10,000 chromatin immunoprecipitation sequencing experiments.

Results

After linkage disequilibrium expansion of the previously reported tag associated SNPs, we identified 192 genetic variants at 8 independent risk loci. Using the Regulatory Element Locus Intersection algorithm, we identified transcriptional regulators with enriched binding at SSNS risk loci (10^-05 < P_corrected < 10^-124), including ZNF530, CIITA, CD74, RFX5, and ZNF425. Many of these regulators have well-described roles in the immune response. RNA polymerase II binding in B cells also demonstrated enriched binding at SSNS risk loci (10^-37<P_corrected<10^-5).

Conclusion

SSNS is a complex disease, and immune dysregulation has been previously implicated as a potential underlying cause. This assessment of established SSNS risk loci and analysis of possible function implicates transcriptional dysregulation, and specifically particular transcriptional regulators with known roles in the immune response, as important in the genetic etiology of SSNS.

Harmonizing Clinical Sequencing and Interpretation for the eMERGE III Network

The advancement of precision medicine requires new methods to coordinate and deliver genetic data from heterogeneous sources to physicians and patients. The eMERGE III Network enrolled >25,000 participants from biobank and prospective cohorts of predominantly healthy individuals for clinical genetic testing to determine clinically actionable findings. The network developed protocols linking together the 11 participant collection sites and 2 clinical genetic testing laboratories. DNA capture panels targeting 109 genes were used for testing of DNA and sample collection, data generation, interpretation, reporting, delivery, and storage were each harmonized. A compliant and secure network enabled ongoing review and reconciliation of clinical interpretations, while maintaining communication and data sharing between clinicians and investigators. A total of 202 individuals had positive diagnostic findings relevant to the indication for testing and 1,294 had additional/secondary findings of medical significance deemed to be returnable, establishing data return rates for other testing endeavors. This study accomplished integration of structured genomic results into multiple electronic health record (EHR) systems, setting the stage for clinical decision support to enable genomic medicine. Further, the established processes enable different sequencing sites to harmonize technical and interpretive aspects of sequencing tests, a critical achievement toward global standardization of genomic testing. The eMERGE protocols and tools are available for widespread dissemination.

17β-Estradiol protects the esophageal epithelium from IL-13-induced barrier dysfunction and remodeling

BACKGROUND

The incidence of eosinophilic esophagitis (EoE) is greater in male than female subjects, and the underlying molecular basis for this sex bias remains unclear.

OBJECTIVE

We sought to delineate the contribution of the sex hormone estrogen to the EoE phenotype and esophageal epithelial barrier function and remodeling.

METHODS

We performed demographic and incidence analyses of EoE in male and female subjects from a single-center pediatric cohort. Estrogen-responsive gene expression analyses and estrogen receptor (ESR) immunofluorescence staining of esophageal biopsy specimens from patients with EoE and control subjects were performed. The effect of 17β-estradiol (E2) on IL-13-induced signaling pathways, gene expression, and esophageal epithelial architecture and barrier function in a primary human esophageal keratinocyte cell (EPC2) culture system (EPC2-air-liquid interface) was examined.

RESULTS

We observed a male predominance in patients with EoE. Analyses of RNA sequencing data sets revealed a significant dysregulation of the estrogen-responsive gene network and expression of ESR1 and ESR2 in esophageal biopsy specimens from patients with EoE compared with control subjects. IL-13 stimulation of EPC2-air-liquid interface cells led to altered cellular architecture with induced dilation of intercellular spaces and barrier dysfunction. Pretreatment of EPC2s with E2 prior to IL-13 exposure abrogated IL-13-induced architectural changes and esophageal barrier dysfunction. Mechanistically, E2-protective effects were dependent on ESR2 and associated with diminishing of IL-13-induced tyrosine kinase 2 and signal transducer and activator of transcription 6 phosphorylation and EoE-dysregulated gene expression.

CONCLUSIONS

Estrogen-responsive genes are modified in patients with EoE compared with control subjects. E2 attenuated IL-13-induced architectural changes and esophageal epithelial barrier dysfunction through inhibition of the IL-13/tyrosine kinase 2/signal transducer and activator of transcription 6 pathway via ESR2-dependent process. Estrogen hormone signaling may protect against development of EoE in female subjects.

New developments in patients with eosinophilic gastrointestinal diseases presented at the CEGIR/TIGERS Symposium at the 2018 American Academy of Allergy, Asthma & Immunology Meeting

The Consortium of Eosinophilic Gastrointestinal Diseases and the International Gastrointestinal Eosinophil Researchers organized a day-long symposium at the recent 2018 Annual Meeting of the American Academy of Allergy, Asthma & Immunology, which was coupled for the first time with the World Allergy Organization meeting to create an international platform. The symposium featured experts in many facets of eosinophilic gastrointestinal diseases, including allergy, immunology, gastroenterology, pathology, and nutrition, and was a well-attended event. The basic science, genetics, cellular immunology, and clinical features of the diseases, with a focus on epithelial, eosinophil, and mast cell responses, as well as current and emerging treatment options, were reviewed. Here we briefly review some of the highlights of the material presented at the meeting.

A Novel Pkhd1 Mutation Interacts with the Nonobese Diabetic Genetic Background To Cause Autoimmune Cholangitis

We previously reported that NOD.c3c4 mice develop spontaneous autoimmune biliary disease (ABD) with anti-mitochondrial Abs, histopathological lesions, and autoimmune T lymphocytes similar to human primary biliary cholangitis. In this article, we demonstrate that ABD in NOD.c3c4 and related NOD ABD strains is caused by a chromosome 1 region that includes a novel mutation in polycystic kidney and hepatic disease 1 (Pkhd1). We show that a long terminal repeat element inserted into intron 35 exposes an alternative polyadenylation site, resulting in a truncated Pkhd1 transcript. A novel NOD congenic mouse expressing aberrant Pkhd1, but lacking the c3 and c4 chromosomal regions (NOD.Abd3), reproduces the immunopathological features of NOD ABD. RNA sequencing of NOD.Abd3 common bile duct early in disease demonstrates upregulation of genes involved in cholangiocyte injury/morphology and downregulation of immunoregulatory genes. Consistent with this, bone marrow chimera studies show that aberrant Pkhd1 must be expressed in the target tissue (cholangiocytes) and the immune system (bone marrow). Mutations of Pkhd1 produce biliary abnormalities in mice but have not been previously associated with autoimmunity. In this study, we eliminate clinical biliary disease by backcrossing this Pkhd1 mutation onto the C57BL/6 genetic background; thus, the NOD genetic background (which promotes autoimmunity) is essential for disease. We propose that loss of functional Pkhd1 on the NOD background produces early bile duct abnormalities, initiating a break in tolerance that leads to autoimmune cholangitis in NOD.Abd3 congenic mice. This model is important for understanding loss of tolerance to cholangiocytes and is relevant to the pathogenesis of several human cholangiopathies.

Selective inhibition of Kv1.3 channels in memory T cells by targeted delivery with nanoparticles suppresses CD40 ligand expression in SLE (THER5P.908)

The pathogenesis of Systemic Lupus Erythematosus (SLE) is characterized by hyperactive memory T cells (TM). In SLE, the TM cells show a Ca2+-dependent increase in the costimulatory CD40 ligand (CD40L) which binds CD40 on B cells, resulting in B cell activation and autoantibody production. CD40L is widely recognized as a potential target for developing new therapies for SLE. Cytosolic Ca2+ levels, which increase during T cell activation and mediate CD40L expression, are regulated by Kv1.3 channels. We have developed lipid nanoparticles that can deliver Kv1.3 siRNAs (Kv1.3-NPs) selectively to TM cells and decrease the activation-induced Ca2+ influx (Hajdu et al., Biomaterials 2013). We studied whether these Kv1.3-NPs decrease the Ca2+-dependent overexpression of CD40L in SLE peripheral blood TM cells. We observed that nuclear translocation of NFAT, a transcription factor upstream to CD40L, in activated TEM cells was reduced by ~50% after treatment with Kv1.3-NPs. Furthermore, Kv1.3-NP treatment selectively reduced CD40L expression in activated TEM cells by ~40% in healthy donors and ~60% in SLE patients, while CD40L levels remained unchanged in cells that did not incorporate the nanoparticles. Interestingly, we observed that treatment with Kv1.3-NPs in SLE patients resulted in T cell phenotype switching from a predominantly TM phenotype to a naïve phenotype. Our findings open the possibility of using Kv1.3-NPs as potential targeted immune suppressive therapeutic agents in SLE.

Lupus risk-variant increases pSTAT1 binding and decreases ETS1 expression (BA4P.137)

Genetic variants near gene ETS1 have been associated with Systemic Lupus Erythematosus (SLE) in independent cohorts of Asian ancestry. ETS1 is a critical driver of immune cell function and differentiation, and mice deficient in ETS1 develop an SLE-like autoimmunity. We performed a fine-mapping study of 14,551 subjects using multi-ancestral cohorts, starting with genotyped variants and imputing to all common variants spanning the ETS1 locus. By constructing genetic models using frequentist and Bayesian association methods, we identified a set of 16 variants that are statistically most likely to be causal. We functionally assessed each of these variants based on their biological function predictions. Of the four variants that we experimentally examined, only rs6590330 differentially binds lysate from B cells. Using mass spectrometry, we found increased binding of the transcription factor signal transducer and activator of transcription 1 (STAT1) to DNA near the risk allele of rs6590330 compared to the non-risk allele. Western blot analysis and chromatin immunoprecipitation of pSTAT1 in B cells heterozygous for rs6590330 confirmed that the risk allele increased binding to the active form of STAT1. eQTL analysis indicates that the risk allele of rs6590330 is only associated with decreased ETS1 expression in Han Chinese. We propose a model in which the risk allele of rs6590330 increases SLE risk by enhancing the binding of pSTAT1, resulting in repression of the ETS1 expression.

Assessment of active play, inactivity and perceived barriers in an inner city neighborhood

Avondale, a disadvantaged neighborhood in Cincinnati, lags behind on a number of indicators of child well-being. Childhood obesity has become increasingly prevalent, as one-third of Avondale's kindergarteners are obese or overweight. The study objective was to determine perceptions of the quantity of and obstacles to childhood physical activity in the Avondale community. Caregivers of children from two elementary schools were surveyed to assess their child's physical activity and barriers to being active. Three hundred and forty surveys were returned out of 1,047 for a response rate of 32%. On school days, 41% of caregivers reported that their children spent more than 2 h watching television, playing video games, or spending time on the computer. While over half of respondents reported that their children get more than 2 h of physical activity on school days, 14% of children were reported to be physically active less than 1 h per day. Caregivers identified violence, cost of extracurricular activities, and lack of organized activities as barriers to their child's physical activity. The overwhelming majority of caregivers expressed interest in a program to make local playgrounds safer. In conclusion, children in Avondale are not participating in enough physical activity and are exposed to more screen time than is recommended by the AAP. Safety concerns were identified as a critical barrier to address in future advocacy efforts in this community. This project represents an important step toward increasing the physical activity of children in Avondale and engaging the local community.

On family-based genome-wide association studies with large pedigrees: observations and recommendations

Family based association studies are employed less often than case-control designs in the search for disease-predisposing genes. The optimal statistical genetic approach for complex pedigrees is unclear when evaluating both common and rare variants. We examined the empirical power and type I error rates of 2 common approaches, the measured genotype approach and family-based association testing, through simulations from a set of multigenerational pedigrees. Overall, these results suggest that much larger sample sizes will be required for family-based studies and that power was better using MGA compared to FBAT. Taking into account computational time and potential bias, a 2-step strategy is recommended with FBAT followed by MGA.

Using Mendelian inheritance errors as quality control criteria in whole genome sequencing data set

Although the technical and analytic complexity of whole genome sequencing is generally appreciated, best practices for data cleaning and quality control have not been defined. Family based data can be used to guide the standardization of specific quality control metrics in nonfamily based data. Given the low mutation rate, Mendelian inheritance errors are likely as a result of erroneous genotype calls. Thus, our goal was to identify the characteristics that determine Mendelian inheritance errors. To accomplish this, we used chromosome 3 whole genome sequencing family based data from the Genetic Analysis Workshop 18. Mendelian inheritance errors were provided as part of the GAW18 data set. Additionally, for binary variants we calculated Mendelian inheritance errors using PLINK. Based on our analysis, nonbinary single-nucleotide variants have an inherently high number of Mendelian inheritance errors. Furthermore, in binary variants, Mendelian inheritance errors are not randomly distributed. Indeed, we identified 3 Mendelian inheritance error peaks that were enriched with repetitive elements. However, these peaks can be lessened with the inclusion of a single filter from the sequencing file. In summary, we demonstrated that erroneous sequencing calls are nonrandomly distributed across the genome and quality control metrics can dramatically reduce the number of mendelian inheritance errors. Appropriate quality control will allow optimal use of genetic data to realize the full potential of whole genome sequencing.

Genetic variant at ETS1 locus increases lupus risk and affects Stat1 binding (BA2P.115)

Over the past 10 years, genetic association studies have identified over 55 systemic lupus erythematous (SLE)-risk loci. Genetic variants in ETS1 have been associated with SLE in several independent studies in populations of Asian ancestry. Several recent studies have implicated Ets1 as a critical driver of B and T cell function; indeed, mice deficient in Ets1 develop an SLE-like autoimmunity. rs1128334, in the 3’ UTR of ETS1, has been associated with the decreased expression of Ets1. We performed a fine-mapping study of over 20,000 subjects of two multi-ancestral cohorts using genotyped and imputed variants spanning the ETS1 locus. By constructing genetic models using frequentist and Bayesian association methods, we identified a set of variants that are most likely to be causal. Of the three variants that we tested, only rs6590330 differentially binds lysate from B cell lines as assessed by electrophoretic mobility shift assays and DNA affinity precipitation assays. We found that the active form of the transcription factor Stat1 binds the risk allele of rs6590330 but not the non-risk allele using mass spectrometry, a finding confirmed by Western blot analysis. rs6590330 is in strong linkage disequilibrium with rs1128334 and is predicted to also be associated with decreased Ets1 expression. We propose a model in which the risk allele of rs6590330 increases SLE risk by binding Stat1 and depressing the expression of Ets1.

X chromosome dose and sex bias in autoimmune diseases: increased 47,XXX in systemic lupus erythematosus and Sjögren’s syndrome (BA4P.211)

Mechanism for female predominance in autoimmunity is unknown. We suspected an X chromosome dose effect and predicted if so, triple X (47,XXX, 1 in ~1,000 live female births) would be increased in female predominant diseases (systemic lupus erythematosus [SLE], primary Sjögren’s syndrome [SS], primary biliary cirrhosis [PBC] and rheumatoid arthritis [RA])compared to diseases without female predominance (sarcoidosis, granulomatosis with polyangiitis [GPA]) and healthy controls. We used single nucleotide polymorphism (SNP) arrays to identify 47,XXX and fluorescent in situ hybridization, or q-PCR to confirm when possible. 47,XXX was found in 7 of 2,948 SLE and 3 of 1,053 SS female patients, but in none of the 4,822 female controls (OR≥21.31, 95% CI: 2.36-∞, p=0.001 and OR≥22.95, 95% CI: 1.89-∞, p=0.006, respectively). One 47,XXX was present for every ~421 SLE women and ~351 SS women. In addition, we identified one 47,XXX from each of 1,159 women with PBC and 943 with sarcoidosis. No 47,XXX was identified among 453 women with RA or 247 with GPA. In conclusion, 47,XXX was present in excess among SLE and SS subjects as predicted by X chromosome dose effect. These estimated prevalence of SLE and SS with 47,XXX being respectively ~2.4 and ~2.8 times higher than in women with 46,XX and ~24 and ~39 times higher than in men with 46,XY. There was no increase of 47,XXX is other female-biased diseases, suggesting multiple pathways to such a bias in autoimmunity.

Allelic heterogeneity in NCF2 associated with systemic lupus erythematosus (SLE) susceptibility across four ethnic populations

Recent reports have associated NCF2, encoding a core component of the multi-protein NADPH oxidase (NADPHO), with systemic lupus erythematosus (SLE) susceptibility in individuals of European ancestry. To identify ethnicity-specific and -robust variants within NCF2, we assessed 145 SNPs in and around the NCF2 gene in 5325 cases and 21 866 controls of European-American (EA), African-American (AA), Hispanic (HS) and Korean (KR) ancestry. Subsequent imputation, conditional, haplotype and bioinformatic analyses identified seven potentially functional SLE-predisposing variants. Association with non-synonymous rs17849502, previously reported in EA, was detected in EA, HS and AA (P(EA) = 1.01 × 10(-54), PHS = 3.68 × 10(-10), P(AA) = 0.03); synonymous rs17849501 was similarly significant. These SNPs were monomorphic in KR. Novel associations were detected with coding variants at rs35937854 in AA (PAA = 1.49 × 10(-9)), and rs13306575 in HS and KR (P(HS) = 7.04 × 10(-7), P(KR) = 3.30 × 10(-3)). In KR, a 3-SNP haplotype was significantly associated (P = 4.20 × 10(-7)), implying that SLE predisposing variants were tagged. Significant SNP-SNP interaction (P = 0.02) was detected between rs13306575 and rs17849502 in HS, and a dramatically increased risk (OR = 6.55) with a risk allele at each locus. Molecular modeling predicts that these non-synonymous mutations could disrupt NADPHO complex assembly. The risk allele of rs17849501, located in a conserved transcriptional regulatory region, increased reporter gene activity, suggesting in vivo enhancer function. Our results not only establish allelic heterogeneity within NCF2 associated with SLE, but also emphasize the utility of multi-ethnic cohorts to identify predisposing variants explaining additional phenotypic variance ('missing heritability') of complex diseases like SLE.

Sub-phenotypes of Systemic Lupus Erythematosus are associated with genetic sequence polymorphisms in the IRF5-TNPO3 region of chromosome 7 (P3317)

Systemic Lupus Erythematosus (lupus) is a systemic autoimmune disorder with a strong genetic etiology. A recent fine-mapping study of the IRF5-TNPO3 lupus association revealed two genetic effects that independently increase lupus risk. We tested the hypothesis that variants in the IRF5-TNPO3 region are also associated with the clinical presentation of lupus. We performed a case-only sub-phenotypic association study using 101 genetic variants in the IRF5-TNPO3 region that were genotyped in 8,395 lupus patients across four ancestral populations. In Europeans Americans with lupus, the age-of-onset (p-value=2.44x10-16, OR=0.68) and the presence of anti-Ro (p-value=2.09x10-7, OR=0.67) and anti-dsDNA (p-value=4.15x10-7, OR=0.75) autoantibodies are associated with genetic variants in the IRF5-TNPO3 locus. In a step-wise logistic regression analysis of age-of-onset, variants are associated in both the IRF5 promoter and the independent genetic effect spanning IRF5 and TNPO3. In contrast, the presence of anti-Ro and anti-dsDNA autoantibodies is only associated with genetic variants in the IRF5 promoter. No other sub-phenotypic analysis in any ancestry demonstrated association after permutation tests were applied to correct for multiple hypothesis tests. In conclusion, genetic variants in the two genetic effects of the IRF5-TNPO3 locus independently affect the age-of-onset and production of anti-dsDNA and anti-Ro autoantibodies in European American lupus patients.

The IRF5-TNPO3 association has two components in systemic lupus erythematosus, which are shared with other autoimmune disorders (P3315)

Improved technical and bioinformatics genetic methods now allows us to capture more complete relevant genetic variation for candidate causal disease risk variant identification. Exploiting genotyping, DNA sequencing, imputation, and trans-ancestral mapping, we modeled the IRF5-TNPO3 genetic association on chromosome 7, now implicated in two immunotherapies and seven autoimmune diseases. Specifically, in systemic lupus erythematosus (SLE) we resolve separate associations in the IRF5 promoter (all ancestries) and an extended European haplotype. We capture 7,650 IRF5-TNPO3 genetic variants across five ethnicities in 8,395 SLE cases and 7,367 controls. The six plausible causative IRF5 promoter variants are confined to 5.7 kb (meta-analysis p-value=6x10^-49; Odds Ratio=1.38-1.97). The 22 potentially causal variants of an 85.5 kb haplotype of IRF5 and TNPO3 (haplotypic p-value in European Americans=2.4x10^-45, Odds Ratio=0.58) (individual p-value in European Americans=10^-27 - 10^-32, Odds Ratio=1.7-1.81). The possible models from this sample virtually eliminate the previously purported IRF5 functional variants as causal. Finally, this model also appears to operate in Sjögren’s syndrome and systemic sclerosis (both components) and primary biliary cirrhosis (haplotype only), demonstrating the nuances of similarity and difference in autoimmune disease risk mechanisms at IRF5-TNPO3.

IRF5 gene polymorphisms in melanoma

Background

Interferon regulatory factor (IRF)-5 is a transcription factor involved in type I interferon signaling whose germ line variants have been associated with autoimmune pathogenesis. Since relationships have been observed between development of autoimmunity and responsiveness of melanoma to several types of immunotherapy, we tested whether polymorphisms of IRF5 are associated with responsiveness of melanoma to adoptive therapy with tumor infiltrating lymphocytes (TILs).

Methods

140 TILs were genotyped for four single nucleotide polymorphisms (rs10954213, rs11770589, rs6953165, rs2004640) and one insertion-deletion in the IRF5 gene by sequencing. Gene-expression profile of the TILs, 112 parental melanoma metastases (MM) and 9 cell lines derived from some metastases were assessed by Affymetrix Human Gene ST 1.0 array.

Results

Lack of A allele in rs10954213 (G > A) was associated with non-response (p < 0.005). Other polymorphisms in strong linkage disequilibrium with rs10954213 demonstrated similar trends. Genes differentially expressed in vitro between cell lines carrying or not the A allele could be applied to the transcriptional profile of 112 melanoma metastases to predict their responsiveness to therapy, suggesting that IRF5 genotype may influence immune responsiveness by affecting the intrinsic biology of melanoma.

Conclusions

This study is the first to analyze associations between melanoma immune responsiveness and IRF5 polymorphism. The results support a common genetic basis which may underline the development of autoimmunity and melanoma immune responsiveness.

Identification of novel coding mutation in C1qA gene in an African-American pedigree with lupus and C1q deficiency

OBJECTIVES

Homozygous C1q deficiency is an extremely rare condition and strongly associated with systemic lupus erythematosus. To assess and characterize C1q deficiency in an African-American lupus pedigree, C1q genomic region was evaluated in the lupus cases and family members.

METHODS

Genomic DNA from patient was obtained and C1q A, B and C gene cluster was sequenced using next generation sequencing method. The identified mutation was further confirmed by direct Sanger sequencing method in the patient and all blood relatives. C1q levels in serum were measured using sandwich ELISA method.

RESULTS

In an African-American patient with lupus and C1q deficiency, we identified and confirmed a novel homozygote start codon mutation in C1qA gene that changes amino acid methionine to arginine at position 1. The Met1Arg mutation prevents protein translation (Met1Arg). Mutation analyses of the patient's family members also revealed the Met1Arg homozygote mutation in her deceased brother who also had lupus with absence of total complement activity consistent with a recessive pattern of inheritance.

CONCLUSION

The identification of new mutation in C1qA gene that disrupts the start codon (ATG to AGG (Met1Arg)) has not been reported previously and it expands the knowledge and importance of the C1q gene in the pathogenesis of lupus especially in the high-risk African-American population.

IL-13 is required and sufficient for airway acidification in allergic airway inflammation (141.16)

Clinical studies have shown acidification of airways in asthma. Importantly, studies have suggested that acidification contributes to the pathophysiological process. However, the mechanism of acidification is unclear. We developed a novel method for measuring the acidity of mouse airways and demonstrated that mouse airways are acidified during models of allergic airway inflammation. Our studies determined that airway acidification does not develop in IL-13-deficient mice and that IL-13 delivery alone is sufficient to induce airway acidification. There are multiple ways IL-13 could lead to acidification, including direct effects on epithelial cells or through recruitment of inflammatory cells. We demonstrated a partial role for eosinophils in airway acidification as CCR3 and IL-5-deficient mice had decreased extent of airway acidification in allergen-challenged mice. Furthermore, using dimethyl amiloride, a specific inhibitor of the Na+/H+ exchanger, we demonstrated significant inhibition of airway acidification in allergic airway inflammation, suggesting a role for ion (proton) channels. In summary, our studies demonstrate that mouse airways are acidified during allergic airway inflammation. We also showed that the mechanism of airway acidification in asthma involves IL-13-mediated pathways including eosinophils and proton channels. These results have considerable implications for the development of therapies that target airway acidification.