Risk Genes Research Articles

Exploring the genetic correlation and causal relationships between breast cancer and meningioma using bidirectional Mendelian randomization.

Previous studies have indicated a significantly higher prevalence of breast cancer (BC) among female patients with meningioma compared to the general female population. Therefore, this study aimed to assess the causal relationship between BC and meningioma at the genetic level. Genetic instrumental variables (IVs) for BC were identified from the Breast Cancer Association Consortium (BCAC), the Discovery Biology and Risk of Inherited Variants in Breast Cancer Consortium (DRIVE), the Collaborative Oncological Gene-environment Study (iCOGS), and 11 other BC genome-wide association studies (GWAS). Meningioma GWAS data were obtained from the FinnGen consortium and were further divided into intracranial and spinal meningioma groups for analysis. The primary analysis employed the inverse-variance weighted (IVW) method, supported by sensitivity analysis to address pleiotropy and enhance robustness. Next, linkage disequilibrium score regression (LDSC) was used to assess the genetic correlation between BC and meningioma. Finally, we applied the Functional Mapping and Annotation (FUMA) platform to conduct an in-depth analysis of the GWAS data. After rigorous screening and Mendelian randomization (MR) tests, genetically predicted overall BC (OR: 1.17, P = 0.0045) and ER(estrogen receptors) + BC (OR: 1.21, P = 0.0006) showed a potential causal association with intracranial meningioma. No causal relationships were found between intracranial meningioma and three BC subtypes. No bidirectional causal relationships were found between spinal meningioma and any BC subtype. The LDSC results suggested a modest positive genetic correlation between overall BC (rg: 0.152, SE: 0.077, P = 0.048), ER + BC (rg: 0.181, SE: 0.086, P = 0.035), and intracranial meningioma. FUMA analysis identified PITPNB, TTC28, and CHEK2 as shared risk genes between overall BC, ER + BC, and intracranial meningioma. These findings suggest that BC, especially ER + BC, may be a risk factor for intracranial meningioma. ER-related signaling pathways and the regulation of DNA damage may play a critical role in the pathogenesis of both diseases.

FOXP1 is a Transcription Factor for the Alzheimer's Disease Risk Gene SORL1.

Sortilin-related receptor 1 (SORL1) is a risk gene of Alzheimer's disease (AD), and some protein-truncating (PTV) and rare missense variants causing the loss of function of SORL1 contribute to AD pathogenesis. SORL1 is an endosomal receptor that interacts with multiple protein sorting complexes to facilitate the transport of various cargoes through the endolysosomal network (ELN). However, the regulatory mechanisms governing SORL1 expression remain unknown. Through biochemical methods, we identified Forkhead Box P1 (FOXP1) as a binding protein to the minimal promoter region of SORL1 gene. Silencing FOXP1 using siRNA significantly decreased the activity of the SORL1 minimal promoter and reduced SORL1 protein and mRNA levels in the neuroblastoma cell line SH-SY5Y. Additionally, using 5xFAD mouse models of AD, we observed significantly decreased FOXP1 and SORL1 expression in neurons within the prefrontal cortex. Disruption of ELN and the autophagy degradation system by bafilomycin A1 (BafA1) appeared to be a specific condition to suppress FOXP1 and hence SORL1 in SH-SY5Y cells. These findings highlight the critical role of FOXP1 in regulating SORL1 expression and suggest that FOXP1 could be a potential target to maintain SORL1 expression for AD prevention and therapy.

DNA methylation and its influence on the pathogenesis of osteoarthritis: a systematic literature review

Purpose Evolving evidence demonstrates the role of epigenetics in the pathogenesis of osteoarthritis (OA), whereas in terms of mechanism, DNA methylation has received the highest attention thus far. This systematic review summarizes the current knowledge of DNA methylation and its influence on the pathogenesis of OA. Methods A protocol in alignment with the PRISMA guidelines was employed to systematically review eight bibliographic databases between 1 January 2015 and 31 January 2021, to identify associations between DNA methylation and articular chondrocytes in OA. Results We identified 23 gene-specific studies and 28 genome-wide methylation analyses. Gene-specific studies focused on pro-inflammatory markers in OA, demonstrating that DNA hypomethylation in the promoter region results in overexpression and hypermethylation is linked to gene silencing. Others reported on the association between OA risk genes and DNA methylation. Genome-wide methylation studies reported on differentially methylated regions (DMRs) comparing OA and non-OA chondrocytes. DMRs were seen in hip OA and knee OA chondrocytes. Conclusion The current body of literature demonstrates the potential and crucial role of DNA methylation in the pathogenesis and progression of OA. This knowledge contributes to the understanding of the pathomechanisms behind OA at gene-specific and genome-wide levels. The observed differences in DNA methylation between healthy and diseased tissues indicate the occurrence of changes in DNA methylation. Based on this, future research in this field that explores the characteristics of potentially reversible changes in DNA methylation may lead to opportunities for causative treatment options for OA.

Arginase 1 genetic variation is associated with the risk of vascular complications in type 2 diabetes.

This study aims to explore the association between arginase 1 (ARG1) genetic variation and susceptibility to type 2 diabetes (T2DM) vascular complications, a primary cause of morbidity and mortality in diabetics. ARG1, a risk gene for cardiovascular disease, was identified from GEO datasets GSE22255 and GSE58294. The ENCODE database identified four candidate single-nucleotide polymorphism (SNP) loci. Nine hundred ninety-two T2DM patients underwent SNP genotyping, and relevant biochemical markers were tested. Logistic regression analysis calculated the odds ratio (OR) and 95% confidence interval (CI) between ARG1 SNP and diabetic vascular complications. Out of 985 patients, 250had CHD, with the TTTG group accounting for 64/250. This group showed a significant reduction in CHD risk (non-TTTG factor-adjusted OR = 1.61, 95% CI: 1.14-2.29, p = 0.008). The combination of the TTTG group, age, central obesity, and hypertension better predicted CHD risk (Area under the curve = 0.72, p < 0.001). ARG1 polymorphisms significantly impact vascular complications in T2DM patients, implying that ARG1 genetic variation may be a potential prevention and treatment target. ChiCTR1800015661.

M6A-mRNA Reader YTHDF2 Identified as a Potential Risk Gene in Autism With Disproportionate Megalencephaly.

Among autistic individuals, a subphenotype of disproportionate megalencephaly (ASD-DM) seen at three years of age is associated with co-occurring intellectual disability and poorer prognoses later in life. However, many of the genes contributing to ASD-DM have yet to be delineated. In this study, we identified additional ASD-DM candidate genes with the aim to better define the genetic etiology of this subphenotype of autism. We expanded the previously studied sample size of ASD-DM individuals ten fold by including probands from the Autism Phenome Project and Simons Simplex Collection, totaling 766 autistic individuals meeting the criteria for megalencephaly or macrocephaly and revealing 154 candidate ASD-DM genes harboring de novo protein-impacting variants. Our findings include 14 high confidence autism genes and seven genes previously associated with DM. Five impacted genes have previously been associated with both autism and DM, including CHD8 and PTEN. By performing functional network analysis, we expanded to additional candidate genes, including one previously implicated in ASD-DM (PIK3CA) as well as 184 additional genes connected withASD or DM alone. Using zebrafish, we modeled a de novo tandem duplication impacting YTHDF2, encoding an N6-methyladenosine (m6A)-mRNA reader, in an ASD-DM proband. Testing zebrafish CRISPR knockdown led to reduced head/brain size, while overexpressing YTHDF2 resulted in increased head/brain size matching that of the proband. Single-cell transcriptomes of YTHDF2 gain-of-function larvae point to reduced expression of Fragile-X-syndrome-associated FMRP-target genes globally and in the developing brain, providing insight into the mechanism underlying autistic phenotypes. We additionally discovered a variant impacting a different gene encoding an m6A reader, YTHDC1, in our ASD-DM cohort. Though we highlight only two cases to date, our study provides support for the m6A-RNA modification pathway as potentially contributing to this severe form of autism.

Carboplatin-resistance-related DNA damage repair prognostic gene signature and its association with immune infiltration in breast cancer

IntroductionBreast cancer is among the most prevalent malignant tumors globally, with carboplatin serving as a standard treatment option. However, resistance often compromises its efficacy. DNA damage repair (DDR) pathways are crucial in determining responses to treatment and are also associated with immune infiltration. This study aimed to identify the DDR genes involved in carboplatin resistance and to elucidate their effects on prognosis, immune infiltration, and drug sensitivity in breast cancer patients.MethodsA 3D-culture model resistant to carboplatin was constructed and sequenced. Co-expressed DDR genes were analyzed to develop a predictive model. Immune infiltration analysis tools were employed to assess the immune microenvironment of patients with varying expression levels of these risk genes. Additionally, drug sensitivity predictions were made to evaluate the efficacy of other DNA damage-related drugs across different risk groups. Molecular assays were performed to investigate the role of the key gene TONSL in breast cancer.ResultsBy integrating data from public database, we established a prognostic signature comprising thirteen DDR genes. Our analysis indicated that this model is associated with immune infiltration patterns in breast cancer patients, particularly concerning CD8+ T cells and NK cells. Additionally, it demonstrated a significant correlation with sensitivity to other DDR-related drugs, suggesting its potential as a biomarker for treatment efficacy. Compared to the control group, TONSL-knockdown cell lines exhibited a diminished response to DNA-damaging agents, marked by a notable increase in DNA damage levels and enhanced drug sensitivity. Furthermore, single-cell analysis revealed elevated TONSL expression in dendritic and epithelial cells, particularly in triple-negative breast cancers.ConclusionsCarboplatin resistance-related DDR genes are associated with prognosis, immune infiltration, and drug sensitivity in breast cancer patients. TONSL may serve as a potential therapeutic target for breast cancer, particularly in triple-negative breast cancer, indicating new treatment strategies for these patients.

Multiomic analyses direct hypotheses for Creutzfeldt-Jakob disease risk genes.

Prions are assemblies of misfolded prion protein that cause several fatal and transmissible neurodegenerative diseases, with the most common phenotype in humans being sporadic Creutzfeldt-Jakob disease (sCJD). Aside from variation of the prion protein itself, molecular risk factors are not well understood. Prion and prion-like mechanisms are thought to underpin common neurodegenerative disorders meaning that the elucidation of mechanisms could have broad relevance. Herein we sought to further develop our understanding of the factors that confer risk of sCJD using a systematic gene prioritization and functional interpretation pipeline based on multiomic integrative analyses. We integrated the published sCJD genome-wide association study (GWAS) summary statistics with publicly available bulk brain and brain cell type gene and protein expression datasets. We performed multiple transcriptome and proteome-wide association studies (TWAS & PWAS) and Bayesian genetic colocalization analyses between sCJD risk association signals and multiple brain molecular quantitative trait loci signals. We then applied our systematic gene prioritization pipeline on the obtained results and nominated prioritized sCJD risk genes with risk-associated molecular mechanisms in a transcriptome and proteome-wide manner. Genetic upregulation of both gene and protein expression of syntaxin-6 (STX6) in the brain was associated with sCJD risk in multiple datasets, with a risk-associated gene expression regulation specific to oligodendrocytes. Similarly, increased gene and protein expression of protein disulfide isomerase family A member 4 (PDIA4), involved in the unfolded protein response, was linked to increased disease risk, particularly in excitatory neurons. Protein expression of mesencephalic astrocyte derived neurotrophic factor (MANF), involved in protection against endoplasmic reticulum stress and sulfatide binding (linking to the enzyme in the final step of sulfatide synthesis, encoded by sCJD risk gene GAL3ST1), was identified as protective against sCJD. In total 32 genes were prioritized into two tiers based on the level of evidence and confidence for further studies. This study provides insights into the genetically-associated molecular mechanisms underlying sCJD susceptibility and prioritizes several specific hypotheses for exploration beyond the prion protein itself and beyond the previously highlighted sCJD risk loci through the newly prioritized sCJD risk genes and mechanisms. These findings highlight the importance of glial cells, sulfatides and the excitatory neuron unfolded protein response in sCJD pathogenesis.

A cross-tissue transcriptome-wide association study identifies new susceptibility genes for benign prostatic hyperplasia

Benign prostatic hyperplasia (BPH) is a prevalent urinary system disorder. Despite evidence of a significant genetic component from previous studies, the specific pathogenic genes and biological mechanisms are still largely unknown. The study utilized the FinnGen R10 dataset, encompassing 177,901 individuals (36,601 cases and 141,300 controls), and the GTEx v8 EQTLs files to conduct single-tissue and cross-tissue transcriptome-wide association studies (TWAS). FUSION method was utilized to validate the findings in specific tissues. Gene Analysis and Multi-marker Analysis of Genomic Annotation (MAGMA) were used to identify potential susceptibility genes. The intersection genes of the above results were analyzed by Mendelian randomization (MR), summary data-based MR (SMR) and colocalization studies. Fine-mapping of causal gene sets (FOCUS) software was employed to accurately locate risk genes. Gene Expression Omnibus (GEO) analysis explores the differential expression of genes. Finally, The GeneMANIA tool was utilized to further understand the functional roles of these susceptibility genes. The cross-tissue TWAS analysis revealed 28 genes associated with BPH susceptibility. Single-tissue TWAS and MAGMA further refined eight genes, and subsequent MR, SMR, FOCUS and colocalization analysis pinpointed INO80B as the key gene. The differential expression of this result was verified by GEO. INO80B may help prevent excessive prostatic cell proliferation by regulating cell cycle-related gene expression. Our research identified the INO80B gene, whose predicted expression is associated with BPH risk and hence provided a new insight into the genetic basis of this disease. However, further functional studies are necessary to elucidate the potential biological activity of these significant signals.

Exploring the therapeutic effect of human recombinant IL11 on lesioned OA human osteochondral explants

ObjectiveTo explore IL11 co-expression profiles in our previously reported RNA-sequencing dataset of OA articular cartilage, in interaction with IL6, and to investigate the effects of hrIL11 administration as potential therapeutic strategy for OA articular cartilage using our biomimetic aged human osteochondral explant model of OA.MethodsWe used RNA-sequencing datasets of macroscopically preserved and lesioned OA articular cartilage (N = 35 patients). Spearman correlations were calculated between IL11 and IL6 expression levels and genes expressed in cartilage (N = 20048 genes). Osteochondral explants were isolated from macroscopically preserved and lesioned areas of the joint and were kept in culture for two weeks, with or without exposure to 200ng/ml hrIL11.ResultsWe found no overlap in correlating genes between IL11 and IL6, indicating their distinct roles in articular cartilage. Moreover, we identified more genes being correlated to IL11 in the lesioned compared to preserved articular cartilage (N = 203 and 106 genes, respectively). Upon treatment of ex vivo OA articular cartilage with hrIL11, we overall observed unbeneficial effects on chondrocyte phenotype, as illustrated by upregulation of MMP13, EPAS1, RUNX2, and POSTN. We did not observe significant differences in Mankin scores upon addition of hrIL11.ConclusionThe current study showed that treatment of OA articular cartilage with hrIL11 is unlikely to be beneficial despite previous indications of hrIL11 as potential druggable target. These findings underscore the importance of functionally investigating OA risk genes. Better understanding of IL11 signaling and the underlying pathways is necessary towards the development of OA treatment strategy.

TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states.

Mutations in cancer risk genes increase susceptibility, but not all carriers develop cancer. Indeed, while DNA mutations are necessary drivers of cancer, only a small subset of mutated cells go on to cause the disease. To date, the mechanisms underlying individual cancer susceptibility remain unclear. Here, we took advantage of a unique mouse model of intrinsic developmental heterogeneity (Trim28+/D9) to investigate whether early-life epigenetic variation influences cancer susceptibility later in life. We found that heterozygosity of Trim28 is sufficient to generate two distinct early-life epigenetic states associated with differing cancer susceptibility. These developmentally primed states exhibit differential methylation patterns at typically silenced heterochromatin, detectable as early as 10 days of age. The differentially methylated loci are enriched for genes with known oncogenic potential, frequently mutated in human cancers and correlated with poor prognosis. This study provides genetic evidence that intrinsic developmental heterogeneity can prime individual, lifelong cancer susceptibility.

Bridging animal models and humans: neuroimaging as intermediate phenotypes linking genetic or stress factors to anhedonia

BackgroundIntermediate phenotypes, such as characteristic neuroimaging patterns, offer unique insights into the genetic and stress-related underpinnings of neuropsychiatric disorders like depression. This study aimed to identify neuroimaging intermediate phenotypes associated with depression, bridging etiological factors to behavioral manifestations and connecting insights from animal models to diverse clinical populations.MethodsWe analyzed datasets from both rodents and humans. The rodent studies included a genetic model (P11 knockout) and an environmental stress model (chronic unpredictable mild stress), while the human data comprised 748 participants from three cohorts. Using the amplitude of low-frequency fluctuations, we identified neuroimaging patterns in rodent models. We then applied a machine-learning approach to cluster neuroimaging subtypes of depression. To assess the genetic predispositions and stress-related changes associated with these subtypes, we analyzed genotype and metabolite data. Linear regression was employed to determine which neuroimaging features predicted core depression symptoms across species.ResultsThe genetic and environmental stress models exhibited distinct neuroimaging patterns in subcortical and sensorimotor regions. Consistent patterns emerged in two neuroimaging subtypes identified across three independent depressed cohorts. The subtype resembling P11 knockout demonstrated higher genetic susceptibility, with enriched expression of risk genes in brain tissues and abnormal metabolites linked to tryptophan metabolism. In contrast, the stress animal-like subtype did not show changes in genetic risk scores but exhibited enriched risk gene expression in somatic and endocrine tissues, along with mitochondrial dysfunction in the antioxidant stress system. Notably, these distinct subcortical-sensorimotor neuroimaging patterns predicted anhedonia, a core symptom of depression, in both rodent models and depressed subtypes.ConclusionsThis cross-species validation suggests that these neuroimaging patterns may serve as robust intermediate phenotypes, linking etiology to anhedonia and facilitating the translation of findings from animal models to humans with depression and other psychiatric disorders.

Heterogeneity analysis and prognostic model construction of HPV negative oral squamous cell carcinoma T cells using ScRNA-seq and bulk-RNA analysis

BackgroundT cells are involved in every stage of tumor development and significantly influence the tumor microenvironment (TME). Our objective was to assess T-cell marker gene expression profiles, develop a predictive risk model for human papilloma virus (HPV)-negative oral squamous cell carcinoma (OSCC) utilizing these genes, and examine the correlation between the risk score and the immunotherapy response.MethodsWe acquired scRNA-seq data for HPV-negative OSCC from the GEO datasets. We performed cell‒cell communication, trajectory, and pathway enrichment analyses of T-cell-associated genes. In addition, we constructed and validated a T-cell-associated gene prognostic model for HPV-negative OSCC patients using TCGA and GEO data and assessed the immune infiltration status of HPV-negative OSCC patients .qRT-PCR was used to detect the expression level of prognosis-related genes in different risk groups.ResultsScRNA-seq was conducted on 28,000 cells derived from 14 HPV-negative OSCC samples and 6 normal samples. We identified 4,635 T cells from these cells and identified 774 differentially expressed genes(DEGs) associated with T cells across five distinct T-cell subtypes. Through the integration of bulk-RNAseq data, we established a prognostic model based on DEGs related to T cells. By separating patients into high-risk and low-risk groups according to these prognostic related genes, we can accurately predict their survival rates and the immune infiltration status of the TME.qRT-PCR results showed that compared with the patients of low risk group, the expression of PMEPA1, SH2D2A, SMS and PRDX4 were significantly up-regulated in high risk group.ConclusionThis study provides a resource for understanding the heterogeneity of T cells in HPV-negative OSCC patients and associated prognostic risk models. It provides new insights for predicting survival and level of immune infiltration in patients with HPV-negative OSCC.

P1296 Exploring the role of BOC mutations in Crohn’s disease using whole exome sequencing and molecular dynamics simulation

Abstract Background Crohn’s disease (CD) is a chronic inflammatory bowel disease, whose pathogenesis involves genetic component. In this study, BOC was identified as a potential risk gene for CD, whose gene product is a member of the cell adhesion molecule family. It is suggested that BOC binds to the N-terminus of Dhh protein (DhhN) through its Fn2-Fn3 domain, facilitating hh protein signal transduction. This signal has been shown to maintain endothelial cell barrier integrity, which is critical in the development of CD. Hence, we hypothesize that mutations in the BOC protein could alter its structure, impairing its ability to bind or release hh proteins, leading to abnormal hh signal transduction and affecting endothelial cell barrier function. Therefore, we employed molecular dynamics simulation to investigate the characteristics and affinity changes of the domain, and the domain with DhhN complex, both before and after mutation. Methods The target risk gene BOC was identified, and employed molecular dynamics simulation to investigate the characteristics and affinity changes of the BOC Fn2-Fn3 domain, and the domain with DhhN complex, both before and after mutation. Results 1. From the list of gene mutations, 121 candidate risk genes were identified. 2. The target risk gene BOC was identified, which is highly expressed on the colorectal endothelial cell membrane surface, and its expression shows a difference between CD patients and normal colorectal tissues. 3. The Arg697 mutation leads to decreased flexibility and increased stability of the BOC Fn2-Fn3 domain. 4. The Arg697 mutation increases the affinity of the domain with the DhhN complex, adding to the number of key amino acids and hydrogen bonds maintaining the complex’s affinity. Conclusion 1. Whole exome sequencing analysis revealed specific BOC gene mutations in CD patients, with differential expression between patients and healthy individuals suggesting an important role for BOC in CD. 2. Molecular dynamics simulations revealed that the Arg697 mutation increases the stability of BOC, and also showed increased stability and affinity of its binding with DhhN, which might prevent BOC from properly releasing hh proteins after binding, leading to abnormal hh signal transduction and thus impairing endothelial cell barrier function, which may promote the development and progression of CD. 3. The increased affinity of the complex following the Arg697 mutation is due to an increase in the number of key amino acid residues at the binding interface, resulting in more hydrogen bonds. Modifying these key amino acids to alter the affinity of the complex could normalize hh signal transduction, thereby restoring endothelial cell barrier function.

Efferocytosis-related gene IL33 predicts prognosis and immune response and mediates proliferation and migration in vitro and in vivo of breast cancer

BackgroundBreast cancer (BRCA) has a high incidence among women, with poor prognosis and high mortality, which is increasing year by year. Efferocytosis is a process of phagocytosis of abnormal cells and is of great value in tumor research. Our study seeks to create a predictive model for BRCA using efferocytosis-related genes (ERGs) to explore the significance of efferocytosis in this disease.MethodsIn this research, Differential analysis, and univariate Cox regression were employed to identify genes linked to prognosis in BRCA patients. Then the BRCA patients were categorized into distinct groups using consensus clustering based on prognosis genes. Survival analysis, PCA, and t-SNE were performed to verify these groups. The enrichment of metabolic pathways within the detected clusters was evaluated using gene set variation analysis (GSVA) and gene set enrichment analysis (GSEA). Additionally, single-sample GSEA (ssGSEA) was used to examine changes in immune infiltration and enrichment. A risk prognostic model was constructed utilizing multivariable Cox regression and Least Absolute Shrinkage and Selection Operator (LASSO) analyses, and subsequently validated its predictive accuracy by stratifying patients according to the median risk score. Ultimately, some crucial independent prognostic genes were pinpointed and their expression, roles, and immune characteristics were explored in both laboratory and live models.ResultsFindings revealed 52 differentially expressed genes (DEGs), of which 21 were significantly linked to BRCA outcomes. These 21 genes were utilized for consensus clustering to categorize BRCA patients into two subtypes. Subtype B was linked to a worse prognosis compared to Subtype A, though both subtypes were distinguishable. The enriched pathways were mainly concentrated in Subtype A and were actively expressed in this group. Following this, a prognostic risk model was constructed using five risk genes, which was proven to possess significant predictive value. A significant link was identified between the immune microenvironment and the risk-associated genes and scores. IL33 was identified as an independent prognostic gene with important research value. Its in vivo expression results aligned with the data analysis findings, showing low expression in BRCA. Furthermore, overexpression of IL33 significantly inhibited BRCA growth and motility in vitro and in vivo, while also enhancing their vulnerability to destruction by activated CD8+ T cells.ConclusionThe ERG-based risk model effectively predicts the prognosis of BRCA patients and shows a strong link with the immune microenvironment. IL33 stands out as a significant prognostic marker, crucial in the onset and advancement of BRCA. This highlights the necessity for additional studies and indicates that IL33 might be a potential target for BRCA treatment.

A network-based systems genetics framework identifies pathobiology and drug repurposing in Parkinson’s disease

Parkinson’s disease (PD) is the second most prevalent neurodegenerative disorder. However, current treatments only manage symptoms and lack the ability to slow or prevent disease progression. We utilized a systems genetics approach to identify potential risk genes and repurposable drugs for PD. First, we leveraged non-coding genome-wide association studies (GWAS) loci effects on five types of brain-specific quantitative trait loci (xQTLs, including expression, protein, splicing, methylation and histone acetylation) under the protein–protein interactome (PPI) network. We then prioritized 175 PD likely risk genes (pdRGs), such as SNCA, CTSB, LRRK2, DGKQ, and CD44, which are enriched in druggable targets and differentially expressed genes across multiple human brain-specific cell types. Integrating network proximity-based drug repurposing and patient electronic health record (EHR) data observations, we identified Simvastatin as being significantly associated with reduced incidence of PD (hazard ratio (HR) = 0.91 for fall outcome, 95% confidence interval (CI): 0.87–0.94; HR = 0.88 for dementia outcome, 95% CI: 0.86–0.89) after adjusting for 267 covariates. In summary, our network-based systems genetics framework identifies potential risk genes and repurposable drugs for PD and other neurodegenerative diseases if broadly applied.

P0210 ORMDL proteins regulate intestinal epithelial cell homeostasis by modulating ER architecture, autophagy, and DNA damage response

Abstract Background ORM1-like protein 3 (ORMDL3) is a risk gene for asthma and inflammatory bowel disease (IBD), identified in genome-wide association studies (GWAS).1,2 It encodes an endoplasmic reticulum (ER)-resident transmembrane protein implicated in calcium homeostasis, sphingolipid biosynthesis, and regulation of the unfolded protein response (UPR) upon ER stress.3,4 However, the role of ORMDL3 and its homologous protein family members ORMDL1 and ORMDL2, which exhibit partly redundant functions, remains unclear in the context of intestinal inflammation. Methods Constitutive and conditional intestinal epithelial cell-specific knockout (KO) mice for Ormdl1, Ormdl2, and Ormdl3 were generated. Histological analysis of small intestinal (SI) Paneth cells (lysozyme immunohistochemistry), goblet cells (periodic acid-Schiff staining) and ER morphology in Paneth cells (transmission electron microscopy [TEM]) was conducted. Interactions between ORMDL proteins and autophagy-related proteins were examined by co-immunoprecipitation and immunoblot assays in irradiated mouse embryonic fibroblasts (iMEFs). Organoids derived from Ormdl1/2/3ΔIEC mice were used for bulk RNA sequencing. Results The Ormdl1/2/3 triple KO was embryonically lethal, while Ormdl3-KO and Ormdl1/3 double KO mice exhibited reduced body size, weight, and embryonic viability, along with fewer Paneth and goblet cells. To eliminate any compensatory effects of the multiple ORMDL proteins, the Ormdl1/2/3ΔIEC mice were analyzed. These mice showed no macroscopic phenotype but displayed microscopic inflammation, reduced Paneth and goblet cells, and increased SI tuft cells. Both constitutive and conditional Ormdl knockout mice showed massive dilation of the ER. While autophagy is a known compensatory mechanism resolving ER stress, we demonstrated that ORMDL3 co-localized and co-precipitated with the autophagy-related protein LC3 (microtubule-associated protein 1A/1B-light chain 3). Consistent with this, loss of ORMDL proteins compromised autophagic flux. Bulk RNA sequencing of SI organoids from Ormdl1/2/3ΔIEC mice revealed reduced expression of genes involved in lipid biosynthesis, tuft cell differentiation via BMP-signalling, and innate immunity, including antimicrobial peptides, likely due to loss of Paneth cells. In contrast, DNA damage response genes were upregulated, as reflected by an increase in γ-H2AX-positive epithelial cells. Conclusion The data suggest a critical regulatory role for ORMDL proteins in the ER-autophagy axis within epithelial cells, shaping mucosal homeostasis and expression of antimicrobial peptides, thereby conferring protection against IBD. Further studies are required to elucidate the molecular basis of the function of ORMDL proteins in intestinal inflammation.

P0039 Deletion of the autophagy-related gene 16 like 1 (Atg16l1) in the myeloid lineage induces systemic inflammation

Abstract Background The autophagy-related gene 16 like 1 (ATG16L1) is essential for the formation of the autophagosome and deletion of this gene leads, among other things, to the disruption of autophagy.1,2 In 2007, a Genome Wide Association Study identified ATG16L1 as a risk gene for Crohn’s Disease.3 This study aims to understand the mechanisms causing the hyperinflammatory systemic phenotype observed in our mouse model carrying a conditional myeloid deletion of Atg16l1 (Atg16l1LysM). Methods The immune phenotype of Atg16l1LysM and Atg16l1fl/fl mice was characterized using histology staining and flow cytometry of lymphatic organs. In addition, single cell RNA sequencing of splenocytes and determination of cytokine levels in the serum were performed to investigate the inflammatory status of the animals. LPS-stimulated bone marrow-derived macrophages (BMDMs) of Atg16l1LysM and Atg16l1fl/fl mice were used as an in-vitro model to study signaling pathways that might be responsible for the inflammatory phenotype. Results Atg16l1LysM mice display a spontaneous hyperinflammatory phenotype that is accompanied by hepatosplenomegaly and increased cytokine levels in serum. Histology staining revealed a disrupted spleen architecture with an increase of red pulp tissue compared to floxed littermates. Flow cytometry and single cell transcriptome data of splenocytes revealed alterations in the cellular composition of Atg16l1LysM spleens confirming an increase of activated myeloid cells and a simultaneous reduction of lymphoid cells, especially T cells. Additionally, the proportion of myeloid-derived suppressor cells (MDSC) in Atg16l1LysM spleen was found to be increased. Moreover, a significant overexpression of type-I interferon signaling genes was discovered in monocytic cells derived from the Atg16l1LysM spleen. Bulk RNA sequencing data of LPS-stimulated Atg16l1 knockout BMDMs confirmed the overactivation of type-I IFN-related genes compared to wild type BMDMs, pointing towards a role for the Stimulator of IFN genes (STING) and Rig-I-like (RLR) pathways in the Atg16l1-deficient scenario. However, neither inhibiting the STING pathway in vitro nor creating Atg16l1STINGLysM double knockout mice lead to a significant reduction of IFN-β production. Conclusion The increased type-I IFN response observed in Atg16l1LysM mice does not seem to be influenced by STING signaling. Future studies are needed to uncover whether RIG-I-like receptors are major contributors of the increased IFN-β response in absence of Atg16l1 and to determine the internal triggers of this reaction. The results also prompt further investigations on aberrant cell activation in autophagy-deficient myeloid cells.

Unveiling causal immune cell–gene associations in multiple myeloma: insights from systematic reviews and Mendelian randomization analyses

BackgroundThe efficacy of novel chimeric antigen receptor T-cell (CAR-T) therapy is inconsistent, likely due to an incomplete understanding of the tumor microenvironment (TME). This study utilized meta-analysis to evaluate CAR-T-cell therapy efficacy and safety and employed two-sample Mendelian randomization (MR) analysis to investigate the causal links between immune cells and Multiple Myeloma (MM).MethodOur literature review, conducted from January 1, 2019, to August 30, 2024, across Medline/PubMed, Scopus, and Web of Science, identified 2,709 articles, 34 of which met our inclusion criteria. We utilized MR analysis of GWAS data to identify immune cells causally related to multiple myeloma, followed by SMR analysis to highlight associated pathogenic genes and colocalisation analysis for validation.ResultsThe meta-analysis revealed an 82.2% overall response rate to CAR-T-cell therapy, characterized by a safe profile with a grade 3 or higher CRS of 6.3% and neurotoxicity of 0.9%. BCMA, CD38, and GPRC5D CAR-T-cell therapies had superior response rates, whereas BCMA and CD3 CAR-T-cell therapy rates lagged at 61.8%. Post-adjustment for multiple testing, the levels of seven types of immune cells (two types of Treg, two types of TNBK, two types of B cells, and one type of Myeloid cell) were found to be elevated in association with an increased risk of multiple myeloma (MM), while the levels of another eight types of immune cells (one types of Treg, three types of TNBK, one type of MT cells, and two types of Myeloid cell and one type of cDC cells) were demonstrated to be associated with a decreased risk of MM. As supported by sensitivity analysis. SMR analysis pinpointed the risk genes VDR, VHL, POMC, and FANCD2, with VHL and POMC correlating at the methylation level. VDR was not significantly correlated with MM after correction for multiple tests. NCAM1 also exhibited a significant methylation-level association with disease.ConclusionOur study supports the efficacy and safety of CAR-T-cell therapy in rrMM patients, with an 82.2% ORR and low rates of severe CRS (6.3%) and neurotoxicity (0.9%). This finding also suggests that BCMA/CD19 bispecific CAR-T cells have a superior ORR, pending clinical confirmation. MR analysis reveals links between immune cells, genes such as VDR and VHL, and MM, enhancing our understanding of its pathophysiology.

Genomic and algorithm-based predictive risk assessment models for benzene exposure

AimIn this research, we leveraged bioinformatics and machine learning to pinpoint key risk genes associated with occupational benzene exposure and to construct genomic and algorithm-based predictive risk assessment models.Subject and methodsWe sourced GSE9569 and GSE21862 microarray data from the Gene Expression Omnibus. Utilizing R software, we performed an initial screen for differentially expressed genes (DEGs), which was followed by the enrichment analyses to elucidate the affected functions and pathways. Subsequent steps included the application of three machine learning algorithms for key gene identification, and the validation of these genes within both a cohort exposed to benzene and a benzene-exposed mice model. We then conducted a functional prediction analysis on these genes using four machine learning models, complemented by GSVA enrichment analysis.ResultsOut of the data, 40 DEGs were identified, primarily linked to cytokine signaling, lipopolysaccharide response, and chemokine pathways. NFKB1, PHACTR1, PTGS2, and PTX3 were pinpointed as significant through machine learning. Validation confirmed substantial changes in NFKB1 and PTX3 following exposure, with PTX3 emerging as paramount, suggesting its utility as a diagnostic biomarker for benzene damage.ConclusionRisk assessment models, informed by oxidative stress markers, successfully discriminated between benzene-injured patients and controls.

Exome sequencing identifies protein-coding variants associated with loneliness and social isolation.

Loneliness and social isolation are serious yet underappreciated public health problems, with their genetic underpinnings remaining largely unknown. We aimed to explore the role of protein-coding variants in the manifestation of loneliness and social isolation. We conducted the first exome-wide association analysis on loneliness and social isolation, utilizing 336,115 participants of white-British ancestry for loneliness and 346,115 for social isolation. Sensitivity analyses were performed to validate the genetic findings. We estimated the genetic burden heritability of loneliness and social isolation and provided biological insights into them. We identified six novel risk genes (ANKRD12, RIPOR2, PTEN, ARL8B, NF1, and PIMREG) associated with loneliness and two (EDARADD and GIGYF1) with social isolation through analysis of rare coding variants. Brain-wide association analysis uncovered 47 associations between identified genes and brain structure phenotypes, many of which are critical for social processing and interaction. Phenome-wide association analysis established significant links between these genes and phenotypes across five categories, mostly blood biomarkers and cognitive measures. The measurements of loneliness and social isolation in UK Biobank are brief for these multi-layer social factors, some relevant aspects may be missed. Our study revealed 13 risk genes associated with loneliness and 6 with social isolation, with the majority being novel discoveries. These findings advance our understanding of the genetic basis of these two traits. The study provides a foundation for future studies aimed at exploring the functional mechanisms of these genes and their potential implications for public health interventions targeting loneliness and social isolation.