Identification of novel common variants associated with chronic pain using conditional false discovery rate analysis with major depressive disorder and assessment of pleiotropic effects of LRFN5

3D genomic features across >50 diverse cell types reveal insights into the genomic architecture of childhood obesity

The prevalence of childhood obesity is increasing worldwide, along with the associated common comorbidities of type 2 diabetes and cardiovascular disease in later life. Motivated by evidence for a strong genetic component, our prior genome-wide association study (GWAS) efforts for childhood obesity revealed 19 independent signals for the trait; however, the mechanism of action of these loci remains to be elucidated. To molecularly characterize these childhood obesity loci we sought to determine the underlying causal variants and the corresponding effector genes within diverse cellular contexts. Integrating childhood obesity GWAS summary statistics with our existing 3D genomic datasets for 57 human cell types, consisting of high-resolution promoter-focused Capture-C/Hi-C, ATAC-seq, and RNA-seq, we applied stratified LD score regression and calculated the proportion of genome-wide SNP heritability attributable to cell type-specific features, revealing pancreatic alpha cell enrichment as the most statistically significant. Subsequent chromatin contact-based fine-mapping was carried out for genome-wide significant childhood obesity loci and their linkage disequilibrium proxies to implicate effector genes, yielded the most abundant number of candidate variants and target genes at the BDNF , ADCY3 , TMEM18 and FTO loci in skeletal muscle myotubes and the pancreatic beta-cell line, EndoC-BH1. One novel implicated effector gene, ALKAL2 - an inflammation-responsive gene in nerve nociceptors - was observed at the key TMEM18 locus across multiple immune cell types. Interestingly, this observation was also supported through colocalization analysis using expression quantitative trait loci (eQTL) derived from the Genotype-Tissue Expression (GTEx) dataset, supporting an inflammatory and neurologic component to the pathogenesis of childhood obesity. Our comprehensive appraisal of 3D genomic datasets generated in a myriad of different cell types provides genomic insights into pediatric obesity pathogenesis.

KEY POINTS

Question: What are the causal variants and corresponding effector genes conferring pediatric obesity susceptibility in different cellular contexts?Findings: Our method of assessing 3D genomic data across a range of cell types revealed heritability enrichment of childhood obesity variants, particularly within pancreatic alpha cells. The mapping of putative causal variants to cis-regulatory elements revealed candidate effector genes for cell types spanning metabolic, neural, and immune systems.Meaning: We gain a systemic view of childhood obesity genomics by leveraging 3D techniques that implicate regulatory regions harboring causal variants, providing insights into the disease pathogenesis across different cellular systems.

A genome-wide association study of alloimmunization in the TOPMed OMG-SCD cohort identifies a locus on chromosome 12

BACKGROUND

Red cell alloimmunization after exposure to donor red cells is a very common complication of transfusion for patients with sickle cell disease (SCD), resulting frequently in accelerated donor red blood cell destruction. Patients show substantial differences in their predisposition to alloimmunization, and genetic variability is one proposed component. Although several genetic association studies have been conducted for alloimmunization, the results have been inconsistent, and the genetic determinants of alloimmunization remain largely unknown.

STUDY DESIGN AND METHODS

We performed a genome-wide association study (GWAS) in 236 African American (AA) SCD patients from the Outcome Modifying Genes in Sickle Cell Disease (OMG-SCD) cohort, which is part of Trans-Omics for Precision Medicine (TOPMed), with whole-genome sequencing data available. We also performed sensitivity analyses adjusting for different sets of covariates and applied different sample grouping strategies based on the number of alloantibodies patients developed.

RESULTS

We identified one genome-wide significant locus on chr12 (p = 3.1e-9) with no evidence of genomic inflation (lambda = 1.003). Further leveraging QTL evidence from GTEx whole blood and/or Jackson Heart Study PBMC RNA-Seq data, we identified a number of potential genes, such as ARHGAP9, STAT6, and ATP23, that may be driving the association signal. We also discovered some suggestive loci using different analysis strategies.

DISCUSSION

We call for the community to collect additional alloantibody information within SCD cohorts to further the understanding of the genetic basis of alloimmunization in order to improve transfusion outcomes.

Two polygenic mouse models of major depressive disorders identify TMEM161B as a potential biomarker of disease in humans

Treatments are only partially effective in major depressive disorders (MDD) but no biomarker exists to predict symptom improvement in patients. Animal models are essential tools in the development of antidepressant medications, but while recent genetic studies have demonstrated the polygenic contribution to MDD, current models are limited to either mimic the effect of a single gene or environmental factor. We developed in the past a model of depressive-like behaviors in mice (H/Rouen), using selective breeding based on behavioral reaction after an acute mild stress in the tail suspension test. Here, we propose a new mouse model of depression (H-TST) generated from a more complex genetic background and based on the same selection process. We first demonstrated that H/Rouen and H-TST mice had similar phenotypes and were more sensitive to glutamate-related antidepressant medications than selective serotonin reuptake inhibitors. We then conducted an exome sequencing on the two mouse models and showed that they had damaging variants in 174 identical genes, which have also been associated with MDD in humans. Among these genes, we showed a higher expression level of Tmem161b in brain and blood of our two mouse models. Changes in TMEM161B expression level was also observed in blood of MDD patients when compared with controls, and after 8-week treatment with duloxetine, mainly in good responders to treatment. Altogether, our results introduce H/Rouen and H-TST as the two first polygenic animal models of MDD and demonstrate their ability to identify biomarkers of the disease and to develop rapid and effective antidepressant medications.

Spatial transcriptomics and single-nucleus RNA sequencing reveal a transcriptomic atlas of adult human spinal cord

Despite the recognized importance of the spinal cord in sensory processing, motor behaviors, and neural diseases, the underlying organization of neuronal clusters and their spatial location remain elusive. Recently, several studies have attempted to define the neuronal types and functional heterogeneity in the spinal cord using single-cell or single-nucleus RNA sequencing in animal models or developing humans. However, molecular evidence of cellular heterogeneity in the adult human spinal cord is limited. Here, we classified spinal cord neurons into 21 subclusters and determined their distribution from nine human donors using single-nucleus RNA sequencing and spatial transcriptomics. Moreover, we compared the human findings with previously published single-nucleus data of the adult mouse spinal cord, which revealed an overall similarity in the neuronal composition of the spinal cord between the two species while simultaneously highlighting some degree of heterogeneity. Additionally, we examined the sex differences in the spinal neuronal subclusters. Several genes, such as SCN10A and HCN1, showed sex differences in motor neurons. Finally, we classified human dorsal root ganglia (DRG) neurons using spatial transcriptomics and explored the putative interactions between DRG and spinal cord neuronal subclusters. In summary, these results illustrate the complexity and diversity of spinal neurons in humans and provide an important resource for future research to explore the molecular mechanisms underlying spinal cord physiology and diseases.

Characterization of genomic regions escaping epigenetic reprogramming in sheep

The mammalian genome undergoes two global epigenetic reprogramming events during the establishment of primordial germ cells and in the pre-implantation embryo after fertilization. These events involve the erasure and re-establishment of DNA methylation marks. However, imprinted genes and transposable elements (TEs) maintain their DNA methylation signatures to ensure normal embryonic development and genome stability. Despite extensive research in mice and humans, there is limited knowledge regarding environmentally induced epigenetic marks that escape epigenetic reprogramming in other species. Therefore, the objective of this study was to examine the characteristics and locations of genomic regions that evade epigenetic reprogramming in sheep, as well as to explore the biological functions of the genes within these regions. In a previous study, we identified 107 transgenerationally inherited differentially methylated cytosines (DMCs) in the F1 and F2 generations in response to a paternal methionine-supplemented diet. These DMCs were found in TEs, non-repetitive regions, and imprinted and non-imprinted genes. Our findings suggest that genomic regions, rather than TEs and imprinted genes, have the propensity to escape reprogramming and serve as potential candidates for transgenerational epigenetic inheritance. Notably, 34 transgenerational methylated genes influenced by paternal nutrition escaped reprogramming, impacting growth, development, male fertility, cardiac disorders, and neurodevelopment. Intriguingly, among these genes, 21 have been associated with neural development and brain disorders, such as autism, schizophrenia, bipolar disease, and intellectual disability. This suggests a potential genetic overlap between brain and infertility disorders. Overall, our study supports the concept of transgenerational epigenetic inheritance of environmentally induced marks in mammals.

Shared genetic links between bladder cancer and obesity-related traits: A conjunctional false discovery rate study

Bladder cancer (BCa) is a common cancer worldwide and is often linked with obesity-related comorbidities, but little is known about the underlying genetic mechanisms. To investigate these mechanisms, we used various quantitative tools, including conditional quantile-quantile (Q-Q) plots, conditional false discovery rate (cFDR), and conjunctional conditional false discovery rate (ccFDR), to explore the pleiotropic enrichment of risk loci between BCa and obesity-related traits. We also performed an expression quantitative trait locus (eQTL) analysis to assess the relationship between shared risk loci and gene expression. Finally, we conducted functional annotation using Kyoto Encyclopedia of Genes and Genomes (KEGG) and gene ontology (GO) analysis. Our findings indicated that there was successive enrichment for a range of obesity-related traits, including body fat percentage, body mass index, fasting insulin, type 2 diabetes mellitus, fasting glucose, high-density lipoprotein cholesterol, total triglycerides, and waist-to-hip ratio. Using the tools mentioned above, we identified 18 significant SNPs and 18 closely related genes (cFDR<0.01) under the condition of 8 obesity-related traits. The SNPs included rs143004880, rs73301337, rs10798572, rs11594929, rs17019138, rs2877, rs149795948, rs142509736, rs12727575, rs1571277, rs12131828, rs635634, rs76895963, rs118081211, rs7044247, rs138895564, rs4135275, and rs148023060. Additionally, we identified 15 novel loci using ccFDR, including rs143004880, rs73301337, rs10798572, rs11594929, rs17019138, rs2877, rs142509736, rs1571277, rs635634, rs76895963, rs12131828, rs118081211, rs7044247, rs138895564, and rs4135275. Of the 2 significant loci that modify gene expression, rs12131828 and rs635634 were identified. The functional annotation indicated that the conditional risk genes mainly participated in the regulation of gene silencing. Our study provided evidence of pleiotropic enrichment between BCa and 8 obesity-related traits, and we identified potential genetic mechanisms underlying this relationship. These findings may help in developing targeted clinical treatments for BCa.

LRFN5 and OLFM4 as novel potential biomarkers for major depressive disorder: a pilot study

Evidences have shown that both LRFN5 and OLFM4 can regulate neural development and synaptic function. Recent genome-wide association studies on major depressive disorder (MDD) have implicated LRFN5 and OLFM4, but their expressions and roles in MDD are still completely unclear. Here, we examined serum concentrations of LRFN5 and OLFM4 in 99 drug-naive MDD patients, 90 drug-treatment MDD patients, and 81 healthy controls (HCs) using ELISA methods. The results showed that both LRFN5 and OLFM4 levels were considerably higher in MDD patients compared to HCs, and were significantly lower in drug-treatment MDD patients than in drug-naive MDD patients. However, there were no significant differences between MDD patients who received a single antidepressant and a combination of antidepressants. Pearson correlation analysis showed that they were associated with the clinical data, including Hamilton Depression Scale score, age, duration of illness, fasting blood glucose, serum lipids, and hepatic, renal, or thyroid function. Moreover, these two molecules both yielded fairly excellent diagnostic performance in diagnosing MDD. In addition, a combination of LRFN5 and OLFM4 demonstrated a better diagnostic effectiveness, with an area under curve of 0.974 in the training set and 0.975 in the testing set. Taken together, our data suggest that LRFN5 and OLFM4 may be implicated in the pathophysiology of MDD and the combination of LRFN5 and OLFM4 may offer a diagnostic biomarker panel for MDD.

Potentially causal associations between placental DNA methylation and schizophrenia and other neuropsychiatric disorders

Increasing evidence supports the role of placenta in neurodevelopment and potentially, in the later onset of neuropsychiatric disorders. Recently, methylation quantitative trait loci (mQTL) and interaction QTL (iQTL) maps have proven useful to understand SNP-genome wide association study (GWAS) relationships, otherwise missed by conventional expression QTLs. In this context, we propose that part of the genetic predisposition to complex neuropsychiatric disorders acts through placental DNA methylation (DNAm). We constructed the first public placental cis-mQTL database including nearly eight million mQTLs calculated in 368 fetal placenta DNA samples from the INMA project, ran cell type- and gestational age-imQTL models and combined those data with the summary statistics of the largest GWAS on 10 neuropsychiatric disorders using Summary-based Mendelian Randomization (SMR) and colocalization. Finally, we evaluated the influence of the DNAm sites identified on placental gene expression in the RICHS cohort. We found that placental cis-mQTLs are highly enriched in placenta-specific active chromatin regions, and useful to map the etiology of neuropsychiatric disorders at prenatal stages. Specifically, part of the genetic burden for schizophrenia, bipolar disorder and major depressive disorder confers risk through placental DNAm. The potential causality of several of the observed associations is reinforced by secondary association signals identified in conditional analyses, regional pleiotropic methylation signals associated to the same disorder, and cell type-imQTLs, additionally associated to the expression levels of relevant immune genes in placenta. In conclusion, the genetic risk of several neuropsychiatric disorders could operate, at least in part, through DNAm and associated gene expression in placenta.

Identification of potentially common loci between childhood obesity and coronary artery disease using pleiotropic approaches

Childhood obesity remains one of the most important issues in global health, which is implicated in many chronic diseases. Converging evidence suggests that a higher body mass index during childhood (CBMI) is significantly associated with increased coronary artery disease (CAD) susceptibility in adulthood, which may partly arise from the shared genetic determination. Despite genome-wide association studies (GWASs) have successfully identified some loci associated with CBMI and CAD individually, the genetic overlap and common biological mechanism between them remains largely unexplored. Here, relying on the results from the two large-scale GWASs (n = 35,668 for CBMI and n = 547,261 for CAD), linkage disequilibrium score regression (LDSC) was used to estimate the genetic correlation of CBMI and CAD in the first step. Then, we applied different pleiotropy-informed methods including conditional false discovery rate ([Formula: see text]) and genetic analysis incorporating pleiotropy and annotation (GPA) to detect potentially common loci for childhood obesity and CAD. By integrating the genetic information from the existing GWASs summary statistics, we found a significant positive genetic correlation ([Formula: see text] = 0.127, p = 2E-4) and strong pleiotropic enrichment between CBMI and CAD (LRT = 79.352, p = 5.2E-19). Importantly, 28 loci were simultaneously discovered to be associated with CBMI, and 13 of them were identified as potentially pleiotropic loci by [Formula: see text] and GPA. Those corresponding pleiotropic genes were enriched in trait-associated gene ontology (GO) terms "amino sugar catabolic process", "regulation of fat cell differentiation" and "synaptic transmission". Overall, the findings of the pleiotropic loci will help to further elucidate the common molecular mechanisms underlying the association of childhood obesity and CAD, and provide a theoretical direction for early disease prevention and potential therapeutic targets.

Identify novel, shared and disorder-specific genetic architecture of major depressive disorder, insomnia and chronic pain

Major depressive disorder (MDD), insomnia (INS) and chronic pain (CP) often have high comorbidity and show high genetic correlation. Here we aimed to better characterize their novel, shared and disorder-specific genetic architecture. Based on genome-wide association study (GWAS) summary data, we applied the conditional false discovery rate (condFDR) and conjunctional FDR (conjFDR) approach to investigate the novel and overlapped genetic loci for MDD, INS and CP. In addition, putative disorder-specific SNP associations were analyzed by conditioning the other two traits. The functions of the identified genomic loci were explored by performing gene set enrichment analysis (GSEA) for the loci mapped genes. We identified 22, 43 and 91 novel risk loci for MDD, INS and CP. GSEA for the loci mapped genes highlighted olfactory signaling pathway for MDD novel loci, breast cancer related gene set for both INS and CP novel loci, and nervous system related development, structure and activity for CP. Furthermore, we identified three loci jointly associated with the three disorders, including 13q14.3 locus with nearby gene OLFM4, 14q21.1 locus with nearby gene LRFN5 and 5q21.2 locus located in intergenic region. In addition, we identified one specific loci for MDD, 7 for INS and 11 for CP respectively by conditioning the other two traits, which were mapped to 68 genes for MDD, 85 for INS and 100 for CP. The MDD specific genes are enriched in immune system related pathways. This study increases understanding of the genetic architectures underlying MDD, INS and CP. The shared underlying genetic risk may help to explain the high comorbidity rates of the disorders.

Systematic review of genome-wide association studies of anxiety disorders and neuroticism

OBJECTIVES

To summarise SNP associations identified by genome-wide association studies (GWASs) of anxiety disorders and neuroticism; to appraise the quality of individual studies, and to assess the ancestral diversity of study participants.

METHODS

We searched PubMed, Scopus, PsychInfo and PubPsych for GWASs of anxiety disorders, non-diagnostic traits (such as anxiety sensitivity), and neuroticism, and extracted all SNPs that surpassed genome-wide significance. We graded study quality using Q-genie scores and reviewed the ancestral diversity of included participants.

RESULTS

32 studies met our inclusion criteria. A total of 563 independent significant variants were identified, of which 29 were replicated nominally in independent samples, and 3 were replicated significantly. The studies had good global quality, but many smaller studies were underpowered. Phenotypic heterogeneity for anxiety (and less so for neuroticism) seemed to reflect the complexity of capturing this trait. Ancestral diversity was poor, with 70% of studies including only populations of European ancestry.

CONCLUSION

The functionality of genes identified by GWASs of anxiety and neuroticism deserves further investigation. Future GWASs should have larger sample sizes, more rigorous phenotyping and include more ancestrally diverse population groups.

Shared genetic architecture between the two neurodegenerative diseases: Alzheimer's disease and glaucoma

BACKGROUND

Considered as the representatives of neurodegenerative diseases, Alzheimer's disease (AD) and glaucoma are complex progressive neuropathies affected by both genetic and environmental risk factors and cause irreversible damages. Current research indicates that there are common features between AD and glaucoma in terms of epidemiology and pathophysiology. However, the understandings and explanations of their comorbidity and potential genetic overlaps are still limited and insufficient.

METHOD

Genetic pleiotropy analysis was performed using large genome-wide association studies summary statistics of AD and glaucoma, with an independent cohort of glaucoma for replication. Conditional and conjunctional false discovery rate methods were applied to identify the shared loci. Biological function and network analysis, as well as the expression level analysis were performed to investigate the significance of the shared genes.

RESULTS

A significant positive genetic correlation between AD and glaucoma was identified, indicating that there were significant polygenetic overlaps. Forty-nine shared loci were identified and mapped to 11 shared protein-coding genes. Functional genomic analyses of the shared genes indicate their modulation of critical physiological processes in human cells, including those occurring in the mitochondria, nucleus, and cellular membranes. Most of the shared genes indicated a potential modulation of metabolic processes in human cells and tissues. Furthermore, human protein-protein interaction network analyses revealed that some of the shared genes, especially MTCH2, NDUFS3, and PTPMT1, as well as SPI1 and MYBPC3, may function concordantly. The modulation of their expressions may be related to metabolic dysfunction and pathogenic processes.

CONCLUSION

Our study identified a shared genetic architecture between AD and glaucoma, which may explain their shared features in epidemiology and pathophysiology. The potential involvement of these shared genes in molecular and cellular processes reflects the "inter-organ crosstalk" between AD and glaucoma. These results may serve as a genetic basis for the development of innovative and effective therapeutics for AD, glaucoma, and other neurodegenerative diseases.

Sources of Individual Differences in Pain

Pain is an immense clinical and societal challenge, and the key to understanding and treating it is variability. Robust interindividual differences are consistently observed in pain sensitivity, susceptibility to developing painful disorders, and response to analgesic manipulations. This review examines the causes of this variability, including both organismic and environmental sources. Chronic pain development is a textbook example of a gene-environment interaction, requiring both chance initiating events (e.g., trauma, infection) and more immutable risk factors. The focus is on genetic factors, since twin studies have determined that a plurality of the variance likely derives from inherited genetic variants, but sex, age, ethnicity, personality variables, and environmental factors are also considered.

Chronic D-ribose and D-mannose overload induce depressive/anxiety-like behavior and spatial memory impairment in mice

The effects of different forms of monosaccharides on the brain remain unclear, though neuropsychiatric disorders undergo changes in glucose metabolism. This study assessed cell viability responses to five commonly consumed monosaccharides-D-ribose (RIB), D-glucose, D-mannose (MAN), D-xylose and L-arabinose-in cultured neuro-2a cells. Markedly decreased cell viability was observed in cells treated with RIB and MAN. We then showed that high-dose administration of RIB induced depressive- and anxiety-like behavior as well as spatial memory impairment in mice, while high-dose administration of MAN induced anxiety-like behavior and spatial memory impairment only. Moreover, significant pathological changes were observed in the hippocampus of high-dose RIB-treated mice by hematoxylin-eosin staining. Association analysis of the metabolome and transcriptome suggested that the anxiety-like behavior and spatial memory impairment induced by RIB and MAN may be attributed to the changes in four metabolites and 81 genes in the hippocampus, which is involved in amino acid metabolism and serotonin transport. In addition, combined with previous genome-wide association studies on depression, a correlation was found between the levels of Tnni3k and Tbx1 in the hippocampus and RIB induced depressive-like behavior. Finally, metabolite-gene network, qRT-PCR and western blot analysis showed that the insulin-POMC-MEK-TCF7L2 and MAPK-CREB-GRIN2A-CaMKII signaling pathways were respectively associated with RIB and MAN induced depressive/anxiety-like behavior and spatial memory impairment. Our findings clarified our understanding of the biological mechanisms underlying RIB and MAN induced depressive/anxiety-like behavior and spatial memory impairment in mice and highlighted the deleterious effects of high-dose RIB and MAN as long-term energy sources.