Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease

Mendelian randomization analysis identifies ERAP1 and IL23R as potential drug targets for ankylosing spondylitis

BACKGROUND

Ankylosing spondylitis (AS) is a chronic inflammatory disease primarily affecting the spine and pelvis, leading to ankylosis, stiffness, and reduced quality of life. Despite therapeutic advances, identifying novel drug targets remains critical.

METHODS

This Mendelian randomization (MR) study leveraged proteome-wide analysis, utilizing data from five genome-wide association studies (GWAS) for proteomics exposure. Outcome data included 3162 European ancestry cases and 294,770 controls from FinnGen R10, and replication analyses used two plasma proteomic datasets (ARIC: 4657 proteins in 7213 individuals; UK Biobank: 4907 proteins in 35,559 participants) and UK Biobank AS GWAS (1344 cases, 324,074 controls). Sensitivity analyses, including Bayesian co-localization and Steiger's direction test, were conducted to ensure robust findings. Protein-protein interaction (PPI) networks were constructed to explore interactions between identified proteins and known AS drug targets.

RESULTS

After FDR adjustment, circulating ERAP1 (OR = 1.30, 95 % CI: 1.21-1.39, P = 8.18 × 10-14) and IL23R (OR = 2.21, 95 % CI: 1.61-3.03, P = 9.47 × 10-7) were genetically linked to increased AS risk, while IL1RL2 showed a protective effect (OR = 0.70, 95 % CI: 0.58-0.85, P = 3.22 × 10-4). Steiger's test confirmed directionality (P < 1.70 × 10-15), and Bayesian co-localization supported shared causal variants (PPH4 > 0.75 for IL23R/IL1RL2). PPI networks revealed interactions between ERAP1, IL23R, and known AS targets. Replication validated ERAP1 and IL23R associations but not IL1RL2.

CONCLUSION

Genetically determined levels of ERAP1 and IL23R are robustly associated with AS risk, highlighting their potential as therapeutic targets. This study demonstrates the utility of MR in identifying drug targets for complex diseases, providing a foundation for further clinical investigation into their therapeutic potential.

A multi-omics target study for glioblastoma multiforme (GBM) based on Mendelian randomization analysis

Background

Glioblastoma multiforme (GBM) is the most frequent type of primary malignant brain tumor. This study utilized Mendelian randomization (MR) analysis to explore the causal link between proteins in plasma and cerebrospinal fluid and GBM.

Aims

This study aimed to identify proteins in both plasma and cerebrospinal fluid (CSF) that could serve as potential therapeutic targets for GBM.

Methods

We employed previously published protein quantitative trait loci (pQTL) data from CSF and plasma as the exposure data, alongside aggregated Genome-Wide Association Study (GWAS) data on GBM for our MR analysis. Furthermore, we conducted Bayesian co-localization analysis and examined the protein-protein interaction (PPI) networks of CSF and plasma proteins related to GBM risk.

Results

MR identified three key proteins linked to GBM risk: ribophorin I (RPN1) in plasma, von Willebrand factor (vWF) and macrophage-stimulating protein (MSP). in CSF. Elevated RPN1 and MSP were associated with decreased GBM risk, while increased vWF was linked to higher risk. External validation confirmed that RPN1 served as a key protein in GBM development. Bayesian co-localization showed a 10.35 % probability of a shared causal variant between RPN1 and GBM. Protein-protein interaction analysis further highlighted related proteins for RPN1.

Conclusions

In summary, the plasma protein RPN1 and the CSF proteins vWF and MSP are causally associated with the risk of GBM. Further research is needed to clarify the roles of these candidate proteins in GBM. Notably, RPN1 may serve as a potential therapeutic target for GBM. Future clinical studies on GBM treatment could explore drugs targeting RPN1.

Causal association of cathepsins with female infertility: a bidirectional Mendelian randomization analysis

OBJECTIVE

This study aimed to systematically evaluate potential causal relationships between nine cathepsins and female infertility using Mendelian randomization (MR).

METHODS

.

METHODS

A bidirectional MR analysis was conducted utilizing single nucleotide polymorphisms as instrumental variables to investigate the potential causal effects between nine cathepsins and female infertility. Genetic data on female infertility were sourced from the FinnGen study, and cathepsin-related data were obtained from genome-wide association studies datasets of European ancestry.

RESULTS

Elevated levels of cathepsin E were significantly and inversely associated with the risk of female infertility, suggesting a potential protective role. This finding was further supported by multivariable MR analysis. However, no significant associations were observed between the other eight cathepsins and female infertility.

CONCLUSION

This study represents the first systematic MR analysis to identify a potential protective effect of cathepsin E on female infertility.

Potential drug targets for Neuromyelitis optica spectrum disorders (NMOSD): A Mendelian randomization analysis

BACKGROUND

Certain peripheral proteins are involved in the development of Neuromyelitis optica spectrum disorders (NMOSD), such as IL-6, complement proteins, and MHC class II molecules. However, the roles of other new protein biomarkers are unclear. Current NMOSD treatments (e.g., intravenous pulse methylprednisolone, or satralizumab for IL-6 receptor inhibition) can only manage symptoms, necessitating the identification of new drug targets to treat NMOSD. The objective of this study is to identify potential drug targets for NMOSD through Mendelian randomization (MR) analysis, thereby addressing the limitations of current treatments and providing better clinical options for patients.

METHODS

NMOSD potential drug targets were evaluated via MR. Data was obtained from a genome-wide association study (GWAS) with 132 individuals with AQP4-IgG-positive NMOSD and 1244 controls. Genetic instruments for plasma and cerebrospinal fluid (CSF) proteins were identified. Sensitivity analyses were conducted using Bayesian co-localization, reverse causality testing and phenotype scanning. Additionally, a comparison and analysis of protein-protein interactions (PPI) were conducted to identify potential causal proteins. The implications of these findings were further explored by evaluating existing NMOSD drugs and their respective targets.

RESULTS

Four proteins were identified at the FDR correction via MR analysis (p < 0.05). Higher levels of PF4V1 (OR = 0.47; 95% CI, 0.29-0.78; p = 3.39 × 10-3) and FAM3B (OR = 0.12; 95% CI, 0.03-0.45; p = 1.65 × 10-3) were associated with a reduced risk of NMOSD, whereas elevated SERPINA1 (OR = 2.28; 95% CI, 1.29-4.04; p= 4.71 × 10-3) and CLEC11A (OR = 13.45; 95% CI, 1.29-4.04; p = 4.71 × 10-3) were related to an increased risk of NMOSD. Bayesian co-localization showed that the protein-related genes shared the same mutation as NMOSD (all PPH4>0.80). Reverse causality testing showed no evidence of NMOSD-driven protein changes (all p > 0.05). PPI analysis revealed SERPINA1 interacts with PF4V1 (combined score = 0.72). Drug evaluation identified Mercaptoethanol and Ferrous gluconate as repurposing candidates.

CONCLUSION

Increased levels of plasma CLEC11A and SERPINA1 are correlated with an elevated risk of NMOSD, whereas elevated levels of plasma PF4V1 and CSF FAM3B are associated with a decreased risk of NMOSD. The opposing effects of risk or protective proteins suggest synergistic targeting could improve efficacy beyond current immunosuppressive regimens. Nonetheless, clinical trials are required to confirm the findings.

Causal roles of lipids and mediating proteins in diabetic retinopathy: insights from metabolomic and proteomic Mendelian randomization

BACKGROUND

This study explores the causal relationships between five major lipids, 249 circulating metabolites, and four diabetic retinopathy (DR) outcomes: overall DR, background DR, severe background DR, and proliferative DR (PDR). We aim to identify plasma proteins that mediate these causal effects, offering insights into potential therapeutic targets.

METHODS

We conducted metabolome-wide Mendelian randomization (MR) analyses to assess associations between major lipids, metabolites, and DR outcomes. Multivariable MR (MVMR) and proteome-wide mediated MR (two-step MR) analyses were performed to ensure robust evaluation and identify mediating plasma proteins.

RESULTS

Triglycerides were identified as a significant risk factor for DR, mediated by proteins like Dickkopf-3 (DKK3), ST6 N-acetylglucosamine transferase 6 (ST4S6), and Neogenin (NEO1). For background DR, HDL-C, specific VLDL particles, and LDL triglycerides were protective, mediated by proteins like chloride intracellular channel 5 (CLIC5), basal cell adhesion molecule (BCAM), and Ribophorin I (RPN1). Additionally, polyunsaturated fatty acids (PUFAs) and total choline were protective against PDR, mediated by Radical Fringe Gene (RFNG).

CONCLUSIONS

This study identifies specific plasma proteins that mediate the effects of lipids and metabolites on DR, establishing a direct molecular link between these biomarkers and disease progression. These findings enhance our understanding of the pathophysiological mechanisms underlying DR and highlight potential targets for therapeutic intervention.

Combining GWAS Summary Data and Proteomics Identified Potential Drug Targets in Dementia

Due to progressive cognitive loss and subsequent incapability of daily life, the development of novel therapeutics is urgently needed for dementia patients. We performed a two-sample bi-directional Mendelian randomization (MR) analysis using summary-level statistics to identify causality between peripheral and cerebrospinal fluid (CSF) proteins and the risk of dementia. Genetic variants were subtracted from the Genome-Wide Association Studies (GWAS) results. Wald ratio (WR) and inverse-variance weighted (IVW) ratio were utilized to estimate the causal effects of plasma and CSF proteins on dementia. Reverse MR, Steiger filtering, Bayesian co-localization phenotype scanning, and external validation were integrated to strengthen the robustness of primary MR results. After sensitivity analysis, six circulating proteins were identified in three dementia classifications, whereas no causality was found in frontotemporal dementia (FTD). Elevated levels of circulating C1R protein increased the odds of developing Alzheimer's disease (AD), while PILRA and CELA2A were estimated to protect against the pathogenesis of AD; genetically predicted increase of α-synuclein and APOE elevated the occurrence of Dementia of Lewy Bodies (DLB); elevated level of circulating CRP was assessed to increase the onset of vascular dementia (VD). Our MR analyses identified a genetically predicted association between circulating C1R, PILRA, and CELA2A and the risk of AD, causal estimates between α-syn, APOE protein, and the onset of DLB, and a robust correlation between CRP and the etiology of VD. This study might guide the discovery of disease etiology and build up a novel disease-modifying paradigm of dementia.

Mendelian Randomization Estimates the Effects of Plasma and Cerebrospinal Fluid Proteins on Intelligence, Fluid Intelligence Score, and Cognitive Performance

Observational studies have revealed associations between levels of plasma and cerebrospinal fluid (CSF) proteins and cognition-related traits. However, these associations may be influenced by confounding factors inherent in observational research. This study aims to identify plasma and CSF proteins associated with intelligence, fluid intelligence score, and cognitive performance through the application of Mendelian randomization (MR). Proteomic quantitative trait locus (pQTL) data for plasma and CSF proteins were sourced from existing genome-wide association study (GWAS). Intelligence, fluid intelligence score, and cognitive performance GWAS summary statistics provided comprehensive data for two-sample MR analysis. Extensive sensitivity analyses, including Steiger testing, reverse MR analysis, and Bayesian co-localization, were conducted to validate associations and identify shared genetic variants. Phenotype scanning explored potential pleiotropic effects. MR analysis identified several proteins in plasma and CSF significantly associated with intelligence, fluid intelligence scores, and cognitive performance. For intelligence, negatively associated proteins in plasma include endoplasmic reticulum aminopeptidase 2 (ERAP2) and secretogranin III (SCG3), while positively associated proteins are myeloperoxidase (MPO), signal regulatory protein alpha (SIRPA), regulator of microtubule dynamics 1 (RMDN1), and endoplasmic reticulum lectin 1 (ERLEC1). In CSF, C1-esterase inhibitor and carboxypeptidase E (CBPE) both exhibited positive associations with intelligence. For fluid intelligence scores, negatively associated proteins in plasma are copine 1 (CPNE1) and SCG3, while positively associated proteins are nudix hydrolase 12 (NUDT12) and RMDN1. In CSF, Macrophage Stimulating Protein (MSP) demonstrated a significant negative impact. For cognitive performance, negatively associated proteins in plasma include ERAP2, tyrosine kinase with immunoglobulin-like and EGF-like domains 1 (TIE1), and SCG3, while positively associated proteins are NUDT12, RMDN1, ERLEC1, and ectonucleotide pyrophosphatase/phosphodiesterase family member 5 (ENPP5). In CSF, C1-esterase inhibitor was positively associated, while MSP and soluble tyrosine kinase with immunoglobulin-like and EGF-like domains 1(sTie-1) showed a negative association. Bayesian co-localization analysis revealed significant genetic overlaps between SIRPA, RMDN1, and ERLEC1 in plasma with intelligence; NUDT12 and SCG3 in plasma with fluid intelligence scores; and TIE1, NUDT12, RMDN1, ERLEC1, and ENPP5 in plasma with cognitive performance. Additionally, significant co-localization was identified between C1-esterase inhibitor and CBPE in CSF with intelligence, as well as between C1-esterase inhibitor and sTie-1 in CSF with cognitive performance. Reverse causality analysis confirmed the causal direction from proteins to cognitive traits. This study identifies specific plasma and CSF proteins that significantly impact intelligence, fluid intelligence scores, and cognitive performance. These proteins could serve as biomarkers and targets for future research and therapeutic interventions aimed at sustaining cognitive abilities and reducing impairment risks.

Plasma proteomes and metabolism with genome-wide association data for causal effect identification in ovarian cancer

BACKGROUND

This study seeks to investigate the relationship between plasma metabolites or proteins and the risk of ovarian cancer through Mendelian randomization analysis and construct, while also developing a predictive model for resistance to chemotherapy.

METHODOLOGY/PRINCIPAL FINDINGS

Appropriate SNPs from GWAS data were selected as instrumental variables. Multiple methods, such as IVW, MR-Egger regression, and WME, were employed to investigate the causal relationship. A predictive model was established utilizing binary logistic regression based on the identified plasma protein genes. Four plasma metabolites and four plasma proteins were recognized as risk factors for ovarian cancer, whereas four plasma proteins were identified as protective factors. A predictive model for chemotherapy resistance was formulated with an AUC of 0.844 (p = 0.002).

CONCLUSIONS

Plasma metabolites and proteins may affect the risk of ovarian cancer and its resistance to chemotherapy. This study presents potential predictive factors and the underlying mechanisms influencing the onset, progression, and resistance of the disease.

Association between autoimmune disease and neurodevelopmental disorder: a Mendelian randomization analysis

INTRODUCTION

Neurodevelopmental disorders such as attention deficit and disruptive behaviour disorders (ADHD), autism spectrum disorder (ASD), and schizophrenia have been increasingly prevalent recently. Previous research has demonstrated that inflammatory activity from autoimmune diseases is involved in neurological diseases. However, some studies question the association between inflammatory activities and neurodevelopmental disorders. Herein, we attempt to clarify this relationship using Mendelian randomization (MR) analysis.

METHODS

We used systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), and type 1 diabetes mellitus (T1D) to represent autoimmune diseases. First, we conducted MR analysis to examine associated SNPs between autoimmune and neurodevelopmental disorders. Second, we performed bidirectional MR analysis to identify 429 types of signalling peptides and proteins or relevant receptors with causality reported diseases. Finally, we compared the genes with the gene loci identified in the available TWAS-hub site.

RESULTS

The MR results of autoimmune diseases on neurodevelopmental disorders did not present any significant association in all models. However, we identified 20-45 factors in ADHD, ASD, and schizophrenia, including semaphorin 3, IL-27 receptor subunit alpha, and fibroblast growth factor 16, which were considered clinically significant pro-inflammatory mediators. GO and KEGG enrichment analyses revealed unequal integrities among the three neurodevelopmental diseases, and we failed to identify a shared pathway linking autoimmune diseases and neurodevelopmental disorders. TWAS analysis indicated that CHRNA5 potentially mediates inflammatory activities in schizophrenia.

CONCLUSION

According to our data, we failed to identify an association between autoimmune diseases and neurodevelopmental disorders. However, we demonstrated that some pro-inflammatory factors are involved in neurodevelopmental disorders.

Unraveling the causal relationship and underlying mechanisms between cathepsins on liver cancer: findings from mendelian randomization and bioinformatics analysis

BACKGROUND

Hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA) are two major types of primary liver cancer (PLC). Earlier research has indicated a potential link between cathepsins and liver cancer. Nonetheless, there have been limited clinical trials examining the connection between cathepsins and PLC. Therefore, we conducted a two-sample Mendelian randomization (MR) study to evaluate the causal relationship between cathepsins and PLC.

METHODS

Data from genome-wide association studies (GWAS) focusing on cathepsins was collected. Additionally, summary data for GCST90018803 (Hepatic bile duct cancer, HBDC), and GCST90018858 (related to hepatic cancer, HC), were employed in the discovery and validation phases of the study, respectively. The inverse variance weighted (IVW) method was served as the primary analytical method in our Mendelian randomization (MR) study, supplemented by the MR-Egger, weighted median, simple mode, and weighted mode methods. To assess heterogeneity and pleiotropy, we conducted the MR-Egger intercept test, Cochran's Q test, as well as the MR-Pleiotropy RESidual Sum and Outlier (MR-PRESSO) analysis, along with the leave-one-out analysis. After that, bioinformatic analysis based on the Gene Expression Omnibus (GEO) databases were utilized, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis were utilized for exploring the underlying mechanisms. Additionally, protein-protein docking was employed to confirm the interaction between related proteins.

RESULTS

The results showed that cathepsin F (CTSF), was causally associated with HBDC. CTSF decrease the risk of HBDC (OR = 0.826, 95% CI 0.711-0.959, P = 0.012). CTSF may play protective roles in patients with HBDC. No heterogeneity or pleiotropy was observed. Additionally, the expression of CTSF genes is lower in patients with HBDC, GO and KEGG functional enrichment analysis revealed CTSF were mainly related to cell cycle, and P53 pathway in HBDC. Docking results showed that CTSF had good binding ability with MDM2, the most well-established negative regulator of p53.

CONCLUSION

This study provided new evidence of the relationship between CTSF and HBDC, suggesting that CTSF plays an inhibition role in HBDC progression. CTSF could be a novel and effective way to for HDBC treatment.

Finding Potential Drug Targets for Pre-Eclampsia Using Mendelian Randomisation and Colocalisation Analysis

INTRODUCTION

Pre-eclampsia (PE) is a common complication of pregnancy and there is an urgent need for new drug targets. We performed whole proteome-wide Mendelian randomisation (MR) and colocalisation analyses to identify potential therapeutic targets for PE.

MATERIAL AND METHODS

A two-sample MR study was conducted using summary-level statistics of 734 plasma proteins retrieved from large genome-proteome-wide association studies. The summary statistics of PE or eclampsia were obtained from the FinnGen consortium. Wald ratio and Inverse variance weighted (IVW) were used to assess the causal association between proteins and PE. Colocalisation analyses were conducted to examine whether the identified proteins and PE shared incidental variants.

RESULTS

Genetically predicted circulating levels of 42 proteins were associated with PE risk after Benjamini-Hochberg correction. Nineteen of the gene-predicted proteins showed evidence of increased PE risk (CRELD1, CPA4, AHSG, NFASC, QDPR, NTM, PZP, FAM171B, RTN4R, FLRT2, ADH4, ADM, SPINK5, LGALS4, CKM, SPON2, UROS, CXCL10 and APOBEC3G); 23 proteins reduced the risk of PE (CLIC5, NEO1, SWAP70, KLK8, VWA2, FSTL1, CXCL11, APOB, NPPB, CNTN4, IL12B, ACHE, TCN1, GFRA2, GNMT, HPGDS, DPT, MANBA, SPARCL1, ACE, FUT8, BST1 and ACP1). Bayesian colocalisation indicated that six proteins (VWA2, ACHE, CXCL10, PZP, AHSG and UROS) and PE, which were identified as high evidence of colocalisation with PE.

CONCLUSIONS

This study provides evidence of the causal association between genetically predicted 42 proteins associated with PE risk, which might be promising drug targets for PE.

Identification of potential therapeutic targets for Alzheimer's disease from the proteomes of plasma and cerebrospinal fluid in a multicenter Mendelian randomization study

BACKGROUND

Certain peripheral proteins are believed to be involved in the development of Alzheimer's disease (AD), but the roles of other new protein biomarkers are still unclear. Current treatments aim to manage symptoms, but they are not effective in stopping the progression of the disease. New drug targets are needed to prevent Alzheimer's disease.

METHODS

We used Mendelian randomization (MR) to study drug targets for Alzheimer's disease. We analyzed data from the European Alzheimer's and Dementia Biobank consortium and replicated our findings in GWAS data from IGAP and FinnGen cohorts. We identified genetic instruments for plasma and cerebrospinal fluid (CSF) proteins and conducted sensitivity analyses using various methods. Additionally, a comparison and analysis of protein-protein interactions (PPI) were conducted to identify potential causal proteins. The implications of these findings were further explored through an examination of existing AD drugs and their respective targets.

RESULTS

Through MR analysis, 10 protein AD pairs were identified as statistically significant at the Bonferroni level (P < 6.35 × 10-5). The specific findings indicate that elevated levels of plasma cathepsin H (CTSH) (OR = 1.06, 95%CI: 1.03-1.08, p = 6.12 × 10-6), plasma signal regulatory protein alpha (SIRPA) (OR = 1.03, 95%CI: 1.02-1.05, p = 1.37 × 10-5), plasma TMEM106B (OR = 1.16, 95%CI: 1.09-1.23, p = 1.92 × 10-6), and CSF bone sialoprotein (BSP) (OR = 1.33, 95%CI: 1.17-1.51, p = 9.34 × 10-6), CSF Interleukin-34 (IL-34) (OR = 2.13, 95%CI: 1.51-3.01, p = 1.85 × 10-5), CSF immunoglobulin-like transcript 2 (ILT-2) (OR = 1.33, 95%CI: 1.17-1.51, p = 9.34 × 10-6) are associated with an increased risk of AD, while increased levels of plasma progranulin gene (GRN) (OR = 0.79, 95%CI: 0.74-0.84, p = 2.19 × 10-12), plasma triggering receptor expressed on myeloid cells 2 (TREM2) (OR = 0.67, 95%CI: 0.58-0.78, p = 6.95 × 10-8), plasma sialic acid-bind immunoglobulin-like lectins (SIGLEC)-9 (OR = 0.67, 95%CI: 0.58-0.78, p = 6.95 × 10-8), and CSF SIGLEC7 (OR = 0.42, 95%CI: 0.28-0.64, p = 4.30 × 10-5) are associated with a decreased risk of AD. Bayesian colocalization found that the above protein-related genes shared the same mutation as AD.

CONCLUSION

Increased levels of plasma CTSH, SIRPA, TMEM106B, CSF BSP, CSF IL-34, and CSF ILT-2 have been found to be correlated with an elevated risk of AD, whereas elevated levels of plasma GRN, TREM2, SIGLEC9, and CSF SIGLEC7 are associated with a decreased risk of developing AD. Further investigation through clinical trials is needed.

Potential drug targets for ovarian cancer identified through Mendelian randomization and colocalization analysis

BACKGROUND

The existing drugs for ovarian cancer (OC) are unsatisfactory and thus new drug targets are urgently required. We conducted proteome-wide Mendelian randomization (MR) and colocalization analysis to pinpoint potential targets for OC.

METHODS

Data on protein quantitative trait loci (pQTL) for 734 plasma proteins were obtained from large genome-proteome-wide association studies. Genetic associations with OC were derived from the Ovarian Cancer Association Consortium, which included 25,509 cases and 40,941 controls. MR analysis was performed to evaluate the association between the proteins and the OC risk. Colocalization analysis was conducted to check whether the identified proteins and OC shared causal variants. In addition, the phenome-wide MR analysis was performed to clarify protein associations across the phenotype, and drug target databases were examined for target validation.

RESULTS

Genetically predicted circulating levels of 44 proteins were associated with OC risk at Benjamini-Hochberg correction. Genetically predicted 17 proteins had evidence of the increased risk of OC (CLEC11A, MFAP2, TYMP, PDIA3, IL1R1, SPINK1, PLAU, DKK2, IL6ST, DLK1, LRRC15, CDON, ANGPTL1, SEMA4D, AKR1A1, TNFAIP6, and FCGR2B); 27 proteins decreased the risk of OC(SIGLEC9, RARRES1, SPINT3, TMEM132A, HAVCR2, CNTN2, TGFBI, GSTA1, HGFAC, TREML2, GRAMD1C, ASAH2, CPNE1, CCL25, MAPKAPK2, POFUT1, PREP, NTNG1, CA10, CACNA2D3, CA8, MAN1C1, MRC2, IL10RB, RBP4, GP5 and CALCOCO2). Bayesian colocalization demonstrated that GRAMD1C, RBP4, PLAU, PDIA3, MFAP2, POFUT1, MAN1C1 and DKK2 shared the same variant with OC. The phe-MR analyses assessed the side effects of these 44 identified proteins, and the drug target database offered information on both approved and investigational indications.

CONCLUSION

This study provides proof of a causal relationship between genetically predicted 44 proteins associated with OC risk, which could serve as promising drug targets for OC.

Potential drug targets for systemic lupus erythematosus identified through Mendelian randomization analysis

So far, there is no clear pathogenesis and no cure for systemic lupus erythematosus (SLE). The therapeutic benefits of existing drug therapies are far from ideal. The proteome is a major source of therapeutic targets. Therefore, new drug targets for SLE need to be discovered. Based on the STROBE-Mendelian randomization (MR) checklist, we performed MR to explore potential drug targets for SLE, using genome-wide association study summary statistics of plasma and cerebrospinal fluid (CSF) and further replicated in the external validation. Bidirectional MR, reverse causality testing by Steiger filtering, Bayesian co-localization were used. In addition, protein-protein interaction networks (PPI) were performed to reveal potential associations between proteins and current SLE drugs. At false discovery rate (FDR) significance (PFDR < .05), MR analysis revealed 8 proteins. Five proteins decreased the SLE risks, whereas the other 3 proteins increased the SLE risks. None of the 8 proteins had reverse causality except sICAM-1. Bayesian co-localization suggested that 5 proteins shared the same variant with SLE. PPI network suggested that intercellular adhesion molecular 1 (ICAM-1), Fc-gamma-RIIb (FCG2B) and N-terminal pro-B-type natriuretic peptide (N-terminal pro-BNP) interacted with targets of current SLE medications. Our integrative analysis revealed that SLE risk is causally associated with ICAM-1, FCG2B, and N-terminal pro-BNP. These 3 proteins have the potential to become drug targets of SLE, especially for ICAM-1 and FCG2B. More further studies are also warranted to support this finding.

Association Analysis of the Circulating Proteome With Sarcopenia-Related Traits Reveals Potential Drug Targets for Sarcopenia

BACKGROUND

Sarcopenia severely affects the physical health of the elderly. Currently, there is no specific drug available for sarcopenia. This study aims to identify pathogenic proteins and druggable targets for sarcopenia through Mendelian randomization (MR)-based analytical framework.

METHODS

A sequential stepwise screening method that includes two-sample MR, Steiger filtering test and colocalization (MRSC) was applied to identify causal proteins associated with sarcopenia-related traits. In the MR analyses, 4372 circulating proteins with valid instrumental variables (IVs) from eight proteomic genome-wide association studies were utilized as exposures, and nine sarcopenia-related traits were utilized as outcomes. IVs were classified into cis-protein quantitative trait loci (pQTLs) and trans-pQTLs based on their positions. We conducted cis-only MRSC analyses and cis + trans MRSC analyses using cis-pQTLs and cis + trans pQTLs as IVs, respectively. Post-MRSC analyses were conducted on the prioritized findings of MRSC, including annotation of protein-altering variants (PAVs), assessment of overlap between pQTLs and expression quantitative trait loci (eQTLs), protein-protein interaction (PPI) analysis, pathway enrichment analysis and annotation of drug targets. Utilizing data from the UK Biobank, we performed an observational study to explore the associations between baseline circulating protein levels and the longitudinal changes in nine sarcopenia-related traits.

RESULTS

A total of 181 causal associations for 65 proteins were prioritized by the cis-only MRSC analyses and 227 associations for 91 proteins were prioritized by the cis + trans MRSC analyses. Among the prioritized proteins, the majority of them employed non-PAVs as IVs and most of their cis-pQTLs overlapped with corresponding eQTLs and exhibited consistent directionality, with only one trans-pQTL overlapping with an eQTL. The PPI network of cis-only MRSC-prioritized proteins (p = 4.04 × 10-4) and cis + trans MRSC-prioritized proteins (p = 8.76 × 10-5) showed significantly more interactions than expected. Reactome, KEGG and GO pathway enrichment analyses for cis-only MRSC-prioritized proteins identified 52, 12 and 79 enriched pathways, respectively (adjusted p < 0.05). For proteins identified by cis + trans MRSC analyses, only 15 pathways were enriched through the GO pathway enrichment analyses. In the observational study, 197 circulating proteins were identified to be associated with one or more sarcopenia-related traits (p < 0.05/2923). Among them, the significant associations of CTSB (negative association) and ASGR1 (positive association) with sarcopenia-related traits were observed to have consistent directional associations in both MR-based studies and observational studies. Drug target annotations suggested that 52 MRSC-prioritized proteins and 145 biomarkers are drug targets or druggable.

CONCLUSIONS

This study identified 89 potential pathogenic proteins and 197 candidate biomarkers for sarcopenia, providing valuable clues for the development of therapeutic drugs for sarcopenia.

Identification of Circulating Proteins Associated With Blood Pressure

BACKGROUND

Circulating proteins in blood are involved in various physiological processes, but their contributions to blood pressure regulation remain partially understood. In traditional observational studies, identifying circulating proteins causally associated with blood pressure is challenging because of potentially unmeasured confounding and possible reverse causality.

METHODS

Two-sample Mendelian randomization analyses were conducted to estimate the causal effects of 2270 circulating proteins (data sourced from 8 genome-wide association studies) on diastolic blood pressure, systolic blood pressure, and pulse pressure. Colocalization analyses were then used to investigate whether the circulating proteins and blood pressure traits shared causal genetic variants. To further verify the findings, we subsequently performed Steiger filtering analyses, annotation of protein-altering variants, assessment of overlap between protein quantitative trait loci and expression quantitative trait loci, protein-protein interaction and functional enrichment analyses, and drug target evaluation. To provide more potential biomarkers, we further evaluated the epidemiological associations of 2923 circulating proteins with blood pressure and hypertension by cross-sectional and longitudinal analyses using individual data in the UK Biobank.

RESULTS

Mendelian randomization and colocalization analyses identified 121 circulating proteins with putative causal effects on at least 1 blood pressure trait. Many of the identified proteins are enriched in the pathways relevant to blood pressure regulation, and a majority of these proteins are either known drug targets or druggable candidates.

CONCLUSIONS

This study has uncovered numerous circulating proteins potentially causally associated with blood pressure, providing insights into the regulatory mechanisms of blood pressure and potential therapeutic targets to facilitate blood pressure management.

Plasma Proteomes and Genome-Wide Association Data for Causal Protein Identification in Stroke

Plasma proteins are promising biomarkers and potential drug targets for stroke. This study aimed to explore whether there is a causal relationship between plasma proteins and subtypes of stroke using a Mendelian randomization (MR) approach. A two-sample bidirectional Mendelian randomization approach was employed to investigate the causal link between plasma proteins and stroke. Data on plasma proteins were obtained from three studies, including INTERVAL, and pooled stroke information was sourced from the MEGASTROKE consortium and the UK Biobank dataset, covering four subtypes of stroke. MR analyses were primarily conducted using inverse variance weighting, and sensitivity analyses were also performed. Finally, potential reverse causality was assessed using bidirectional MR. We identified two proteins causally associated with stroke: one as a potential therapeutic target and another as a protective factor. CXCL8 was found to be positively associated with the risk of developing large-artery atherosclerotic (LAA) stroke (OR, 1.005; 95% CI 1.001 to 1.010; p = 0.022), whereas TNFRSF11b was negatively correlated with the risk of developing LAA stroke (OR, 0.937; 95% CI 0.892 to 0.984; p = 0.010), independently of other stroke subtypes. Reverse bivariate analysis did not indicate that ischemic stroke was causally associated with CXCL8 and TNFRSF11b. There is a causal relationship between CXCL8 and TNFRSF11b with LAA stroke, independent of other subtypes. This study offers a new perspective on the genetics of stroke.

The Causal Relationships and Therapeutic Targets of Plasma Proteins in Ankylosing Spondylitis

Objective: The purpose of this study was to assess the causal effects of circulating plasma proteins on ankylosing spondylitis (AS) and to explore potential therapeutic targets. Methods: The study used protein quantitative trait loci (pQTLs) for thousands of plasma proteins from nine genome-wide association studies (GWAS) as instrumental variables. The relationship between genetically predicted plasma proteins and AS was assessed through Mendelian randomization (MR) analysis. Further analyses, including colocalization analysis, Steiger filtering analysis, protein-altering variant assessment, protein-protein interaction (PPI), and pathway enrichment analysis, were conducted to validate the robustness and causal direction of the results, as well as to investigate the protein functions and potential drug targets. Results: Nine unique proteins were found to have strong causal associations with AS. Steiger filtering analysis confirmed that all associations identified by MR analysis have a direct causal link from the proteins to AS. Colocalization analysis identified four unique proteins-Interleukin-6 receptor alpha (IL-6Rα), Interleukin-23 receptor (IL-23R), Thrombospondin-2 (THBS2), and Interleukin-1 receptor type 2 (IL-1R2)-that share the same causal variants with AS. PPI and pathway enrichment analysis revealed the potential roles of these proteins in inflammatory responses and immune regulation. Moreover, these proteins were valuable drug targets or considered druggable. Conclusions: This study has identified multiple plasma proteins associated with AS, revealing the important roles of these proteins in the pathogenesis of AS and providing potential therapeutic targets for AS.

The effect of coagulation traits on the risk of retinal vein occlusion: a mendelian randomization study

Retinal vein occlusion (RVO) is the leading cause of vision loss due to an obstruction in the retinal venous system. While RVO is often linked to thrombotic tendencies and coagulation abnormalities, the exact role of coagulation traits in its development is not fully understood. This study aims to investigate the potential causal relationship between coagulation traits and the risk of RVO by analyzing publicly available genome-wide association study (GWAS) summary statistics. A two-sample Mendelian randomization (MR) analysis framework was employed to investigate the causal relationship between coagulation traits and the risk of RVO. Stringent quality control measures were applied to select appropriate instrumental variables strongly linked to exposure, such as coagulation factor III (FIII), coagulation factor V (FV), coagulation factor VIII (FVIII), coagulation factor XI (FXI), coagulation factor VII (FVII) and coagulation factor X (FX), as well as plasmin, platelet count, platelet crit (PCT), mean platelet volume (MPV), and platelet distribution width (PDW). The study utilized the FinnGen project RVO GWAS summary statistics cohort, consisting of 372 RVO cases and 182,573 controls. The analysis focused on 11 coagulation traits. The research suggests that genetically predicted plasma levels of FIII, FVII, MPV, and PCT may be potentially causative for reducing the risk of RVO, and that levels of FVIII may be potentially causative for increasing the risk of RVO. Our MR analysis, utilizing GWAS data from a comprehensive population-based study, revealed a causal association between plasma levels of FIII, FVII, FVIII, MPV, and PCT with the risk of RVO.

Identification of potential druggable targets for endometriosis through Mendelian randomization analysis

Introduction

Endometriosis (EM) is a widely recognized disorder in gynecological endocrinology. Although hormonal therapies are frequently employed for EM, their side effects and outcome limitations underscore the need to explore the genetic basis and potential drug targets for developing innovative therapeutic approaches. This study aimed to identify both cerebrospinal fluid (CSF) and plasma protein markers as promising therapeutic targets for EM.

Methods

We utilized Mendelian randomization (MR) analysis to explore potential disease-causing proteins, utilizing genetic datasets from genome-wide association studies (GWAS) and protein quantitative trait loci (pQTL) analyses. We applied a range of validation techniques, including reverse causality detection, phenotype scanning, Bayesian co-localization (BC) analysis, and external validations to substantiate our findings. Additionally, we conducted a protein-protein interaction (PPI) network as well as functional enrichment analyses to unveil potential associations among target proteins.

Results

MR analysis revealed that a decrease of one standard deviation (SD) in plasma R-Spondin 3 (RSPO3) level had a protective effect on EM (OR = 1.0029; 95% confidence interval (95% CI): 1.0015-1.0043; P = 3.2567e-05; Bonferroni P < 5.63 × 10-5). BC analysis showed that RSPO3 shared the same genetic variant with EM (coloc.abf-PPH4 = 0.874). External validation further supported this causal association. Galectin-3 (LGALS3; OR = 0.9906; 95% CI: 0.9835-0.9977; P = 0.0101), carboxypeptidase E (CPE; OR = 1.0147; 95% CI: 1.0009-1.0287; P = 0.0366), and alpha-(1,3)-fucosyltransferase 5 (FUT5; OR = 1.0053; 95% CI: 1.0013-1.0093; P = 0.002) were detected as potential targets for EM in CSF. PPI analysis showed that fibronectin (FN1) had the highest combined score. Furthermore, several EM-linked proteins were involved in the glycan degradation pathway.

Discussion

In conclusion, this comprehensive study offers valuable insights into potential drug targets for EM, with RSPO3 emerging as a promising candidate. Additionally, mechanistic roles of FN1, glycan degradation pathway, LGALS3, CPE, and FUT5 in EM warrant further investigation.

Effects of the maternal and fetal proteome on birth weight: a Mendelian randomization analysis

Background

Fetal growth is an important indicator of survival, regulated by maternal and fetal genetic and environmental factors. However, little is known about the underlying molecular mechanisms. Proteins play a major role in a wide range of biological processes and could provide key insights into maternal and fetal molecular mechanisms regulating fetal growth.

Method

We used intergenerational two-sample Mendelian randomization to explore the effects of 1,139 maternal and fetal genetically-instrumented plasma proteins on birth weight. We used genome-wide association summary data from the Early Growth Genetics (EGG) consortium (n=406,063 with maternal and/or fetal genotype), with independent replication in the Norwegian Mother, Father and Child Cohort Study (MoBa; n=74,932 mothers and n=62,108 offspring). Maternal and fetal data were adjusted for the correlation between fetal and maternal genotype, to distinguish their independent genetic effects.

Results

We found that higher genetically-predicted maternal levels of NEC1 increased birth weight (mean-difference: 12g (95% CI [6g, 18g]) per 1 standard deviation protein level) as did PRS57 (20g [10g, 31g]) and ULK3 (140g [81g, 199g]). Higher maternal levels of Galectin_4 decreased birth weight (-206g [-299g, -113g]). In contrast, in the offspring, higher genetically-predicted offspring levels of NEC1 decreased birth weight (-10g [-16g, -5g]), alongside sLeptin_R (-8g [-12g, -4g]), and UBS3B (-78g [-116g, -41g]). Higher fetal levels of Galectin_4 increased birth weight (174g [89g, 258g]). We replicated these results in MoBa, and found supportive evidence for shared causal variants from genetic colocalization analyses and protein-protein network associations.

Conclusions

We find strong evidence for causal effects, sometimes in opposing directions, of maternal and fetal genetically-instrumented proteins on birth weight. These provide new insights into maternal and fetal molecular mechanisms regulating fetal growth, involving glucose metabolism, energy balance, and vascular function that could be used to identify new intervention targets to reduce the risk of fetal growth disorders, and their associated adverse maternal and fetal outcomes.

Proteome-wide mendelian randomization identifies causal plasma proteins in interstitial lung disease

Interstitial lung disease (ILD) has shown limited treatment advancements, with minimal exploration of circulating protein biomarkers causally linked to ILD and its subtypes beyond idiopathic pulmonary fibrosis (IPF). In this study, we aimed to identify potential drug targets and circulating protein biomarkers for ILD and its subtypes. We utilized the most recent large-scale plasma protein quantitative trait loci (pQTL) data detected from the antibody-based method and ILD and its subtypes' GWAS data from the updated FinnGen database for Mendelian randomization analysis. To enhance the reliability of causal associations, we conducted external validation and sensitivity analyses, including Bayesian colocalization and bidirectional Mendelian randomization analysis. Our study identified eight plasma proteins genetically associated with ILD or its subtypes. Among these, three proteins-CDH15 (Cadherin-15), LTBR (Lymphotoxin-beta receptor), and ADAM15 (A disintegrin and metalloproteinase 15)-emerged as priority biomarkers and potential therapeutic targets, demonstrating more reliable associations by passing a series of sensitivity analyses compared to the others. Based on these findings, we propose for the first time that CDH15, ADAM15, and LTBR hold promise as novel potential circulating protein biomarkers and therapeutic targets for the diagnosis and treatment of ILD, IPF, and sarcoidosis, respectively, especially ADAM15, and these findings have the potential to provide new perspectives for advancing the research on the heterogeneity of ILD.

Potential drug targets for asthma identified through mendelian randomization analysis

BACKGROUND

The emergence of new molecular targeted drugs marks a breakthrough in asthma treatment, particularly for severe cases. Yet, options for moderate-to-severe asthma treatment remain limited, highlighting the urgent need for novel therapeutic drug targets. In this study, we aimed to identify new treatment targets for asthma using the Mendelian randomization method and large-scale genome-wide association data (GWAS).

METHODS

We utilized GWAS data from the UK Biobank (comprising 56,167 patients and 352,255 control subjects) and the FinnGen cohort (including 23,834 patients and 228,085 control subjects). Genetic instruments for 734 plasma proteins and 154 cerebrospinal fluid proteins were derived from recently published GWAS. Bidirectional Mendelian randomization analysis, Steiger filtering, colocalization, and phenotype scanning were employed for reverse causal inference detection, further substantiating the Mendelian randomization results. A protein-protein interaction network was also constructed to reveal potential associations between proteins and asthma medications.

RESULTS

Under Bonferroni significance conditions, Mendelian randomization analysis revealed causal relationships between seven proteins and asthma. In plasma, we observed that an increase of one standard deviation in IL1R1[1.30 (95% CI 1.20-1.42)], IL7R[1.07 (95% CI 1.04-1.11)], ECM1[1.03 (95% CI 1.02-1.05)], and CD200R1[1.18 (95% CI 1.09-1.27)] were associated with an increased risk of asthma, while an increase in ADAM19 [0.87 (95% CI 0.82-0.92)] was found to be protective. In the brain, each 10-fold increase in IL-6 sRa [1.29 (95% CI 1.15-1.45)] was associated with an increased risk of asthma, while an increase in Layilin [0.61 (95% CI 0.51-0.73)] was found to be protective. None of the seven proteins exhibited a reverse causal relationship. Colocalization analysis indicated that ECM1 (coloc.abf-PPH4 = 0.953), IL-6 sRa (coloc.abf-PPH4 = 0.966), and layilin (coloc.abf-PPH4 = 0.975) shared the same genetic variation as in asthma.

CONCLUSION

A causal relationship exists between genetically determined protein levels of IL1R1, IL7R, ECM1, CD200R1, ADAM19, IL-6 sRa, and Layilin (LAYN) and asthma. Moreover, the identified proteins may serve as attractive drug targets for asthma, especially ECM1 and Layilin (LAYN). However, further research is required to comprehensively understand the roles of these proteins in the occurrence and progression of asthma.

Revealing potential drug targets in schizophrenia through proteome-wide Mendelian randomization genetic insights

BACKGROUND

Schizophrenia (SCZ) is a severe, chronic mental disorder with no current cure. Identifying novel pharmacological targets is crucial for developing more effective treatments.

METHODS

We performed two-sample Mendelian randomization (MR) analyses to estimate the associations between cerebrospinal fluid (CSF) containing 154 proteins and plasma containing 734 proteins and risk of SCZ. Bidirectional MR analysis, steiger filtering, bayesian colocalization, phenotypic scanning, and validation analysis were examined to validate the assumptions of MR. For proteins significantly associated with SCZ identified by MR, we explored their potential impact on brain structures, including cortical surface area (SA), thickness (TH), and the volume of subcortical structures.

RESULTS

MR analysis identified 13 protein-SCZ pairs at Bonferroni significance (P < 5.63 × 10-5). Notably, the genetically proxied protein level of neuromedin B (NMB) was associated with an increased risk for SCZ (odds ratio [OR] = 1.41; 95 % CI, 1.27 to 1.58; P = 6.68 × 10-10). Bayesian colocalization suggested that NMB shares genetic variations with SCZ. Further, NMB interacts with target proteins of current SCZ drugs and was validated in the UK Biobank. The genetically proxied NMB was positively associated with an increase in the surface area (SA) of the parahippocampal gyrus (β = 8.93 mm2, 95 % CI, 1.58 to 16.3, P = .02). Additionally, an increase in the genetically proxied SA of the parahippocampal gyrus was inversely associated with the risk of SCZ (OR = 0.996, 95 % CI, 0.993 to 0.999, P = .04).

CONCLUSIONS

The findings suggest that NMB may represent a promising target for pharmacological intervention in SCZ. This warrants further investigation into the specific constituents involved, which could have potential for follow-up studies.

Identification of Drug-Targetable Genes for Eczema and Dermatitis Using Integrated Genomic and Proteomic Approaches

Background: Eczema and dermatitis are common inflammatory skin conditions with significant morbidity. Identifying drug-targetable genes can facilitate the development of effective treatments. Methods: This study analyzed data obtained by meta-analysis of 2 genome-wide association studies on eczema/dermatitis (57,311 cases and 896,779 controls, European ancestry). We identified drug-targetable genes from the Drug-Gene Interaction Database and Finan et al's findings. Cis-expression quantitative trait loci (eQTL) data from human blood and skin tissues were used for Mendelian randomization (MR) analysis. Bayesian colocalization, proteomic MR, and meta-analysis validated the causal relationships. Finally, protein-protein interactions (PPIs) and correlation analysis of potential drug targets and cytokines were performed. Results: We identified 2532 drug-targetable genes; 3378 Single Nucleotide Polymorphism (SNPs) were associated with 1531 genes in blood cis-eQTLs, 664 SNPs with 667 genes in sun-exposed skin eQTLs, and 572 SNPs with 574 genes in nonsun-exposed skin eQTLs. Five genes (SLC22A5, NOTCH4, AGER, HLA-DRB5, and EHMT2) showed causal relationships with eczema/dermatitis across multiple datasets. Single-variable and multi-variable Mendelian randomization (SMR) and multi-SNP SMR analysis identified 8 genes (PIK3R4, DHODH, CXCR2, Interleukin (IL)18, LGALS9, RPS6KB2, SLC22A5, and AGER) across all tissues. Functional Summary Information for Variants in the Online Network (FUSION) analysis confirmed associations for SLC22A5 and AGER. Bayesian colocalization indicated AGER (PPH4: 0.95) as a shared causal variant. Proteomic MR and meta-analysis showed that increased AGER protein levels were associated with a lower risk of eczema or dermatitis (odds ratio: 0.995, 95% confidence interval: 0.997-0.993, P = 0.0002). A PPI network revealed interactions of AGER with NOTCH4 and multiple cytokines, whereas SLC22A5 showed no cytokine interactions. Conclusions: This study identified potential drug-targetable genes, with AGER showing strong potential as a target for reducing eczema/dermatitis risk. These findings provide a basis for developing targeted therapies.

Exploration of potential drug targets for Glaucoma by plasma proteome screening

BACKGROUND

Glaucoma is the leading cause of irreversible blindness. However, the current available treatment methods are still unsatisfactory. Therefore, the exploration of new drug targets for the treatment of glaucoma is of paramount importance.

METHODS

We conducted two-sample Mendelian randomization (MR) using plasma protein quantitative trait loci (pQTL) data from two datasets (n = 734, n = 4907) and their instrumental variables to investigate the causal relationship between plasma proteins and glaucoma. The analysis was validated by replacing the exposure and outcome cohorts. Additionally, we utilized protein-protein interaction networks to assess the associations between these potential drug targets and existing drug targets.

RESULTS

Through two-sample Mendelian randomization analysis, we identified causal relationships between Glaucoma and the following proteins: AZU1, OBP2B, ENPP5, INPP5B, KREMEN1, LYPLAL1, and PTPRJ. External validation confirmed the protective effect of LYPLAL1 on Glaucoma, while ENPP5, KREMEN1, and PTPRJ increased the risk of Glaucoma. Reverse MR and Steiger filtering did not indicate any reverse causal associations of the aforementioned proteins with Glaucoma.

CONCLUSION

Our study demonstrates a causal impact of ENPP5, KREMEN1, PTPRJ, and LYPLAL1 on the risk of Glaucoma. These findings suggest that these four proteins may serve as promising drug targets for Glaucoma treatment.

SIGNIFICANCE

Currently, the pharmacological treatment of glaucoma primarily focuses on lowering intraocular pressure, which has its limitations. Targeted therapy is a personalized treatment approach that aims to inhibit or block the development and progression of diseases such as cancer and inflammation by selectively acting on specific biomolecules or signaling pathways. Our research employs a two-sample Mendelian randomization (MR) method, integrating a large amount of GWAS and pQTL data to perform MR analysis. This has enabled us to explore several plasma proteins as potential drug targets for glaucoma, providing direction and a research foundation for future investigations into glaucoma drug targets.

DMRdb: a disease-centric Mendelian randomization database for systematically assessing causal relationships of diseases with genes, proteins, CpG sites, metabolites and other diseases

Exploring the causal relationships of diseases with genes, proteins, CpG sites, metabolites and other diseases is fundamental to the life sciences. However, large-scale research using Mendelian randomization (MR) analysis is currently lacking. To address this, we introduce DMRdb (http://www.inbirg.com/DMRdb/), a disease-centric Mendelian randomization database, designed to systematically assess causal relationships of diseases with genes, proteins, CpG sites, metabolites and other diseases. The database consists of three main components: (i) 6640 high-quality disease genome-wide association studies (GWASs) from public sources that were subjected to rigorous quality filtering and standardization; (ii) over 497 billion results from MR analyses involving 6640 disease GWAS datasets, 16 238 expression quantitative trait loci (eQTLs) data, 2564 protein quantitative trait loci (pQTLs) data, 12 000 methylation quantitative trait locus (meQTLs) data and 825 metabolites data and (iii) over 380 000 causal relationship pairs from 1223 literature sources relevant to MR analyses. A user-friendly online database was developed to allow users to query, search, and download all the results. In summary, we anticipate that DMRdb will be a valuable resource for advancing our understanding of disease mechanisms and identifying new biomarkers and therapeutic targets.

Evaluating the Causal Effect of Circulating Proteome on Glycemic Traits: Evidence From Mendelian Randomization

Exploring the mechanisms underlying abnormal glycemic traits is important for deciphering type 2 diabetes and characterizing novel drug targets. This study aimed to decipher the causal associations of circulating proteins with fasting glucose (FG), 2-h glucose after an oral glucose challenge (2hGlu), fasting insulin (FI), and glycated hemoglobin (HbA1c) using large-scale proteome-wide Mendelian randomization (MR) analyses. Genetic data on plasma proteomes were obtained from 10 proteomic genome-wide association studies. Both cis-protein quantitative trait loci (pQTLs) and cis + trans-pQTLs MR analyses were conducted. Bayesian colocalization, Steiger filtering analysis, assessment of protein-altering variants, and mapping expression QTLs to pQTLs were performed to investigate the reliability of the MR findings. Protein-protein interaction, pathway enrichment analysis, and evaluation of drug targets were performed. Thirty-three proteins were identified with causal effects on FG, FI, or HbA1c but not 2hGlu in the cis-pQTL analysis, and 93 proteins had causal effects on glycemic traits in the cis + trans-pQTLs analysis. Most proteins were either considered druggable or drug targets. In conclusion, many novel circulating protein biomarkers were identified to be causally associated with glycemic traits. These biomarkers enhance the understanding of molecular etiology and provide insights into the screening, monitoring, and treatment of diabetes.

ARTICLE HIGHLIGHTS

Genetic Associations Among Inflammation, White Matter Architecture, and Extracellular Free Water

Phenotypic and genetic relationships between white matter microstructure (i.e., fractional anisotropy [FA]) and peripheral inflammatory responses (i.e., circulating cytokines) have important implications for health and disease. However, it is unclear whether previously discovered genetic correlations between the two traits are due to tissue-specific white matter architecture or increased free water in the extracellular space. We applied a two-compartment model to diffusion tensor imaging (DTI) data and estimated tissue-specific white matter microstructure (FAT) and free water volume (FW). We then quantified their heritability and their genetic correlations with two peripherally circulating proinflammatory cytokines (IL-8 and TNFα), and compared these correlations to those obtained using traditional FA measures from one-compartment DTI models. All DTI and cytokine measures were significantly moderately heritable. We confirmed phenotypic and genetic correlations between circulating cytokine levels and single-compartment FA across the brain (IL-8: ρp = -0.16, FDRp = 4.8 × 10-07; ρg = -0.37 (0.12), FDRp = 0.01; TNFα: ρp = -0.15, FDRp = 2.4 × 10-07; ρg = -0.34 (0.12), p = 0.01). However, this relationship no longer reached significance when FA measures were derived using the two-compartment DTI model (IL-8: ρp = -0.04, FDRp = 0.17; ρg = -0.14 (0.13), FDRp = 0.29; TNFα: ρp = -0.05, FDRp = 0.10; ρg = -0.22 (0.13), FDRp = 0.10). There were significant phenotypic and genetic correlations between FW and both IL-8 (ρp = 0.19, FDRp = 2.1 × 10-10; ρg = 0.34 (0.11), FDRp = 0.01) and TNFα (ρp = 0.16, FDRp = 1.89 × 10-07; ρg = 0.30 (0.12), FDRp = 0.02). These results have important implications for understanding the mechanisms linking the two phenomena, but they also serve as a cautionary note for those examining associations between white matter integrity using single-compartment models and inflammatory processes.

Causal effects of circulating inflammatory proteins on knee and hip osteoarthritis: A two sample Mendelian randomization study

INTRODUCTION

Numerous circulating proteins are linked to the presence or severity of joint inflammation. However, traditional studies could not explain whether these protein biomarkers are proximate to disease progression.

METHOD

We conducted a study to explore the causal effects of 91 circulating inflammation-related proteins (CIPs) on knee osteoarthritis (KOA) and hip osteoarthritis (HOA), using two-sample Mendelian randomization (MR). The primary analysis utilized the inverse variance weighted (IVW) method, augmented by complementary approaches including weighted median, weighted mode, simple median, MR-Egger, and MR-PRESSO analysis. Sensitivity analysis validated the robustness of the results and ensured the absence of heterogeneity and horizontal pleiotropy.

RESULTS

We identified 2 CIPs with a causal effect on KOA, including CXCL9 (OR = 1.249, 95% CI = 1.046-1.492, P = 0.014) and TNF-β (OR = 1.105, 95% CI = 1.014-1.204, P = 0.023). Additionally, 3 CIPs were found to have a causal effect on HOA, including CXCL6 (OR = 1.058, 95% CI = 1.004-1.116, P = 0.035), RANKL (OR = 1.067, 95% CI = 1.002-1.137, P = 0.044), and VEGFA (OR = 1.072, 95% CI = 1.008-1.140, P = 0.027).

CONCLUSIONS

In the current study, our findings indicated that CXCL9 and TNF-β had the potential to influence the risk of KOA, while CXCL6, RANKL, and VEGFA could impact the risk of HOA. These discoveries underscored the significance of these proteins as potential targets for intervention in the prevention and treatment of KOA and HOA. Key Points • We presented genetic evidence supporting a causal link between circulating inflammatory proteins associated with joint inflammation using MR methods. • 5 CIPs have demonstrated promotive effects on the occurrence of KOA and HOA.

Decoding the Therapeutic Target SVEP1: Harnessing Molecular Trait GWASs to Unravel Mechanisms of Human Disease

Although human genetics has substantial potential to illuminate novel disease pathways and facilitate drug development, identifying causal variants and deciphering their mechanisms remain challenging. We believe these challenges can be addressed, in part, by creatively repurposing the results of molecular trait genome-wide association studies (GWASs). In this review, we introduce techniques related to molecular GWASs and unconventionally apply them to understanding SVEP1, a human coronary artery disease risk locus. Our analyses highlight SVEP1's causal link to cardiometabolic disease and glaucoma, as well as the surprising discovery of SVEP1 as the first known physiologic ligand for PEAR1, a critical receptor governing platelet reactivity. We further employ these techniques to dissect the interactions between SVEP1, PEAR1, and the Ang/Tie pathway, with therapeutic implications for a constellation of diseases. This review underscores the potential of molecular GWASs to guide drug discovery and unravel the complexities of human health and disease by demonstrating an integrative approach that grounds mechanistic research in human biology.

Systematic proteome-wide Mendelian randomization to prioritize causal plasma proteins for skin cancers

Skin cancer is one of the most common cancers worldwide. Some risk factors including sun exposure and MC1R variants are recognized; however, the identification of additional genetic factors is essential for the development of novel therapeutic strategies. Here, we conducted a proteome-wide Mendelian randomization (MR) using plasma protein quantitative trait loci (pQTLs) from a published study and the UK Biobank genome-wide association study (GWAS) of skin cancers. We replicated the published result of ASIP, which was significantly associated with increased risks of basal cell carcinoma (BCC) and malignant melanoma. Moreover, we newly identified CTSS, which was significantly associated with a decreased risk of BCC. A series of replication analyses using the DeCODE pQTLs and the FinnGen GWAS, and sensitivity analyses including Steiger filtering, reverse MR, and Bayesian colocalization, supported our primary results. Our findings highlighted the possibility of prioritizing proteins for novel therapeutic or preventive targets and biomarkers for skin cancers.

Causal associations of tea consumption on risk of pancreatic adenocarcinoma and the mediating role of vascular endothelial growth factor D levels

Tea is one of the most widely consumed beverages in the world. However, the association between tea and risk of pancreatic adenocarcinoma remains controversial. This study aimed to investigate the causal relationship between tea consumption and risk of pancreatic adenocarcinoma and to explore their mediating effects. The two-sample Mendelian randomisation (MR) analysis showed an inverse causal relationship between tea intake and pancreatic adenocarcinoma (OR: 0·111 (0·02, 0·85), P < 0·04). To examine the mediating effects, we explored the potential mechanisms by which tea intake reduces the risk of pancreatic adenocarcinoma. Based on the oral bioavailability and drug-like properties in Traditional Chinese Medicine Systems Pharmacology database, we selected the main active ingredients of tea. We screened out the fifteen representative targeted genes by Pharmmapper database, and the gene ontology enrichment analysis showed that these targeted genes were related to vascular endothelial growth factor (VEGF) pathway. The two-step MR analysis of results showed that only VEGF-D played a mediating role, with a mediation ratio of 0·230 (0·066, 0·394). In conclusion, the findings suggest that VEGF-D mediates the effect of tea intake on the risk of pancreatic adenocarcinoma.

Unveiling Novel Protein Biomarkers for Psoriasis Through Integrated Analysis of Human Plasma Proteomics and Mendelian Randomization

Background

Current pharmacological treatments for psoriasis are generally non-specific and have significant limitations, particularly in the realm of targeted biologic therapies. There is an urgent need to identify and develop new therapeutic targets to improve treatment options.

Objective

The aim of this study was to explore the proteome associated with psoriasis in large population cohorts to discover novel biomarkers that could guide therapy.

Methods

We analyzed data from 54,306 participants enrolled in the UK Biobank Pharmacological Proteomics Project (UKB-PPP). We investigated the relationship between 2923 serum proteins and the risk of psoriasis using multivariate Cox regression models initially. This was complemented by two-sample Mendelian randomization (TSMR), Summary-data-based Mendelian Randomization (SMR), and coloc colocalization studies to identify genetic correlations with protein targets linked to psoriasis. A protein scoring system was created using the Cox proportional hazards model, and cumulative risk curves were generated to analyze psoriasis incidence variations.

Results

Our study pinpointed 62 proteins significantly linked to the risk of developing psoriasis. Further analysis through TSMR narrowed these down to ten proteins with strong causal relationships to the disease. Additional deep-dive analyses such as SMR, colocalization, and differential expression studies highlighted four critical proteins (MMP12, PCSK9, PRSS8, and SCLY). We calculated a protein score based on the levels of these proteins, with higher scores correlating with increased risk of psoriasis.

Conclusion

This study's integration of proteomic and genetic data from a European adult cohort provides compelling evidence of several proteins as viable predictive biomarkers and potential therapeutic targets for psoriasis, facilitating the advancement of targeted treatment strategies.

Proteome-wide Mendelian randomization and functional studies uncover therapeutic targets for polycystic ovarian syndrome

Polycystic ovarian syndrome (PCOS) is an endocrine syndrome that affects a large portion of women worldwide. This proteogenomic and functional study aimed to uncover candidate therapeutic targets for PCOS. We comprehensively investigated the causal association between circulating proteins and PCOS using two-sample Mendelian randomization analysis. Cis-protein quantitative trait loci were derived from six genome-wide association studies (GWASs) on plasma proteome. Genetic associations with PCOS were obtained from a large-scale GWAS meta-analysis, FinnGen cohort, and UK Biobank. Colocalization analyses were performed to prioritize the causal role of candidate proteins. Protein-protein interaction (PPI) and druggability evaluation assessed the druggability of candidate proteins. We evaluated the enrichment of tier 1 and 2 candidate proteins in individuals with PCOS and a mouse model and explored the potential application of the identified drug target. Genetically predicted levels of 65 proteins exhibited associations with PCOS risk, with 30 proteins showing elevated levels and 35 proteins showing decreased levels linked to higher susceptibility. PPI analyses revealed that FSHB, POSTN, CCN2, and CXCL11 interacted with targets of current PCOS medications. Eighty medications targeting 20 proteins showed their potential for repurposing as therapeutic targets for PCOS. EGLN1 levels were elevated in granulosa cells and the plasma of individuals with PCOS and in the plasma and ovaries of dehydroepiandrosterone (DHEA)-induced PCOS mouse model. As an EGLN1 inhibitor, administration of roxadustat in the PCOS mouse model elucidated the EGLN1-HIF1α-ferroptosis axis in inducing PCOS and validated its therapeutic effect in PCOS. Our study identifies candidate proteins causally associated with PCOS risk and suggests that targeting EGLN1 provides a promising treatment strategy.

Evaluating the association between immunological proteins and common intestinal diseases using a bidirectional two-sample Mendelian randomization study

Dysregulation of intestinal homeostasis, characterized by imbalanced immunological proteins, contributes to the pathogenesis of common intestinal diseases, e.g., irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and colorectal cancer (CRC). However, the potential causal relationships between specific immunological proteins and these diseases remain to be fully elucidated. In this study, we employed the bidirectional two-sample Mendelian randomization analysis to infer potential causal relationships between representative immunological proteins and these intestinal diseases. Genome-wide association study (GWAS) summary statistics of IBS, IBD, and CRC were obtained from public databases and utilized in MR analysis. Multiple sensitivity analyses were performed to evaluate the robustness, with p-values adjusted using the Benjamini-Hochberg method for multiple comparisons. Our findings revealed a significant association between IL-1β (OR = 0.783, 95 % CI: 0.676 to 0.908, adjusted P = 0.048) and a decreased risk of IBS. Furthermore, genetic predisposition to IBS was related to the reduced levels of IL-25 (β =  - 0.233, 95 % CI: -0.372 to -0.094, adjusted P = 0.047). Additionally, genetic predisposition to IBD was correlated with elevated levels of IL-6 (β = 0.046, 95 % CI: 0.022-0.069, adjusted P = 0.010). The levels of TNF-α (OR = 1.252, 95 % CI: 1.102 to 1.423, adjusted P = 0.047) were associated with an increased risk of CRC. Our study suggests associations between specific immunological proteins and intestinal diseases, which would provide valuable insights for developing targeted immunomodulation therapies for these conditions. Further investigation into underlying mechanisms remains a research priority in the future.

Association Between Neuroinflammation and Parkinson's Disease: A Comprehensive Mendelian Randomization Study

The objective of the study is to determine the causal relationship and potential mechanisms between Parkinson's disease (PD) and neuroinflammatory and neurotoxic mediators. We conducted two-sample Mendelian randomization (2SMR) study and multivariable Mendelian randomization (MVMR) analysis to investigate the causality between PD and neuroinflammatory and neurotoxic mediators. The mediation analysis with MR was also conducted to determine the potential mediating effect of neuroinflammatory and neurotoxic mediators between asthma and PD. Genetically predicted levels of nine neuroinflammation were associated with changes in PD risk. The associations of PD with CCL24, galectin-3 levels, haptoglobin, and Holo-Transcobalamin-2 remained significant in multivariable analyses. The mediation analysis with MR revealed that asthma affects PD through CCL24 and galectin-3. The results showed neuroinflammation could affect the pathogenesis of PD. In the combined analysis of these nine variables, CCL24, galectin-3 levels, HP, and Holo-Transcobalamin-2 alone were found to be significant. Asthma plays an intermediary role through CCL24 and galectin-3 levels.

Novel Drug Targets for Atrial Fibrillation Identified Through Mendelian Randomization Analysis of the Blood Proteome

PURPOSE

Novel, effective, and safe preventive therapy targets for AF are still needed. Circulating proteins with causal genetic evidence are promising candidates. We aimed to systematically screen circulating proteins for AF drug targets and determine their safety and efficacy using genetic methods.

METHODS

The protein quantitative trait loci (pQTL) of up to 1949 circulating proteins were retrieved from nine large genome-proteome-wide association studies. Two-sample Mendelian Randomization (MR) and colocalization analyses were used to estimate the causal effects of proteins on the risk of AF. Furthermore, phenome-wide MR was conducted to depict side effects and the drug-target databases were searched for drug validation and repurposing.

RESULTS

Systematic MR screen identified 30 proteins as promising AF drug targets. Genetically predicted 12 proteins increased AF risk (TES, CFL2, MTHFD1, RAB1A, DUSP13, SRL, ANXA4, NEO1, FKBP7, SPON1, LPA, MANBA); 18 proteins decreased AF risk (PMVK, UBE2F, SYT11, CHMP3, PFKM, FBP1, TNFSF12, CTSZ, QSOX2, ALAD, EFEMP1, FLRT2, LRIG1, OLA1, SH3BGRL3, IL6R, B3GNT8, FCGR2A). DUSP13 and TNFSF12 possess strong colocalization evidence. For the proteins that were identified, extended phe-MR analysis was conducted to assess their side-effect profiles, while drug-target databases provided information on their approved or investigated indications.

CONCLUSION

We identified 30 circulating proteins as potential preventive targets for AF.

Circulating YKL-40 levels but not CHI3L1 or TRIB1 gene variants predict long-term outcomes in patients with angiographically confirmed multivessel coronary artery disease

YKL-40 is significantly associated with the prevalence and severity of coronary artery disease (CAD). YKL-40 levels are significantly associated with variations in the CHI3L1 and TRIB1 genes. We investigated candidate genes for YKL-40 levels and evaluated the prognostic value of this biomarker and corresponding variants for long-term outcomes in patients with CAD. We included 4664 and 521 participants from the Taiwan Biobank (TWB) and CAD cohorts, respectively. Candidate variants for circulating YKL-40 levels were investigated using genome-wide association study (GWAS) data from the TWB cohort, and the results were validated in the CAD cohort. The primary endpoint was all-cause mortality. The secondary endpoint was major adverse cardiac events (MACEs), which included the composite endpoints of all-cause mortality, nonfatal acute coronary syndrome, hospitalization for heart failure, and nonfatal stroke. According to the GWAS data from the TWB cohort, three CHI3L1 variants (rs4950928, rs10399931, and rs872129) and one TRIB1 variant (rs6982502) were independently associated with YKL-40 levels. These findings were validated in the CAD cohort. The combined CHI3L1 and TRIB1 weighted genetic risk scores (WGRSs) were not associated with the long-term outcomes (median follow-up period of 3.7 years) in patients with CAD. Conversely, patients with YKL-40 levels in the upper tertile had the highest rates of all-cause mortality and MACEs (log-rank p = 9.58 × 10-8 for all-cause mortality and 1.34 × 10-7 for MACEs). Furthermore, YKL-40 levels predicted poor clinical outcomes only in patients with multivessel CAD (log-rank p = 3.0 × 10-6 for all-cause mortality and 1.10 × 10-5 for MACEs) and not in patients with single-vessel CAD. This study revealed that YKL-40 levels but not the combined CHI3L1 and TRIB1 WGRSs were found to be independent predictors of poor clinical outcomes in patients with multivessel CAD.

Evidence of a Causal Relationship Between Body Mass Index and Immune-Mediated and Inflammatory Skin Diseases and Biomarkers: A Mendelian Randomization Study

Aim

Increasing observational studies are revealing a positive correlation between body mass index (BMI) and the risk of Immune-mediated and Inflammatory Skin Diseases (IMID), however the causal relationship is not yet definite.

Objective

The aim of the study was to conduct a two-sample Mendelian randomization (TSMR) to explore the potential causality between BMI, and IMID and biomarkers.

Methods

The summary statistics for BMI (n = 322,154), at genome-wide significant level, were derived from the Genetic Investigation of Anthropometric Traits consortium (GIANT). The outcome data for IMID (Psoriasis, vitiligo, Atopic dermatitis (AD), acne, Bullous diseases, Dermatitis herpetiformis, Systemic lupus erythematosus (SLE), Alopecia Areata (AA), Hidradenitis suppurativa (HS) and Systemic sclerosis), and biomarkers were obtained from genome-wide association studies (GWAS). The TSMR analyses were performed in four methods, including inverse variance weighted (IVW) method, MR-Egger regression, the weighted median estimator (WME) and simple mode.

Results

The IVW analysis showed that the per standard deviation (SD) increase in BMI increased a 57% risk of psoriasis. We also observed the suggestive evidence of a causal relationship between BMI and AD and HS. This analysis did not support causality of Vitiligo, Acne, Bullous pemphigoid, Dermatitis herpetiformis, SLE, AA and Systemic sclerosis. The higher risk of BMI may be explained by higher levels of Triglycerides, C-reactive protein (CRP), Interleukin 6, Erythrocyte sedimentation rate (ESR) and Neutrophil count. The high-density lipoprotein (HDL) has an inverse relationship with BMI. No influences were defined for Total cholesterol, low-density lipoprotein (LDL), Rheumatoid factor (RF), Basophil count and Eosinophil count.

Conclusion

Our two-sample MR analysis proved the causal evidence for the associations between BMI and IMID, including psoriasis, AD and HS, which might be related to the elevated expression of biomarkers, including Triglycerides, CRP, Interleukin 6, ESR and neutrophil count.

Exploring causal associations between interleukins, their receptors, and acute respiratory distress syndrome: a bidirectional-Mendelian Randomization study

Background

Acute Respiratory Distress Syndrome (ARDS) is a severe lung condition posing significant health risks. Observational studies have indicated a potential linkage between ARDS and various interleukins, such as Interleukin-8, -2, -6, and -1β. However, the causal relationships between specific interleukins, their receptors, and ARDS remain unclear.

Methods

This study employed bidirectional Mendelian Randomization (MR) to investigate the causal associations between 197 different interleukins, interleukin receptors, and ARDS. GWAS summary data for interleukins and their receptors were sourced from publicly available studies, while ARDS data were derived from the FinnGen database. Wald Ratio and Inverse Variance Weighted (IVW) methods were primarily utilized in the MR analyses. Reverse MR was also conducted to explore reverse causations.

Results

The study identified significant causal relationships between several interleukins, their receptors and ARDS. Specifically, Interleukin-17 receptor D (IL-17RD) (OR = 0.67, 95%CI = 0.51-0.89, p = 0.006), Interleukin-22 receptor subunit alpha-1 (IL22RA-1) (OR = 1.45, 95%CI = 1.08-1.96, p = 0.014), Interleukin-20 receptor subunit alpha (IL20RA) (OR = 0.53, 95%CI = 0.32-0.89, p = 0.016), Interleukin-22 (IL-22) (OR = 3.60, 95%CI = 1.20-10.83, p = 0.022), Interleukin-23 receptor (IL-23R) (OR = 2.14, 95%CI = 1.10-4.17, p = 0.025), Single Ig IL-1-related receptor (SIGIRR) (OR = 1.22, 95%CI = 1.00-1.48, p = 0.047) showed notable associations with ARDS. No reverse causal relationships were found on results above, and neither heterogeneity nor pleiotropy was detected in the analysis.

Conclusion

This study elucidates the causal connections between specific interleukins, their receptors and ARDS, contributing significantly to the understanding of ARDS pathogenesis. These findings offer a foundation for further research and potential therapeutic interventions targeting these interleukins and receptors in ARDS management. The absence of reverse causation and pleiotropy, heterogeneity reinforces the robustness of these associations.

Genetic variation perspective reveals potential drug targets for subtypes of endometrial cancer

The study aims to identify potential drug targets for endometrial cancer (EC) subtypes through a Mendelian randomization (MR) approach, assessing their clinical relevance. We utilized genetic instruments for 4,907 plasma proteins from the deCODE Genetics study dataset, and data with EC (n = 12,906) from a genome-wide study (GWAS) meta-analysis in European populations for MR analyses. Complementary analyses included protein-protein interactions (PPI) network analysis, therapeutic efficacy evaluation, differential gene expression assessment, and prognosis evaluation. The expression levels of key drug targets were quantitatively measured at both the transcriptional and translational stages utilizing reverse transcription quantitative PCR (RT-qPCR) and immunohistochemistry (IHC). Additionally, we analyzed various clinicopathological features. Five drug targets for EC (CBR3, GSTO1, HHIP, IGF2R, and MMP10), seven for endometrioid subtypes (ACAP2, CBR3, GSTO1, HHIP, IGF2R, MMP10, and TLR2), and seven for non-endometrioid subtypes (CST3, DNAJB14, FSTL5, GMPR2, IFI16, MAPK9, and NEO1) were identified. Among these, IGF2R (OR = 1.165; 95% CI 1.067-1.272; p = 1.046 × 10- 2) and CST3 (OR = 0.523; 95% CI 0.339-0.804; p = 7.010 × 10- 3) were highlighted as key drug targets with causal evidence both at transcriptional and translational levels. This study preliminarily confirms that IGF2R and CST3 may serve as novel targets for the treatment of EC, providing a foundational reference for innovative clinical approaches to this disease.

CCN3/NOV as a potential therapeutic target for diverticular disease: A proteome-wide Mendelian randomization study

Genome-wide association studies (GWAS) identified over 100 susceptibility loci and candidate causal genes for diverticular disease (DD) at the transcriptional level. However, effective therapeutics or preventions based on underlying disease mechanisms remain to be elucidated. In this study, we explored potential causal genes for DD at the protein level. We used 2 GWAS summary statistics of DD; 1 was obtained from the United Kingdom Biobank (UKBB) with 31,917 cases and 419,135 controls, and the other from the FinnGen consortium with 30,649 cases and 301,931 controls. For the primary analysis, we employed proteome-wide Mendelian randomization (MR) studies using 738 cis-acting protein quantitative trait loci (pQTLs) for 735 plasma proteins from the 5 published studies. For external validation, we conducted 2-sample MR analyses using plasma pQTLs of the screened proteins from another study by deCODE genetics. Moreover, we performed a series of sensitivity analyses including reverse MR and Bayesian colocalization tests. The primary MR identified 4 plasma proteins that were associated with DD risk including CCN3/NOV (odds ratio [OR], 0.98; 95% confidence interval [CI], 0.97-0.99; P = 1.2 × 10-11 for UKBB. OR, 0.73; 95% CI, 0.66-0.81; P = 7.2 × 10-10 for FinnGen). The validation MR well replicated the primary result of CCN3/NOV (OR, 0.95; 95% CI, 0.93-0.96; P = 1.9 × 10-11 for UKBB. OR, 0.43; 95% CI, 0.33-0.56; P = 7.0 × 10-10 for FinnGen). Sensitivity analyses supported the causal association. We prioritized plasma CCN3/NOV protein as a protective factor for DD for follow-up functional studies to elucidate the disease mechanisms and therapeutics.

Investigating potential drug targets for IgA nephropathy and membranous nephropathy through multi-queue plasma protein analysis: a Mendelian randomization study based on SMR and co-localization analysis

BACKGROUND

Membranous nephropathy (MN) and IgA nephropathy (IgAN) pose challenges in clinical treatment with existing therapies primarily focusing on symptom relief and often yielding unsatisfactory outcomes. The search for novel drug targets remains crucial to address the shortcomings in managing both kidney diseases.

METHODS

Utilizing GWAS data for MN (ncase = 2150, ncontrol = 5829) and IgAN (ncase = 15587, ncontrol = 462197), instrumental variables for plasma proteins were derived from recent GWAS. Sensitivity analysis involved bidirectional Mendelian randomization analysis, MR Steiger, Bayesian co-localization, and Phenotype scanning. The SMR analysis using eQTL data from the eQTLGen Consortium was conducted to assess the availability of selected protein targets. The PPI network was constructed to reveal potential associations with existing drug treatment targets.

RESULTS

The study, subjected to the stringent Bonferroni correction, revealed significant associations: four proteins with MN and three proteins with IgAN. In plasma protein cis-pQTL data from two cohorts, an increase in one standard deviation in PLA2R1 (OR = 2.01, 95%CI = 1.83-2.21), AIF1 (OR = 9.04, 95%CI = 4.69-17.41), MLN (OR = 3.79, 95%CI = 2.12-6.78), and NFKB1 (OR = 29.43, 95%CI = 7.73-112.0) was associated with an increased risk of MN. Additionally, in plasma protein cis-pQTL data, a standard deviation increase in FCGR3B (OR = 1.15, 95%CI = 1.09-1.22) and BTN3A1 (OR = 4.05, 95%CI = 2.65-6.19) correlated with elevated IgAN risk, while AIF1 (OR = 0.58, 95%CI = 0.46-0.73) exhibited IgAN protection. Bayesian co-localization indicated that PLA2R1 (coloc.abf-PPH4 = 0.695), NFKB1 (coloc.abf-PPH4 = 0.949), FCGR3B (coloc.abf-PPH4 = 0.909), and BTN3A1 (coloc.abf-PPH4 = 0.685) share the same variants associated with MN and IgAN. The SMR analysis indicated a causal link between NFKB1 and BTN3A1 plasma protein eQTL in both conditions, and BTN3A1 was validated externally.

CONCLUSION

Genetically influenced plasma levels of PLA2R1 and NFKB1 impact MN risk, while FCGR3B and BTN3A1 levels are causally linked to IgAN risk, suggesting potential drug targets for further clinical exploration, notably BTN3A1 for IgAN.

Potential Drug Targets for Diabetic Retinopathy Identified Through Mendelian Randomization Analysis

Purpose

This study aimed to investigate the causal effect of plasma proteins on diabetic retinopathy (DR) risk and identify potential drug targets for this disease.

Methods

Two-sample Mendelian randomization was performed to explore potential drug targets for DR. A total of 734 proteins were selected as instrumental variables. The Steiger filtering test and colocalization analysis were conducted to determine the causal direction and genetic pleiotropy. Plasma proteins from the decode study were used to validate the findings.

Results

Eleven plasma proteins were associated with DR risk. Genetically predicted high levels of CCL3L1 (odds ratio [OR] = 0.582; 95% confidence interval [CI], 0.343-0.986; P = 0.044), PAM (OR = 0.782; 95% CI, 0.652-0.937; P = 0.008), GP1BA (OR = 0.793; 95% CI, 0.632-0.994; P = 0.044), GALNT16 (OR = 0.832; 95% CI, 0.727-0.952; P = 0.008), POGLUT1 (OR = 0.836; 95% CI = 0.703-0.995; P = 0.043), and DKK3 (OR = 0.859; 95% CI, 0.777-0.950; P = 0.003) have the protective effect on DR risk. Genetically predicted high levels of GFRA2 (OR = 1.104; 95% CI, 1.028-1.187; P = 0.007), PATE4 (OR = 1.405; 95% CI, 1.060-1.860; P = 0.018), GSTA1 (OR = 1.464; 95% CI, 1.163-1.842; P = 0.001), SIRPG (OR = 1.600, 95% CI, 1.244-2.057; P = 2.51E-04), and MAPK13 (OR = 1.731; 95% CI, 1.233-2.431; P = 0.002) were associated with an increased risk of DR. However, the colocalization analysis results suggested that SIRPG and GP1BA have a shared causal variant with DR.

Conclusions

CCL3L1, PAM, GALNT16, POGLUT1, DKK3, GFRA2, PATE4, GSTA1, and MAPK13 were associated with DR risk and were identified as potential drug targets for DR.

Translational Relevance

The present study has highlighted the role of CCL3L1, PAM, GALNT16, POGLUT1, DKK3, GFRA2, PATE4, GSTA1, and MAPK13 in the development of DR.

The genetic landscape of neuro-related proteins in human plasma

Understanding the genetic basis of neuro-related proteins is essential for dissecting the molecular basis of human behavioural traits and the disease aetiology of neuropsychiatric disorders. Here the SCALLOP Consortium conducted a genome-wide association meta-analysis of over 12,000 individuals for 184 neuro-related proteins in human plasma. The analysis identified 125 cis-regulatory protein quantitative trait loci (cis-pQTL) and 164 trans-pQTL. The mapped pQTL capture on average 50% of each protein's heritability. At the cis-pQTL, multiple proteins shared a genetic basis with human behavioural traits such as alcohol and food intake, smoking and educational attainment, as well as neurological conditions and psychiatric disorders such as pain, neuroticism and schizophrenia. Integrating with established drug information, the causal inference analysis validated 52 out of 66 matched combinations of protein targets and diseases or side effects with available drugs while suggesting hundreds of repurposing and new therapeutic targets.

Novel targets for the treatment and prevention of Alzheimer's disease in the European population, inspiration from amyloid beta and tau protein

Alzheimer's disease (AD) is a gradual neurodegenerative ailment that lacks any disease-modifying intervention. Our objective was to pinpoint pharmacological targets with a focus on amyloid beta (Aβ) and tau to treat and prevent AD in the European population. A proteome-wide Mendelian randomization (MR) analysis was carried out to estimate the associations between proteins and cerebrospinal fluid (CSF) Aβ-42 and phosphorylated Tau (p-Tau). We utilized colocalization and MR analysis to investigate whether the identified proteins were associated with the risk of AD. Additionally, we expanded our investigation to include non-AD phenotypes by conducting a phenome-wide MR analysis of 1646 disease traits based on the FinnGen and UK Biobank databases to explore potential side effects. We identified 11 proteins that were genetically associated with both CSF Aβ-42 and p-Tau levels. The genetically predicted levels of three proteins, GAL3ST2, POLR1C, and BIN1, were found to be associated with an increased risk of AD with high colocalization. In the phenome-wide MR analysis, two out of the three biomarkers were associated with at least one disease, except for GAL3ST2, which was not associated with any disease under the threshold of FDR <0.1. POLR1C was found to be associated with the most disease traits, and all disease associations with genetically inhibited BIN1 were protective. The proteome-wide MR investigation revealed 11 proteins that were associated with the level of CSF Aβ-42 and p-Tau. Among them, GAL3ST2, POLR1C, and BIN1 were identified as potential therapeutic targets for AD and warrant further investigation.

Unveiling new protein biomarkers and therapeutic targets for acne through integrated analysis of human plasma proteomics and genomics

Background

The current landscape of acne therapeutics is notably lacking in targeted treatments, highlighting a critical need for the discovery of new drug targets to improve treatment outcomes.

Objectives

This study aims to investigate the connections between proteomics and genetics in relation to acne across extensive population cohorts, aspiring to identify innovative preventive and therapeutic approaches.

Methods

Employing a longitudinal cohort of 54,306 participants from the UK Biobank Pharmacological Proteomics Project (UKB-PPP), we performed an exhaustive evaluation of the associations between 2,923 serum proteins and acne risk. Initial multivariate Cox regression analyses assessed the relationship between protein expression levels and acne onset, followed by two-sample Mendelian Randomization (TSMR), Summary-data-based Mendelian Randomization (SMR), and colocalization to identify genetic correlations with potential protein targets.

Results

Within the UKB cohort, we identified 19 proteins significantly associated with the risk of acne. Subsequent analysis using Two-Sample Mendelian Randomization (TSMR) refined this to two specific proteins: FSTL1 and ANXA5. Each one-standard deviation increase in the expression levels of FSTL1 and ANXA5 was associated with a 24% and 32% increase in acne incidence, respectively. These results were further validated by additional Summary-data-based Mendelian Randomization (SMR) and differential expression analyses.

Conclusions

Our comprehensive analysis of proteomic and genetic data from a European adult cohort provides compelling causal evidence that several proteins are promising targets for novel acne treatments.

Identification of potential novel targets for treating inflammatory bowel disease using Mendelian randomization analysis

BACKGROUND

Inflammatory bowel disease (IBD) is a complex autoimmune disorder, although some medications are available for its treatment. However, the long-term efficacy of these drugs remains unsatisfactory. Therefore, there is a need to develop novel drug targets for IBD treatment.

METHODS

We conducted two-sample Mendelian randomization (MR) analysis using Genome-Wide Association Study (GWAS) data to assess the causal relationships between plasma proteins and IBD and its subtypes. Subsequently, the presence of shared genetic variants between the identified plasma proteins and traits was explored using Bayesian co-localization. Phenome-wide MR was used to evaluate evaluated adverse effects, and drug target databases were examined for therapeutic potential.

RESULTS

Using the Bonferroni correction (P < 3.56e-05), 17 protein-IBD pairs were identified. Notably, the genetic associations of IBD shared a common variant locus (PP.H4 > 0.7) with five proteins (MST1, IL12B, HGFAC, FCGR2A, and IL18R1). As a subtype of IBD, ulcerative colitis shares common variant loci with FCGR2A, IL12B, and MST1. In addition, we found that ANGPTL3, IL18R1, and MST1 share a common variant locus with Crohn's disease. Furthermore, phenome-wide MR analysis revealed that except for ANGPTL3, no other proteins showed potential adverse effects. In the drug database, identified plasma proteins such as FCGR2A and IL18R1 were found to be potential drug targets for the treatment of IBD and its subtypes.

CONCLUSION

Six proteins (FCGR2A, IL18R1, MST1, HGFAC, IL12B, and ANGPTL3) were identified as potential drug targets for the treatment of IBD and its subtypes.

Cathepsins and neurological diseases: a Mendelian randomization study

Background

The causal relationship between cathepsins and neurological diseases remains uncertain. To address this, we utilized a two-sample Mendelian randomization (MR) approach to assess the potential causal effect of cathepsins on the development of neurological diseases.

Methods

This study conducted a two-sample two-way MR study using pooled data from published genome-wide association studies to evaluate the relationship between 10 cathepsins (B, D, E, F, G, H, L2, O, S, and Z) and 7 neurological diseases, which included ischemic stroke, cerebral hemorrhage, Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, and epilepsy. The analysis employed various methods such as inverse variance weighting (IVW), weighted median, MR Egger regression, MR pleiotropy residual sum and outlier, Cochran Q statistic, and leave-one-out analysis.

Results

We found a causal relationship between cathepsins and neurological diseases, including Cathepsin B and Parkinson's disease (IVW odds ratio (OR): 0.89, 95% confidence interval (CI): 0.83, 0.95, p = 0.001); Cathepsin D and Parkinson's disease (OR: 0.80, 95%CI: 0.68, 0.95, p = 0.012); Cathepsin E and ischemic stroke (OR: 1.05, 95%CI: 1.01, 1.09, p = 0.015); Cathepsin O and ischemic stroke (OR: 1.05, 95%CI: 1.01, 1.10, p = 0.021). Reverse MR analyses revealed that multiple sclerosis and Cathepsin E (OR: 1.05, 95%CI: 1.01, 1.10, p = 0.030). There is currently no significant relationship has been found between other cathepsins and neurological diseases.

Conclusion

Our study reveals a causal relationship between Cathepsins B, D, E, and O and neurological diseases, offering valuable insights for research aimed at improving the diagnosis and treatment of such conditions.