Functional mapping and annotation of genetic associations with FUMA. Nat Commun. 2017;8:1826. [PMID: 29184056 PMCID: PMC5705698 DOI: 10.1038/s41467-017-01261-5]

A GWAS of angiotensin-converting enzyme inhibitor-induced angioedema in a South African population

Background

Angiotensin-converting enzyme inhibitor-induced angioedema (AE-ACEI) is a life-threatening adverse event; globally, it is the most common cause of emergency presentations with angioedema. Several genome-wide association studies (GWASs) have found genomic associations with AE-ACEI. However, despite African Americans having a 5-fold increased risk of AE-ACEI, there are no published GWASs from Africa.

Objective

The aim of this study was to conduct a GWAS of AE-ACEI in a South African population and perform a meta-analysis with an African American and European American population.

Methods

The GWAS included 202 South African adults with a history of AE-ACEI and 513 controls without angioedema following angiotensin-converting enzyme inhibitor (ACEI) treatment for at least 2 years. A meta-analysis was conducted with GWAS summary statistics from an African American and European American cohort (from the Vanderbilt-Marshfield cohort, which consisted of 174 case patients and 489 controls).

Results

No single-nucleotide polymorphisms (SNPs) attained genome-wide significance; however, 26 SNPs in the postimputation standard GWAS of the South African cohort and 73 SNPs in the meta-analysis attained suggestive thresholds (P < 5.0 × 10-06). Some of these SNPs were found to be located close to the genes PRKCQ (protein kinase C theta), RAD51B (RAD51 Paralog B), and RIMS1 (regulating synaptic membrane exocytosis 1), which were previously linked with drug-induced angioedema, and also close to the CSMD1 (CUB and sushi multiple domains 1) gene, which has been linked to ACEI cough, providing replication at the gene level but with novel lead SNPs. The study also replicated SNP rs500766 on chromosome 10, which was previously found to be associated with AE-ACEI.

Conclusions

Our results highlight the importance of African populations for detection of novel variants in replication studies. Further increased sampling across the continent and matched functional work are needed to confirm the importance of genetic variation in understanding the biology of AE-ACEI.

Sex dependent genetic architecture of biochemically verified tobacco use

BACKGROUND

Tobacco use differs by genetics and sex, and dose-dependently increases the risk for numerous diseases. Nicotine is metabolized to cotinine (COT) which is further metabolized to 3'hydroxycotinine (3HC). COT and COT+3HC are biomarkers which capture tobacco intake more accurately than self-reported measures such as cigarettes/day. It is currently not known whether genetic risk factors for heavier tobacco intake, measured using these biomarkers, differ by sex.

METHODS

We conducted a genome-wide genotype-by-sex (GxS) interaction analysis of COT and COT+3HC measured from blood in European treatment-seeking smokers (n = 541 males, n = 389 females) (NCT01314001). Linear regression models included Genotypes (coded additively), Sex, a GxS interaction term, covariates, and all covariate-by-genotype and covariate-by-sex interaction terms.

RESULTS

For COT, five suggestive (P < 5 × 10-6) loci on chr 4, 15, 19, 12, and 1 were identified; the top variant was rs11520555 (5' of SPOCK3; beta=0.38, se=0.08, GxS P = 7.39 × 10-7). For COT+3HC, eight suggestive loci on chr 21, 18, 17 (2 loci), 13, 5, 8, and 19 were identified; the top variant was rs73157714 (3' of HSPA13; beta=0.33, se=0.06, GxS P = 3.48 × 10-7). Overall, 26 genes were mapped, with 9 showing moderate to high expression in brain, and 5 showing prior associations with psychiatric traits in the GWAS Catalog.

CONCLUSIONS

Our findings suggest that the genetic architecture of tobacco intake, measured accurately using biomarkers, differs between women and men. A more granular understanding of factors influencing tobacco intake in women versus men may identify risk factors for heavier use and sex-specific opportunities to promote smoking cessation and mitigate disease risk.

IMPLICATIONS

This genome-wide interaction study suggested that some of the genetic influences on tobacco intake, measured accurately using biomarkers, differ by sex. The loci identified in our study could be a starting point for developing new genetic biomarkers that predict sex-specific differences in tobacco intake and disease risk.

Genetic Distinctions Between Reticular Pseudodrusen and Drusen: A Genome-Wide Association Study

OBJECTIVE

To identify genetic determinants specific to reticular pseudodrusen (RPD) compared with drusen.

DESIGN

Genome-wide association study (GWAS) SUBJECTS: Participants with RPD, drusen, and controls from the UK Biobank (UKBB), a large, multisite, community-based cohort.

METHODS

Participants with RPD, drusen, and controls from the UK Biobank (UKBB), a large, multisite, community-based cohort, were included. A deep learning framework analyzed 169,370 optical coherence tomography (OCT) volumes to identify cases and controls within the UKBB. Five retina specialists validated the cohorts using OCT and color fundus photographs. Several GWAS were undertaken utilizing the quantity and presence of RPD and drusen. Genome-wide significance was defined as P < 5e-8.

MAIN OUTCOMES MEASURES

Genetic associations were examined with the number of RPD and drusen within 'pure' cases, where only RPD or drusen were present in either eye. A candidate approach assessed 46 previously known AMD loci. Secondary GWAS were conducted for number of RPD and drusen in mixed cases, and binary case-control analyses for pure RPD and pure drusen.

RESULTS

The study included 1787 participants: 1037 controls, 361 pure drusen, 66 pure RPD, and 323 mixed cases. The primary pure RPD GWAS identified four genome-wide significant loci: rs11200630 near ARMS2-HTRA1 (P = 1.9e-09), rs79641866 at PARD3B (P = 1.3e-08), rs143184903 near ITPR1 (P = 8.1e-09), and rs76377757 near SLN (P = 4.3e-08). The latter three are uncommon variants (minor allele frequency <5%). A significant association at the CFH locus was also observed using a candidate approach (P = 1.8e-04). For pure drusen, two loci reached genome-wide significance: rs10801555 at CFH (P = 6.0e-33) and rs61871744 at ARMS2-HTRA1 (P = 4.2e-20).

CONCLUSIONS

The study highlights a clear association between the ARMS2-HTRA1 locus and higher RPD load. Although the CFH locus association did not achieve genome-wide significance, a suggestive link was observed. Three novel associations unique to RPD were identified, albeit for uncommon genetic variants. Further studies with larger sample sizes are needed to explore these findings.

Multiomics analysis demonstrated a strong correlation between lipid-mediated chronic kidney disease and stroke: Potential benefits of affected patient cohorts

OBJECTIVE

Patients with chronic kidney disease (CKD) exhibit a disproportionately elevated risk of stroke, frequently compounded by renal impairment. Therapeutic strategies for stroke based on Traditional Chinese Medicine's 'kidney-brain axis' theory demonstrate clinical efficacy, indicating that there may be a potential association between chronic kidney disease and stroke, which needs further exploration and verification.

METHODS

In this study, databases such as GEO, NHANES, and GWAS were used to collect data related to CKD and stroke. GEO gene data enrichment analysis was used to explore possible mediating factors between CKD and stroke. NHANES clinical data were used to verify the GEO data analysis results. Mendelian randomization was used to confirm the causal relationship between CKD and stroke and verify the association effect of mediating factors in these two diseases.

RESULTS

Cross-gene analysis and transcription factor analysis of GEO data revealed that lipid-related pathways may have a mediating effect on the relationship between CKD and stroke. Logistic regression analysis based on NHANES data revealed that changes in LDL-C, HDL-C, TC, and TG can affect the occurrence of stroke. Mendelian randomization analysis was used to determine the causal relationship between CKD and stroke and verified the mediating effects of lipid factors, such as LDL-C, HDL-C, TC, and TG, indicating that LDL-C, HDL-C, TC, and TG may be potential mediating factors for these two diseases. Our findings highlight the clinical relevance of lipid pathways in bridging CKD and stroke. By integrating predictive biomarkers and multi-level diagnostics, this study paves the way for AI-driven precision medicine in stroke prevention. Specifically, machine learning approaches could enhance risk stratification of high-risk CKD cohorts, enabling tailored interventions such as lipid-lowering therapies and personalized monitoring protocols. These strategies align with emerging paradigms in healthcare benefits and population-specific management.

CONCLUSION

This study provides new insights into the interactive relationship between CKD and stroke and provides a scientific basis for the process of syndrome differentiation and the treatment of stroke under the guidance of the "kidney-brain correlation". Moreover, the influence of mediating factors related to lipid metabolism on the occurrence of these two diseases was investigated, which deepened researchers' understanding of the potential association mechanism between the two diseases.

Genetic associations of neuropathic pain and sensory profile in a deeply phenotyped neuropathy cohort

ABSTRACT

We aimed to investigate the genetic associations of neuropathic pain in a deeply phenotyped cohort. Participants with neuropathic pain were cases and compared with those exposed to injury or disease but without neuropathic pain as control subjects. Diabetic polyneuropathy was the most common aetiology of neuropathic pain. A standardised quantitative sensory testing protocol was used to categorize participants based on sensory profile. We performed genome-wide association study, and in a subset of participants, we undertook whole-exome sequencing targeting analyses of 45 known pain-related genes. In the genome-wide association study of diabetic neuropathy (N = 1541), a top significant association was found at the KCNT2 locus linked with pain intensity (rs114159097, P = 3.55 × 10 -8 ). Gene-based analysis revealed significant associations between LHX8 and TCF7L2 and neuropathic pain. Polygenic risk score for depression was associated with neuropathic pain in all participants. Polygenic risk score for C-reactive protein showed a positive association, while that for fasting insulin showed a negative association with neuropathic pain, in individuals with diabetic polyneuropathy. Gene burden analysis of candidate pain genes supported significant associations between rare variants in SCN9A and OPRM1 and neuropathic pain. Comparison of individuals with the "irritable" nociceptor profile to those with a "nonirritable" nociceptor profile identified a significantly associated variant (rs72669682, P = 4.39 × 10 -8 ) within the ANK2 gene. Our study on a deeply phenotyped cohort with neuropathic pain has confirmed genetic associations with the known pain-related genes KCNT2 , OPRM1 , and SCN9A and identified novel associations with LHX8 and ANK2 , genes not previously linked to pain and sensory profiles, respectively.

Genome-wide association study identifying novel risk variants associated with glycaemic traits in the continental African AWI-Gen cohort

AIMS/HYPOTHESIS

Glycaemic traits such as high fasting glucose levels and insulin resistance are positively associated with the risk of type 2 diabetes and other cardiometabolic diseases. Genetic association studies have identified hundreds of associations for each glycaemic trait, yet very few studies have involved continental African populations. We report the results of genome-wide association studies (GWASs) in a pan-African cohort for four glycaemic traits, namely fasting glucose, fasting insulin, insulin resistance (HOMA-IR) and beta cell function (HOMA-B), which are quantitative variables that affect the risk of developing type 2 diabetes.

METHODS

GWASs for the four traits were conducted in approximately 10,000 individuals from the Africa Wits-INDEPTH Partnership for Genomics Studies (AWI-Gen) cohort, with participants from Burkina Faso, Ghana, Kenya and South Africa. Association testing was performed using linear mixed models implemented in BOLT-LMM, with age, sex, BMI and principal components as covariates. Replication, fine mapping and functional annotation were performed using standard approaches.

RESULTS

We identified a novel signal (rs574173815) in the intron of the ankyrin repeat domain 33B (ANKRD33B) gene associated with fasting glucose, and a novel signal (rs114029796) in the intronic region of the WD repeat domain 7 (WDR7) gene associated with fasting insulin. SNPs in WDR7 have been shown to be associated with type 2 diabetes. A variant (rs74806991) in the intron of ADAM metallopeptidase with thrombospondin type 1 motif 16 (ADAMTS16) and another variant (rs6506934) in the β-1,4-galactosyltransferase 6 gene (B4GALT6) are associated with HOMA-IR. Both ADAMTS16 and B4GALT6 are implicated in the development of type 2 diabetes. In addition, our study replicated several well-established fasting glucose signals in the GCK-YTK6, SLC2A2 and THORLNC gene regions.

CONCLUSIONS/INTERPRETATION

Our findings highlight the importance of performing GWASs for glycaemic traits in under-represented populations, especially continental African populations, to discover novel associated variants and broaden our knowledge of the genetic aetiology of glycaemic traits. The limited replication of well-known signals in this study hints at the possibility of a unique genetic architecture of these traits in African populations.

DATA AVAILABILITY

The dataset used in this study is available in the European Genome-Phenome Archive (EGA) database ( https://ega-archive.org/ ) under study accession code EGAS00001002482. The phenotype dataset accession code is EGAD00001006425 and the genotype dataset accession code is EGAD00010001996. The availability of these datasets is subject to controlled access by the Data and Biospecimen Access Committee of the H3Africa Consortium. GWAS summary statistics are accessible through the NHGRI-EBI GWAS Catalog ( https://www.ebi.ac.uk/gwas/ ).

A multilevel study on the genetic relationship between schizophrenia and inflammatory bowel disease

BACKGROUND

Schizophrenia (SCZ) and Inflammatory Bowel Disease (IBD) represent significant clinical challenges, frequently co-morbid and potentially linked by a genetic correlation. However, the precise mechanism underlying this correlation remains elusive.

METHODS

we utilized genome-wide association study (GWAS) data for SCZ and IBD to evaluate their genetic correlation. Initially, we performed an overall assessment using Linkage Disequilibrium Score Regression (LDSC), Genetic Covariance Analysis (GNOVA), and High-Dimensional Likelihood (HDL) methods. Subsequently, we conducted a more detailed local analysis using the Local Analysis of Variant Association (LAVA) method. To quantify the genetic overlap between these traits, we employed the Conditional/Joint False Discovery Rate (cond/conjFDR) statistical framework. Finally, by integrating the conjFDR analysis with Multi-Trait GWAS (MTAG), we successfully identified multiple shared genetic loci, shedding light on the genetic intersection between these two traits.

RESULTS

At the genomic level, three independent methods confirmed the overall genetic correlation between SCZ and IBD, including CD and UC. Local genetic correlations were also observed across multiple chromosomal regions. At the single-nucleotide polymorphism (SNP) level, we performed a conjFDR analysis, which indicated a genetic overlap between the two traits. By integrating conjFDR analysis with MTAG, we successfully identified several shared genetic loci, including SLC39A8, BACH2, ZNF365, NOD2, PLCL1, and KIF21B.

CONCLUSION

The present study provides a novel perspective on the correlation between SCZ and IBD, potentially advancing the understanding of the genetic architecture and mechanisms of co-morbidities in both diseases.

Developing brain asymmetry shapes cognitive and psychiatric outcomes in adolescence

Cerebral asymmetry, fundamental to various cognitive functions, is often disrupted in neuropsychiatric disorders. While brain growth has been extensively studied, the maturation of brain asymmetry in children and the factors influencing it in adolescence remain poorly understood. We analyze longitudinal data from 11,270 children aged 10-14 years in the Adolescent Brain Cognitive Development (ABCD) study. Our analysis maps the developmental trajectory of structural brain asymmetry. We identify significant age-related, modality-specific development patterns. These patterns link to crystallized intelligence and mental health problems, but with weak correlations. Genetically, structural asymmetry relates to synaptic processes and neuron projections, likely through asymmetric synaptic pruning. At the microstructural level, corpus callosum integrity emerged as a key factor modulating the developing asymmetry. Environmentally, favorable perinatal conditions were associated with prolonged corpus callosum development, which affected future asymmetry patterns and cognitive outcomes. These findings underscore the dynamic yet predictable interactions between brain asymmetry, its structural determinants, and cognitive and psychiatric outcomes during a pivotal developmental stage. Our results provide empirical support for the adaptive plasticity theory in cerebral asymmetry and offer insights into both cognitive maturation and potential risk for early-onset mental health problems.

Unraveling the genetics of gulf war illness in diverse participants enrolled in the million veteran program

Gulf War Illness (GWI) is a multi-symptom chronic condition that affects Veterans who served in the 1990-1991 Gulf War (GW). To generate novel information about GWI pathogenesis, we used genome-wide data available from 33 523 Veterans of diverse ancestral backgrounds who served during the 1990-1991 Gulf War era (34% deployed). Polygenic score (PGS) analysis showed GWI pleiotropy for several traits with the strongest evidence for type-2 diabetes (T2D), anxiety, and depression. While T2D PGS was associated with higher GWI odds in GW Veterans, anxiety and depression PGSs were associated with higher odds of GWI in non-deployed GW-era Veterans. Seven independent variants were identified (P < 5 × 10-8). Two of them were supported by independent transcriptomic and phenome-wide analyses. Rs4675853 was associated with AGXT, MAB21L4, and ATG4Btranscriptomic regulation and with sex hormone-binding globulin levels. Rs138168412 was associated with AOPEPtranscriptomic regulation and with respiratory function and physical strength. The TWAS identified five additional loci such as CEMIPin the cerebellum and SNCGin the adrenal gland. The results provide a comprehensive assessment of the polygenic architecture of GWI research definitions, identifying mechanisms potentially relevant to the disease pathogenesis.

Dissecting the genetic determinants and biological associations between body mass index and female reproductive disorders based on genome-wide association study

BACKGROUND

While the phenotypic link between body mass index (BMI) and some female reproductive disorders is well established, the genetic architecture and causal relationships have not been systematically studied. We aimed to create an atlas of the shared genetic associations of BMI and 16 female reproductive disorders and to identify their common risk loci, biological pathways, and potential mechanisms.

METHODS

We assessed the genetic correlations between BMI and 16 reproductive disorders using summary data from large-scale genome-wide association studies. Cross-trait pleiotropic analysis identified shared loci and genes, while functional annotation and tissue-specific analysis revealed relevant biological pathways and tissues. Multi-trait colocalization analysis examined the role of hormones and metabolites in these traits. Additionally, bidirectional Mendelian randomization (MR) analysis was employed to assess causal relationships between BMI and reproductive outcomes. We also conducted summary data-based MR (SMR) analysis to identify potential drug targets.

RESULTS

Our results revealed a significant genetic correlation between BMI and eight female reproductive diseases. Furthermore, we identified 50 shared pleiotropic loci between BMI and these traits, with 21 of them showing significant colocalization, suggesting a complex shared genetic architecture across the genome. In addition, the top biological pathways and tissues enriched with these pleiotropic loci were associated with RNA metabolism, macromolecule biosynthesis, type B pancreatic cell apoptosis, various brain regions, and the pituitary. Moreover, multi-trait colocalization indicated that insulin, lipid metabolites, glucose, glycine, and glutamine mediate shared mechanisms between BMI, gestational diabetes mellitus (GDM), and endometrial cancer. MR analysis suggested BMI may cause several reproductive diseases, with only GDM affecting BMI reversely. Finally, SMR analysis revealed EIF2S2P3 and MCM6, which may have a causative effect on both BMI & GDM and BMI & gestational hypertension.

CONCLUSION

Our results suggest a significant genetic link between BMI and eight female reproductive diseases, highlighting a shared and causal genetic basis. Reducing BMI in women may serve as an effective strategy to lower the risk of female reproductive disorders. The identified pleiotropic loci, genes, and shared pathways could provide new therapeutic targets for both obesity and reproductive diseases, along with their comorbidities.

CLINICAL TRIAL NUMBER

Not applicable.

Characterizing pleiotropy among bipolar disorder, schizophrenia, and major depression: a genome-wide cross-disorder meta-analysis

BACKGROUND

To understand the pathogenetic mechanisms shared among schizophrenia (SCZ), bipolar disorder (BP), and major depression (MDD), we investigated the pleiotropic mechanisms using large-scale genome-wide and brain transcriptomic data.

METHODS

We analyzed SCZ, BP, and MDD genome-wide association datasets available from the Psychiatric Genomics Consortium using the PLEIO framework and characterized the pleiotropic loci identified using pathway and tissue enrichment analyses. Pleiotropic and disorder-specific loci were also assessed.

RESULTS

Our pleiotropy-informed genome-wide analysis identified 553 variants that included 192 loci not reaching genome-wide significance in input datasets. These were enriched for five molecular pathways: cadherin signaling (p = 2.18 × 10-8), Alzheimer's disease-amyloid secretase (p = 4 × 10-4), oxytocin receptor-mediated signaling (p = 1.47 × 10-3), metabotropic glutamate receptor group III (p = 5.82 × 10-4) and Wnt signaling (p = 1.61 × 10-11). Pleiotropic loci demonstrated the strongest enrichment in the brain cortex (p = 5.8 × 10-28), frontal cortex (p = 3 × 10-31), and cerebellar hemisphere (p = 9.8 × 10-28). SCZ-BP-MDD pleiotropic variants were also enriched for neurodevelopmental brain transcriptomic profiles related to the second-trimester post-conception (week 21, p = 7.35 × 10-5; week 17, p = 6.36 × 10-4) and first year of life (p = 3.25 × 10-5).

CONCLUSIONS

Genetic mechanisms shared among SCZ, BP, and MDD appear to be related to early neuronal development. Because the genetic architecture of psychopathology transcends diagnostic boundaries, pleiotropy-focused analyses can lead to increased gene discovery and novel insights into relevant pathogenic mechanisms.

Metabolome-wide association identifies ferredoxin-1 (FDX1) as a determinant of cholesterol metabolism and cardiovascular risk in Asian populations

The burden of cardiovascular disease is rising in the Asia-Pacific region, in contrast to falling cardiovascular disease mortality rates in Europe and North America. Here we perform quantification of 883 metabolites by untargeted mass spectroscopy in 8,124 Asian adults and investigate their relationships with carotid intima media thickness, a marker of atherosclerosis. Plasma concentrations of 3beta-hydroxy-5-cholestenoate (3BH5C), a cholesterol metabolite, were inversely associated with carotid intima media thickness, and Mendelian randomization studies supported a causal relationship between 3BH5C and coronary artery disease. The observed effect size was 5- to 6-fold higher in Asians than Europeans. Colocalization analyses indicated the presence of a shared causal variant between 3BH5C plasma levels and messenger RNA and protein expression of ferredoxin-1 (FDX1), a protein that is essential for sterol and bile acid synthesis. We validated FDX1 as a regulator of 3BH5C synthesis in hepatocytes and macrophages and demonstrated its role in cholesterol efflux in macrophages and aortic smooth muscle cells, using knockout and overexpression models.

Deciphering the influence of socioeconomic status on brain structure: insights from Mendelian randomization

Socioeconomic status (SES) influences physical and mental health, however its relation with brain structure is less well documented. Here, we examine the role of SES on brain structure using Mendelian randomisation. First, we conduct a multivariate genome-wide association study of SES using educational attainment, household income, occupational prestige, and area-based social deprivation, with an effective sample size of N = 947,466. We identify 554 loci associated with SES and distil these loci into those that are common across those four traits. Second, using an independent sample of ~35,000 we provide evidence to suggest that SES is protective against white matter hyperintensities as a proportion of intracranial volume (WMHicv). Third, we find that differences in SES still afford a protective effect against WMHicv, independent of that made by cognitive ability. Our results suggest that SES is a modifiable risk factor, causal in the maintenance of cognitive ability in older-age.

Post-genome-wide association study dissects genetic vulnerability and risk gene expression of Sjögren's disease for cardiovascular disease

OBJECTIVES

This study aims to clarify the genetic associations between Sjögren's Disease (SD) and cardiovascular disease (CVD) outcomes, and to conduct an in-depth exploration of specific pleiotropic susceptibility genes.

METHODS

We performed two-sample and multivariable Mendelian randomization (MR) analysis to investigate the association between SD and the risk of ischemic heart disease (IHD) and stroke. Linkage disequilibrium score regression (LDSC) and Bayesian co-localization analyses were employed to assess the genetic associations between traits. Cross-phenotype analyses were employed to identify shared variants and genes, followed by a Transcriptome-Wide Association Study (TWAS) and Multi-marker Analysis of Genomic Annotation (MAGMA) based on Multi-Trait Analysis of GWAS (MTAG) results. To validate the pleiotropic genes, we further analyzed tissue-specific differentially expressed genes (DEGs) related to SD using RNA sequencing data.

RESULTS

The two-sample and multivariable MR analyses revealed that SD confers a genetic vulnerability to IHD and stroke. LDSC and co-localization analyses indicated a strong genetic linkage between SD and CVDs. Cross-phenotype analyses identified 38 and 37 pleiotropic single nucleotide polymorphisms (SNPs) for SD-Stroke and SD-IHD, respectively, primarily located within the MHC class region on 6p21.32:33 loci. Additionally, TWAS and MAGMA analyses identified pleiotropic genes located outside the MHC regions-seven associated with stroke (UHRF1BP1, SNRPC, BLK, FAM167A, ARHGAP27, C8orf12, and PLEKHM1) and two associated with IHD (UHRF1BP1 and SNRPC). Proxy variants within these genes in SD suggested an increased causal risk for stroke or IHD. Co-localization analysis further reinforced that SD and stroke share significant SNPs within the loci of FAM167A, BLK, C8orf12, SNRPC, and UHRF1BP1. DEG analysis revealed a significant up-regulation of the identified genes in SD-specific tissues.

CONCLUSIONS

SD appears genetically predisposed to an increased risk of CVDs. Moreover, this research not only identified pleiotropic genes shared between SD and CVDs, but also, for the first time, detected key gene expressions that elevate CVD risk in SD patients-findings that may offer promising therapeutic targets for patient management.

Genome-wide association study for lung cancer in 6531 African Americans reveals new susceptibility loci

Despite lung cancer affecting all races and ethnicities, disparities are observed in incidence and mortality rates among different ethnic groups in the United States. Non-Hispanic African Americans had a high incidence rate of lung cancer at 55.8 per 100 000 people, as well as the highest death rate at 37.2 per 100 000 people from 2016 to 2020. While previous genome-wide association studies (GWAS) have identified over 45 susceptibility risk loci that influence lung cancer development, few GWAS have investigated the etiology of lung cancer in African Americans. To address this gap in knowledge, we conducted GWAS of lung cancer focused on studying African Americans, comprising 2267 lung cancer cases and 4264 controls. We identified three loci associated with lung cancer, one with lung adenocarcinoma, and four with lung squamous cell carcinoma in this population at the genomic-wide significance level. Among them, three novel loci were identified near VWF at 12p13.31 for overall lung cancer and GACAT3 at 2p24.3 and LMAN1L at 15q24.1 for lung squamous cell carcinoma. In addition, we confirmed previously reported risk loci with known or new lead variants near CHRNA5 at 15q25.1 and CYP2A6 at 19q13.2 associated with lung cancer and TRIP13 at 5p15.33 and ERC1 at 12p13.33 associated with lung squamous cell carcinoma. Further multi-step functional analyses shed light on biological mechanisms underlying these associations of lung cancer in this population. Our study highlights the importance of ancestry-specific studies for the potential alleviation of lung cancer burden in African Americans.

Chromatin state origins of uterine leiomyoma

Aberrations in the regulatory genome play a pivotal role in population-level disease predisposition. Annotation of the regulatory regions using appropriate primary tissues - instead of cell lines affected by selection and other confounding factors - could shed new light into mechanisms underlying common conditions. We test this approach in uterine leiomyomas, highly prevalent benign neoplasms of the myometrium, by creating 15-state chromatin annotations for myometrium and uterine leiomyomas. Integration with RNA-seq, ATAC-seq, HiChIP and methylation data enables us to compare the epigenomes of myometrium and ULs with distinct driver mutations, highlighting the role of bivalent regions in the neoplastic process. Subsequently, a genome wide association study meta-analysis is performed, using three different cohorts. Disease association loci are enriched at active chromatin, especially at enhancers, and harbor tumor- and driver mutation-specific chromatin states. At SATB2 locus we show the effect of the risk genotype already in the normal tissue. Integration of genome-wide association studies and deep regulatory genomics data from the correct tissue type represents a powerful approach in understanding population-level disease predisposition.

Systematic review and independent validation of genetic factors of radiographic outcome in rheumatoid arthritis identifies a genome-wide association with CARD9

OBJECTIVES

This study aimed to investigate non-HLA genetic mechanisms underlying radiographic severity in rheumatoid arthritis (RA).

METHODS

A systematic review of publications reporting non-HLA genetic associations with radiographic severity in RA across ancestries was undertaken. Experimental validation was performed in the Norfolk Arthritis Register, comprising 1407 patients with available genetic and treatment data followed prospectively for up to 10 years, with 2198 longitudinal radiographs. Genome-wide genotyping was performed with Illumina Human Core Exome Array. Radiographic outcomes (presence of erosions; Larsen score) were modelled longitudinally. Fine mapping and functional annotations to refine associations to potential causative loci were undertaken using FUMA, PolyPhen2, and RegulomeDB.

RESULTS

The systematic review identified 102 publications reporting 139 independent associations with radiographic outcome. Association with 15 independent polymorphisms were replicated in the Norfolk Arthritis Register data set, implicating adaptive immune processes (Th1, Th2, and Th17 pathways), cytokine regulation, and osteoclast differentiation. Notably, we refined the association of rs59902911 at the CARD9 locus to an intronic polymorphism within an active enhancer (rs78892335), achieving genome-wide significance and with an effect size exceeding the minimal clinically important difference for each copy of the minor allele (4.78 Larsen units/copy; 95% CI, 3.15-6.41; p = 9.01 × 10-9). This polymorphism is associated with the expression of CARD9 in immune cells, including B cells.

CONCLUSIONS

We provide a comprehensive list of validated genetic associations with RA outcome and demonstrate that non-HLA polymorphisms can associate with radiographic severity independently of disease susceptibility. This highlights the importance of dedicated genetic outcome studies for patient stratification in precision medicine for RA.

Genome-wide association meta-analysis of age at onset of walking in over 70,000 infants of European ancestry

Age at onset of walking is an important early childhood milestone which is used clinically and in public health screening. In this genome-wide association study meta-analysis of age at onset of walking (N = 70,560 European-ancestry infants), we identified 11 independent genome-wide significant loci. SNP-based heritability was 24.13% (95% confidence intervals = 21.86-26.40) with ~11,900 variants accounting for about 90% of it, suggesting high polygenicity. One of these loci, in gene RBL2, co-localized with an expression quantitative trait locus (eQTL) in the brain. Age at onset of walking (in months) was negatively genetically correlated with ADHD and body-mass index, and positively genetically correlated with brain gyrification in both infant and adult brains. The polygenic score showed out-of-sample prediction of 3-5.6%, confirmed as largely due to direct effects in sib-pair analyses, and was separately associated with volume of neonatal brain structures involved in motor control. This study offers biological insights into a key behavioural marker of neurodevelopment.

Genome-wide analyses of variance in blood cell phenotypes provide new insights into complex trait biology and prediction

Blood cell phenotypes are routinely tested in healthcare to inform clinical decisions. Genetic variants influencing mean blood cell phenotypes have been used to understand disease aetiology and improve prediction; however, additional information may be captured by genetic effects on observed variance. Here, we mapped variance quantitative trait loci (vQTL), i.e. genetic loci associated with trait variance, for 29 blood cell phenotypes from the UK Biobank (N ~ 408,111). We discovered 176 independent blood cell vQTLs, of which 147 were not found by additive QTL mapping. vQTLs displayed on average 1.8-fold stronger negative selection than additive QTL, highlighting that selection acts to reduce extreme blood cell phenotypes. Variance polygenic scores (vPGSs) were constructed to stratify individuals in the INTERVAL cohort (N ~ 40,466), where the genetically most variable individuals had increased conventional PGS accuracy (by ~19%) relative to the genetically least variable individuals. Genetic prediction of blood cell traits improved by ~10% on average combining PGS with vPGS. Using Mendelian randomisation and vPGS association analyses, we found that alcohol consumption significantly increased blood cell trait variances highlighting the utility of blood cell vQTLs and vPGSs to provide novel insight into phenotype aetiology as well as improve prediction.

Transdiagnostic and Disorder-Level GWAS Enhance Precision of Substance Use and Psychiatric Genetic Risk Profiles in African and European Ancestries

BACKGROUND

Substance use disorders (SUDs) and psychiatric disorders frequently co-occur, and their etiology likely reflects both transdiagnostic (i.e., common/shared) and disorder-level (i.e., independent/nonshared) genetic influences. Understanding the genetic influences that are shared and those that operate independently of the shared risk could enhance precision in diagnosis, prevention, and treatment, but this remains underexplored, particularly in non-European ancestry groups.

METHODS

We applied genomic structural equation modeling to examine the common and independent genetic architecture among SUDs and psychotic, mood, and anxiety disorders using summary statistics from genome-wide association studies (GWAS) conducted in European- (EUR) and African-ancestry (AFR) individuals. To characterize the biological and phenotypic associations, we used FUMA, conducted genetic correlations, and performed phenome-wide association studies (PheWAS).

RESULTS

In EUR individuals, transdiagnostic genetic factors represented SUDs, psychotic, and mood/anxiety disorders, with GWAS identifying two novel lead single-nucleotide polymorphisms (SNPs) for the mood factor. In AFR individuals, genetic factors represented SUDs and psychiatric disorders, and GWAS identified one novel lead SNP for the SUD factor. In EUR individuals, second-order factor models showed phenotypic and genotypic associations with a broad range of physical and mental health traits. Finally, genetic correlations and PheWAS highlighted how common and independent genetic factors for SUD and psychotic disorders were differentially associated with psychiatric, sociodemographic, and medical phenotypes.

CONCLUSIONS

Combining transdiagnostic and disorder-level genetic approaches can improve our understanding of co-occurring conditions and increase the specificity of genetic discovery, which is critical for identifying more effective prevention and treatment strategies to reduce the burden of these disorders.

Relationship Between Problematic Alcohol Use and Various Psychiatric Disorders: A Genetically Informed Study

OBJECTIVE

Problematic alcohol use (PAU) adversely affects the clinical course of psychiatric disorders. Genetic studies have suggested that genetic factors underlie the co-occurrence of PAU with psychiatric disorders. This study aimed to elucidate shared genetic architectures, prioritizing genes that disorders may have in common.

METHODS

Using genome-wide association data of PAU including 435,563 samples from people of European ancestry, this study investigated the genetic relationship between PAU and 11 psychiatric disorders using a bivariate causal mixture model (MiXeR). Local genetic correlation and colocalization analyses were conducted to identify the genomic regions significantly associated with PAU and each psychiatric disorder. Postanalysis included the false discovery rate (FDR) and transcriptome-wide association studies (TWASs), as well as summary-data-based Mendelian randomization to prioritize shared genes by integrating brain transcriptome data.

RESULTS

MiXeR analysis revealed a substantial polygenic overlap (39%-73%) between PAU and psychiatric disorders. Four bivariate genomic regions with high correlations suggest shared causal variants of PAU with major depression and schizophrenia. Within these regions, four and six genes for the PAU-major depression and PAU-schizophrenia pairs, respectively, were mapped by conjunctional FDR analysis. Furthermore, TTC12 and ANKK1 were identified as potential causal genes for PAU and these disorders. The findings were replicated in multi-ancestry analyses of colocalization and TWASs.

CONCLUSIONS

Despite the varying degrees of genetic overlap and directions of shared genetic effect correlations, these results imply the presence of shared genetic factors influencing the comorbidity of PAU and psychiatric disorders. Additionally, TTC12 and ANKK1, located near DRD2, may be causally associated with comorbid conditions.

Pharmacogenomics and Pharmacokinetics of Aspirin in Preeclampsia Prevention

BACKGROUND

It has become evident that some women develop preeclampsia despite aspirin. This study aimed to examine how such aspirin nonresponsiveness develops in high-risk preeclampsia pregnancies by exploring the role of genetic polymorphisms and aspirin metabolism.

METHODS

The study involved pregnant women who developed preeclampsia despite low-dose aspirin and those who did not. First, we conducted a pharmacogenomic association study exploring the association of potential genetic variants with aspirin nonresponsiveness. Next, we analyzed the rate of enzymatic aspirin hydrolysis in maternal plasma. The extent of placental exposure to acetylsalicylic acid and its bioactive metabolites, that is, salicylic acid and gentisic acid, was determined by liquid chromatography-mass spectrometry. The expressions of AMEs (aspirin metabolizing enzymes), that is, GLYAT (glycine-N-acyltransferase), UGT1A6, CYP2E1, and NAT2 in the placenta, were analyzed by quantitative reverse transcription polymerase chain reaction, immunohistochemistry staining, and ELISA. Finally, the effects of AMEs were further examined on HTR-8/SVneo and human primary cytotrophoblast cells.

RESULT

Our genetic study showed that single-nucleotide polymorphisms (SNPs) of genes involved in aspirin pharmacokinetics and pharmacodynamics were not associated with aspirin nonresponsiveness in preeclampsia. Rates of aspirin hydrolysis in maternal plasma and the concentrations of acetylsalicylic acid, salicylic acid, and gentisic acid in the placenta did not differ between aspirin-responsive and aspirin-nonresponsive women. Intriguingly, GLYAT was significantly upregulated in the aspirin-nonresponsive placenta and associated with aspirin nonresponsiveness. This overexpression of GLYAT was found to diminish the proangiogenic, anti-inflammatory, and antisenescence effects of salicylic acid in HTR-8/SVneo and human primary cytotrophoblast cells.

CONCLUSIONS

Our study revealed that maternal genetic factors and plasma aspirin hydrolysis are not among the decisive factors in determining the effectiveness of low-dose aspirin in preventing preeclampsia among high-risk women. Instead, placental GLYAT appears to play a key role by limiting the effect of salicylic acid in the placenta.

X-chromosome association study reveals genetic susceptibility loci of hypospadias in southern Chinese population

PURPOSE

X-chromosome variants contribute significantly to hypospadias risk but have not been fully elucidated in the Chinese population. Here we aim to assess how X-chromosome variants contribute to hypospadias susceptibility in the Chinese population.

METHODS

We recruited 1,073 boys with hypospadias and 5,150 controls in a southern Chinese population. Single-variant and gene/pathway-based association analyses were conducted for the distal and proximal hypospadias. Haplotype analysis was performed on top susceptibility genes. Additionally, we performed a multi-ancestral comparison between the East Asian and European populations.

RESULTS

We performed an X-chromosome-wide association study on 987 patients and 4,761 controls that met quality control standards. We confirmed DGKK variants as multi-ancestral susceptibility loci for distal hypospadias (lead SNP: rs5961181, P = 1.82 × 10- 7), but not for the proximal subtype. Distinct association signals were identified for distal hypospadias (DGKK-CCNB3-AKAP4, PNPLA4, AR-OPHN1, TAF7L, IL1RAPL1) and proximal hypospadias (SMIM10L2A, PRR32 and Xq28 gene cluster). Pathway analysis revealed that distal hypospadias is associated with male gamete generation, epithelial cell polarity, and lipid/sterol metabolism, while proximal hypospadias is linked to amino acid metabolism and gastrulation. Except for DGKK, all candidate genes showed population-favored associations compared to European studies. Haplotype analysis of DGKK, PNPLA4, OPHN1 and IL1RAPL1 showed increased risk for specific risk haplotypes (OR ranged from 4.35 to 6.25).

CONCLUSION

Our findings highlight the importance of X chromosome variants in hypospadias etiology and reveal subtype- and population-specific genetic architecture. Our results improve the understanding of genetic susceptibility for hypospadias risk and provide insights into risk prediction and personalized prevention strategies in hypospadias management.

Multi-ancestry genome-wide association meta-analysis of buprenorphine treatment response

Although the mu-opioid partial agonist buprenorphine is increasingly being prescribed to treat opioid use disorder, patients' responses to the drug vary and few clinical and no genetic predictors of treatment response have been identified. We conducted a genome-wide association study (GWAS) meta-analysis of buprenorphine treatment response (defined using urine drug screen results) in 4394 Veterans with opioid use disorder from the VA Million Veteran Program (751 of African-like ancestry [AFR] and 3643 of European-like ancestry [EUR]) and 296 participants from a clinical trial of extended-release buprenorphine (nAFR = 104, nEUR = 192). We conducted within-ancestry GWAS in both cohorts, followed by cross-ancestry, fixed-effects GWAS meta-analyses within and across cohorts. We also examined associations between demographic and clinical characteristics and buprenorphine treatment response. The cross-ancestry meta-analysis of both cohorts identified one genome-wide significant locus (rs149319538) that maps to SLC39A10, a gene that encodes a zinc transporter. Phenome-wide association analyses of the lead variant implicated connectivity of the uncinate fasciculus, a limbic white matter fiber tract. Of the clinical characteristics, only the presence of chronic pain and a lower maximum buprenorphine dosage were related to higher odds of treatment response in adjusted models. We report here the first genome-wide significant variant associated with buprenorphine treatment response. Larger samples are needed to replicate these findings and identify additional clinical and genetic factors that predict buprenorphine treatment efficacy to enable the use of a precision approach to OUD treatment.

The genetic overlap and causal relationship between attention deficit hyperactivity disorder and obstructive sleep apnea: a large-scale genomewide cross-trait analysis

BACKGROUND

Attention deficit hyperactivity disorder (ADHD) and Obstructive sleep apnea (OSA) are highly clinically co-occurring, but the mechanisms behind this remain unclear, so this article analyzes the reasons for the co-morbidities from a genetic perspective.

METHODS

We examined the genetic architecture of ADHD and OSA based on the large genome-wide association studies (GWAS). The global genetic relationship between OSA and ADHD was explored. Cross-trait analysis from single nucleotide polymorphism (SNP) and gene level was performed subsequently to detect the crucial genomic regions. Finally, we revealed the anatomical change on which genetic overlap relies and further explored whether genetic factors exert a causal effect.

RESULTS

After using both linkage disequilibrium score regression (LDSC) and High-definition likelihood inference (HDL) methods, we identified a significant genetic correlation between OSA and ADHD (PLDSC = 2.45E-28, PHDL = 1.09E-25), demonstrating a consistent direction. Furthermore, through the application of various cross-trait methods, we pinpointed 5 loci and 57 genes involved in regulating the co-occurrence of these disorders. These genetic regions were thought to be associated with the prefrontal lobes (P = 3.07E-06) and the nucleus accumbens basal ganglia (P = 2.85E-06). Lastly, utilizing Mendelian randomization (MR), we established a link indicating that individuals with ADHD were at an elevated risk of developing OSA (PIVM = 0.02, OR (95%CI):1.09 (1.01-1.17)).

CONCLUSIONS

This study reveals a strong genetic correlation between ADHD and OSA. It offers insights for future drug target development and sleep management in ADHD.

Genome-wide Pleiotropy Analysis Reveals Shared Genetic Associations between Type 2 Diabetes Mellitus and Subcortical Brain Volumes

Type 2 diabetes mellitus (T2DM), a prevalent metabolic disorder marked by insulin resistance and hyperglycemia, has been linked to volumetric changes in subcortical regions, yet the genetic basis of this relationship remains unclear. We analyzed genome-wide association study summary data for T2DM and 14 subcortical volumetric traits, using MiXeR to quantify shared genetic architecture and applying conditional/conjunctional false discovery rate analyses to detect novel and shared genomic loci. Enrichment and gene expression analyses were subsequently performed to explore the biological functions and mechanisms of genes associated with these loci. We observed a substantial proportion of trait-influencing variants shared between T2DM and subcortical structures, with Dice coefficients ranging from 22.4% to 49.6%. Additionally, 70 distinct loci were identified as being jointly associated with T2DM and subcortical volumes, 5 and 22 of which were novel for T2DM and subcortical volumes, respectively. The 769 protein-coding genes mapped to these shared loci are enriched in metabolic and neurodevelopmental pathways and exhibit specific developmental trajectories, with 117 genes showing expression levels linked to both T2DM and subcortical structures. This study uncovered polygenic overlap between T2DM and subcortical structures, deepening our comprehension of the genetic factors linking metabolic disorders and brain health.

Multitrait GWAS of non-suicidal self-injury and the polygenetic effects on child psychopathology and brain structures

Non-suicidal self-injury (NSSI) is highly prevalent in recent years, but the genetic architecture remains unknown. We perform a multitrait analysis of genome-wide association study on NSSI, incorporating self-harm and suicide attempt. Common genetic variants account for 6.03% of NSSI variance. Three risk loci are associated with NSSI at 7q31.2 (rs62474683), DCC (rs4372758), and LCA5L/GET1/GET1-SH3BGR (rs2837022). Increased expression levels of GET1/SH3BGR in hippocampus relates to NSSI risk. Fine-mapping identifies seven likely causal variants, and colocalization with rs4281987 and rs2837022 evidences SH3BGR/GET1 expression in hippocampus to NSSI. In an independent sample, polygenic risk score for NSSI is associated with children's NSSI behavior, suicidal ideation, and suicide attempt (odds ratios [ORs]: 1.14-1.37). Reduction in right temporal pole volume mediates NSSI genetic liability for children's NSSI behavior. Walking for pleasure and exercises like swimming and bowling reduces NSSI risk, whereas smoking increases it. This study elucidates the NSSI genetic basis and its impact on children's emotions, behavior, and brain structure.

Integrating a multi-omics strategy framework to screen potential targets in cognitive impairment-related epilepsy

Epilepsy is a prevalent neurological disorder that affects over 70 million individuals worldwide and is often associated with cognitive impairments. Despite the widespread impact of epilepsy and cognitive impairments, the genetic basis and causal relationships underlying these conditions remain uncertain, prompting us to conduct a comprehensive investigation into the molecular mechanisms involved. In this study, we utilized statistical data from the third National Health and Nutrition Examination Survey (NHANES III) to evaluate correlation and large-scale pan-phenotype genome-wide association study (GWAS) data to establish genetic correlation and causality. Leveraging multi-omics datasets, we performed a comprehensive post-analysis that included variant prioritization, gene analysis, tissue and cell type enrichment, and pathway annotation. An integrated strategy-multi-trait analysis of GWAS (MTAG), transcriptome-wide association study (TWAS), summary-data-based Mendelian Randomization (SMR), and protein quantitative trait locus (pQTL)-MR-was performed to investigate the shared genetic architecture. Based on multiple orthogonal lines of evidence, we thereby identified 40 single nucleotide polymorphisms (SNPs) and 85 genes common to both conditions. Additionally, we optimized candidate genes such as GNAQ, FADS1, and PTK2 by single-cell expression analysis and molecular pathway mechanisms, thereby highlighting potential shared genetic pathways. These findings elucidate the genetic interplay and co-occurring mechanisms between epilepsy and cognitive impairments, providing crucial insights for future research and therapeutic strategies.

Genetic Links Between Subcortical Brain Morphometry and Suicide Attempt Risk in Children and Adults

Genome-wide association studies (GWAS) have uncovered genetic variants associated with suicide attempt (SA) risk and regional brain volumes (RBVs). However, the extent of their genetic overlap remains unclear. To address this, we investigated whether the genetic architecture of SA and various RBVs (i.e., caudate nucleus, hippocampus, brainstem, ventral diencephalon, thalamus, globus pallidus, putamen, nucleus accumbens, amygdala and intracranial volume (ICV)) was shared. We leveraged GWAS summary statistics from the largest available datasets on SA (N = 958,896) and intracranial and subcortical RBVs (N = 74,898). Using linkage disequilibrium score regression, we estimated genome-wide genetic correlations between SA and individual RBVs. GWAS-pairwise analyses identified genomic segments associated with both SA and RBVs, followed by functional annotation. Additionally, we examined whether polygenic scores (PGS) for SA were associated with ICV and subcortical brain structure phenotypes in youth of European ancestry (N = 5276) in the Adolescent Brain Cognitive Development (ABCD) study. Linkage disequilibrium score regression results indicated a significant genetic correlation between SA and ICV (rG = -0.10, p-value = 1.9 × 10-3). GWAS-pairwise analyses and functional annotation revealed 10 genomic segments associated with SA and at least one RBV (thalamus, putamen and caudate nucleus). After adjusting for multiple tests, PGS association analysis indicated that a higher PGS for SA was significantly associated with a smaller volume of the right nucleus accumbens (b = -7.05, p = 0.018). Our findings highlight a negative genetic correlation between SA and ICV amongst adults and suggest different neural correlates associated with genetic risk for SA across developmental periods. This study advances our understanding of the shared genetic underpinnings of SA and brain structure, potentially informing future research and clinical interventions.

Sex-differentiated placental methylation and gene expression regulation has implications for neonatal traits and adult diseases

Sex differences in physiological and disease traits are pervasive and begin during early development, but the genetic architecture of these differences is largely unknown. Here, we leverage the human placenta, a transient organ during pregnancy critical to fetal development, to investigate the impact of sex in the regulatory landscape of placental autosomal methylome and transcriptome, and its relevance to health and disease. We find that placental methylation and its genetic regulation are extensively impacted by fetal sex, whereas sex differences in placental gene expression and its genetic regulation are limited. We identify molecular processes and regulatory targets that are enriched in a sex-specific manner, and find enrichment of imprinted genes in sex-differentiated placental methylation, including female-biased methylation within the well-known KCNQ1OT1/CDKN1C imprinting cluster of genes expressed in a parent-of-origin dependent manner. We establish that several sex-differentiated genetic effects on placental methylation and gene expression colocalize with birthweight and adult disease genetic associations, facilitating mechanistic insights on early life origins of health and disease outcomes shaped by sex.

The role of inflammation in the development of tic symptoms in subjects with ADHD

Tourette's syndrome is characterized by multiple motor and 1 or more vocal tics that persist for more than 1 year since first tic onset. It is well known that subjects with Tourette's syndrome show varieties of comorbidities, and ADHD is one of the most prevalent comorbid symptoms. In most cases, ADHD symptoms is known to precede the onset of tic symptoms, but how subjects with ADHD develop Tourette's syndrome later in life remains unclear. Both Tourette's syndrome and ADHD is highly heritable, and genome wide association studies of ADHD and Tourette's syndrome showed that Tourette's syndrome and ADHD are genetically related. In order to identify the factor to cause tic symptoms in subjects with ADHD, we conducted two-sample mendelian randomization analysis, gene-set analysis and identified neutrophil degranulation is a pathways specific to Tourette's syndrome. Molecular analysis showed that Neutrophil-lymphocyte ratio may be relatively upregulated within the normal range in subjects with ADHD and Tourette's syndrome compared to subjects with ADHD only. As the molecular analysis is still in its preliminary stages, the current results suggest that inflammation may be a contributing factor in the development of symptoms of Tourette's syndrome in subjects with ADHD. If these results can be replicated, neutrophil-lymphocyte ratio could serve as a potential a biomarker for the risk of Tourette's syndrome.

Investigating the causal and genetic relationship between migraine and Parkinson's disease

OBJECTIVE

The relationship between migraine and Parkinson's disease (PD) remains controversial. We aimed to investigate the causal and genetic associations between migraine and PD.

METHODS

Genetic data for migraine [any migraine (AM), migraine without aura (MO), and migraine with aura (MA)] and PD were sourced from the latest genome-wide meta-analyses conducted by the International Headache Genetics Consortium and the International Parkinson's Disease Genomics Consortium, respectively. Various analyses were performed to evaluate the potential causal associations and explore genetic correlations between these conditions.

RESULTS

The analyses indicated that AM (odds ratio [OR] 1.02, 95% confidence interval [CI] 0.91-1.14; p = 0.785), MO (OR 0.94, 95% CI 0.84-1.07; p = 0.358), and MA (OR 1.01, 95% CI 0.95-1.06; p = 0.846) were not significantly associated with the risk of PD. Similarly, reverse analyses also demonstrated no significant causality between PD and the risks of migraine or its subtypes. After adjusting for coronary heart disease, AM (OR 0.99, 95% CI 0.90-1.10; p = 0.897), MO (OR 0.94, 95% CI 0.86-1.03; p = 0.207), and MA (OR 1.00, 95% CI 0.93-1.07; p = 0.902) remained unrelated to PD risk. Likewise, PD was found to be unassociated with AM (OR 0.96, 95% CI 0.92-1.02; p = 0.168), MO (OR 0.95, 95% CI 0.86-1.05; p = 0.287), and MA (OR 1.02, 95% CI 0.93-1.13; p = 0.669). These null findings persisted even when adjusting for hypertension. Apart from above causal inference results, no significant genetic correlation was found between AM (rg = -0.06, p = 0.127), MA (rg = -0.05, p = 0.516), or MO (rg = -0.06, p = 0.492) and PD, and no correlations were observed across specific genomic regions. Additionally, no shared heritability was observed between PD and migraine, or its subtypes, in tissue expression.

CONCLUSION

Our study suggests that there is no significant causal association or genetic correlation between migraine and PD from a genetic perspective.

Whole exome sequencing identified six novel genes for depressive symptoms

Previous genome-wide association studies of depression have primarily focused on common variants, limiting our comprehensive understanding of the genetic architecture. In contrast, whole-exome sequencing can capture rare coding variants, helping to explore the phenotypic consequences of altering protein-coding genes. Here, we conducted a large-scale exome-wide association study on 296,199 participants from the UK Biobank, assessing their depressive symptom scores through the Patient Health Questionnaire-4. We identified 22 genes associated with depressive symptoms, including 6 newly discovered genes (TRIM27, UBD, SVOP, ADGRB2, IRF2BPL, and ANKRD12). Both ontology enrichment analysis and plasma proteomics association analysis consistently revealed that the identified genes were associated with immune responses. Furthermore, we identified associations between these genes and brain regions related to depression, such as anterior cingulate cortex and orbitofrontal cortex. Additionally, phenome-wide association analysis demonstrated that TRIM27 and UBD were associated with neuropsychiatric, cognitive, biochemistry, and inflammatory traits. Our findings offer new insights into the potential mechanisms and genetic architecture of depressive symptoms.

Causal relationship between hippocampal subfield volume and alzheimer's disease: a mendelian randomization study

BACKGROUND AND OBJECTIVE

Numerous studies suggest that the development of Alzheimer's Disease (AD) leads to a reduction in overall hippocampal volume. However, there is limited research exploring whether pre-morbid differences in hippocampal volume impact the risk of AD. This study aims to delve into the causal relationship between hippocampal subregional volume and AD using bidirectional Mendelian Randomization (MR) methods.

METHODS

We extracted 44 instrumental variables for hippocampal subregional volume from the GWAS Catalog, involving 21,282 European individuals. Data on Alzheimer's Disease were sourced from the Psychiatric Genomics Consortium, comprising 1,126,563 European individuals. Rigorous methods were employed to select instrumental variables, with the primary analysis conducted using the Inverse Variance Weighted method. Several sensitivity analyses included tests for heterogeneity, pleiotropy, and outliers. The obtained SNPs were mapped to genes for pathway enrichment analysis to explore the potential mechanisms underlying the regulation of hippocampal volume in Alzheimer's disease.

RESULTS

The study found significant causal associations between increased volume of the 5 hippocampal subfields with increased risk of AD. Conversely, increased Left hippocampus amygdala-transition-area volume was associated with reduced risk of AD. In reverse MR, AD was found to decrease the volume of 8 hippocampal subfields, while increasing the volume of the left hippocampal-fissure region. Amyloid-beta formation, leukocyte activation, and positive regulation of immune response mediated the changes in hippocampal subregional volume due to AD.

CONCLUSION

This MR study provides evidence that AD is causally related to hippocampal subfield volume, highlighting the roles of amyloid-beta formation and immune alterations in this context.

Multi-ancestry genome-wide association meta-analysis identifies novel associations and informs genetic risk prediction for Hirschsprung disease

BACKGROUND

Hirschsprung disease (HSCR) is a rare, congenital disease characterized by the absence of enteric ganglia in the hindgut. Common genetic variation contributes substantially to the heritability of the disease yet only three HSCR-associated loci were identified from genome-wide association studies (GWAS) thus far.

METHODS

We performed the largest multi-ancestry meta-analysis of GWAS to date, totalling 1250 HSCR cases and 7140 controls. Prioritized candidate genes were further characterized using single-cell transcriptomic data of developing human and mouse gut for their roles in development of enteric nervous system (ENS). Functional characterisation using human cells and zebrafish models was performed. Global and ancestry-matched polygenic risk score (PRS) models were derived and evaluated for predicting risk of HSCR.

FINDINGS

We identified four HSCR-susceptibility loci, with three loci (JAG1, HAND2 and ZNF25) reaching genome-wide significance and one putative locus (UNC5C) prioritized by functional relevance. Spatiotemporal analysis revealed hotspots of gene dysregulation during ENS development. Functional analyses further demonstrated that knockdown of the candidate genes impaired cell migration and zebrafish knockouts displayed abnormal ENS development. We also demonstrated comparable performance for a PRS model derived from multi-ancestry meta-analysis to those of ancestry-matched PRS models, supporting its potential clinical application in risk prediction of HSCR across populations.

INTERPRETATION

Overall, the meta-analysis implicated novel genes, pathways and spatiotemporal developmental hotspots in the genetic aetiology of HSCR. Development of a PRS universally applicable irrespective of ancestries may leverage its clinical utility in risk prediction.

FUNDING

The full list of funding bodies can be found in the Acknowledgements section.

Brain-based gene expression and corresponding behavioural relevance of risk genes for broad antisocial behaviour

Antisocial behaviour (ASB) involves persistent irresponsible, delinquent activities violating rights and safety of others. A meta-analysis of genome-wide association studies revealed significant genetic associations with ASB, yet their brain expression patterns and behavioural relevance remain unclear. Our investigation of fifteen genes associated with ASB examined their biological role and distribution across tissues, integrating post-mortem brain sample data from the Allen-Human-Brain Atlas and the Genotype-Tissue Expression project. We found that these genes were differentially expressed in the brain, particularly in regions like the cerebellum, putamen, and caudate, and were notably downregulated in the pancreas. Single cell type expression analysis revealed that ASB-associated genes had strong correlations with ductal and endothelial cells in the pancreas, indicating a possible metabolic influence on ASB. Certain genes like NTN1, SMAD5, NCAM2, and CDC42EP3 displayed specificity for cognitive terms including chronic pain, heart rate, and aphasia. These expression patterns aligned with neurocognitive domains related to thinking, and learning, distress, motor skills, as determined by fMRI analysis. This study connects specific brain gene expression with potential genetic and metabolic factors in ASB, offering novel insights into its biological basis and possible interdisciplinary approaches to understanding and addressing aggressive behaviours.

Polygenic overlap with granulocyte counts identifies novel loci for clozapine metabolism and clozapine-induced agranulocytosis

While clozapine is the most effective antipsychotic drug, its use is limited due to hematological adverse effects involving the reduction of granulocyte counts with potential life-threatening agranulocytosis. It is not yet possible to predict or prevent the risk of agranulocytosis, and the mechanisms are unknown but likely related to clozapine metabolism. Genome-wide association studies (GWASs) of clozapine metabolism and clozapine-induced agranulocytosis have identified few genetic loci. We used the largest available GWAS summary statistics of clozapine metabolism (clozapine-to-norclozapine ratio) and clozapine-induced agranulocytosis, applying the conditional false discovery rate (condFDR) method to increase power for genetic discovery by conditioning on granulocyte counts variants. To investigate potential causal effects of shared loci, we performed Mendelian Randomization analyses. After conditioning on granulocyte counts, we identified two novel loci associated with clozapine-to-norclozapine ratio. These loci were significantly associated with clozapine metabolism in a validation sample of 392 clozapine-treated individuals. For clozapine-induced agranulocytosis, five loci were identified after conditioning on granulocyte counts. These five loci were significantly associated with reduced granulocyte counts in a small independent sample of clozapine-treated individuals. Genetic liability to slow clozapine metabolism (high clozapine-to-norclozapine ratio) showed evidence of a causal effect on reduced neutrophil counts, and genetic liability to low neutrophil counts exhibited weak evidence of a causal effect on clozapine-induced agranulocytosis. Our findings of shared genetic variants associated with clozapine metabolism and granulocyte counts may form the basis for developing prediction models for clozapine-induced agranulocytosis.

Shared genetic architecture of gastroesophageal reflux disease and age related phenotypes

Increasing age is a risk factor of gastroesophageal reflux disease. This study aims to uncover the shared genetic architecture of gastroesophageal reflux disease (GERD) and age-related phenotypes. Based on publicly available GWAS statistics, this genome-wide pleiotropic association research was performed with multiple genetic approaches sequentially to explore the pleiotropic associations from single-nucleotide polymorphism (SNP) and gene levels, to reveal the underlying shared genetic etiology between GERD and age-related phenotypes. This study featured shared genetic mechanisms between GERD and age-related phenotypes, including frailty index (FI), telomere length (TL), longevity, and parental lifespan (PL). Strong genetic association were observed. A set of pleiotropic loci and genes were identified by PLACO, FUMA, Bayesian colocalization and additional MAGMA analysis. Our research provided strong evidence of genetic correlation between GERD and several age-related phenotypes, especially frailty index (FI) and telomere length (TL), brought novel insight into the shared genetic architecture between GERD and aging.

Blunted cortisol as a biomarker of depression based on the attenuation hypothesis: A Mendelian randomization analysis using depression as exposure

BACKGROUND

Both elevated and blunted cortisol responses have been associated with depression. Previous Mendelian randomization (MR) studies have largely ruled out cortisol as a cause of depression. Based on the attenuation hypothesis, this MR study used depression as exposure to assess whether cortisol might be a consequence and therefore a biomarker of depression.

METHODS

Strong (P < 5 × 10-8) and independent (r2 < 0.001) single nucleotide polymorphisms (SNPs) associated with broadly defined depression (294,322 cases, 741,438 controls) were used as instruments. These were applied to genetic associations with morning, fasting, and random plasma cortisol in the CORtisol NETwork (CORNET) consortium (n = 25,314), METabolic Syndrome in Men (METSIM) study (n = 6667), and Canadian Longitudinal Study on Aging (CLSA) cohort (n = 8299). Multivariable MR, adjusting for childhood maltreatment and major mental disorders, was conducted to address potential horizontal pleiotropy from dichotomous depression. Instruments were also selected by evidence of colocalization with major depressive disorder to address non-specificity.

RESULTS

Using 133 SNPs as instruments, depression was inversely associated with morning plasma cortisol (β per log-odds of genetic liability to depression = -0.107 [95 % CI, -0.181 to -0.032]) in the CORNET consortium. Replication in the METSIM study (β = -0.203 [95 % CI, -0.367 to -0.040]) and CLSA cohort (β = -0.091 [95 % CI, -0.220 to 0.039]) showed consistent but not always significant associations. Multivariable MR and follow-up analysis incorporating colocalization supported these findings.

CONCLUSIONS

Consistent with the attenuation hypothesis, blunted cortisol response appeared to be a consequence and potentially a biomarker of depression. Future studies are needed to provide more interpretable effect sizes and validate other biomarker measures.

Trans-ancestry transcriptome-wide association and functional studies to uncover novel susceptibility genes and therapeutic targets for colorectal cancer

By integrating findings from large-scale omics analyses with experimental tests, this study aims to decipher susceptibility genes and the underlying biological mechanisms involved in the development of colorectal cancer (CRC). We first conducted a trans-ancestry transcriptome-wide association study (TWAS) among 57,402 CRC cases and 119,110 controls, aiming to examine how altered gene expression influences CRC risk in European and Asian populations. Then, functional experiments in (i) CRC cell lines and (ii) tumor xenografts were conducted to examine potential underlying mechanisms involved in colorectal carcinogenesis. Further, a drug sensitivity test was employed to explore possible clinical implications for CRC treatment. The TWAS identified 67 genes highly associated with CRC risk, 23 of which were novel findings. Functional annotation of variants within TWAS-identified loci revealed that the majority (93.6%) showed evidence of transcriptional regulatory mechanisms via proximal promoter or distal enhancer-promoter interactions. Among the identified susceptibility genes, splicing factor 3a subunit 3 (SF3A3) may act as an oncogene on the basis that overexpression of this gene was significantly associated with increased risk of CRC (P = 5.75 × 10-11). Further cell and animal experiments confirmed that SF3A3 plays an oncogenic role in CRC development, and the underlying biological mechanism is likely to be related to its anti-apoptosis effect. The drug sensitivity test suggested that phenethyl isothiocyanate (PEITC) targeting SF3A3 can inhibit CRC progression. This study identified novel CRC susceptibility genes and potential biological mechanisms of SF3A3 involved in CRC development, providing important insight into the etiology and potential leads to the treatment of CRC.

Multi-cohort cross-omics analysis reveals disease mechanisms and therapeutic targets in HTLV-1-associated myelopathy, a neglected retroviral neuroinflammatory disorder

HTLV-1 is an enigmatic retrovirus triggering a debilitating neuroinflammatory disease, HTLV-1-associated myelopathy (HAM), with unknown pathogenesis. Both HTLV-1 infection and HAM predominantly affect women and non-white neglected populations. HAM is lacking disease-modifying treatment, as current treatment is mostly symptomatic and inspired by either HIV-1 or multiple sclerosis therapeutic strategies. We used systems biology analyses of novel and publicly available data comprising (epi)genomics, transcriptomics, metabolomics and proteomics of multi-ancestry cohorts from a total of > 2500 People Living with HTLV-1 from 5 countries (Brazil, Peru, Japan, UK, US). Leveraging an unique admixed Brazilian cohort, genome-wide association study (GWAS) revealed African-specific variants in inflammasome sensor AIM2 with genome-wide significance (p < 5x10-8). Suggestive loci (p > 5x10-8) corresponding to metabolic, immune and neuronal genes were validated using published Japanese GWAS. Polygenic risk score and proviral load were independent disease predictors across ancestries. Systems biology analysis revealed neuronal/synaptic signaling, monocyte count, glucose/lipid metabolism, and neurocognition/depression as genetically linked to HAM. In silico drug screening identified estrogen blocker Fulvestrant as the top hit, while also confirming existing (pre)clinical data for HDAC inhibitors and immunosuppressants. Validated GWAS genes were overexpressed in HAM patients' whole blood and CD4 T-cells, as well as in spinal cord astrocytes, oligodendrocytes, and microglia by single-cell RNAseq. We experimentally confirmed decreased ApoA1/lipid/cholesterol levels, higher monocyte levels and lower neurocognitive scores in multi-ancestry cohorts. We found striking biological similarities between retroviral Hbz/Tax overexpression, Hbz interactome and HAM multi-omics findings: enrichment for lipid/cholesterol metabolism, estrogen signaling, neurodegenerative diseases, and viral pathways including EBV, recently identified as the major driver of multiple sclerosis. In conclusion, our data-driven approach uncovers novel disease mechanisms and therapeutic targets, and a validated polygenic risk score allowing targeted surveillance for high-risk individuals. A strong molecular overlap to other neurodegenerative/neuroinflammatory diseases reveals shared neuropathogenic pathways between unrelated viruses.

Exploring the association between systemic lupus erythematosus and osteonecrosis by Mendelian randomization analysis

Patients with systemic lupus erythematosus (SLE) have been shown to have a high risk of osteonecrosis, but the potential causal relationship between genetic susceptibility and risk of osteonecrosis is unclear. In this study, we used Mendelian randomization to investigate the effects of SLE, gout and rheumatoid arthritis on osteonecrosis, and performed post-GWAS localization and functional analyses of GWAS studies related to osteonecrosis, with the aim of obtaining a more in-depth understanding of the mechanisms of osteonecrosis. In this study, a total of 45 single nucleotide polymorphisms (SNPS) data associated with SLE from publicly available genome-wide association study (GIS) datasets were selected for magnetic resonance estimation using inverse-variance weighting, MR-Eagle method and weighted median method. The Cochrane Q-test, MR-Egger interception, MR-multidirectional residual and outlier methods, entrance/exit analysis and funnel plot were applied for sensitivity analysis. Two-sample Mendelian randomization analysis of the 19 SNPs obtained from screening showed no significant causal effect of SLE and osteonecrosis, and IVW and MR-Egger heterogeneity analyses showed no significant heterogeneity between the instrumental variables (P > 0.05). Multi-phenotype MR analysis showed no significant causal effect between gout and rheumatoid arthritis and osteonecrosis (p > 0.05). The available evidence does not support a significant causal effect of gout and rheumatoid arthritis on osteonecrosis, and the causal effect of SLE on the increased risk of osteonecrosis is only supported by the IVW method, which is of insufficient evidence validity, but suggests a better theoretical basis for the study of heritability related to SLE.

GWAS study of myelosuppression among NSCLC patients receiving platinum-based combination chemotherapy

Platinum-based chemotherapy remains the mainstay for non-small cell lung cancer (NSCLC), but it frequently causes dose-limiting myelosuppression, with significant individual variability in susceptibility. However, the genetic basis of myelosuppression side effects remains elusive, greatly hindering personalized therapeutic approaches. In this study, we perform a comprehensive genome-wide association analysis on 491 NSCLC patients receiving platinum-based chemotherapy, examining 4,690,998 single-nucleotide polymorphisms (SNPs) to identify relevant genetic variants. LDBlockShow, FUMA, and MAGMA are utilized to explore linkage disequilibrium, expression quantitative trait loci (eQTLs), chromatin interaction, and conduct gene-based and gene set-based analysis of candidate SNPs. The GWAS results reveal that rs6856089 and its linked SNPs are significantly associated with platinum-based chemotherapy-induced myelosuppression. Specifically, patients with the A allele of rs6856089 have a significantly lower risk of myelosuppression (odds ratio (OR) = 0.1300, P = 7.59 × 10 -8). Furthermore, gene-based analysis reveals that EMCN ( P = 2.47 × 10 -5), which encodes endomucin, a marker for hematopoietic stem cells, might mediate myelosuppression. This study provides a scientific basis for the individual differences in platinum-based chemotherapy-induced myelosuppression.

Genetic approach uncovering the pathways between childhood maltreatment and suicide attempt

Childhood maltreatment significantly heightens the risk of suicide attempt, but the causal mechanisms and underlying pathways are not fully understood. Using genetic instruments for both childhood maltreatment (n = 185,414) and suicide attempt (cases = 29,782; controls = 519,961), we performed two-sample Mendelian randomization analyses. Our results show that higher level of childhood maltreatment is causally associated with an increased risk of suicide attempt (OR = 3.40; 95% CI, 2.34-4.96, P = 1.3e-10). We then conducted a two-step Mendelian randomization mediation analysis, identifying 11 out of 58 potential mediators between childhood maltreatment and suicide attempt. These mediators included neurobiological, psychopathological and behavioral factors. The psychopathological factors had the most significant impact, accounting for 10.4-50.2% the mediation. This study confirms the causal relationship between childhood maltreatment and suicide attempt, highlighting specific mediators-especially within the psychopathological dimension-that can guide targeted interventions to alleviate the adverse effects of childhood maltreatment and prevent suicide attempt.

Genome-wide association study of plasma amino acids and Mendelian randomization for cardiometabolic traits

Plasma amino acids (AAs) have emerged as promising biomarkers for metabolic disorders, yet their causality remains unclear. We aimed to investigate the genetic determinants of AA levels in a cohort of 10,333 individuals and their causal effects on cardiometabolic traits using Mendelian randomization (MR). Plasma levels of 20 AAs were quantified using capillary electrophoresis mass spectrometry. Genome-wide association studies were conducted using BOLT-LMM and heritability estimation via LDSC analysis. Causal effects of AAs on 11 cardiometabolic traits were examined using two-sample MR analyses. We identified 85 locus-metabolite associations across 43 genes for 18 AAs, including 44 novel loci linked to metabolic genes. Heritability for AAs was estimated at 16%. MR analysis demonstrated cystine to positively associate with systolic blood pressure (SBP) (β = 0.056, SE = 0.010), while serine indicated protective effects on SBP (β = - 0.040, SE = 0.011), diastolic BP (β = - 0.044, SE = 0.010), and coronary artery disease (odds ratio 0.888, SE = 0.028). We identified potentially novel genetic loci associated with AA levels and demonstrated robust causal associations between several AAs and cardiometabolic traits. These findings reinforce the importance of AAs as potential biomarkers and therapeutic targets in cardiometabolic health.

Deciphering distinct genetic risk factors for FTLD-TDP pathological subtypes via whole-genome sequencing

Frontotemporal lobar degeneration with neuronal inclusions of the TAR DNA-binding protein 43 (FTLD-TDP) is a fatal neurodegenerative disorder with only a limited number of risk loci identified. We report our comprehensive genome-wide association study as part of the International FTLD-TDP Whole-Genome Sequencing Consortium, including 985 patients and 3,153 controls compiled from 26 institutions/brain banks in North America, Europe and Australia, and meta-analysis with the Dementia-seq cohort. We confirm UNC13A as the strongest overall FTLD-TDP risk factor and identify TNIP1 as a novel FTLD-TDP risk factor. In subgroup analyzes, we further identify genome-wide significant loci specific to each of the three main FTLD-TDP pathological subtypes (A, B and C), as well as enrichment of risk loci in distinct tissues, brain regions, and neuronal subtypes, suggesting distinct disease aetiologies in each of the subtypes. Rare variant analysis confirmed TBK1 and identified C3AR1, SMG8, VIPR1, RBPJL, L3MBTL1 and ANO9, as novel subtype-specific FTLD-TDP risk genes, further highlighting the role of innate and adaptive immunity and notch signaling pathway in FTLD-TDP, with potential diagnostic and novel therapeutic implications.

Genome-wide association study reveals a novel tuberculosis susceptibility locus in multiple East Asian and European populations

Background

Tuberculosis (TB) continues to be a leading cause of morbidity and mortality worldwide. Past genome-wide association studies (GWAS) have explored TB susceptibility across various ethnic groups, yet a significant portion of TB heritability remains unexplained.

Methods

We conducted GWAS in the Singapore Chinese and Vietnamese, followed by a comprehensive meta-analysis incorporating 4 independent East Asian datasets, resulting in a total of 11,841 cases and 197,373 population controls.

Findings

We identified a novel susceptibility locus for pulmonary TB (PTB) at 22q12.2 in East Asians [rs6006426, OR (95%Cl) =1.097(1.066, 1.130), P meta =3.31×10 -10 ]. The association was further validated in Europeans [OR (95%Cl) =1.101(1.002, 1.211), P =0.046] and was strengthened in the combined meta-anlaysis including 12,736 PTB cases and 673,864 controls [OR (95%Cl) =1.098(1.068, 1.129), P meta =4.33×10 -11 ]. rs6006426 affected SF3A1 expression in various immune cells ( P from 0.003 to 6.17×10 -18 ) and OSM expression in monocytes post lipopolysaccharide stimulation ( P =5.57×10 -4 ). CRISPR-Cas9 edited zebrafish embryos with osm depletion resulted in decreased burden of Mycobacterium marinum ( M.marinum ) in infected embryos ( P =0.047).

Interpretation

Our findings offer novel insights into the genetic factors underlying TB and reveals new avenues for understanding its etiology.

Genetic variants associated with metabolic dysfunction-associated fatty liver diseases in a Korean population

BACKGROUND

Susceptibility to metabolic dysfunction-associated fatty liver diseases (MAFLD) shows a large inter-ethnic variability. Currently, large-scale genome-wide association studies (GWAS) on MAFLD in a Korean population are limited. This study aimed to investigate genes underlying MAFLD in a Korean population.

METHODS

A total of 13,457 Korean adults (4061 cases and 9396 controls) who underwent abdominal ultrasonography, biochemical testing, and genetic studies at a comprehensive health promotion center from 2019 to 2023 were included. Genome-wide genotyping was conducted using Infinium Asian Screening Array and an iSCAN system (Illumina, San Diego, CA, USA). Gene-based approach was conducted with Multi-Marker Analysis for Genomic Annotation (MAGMA) and Functional Mapping and Annotation (FUMA). Expression quantitative trait loci (eQTLs) mapping was done using GTEx v8 data.

RESULTS

The 22q13.3, 19p13.11, and 2p23.3 loci were associated with MAFLD after adjusting for age, sex, and body mass index (p < 5 × 10-8). Of these, 154 (89%) variants were identified as eQTLs (FDR < 0.05). Gene-based approach showed that PNPLA3, SAMM50, and PARVB were significantly associated with MAFLD (Bonferroni-corrected p < 2.99 × 10-6), followed by PDLIM4, GCKR, APOB, GPAM, HMGA1, C5orf56, and APOC1.

CONCLUSIONS

This is the largest-scale GWAS of MAFLD in a Korean adult population. Genotyping PARVB as well as PNPLA3 might help us identify individuals with the highest risk of MAFLD in Korean adults. These findings would contribute to our understanding of genetic pathogenesis of MAFLD in the Korean population.

The phenotypic and genetic association between endometriosis and immunological diseases

STUDY QUESTION

Is there an increased risk of immunological diseases among endometriosis patients, and does a shared genetic basis contribute to this risk?

SUMMARY ANSWER

Endometriosis patients show a significantly increased risk of autoimmune, autoinflammatory, and mixed-pattern diseases, including rheumatoid arthritis, multiple sclerosis, coeliac disease, osteoarthritis, and psoriasis, with genetic correlations between endometriosis and osteoarthritis, rheumatoid arthritis, and multiple sclerosis, and a potential causal link to rheumatoid arthritis.

WHAT IS KNOWN ALREADY

The epidemiological evidence for an increased risk of immunological diseases among women with endometriosis is limited in scope and has varied in robustness due to the opportunity for biases. The presence of a biological basis for increased comorbidity across immunological conditions has not been investigated. Here we investigate the phenotypic and genetic association between endometriosis and 31 immune conditions in the UK Biobank.

STUDY DESIGN, SIZE, DURATION

Phenotypic analyses between endometriosis and immune conditions (17 classical autoimmune, 10 autoinflammatory, and 4 mixed-pattern diseases) were conducted using two approaches (8223 endometriosis, 64 620 immunological disease cases): (i) retrospective cohort study design to incorporate temporality between diagnoses and (ii) cross-sectional analysis for simple association. Genome-wide association studies (GWAS) and meta-analyses for those immune conditions that showed phenotypic association with endometriosis (1493-77 052 cases) were conducted.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Comprehensive phenotypic association analyses were conducted in females in the UK Biobank. GWAS for immunological conditions were conducted in females-only and sex-combined study populations in UK Biobank and meta-analysed with existing largest available GWAS results. Genetic correlation and Mendelian randomization (MR) analyses were conducted to investigate potential causal relationships. Those immune conditions with significant genetic correlation with endometriosis were included in multi-trait analysis of GWAS to boost discovery of novel and shared genetic variants. These shared variants were functionally annotated to identify affected genes utilizing expression quantitative trait loci (eQTL) data from GTEx and eQTLGen databases. Biological pathway enrichment analysis was conducted to identify shared underlying biological pathways.

MAIN RESULTS AND THE ROLE OF CHANCE

In both retrospective cohort and cross-sectional analyses, endometriosis patients were at significantly increased (30-80%) risk of classical autoimmune (rheumatoid arthritis, multiple sclerosis, coeliac disease), autoinflammatory (osteoarthritis), and mixed-pattern (psoriasis) diseases. Osteoarthritis (genetic correlation (rg) = 0.28, P = 3.25 × 10-15), rheumatoid arthritis (rg = 0.27, P = 1.5 × 10-5) and multiple sclerosis (rg = 0.09, P = 4.00 × 10-3) were significantly genetically correlated with endometriosis. MR analysis suggested a causal association between endometriosis and rheumatoid arthritis (OR = 1.16, 95% CI = 1.02-1.33). eQTL analyses highlighted genes affected by shared risk variants, enriched for seven pathways across all four conditions, with three genetic loci shared between endometriosis and osteoarthritis (BMPR2/2q33.1, BSN/3p21.31, MLLT10/10p12.31) and one with rheumatoid arthritis (XKR6/8p23.1).

LIMITATIONS, REASONS FOR CAUTION

We conducted the first female-specific GWAS analyses for immune conditions. Given the novelty of these analyses, the sample sizes from which results were derived were limited compared to sex-combined GWAS meta-analyses, which limited the power to use female-specific summary statistics to uncover the shared genetic basis with endometriosis in follow-up analyses. Secondly, the 39 genome-wide significant endometriosis-associated variants used as instrumental variables in the MR analysis explained approximately 5% of disease variation, which may account for the nominal or non-significant MR results.

WIDER IMPLICATIONS OF THE FINDINGS

Endometriosis patients have a moderately increased risk for osteoarthritis, rheumatoid arthritis, and to a lesser extent, multiple sclerosis, due to underlying shared biological mechanisms. Clinical implications primarily involve the need for increased awareness and vigilance. The shared genetic basis opens up opportunities for developing new treatments or repurposing therapies across these conditions.

STUDY FUNDING/COMPETING INTEREST(S)

We thank all the UK Biobank and 23andMe participants. Part of this research was conducted using the UK Biobank Resource under Application Number 9637. N.R. was supported by a grant from the Wellbeing of Women UK (RG2031) and the EU Horizon 2020 funded project FEMaLe (101017562). A.P.M. was supported in part by Versus Arthritis (grant 21754). H.F. was supported by the National Natural Science Foundation of China (grant 32170663). N.R., S.A.M., and K.T.Z. were supported in part by a grant from CDMRP DoD PRMRP (W81XWH-20-PRMRP-IIRA). K.T.Z. and C.M.B. reported grants in 3 years prior, outside the submitted work, from Bayer AG, AbbVie Inc., Volition Rx, MDNA Life Sciences, PrecisionLife Ltd., and Roche Diagnostics Inc. S.A.M. reports grants in the 3 years prior, outside this submitted work, from AbbVie Inc. N.R. is a consultant for Endogene.bio, outside this submitted work. The other authors have no conflicts of interest to declare.

TRIAL REGISTRATION NUMBER

N/A.

A multi-trait genome-wide association study of coronary artery disease and subclinical atherosclerosis traits

Measures of subclinical atherosclerosis, such as coronary artery calcification (CAC) and carotid intima-media thickness (CIMT), reflect the underlying pathophysiology of coronary artery disease (CAD) and are genetically correlated with CAD and related risk factors. Leveraging summary statistics from genome-wide association studies of CAD, CIMT, CAC, type 2 diabetes, low-density lipoprotein cholesterol, and systolic blood pressure, we performed 15 separate multi-trait GWAS to identify shared susceptibility loci and elucidate the pleiotropic architecture underlying atherosclerosis. We identified 442 shared risk loci across all analyses that met an experiment-wide Bonferroni threshold of 3.3 × 10-9, uncovering 195 novel atherosclerosis loci. Multi-trait colocalization confirmed a shared causal signal in 25 shared novel loci for atherosclerosis. Trait-eQTL colocalization identified evidence of a shared causal signal in arterial, subcutaneous adipose, and cardiac tissues, implicating genes such as PRRX2, BNC2, CLIC4, SCAI, and PPP6C, and pathways related to vascular remodeling, inflammation, and metabolic regulation.