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

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.

Transcriptomics, Proteomics and Bioinformatics in Atrial Fibrillation: A Descriptive Review

Atrial fibrillation (AF) is the most frequent cardiac arrhythmia, with an estimated five million cases globally. This condition increases the likelihood of developing cardiovascular complications such as thromboembolic events, with a fivefold increase in risk of both heart failure and stroke. Contemporary challenges include a better understanding AF pathophysiology and optimizing therapeutical options due to the current lack of efficacy and adverse effects of antiarrhythmic drug therapy. Hence, the identification of novel biomarkers in biological samples would greatly impact the diagnostic and therapeutic opportunities offered to AF patients. Long noncoding RNAs, micro RNAs, circular RNAs, and genes involved in heart cell differentiation are particularly relevant to understanding gene regulatory effects on AF pathophysiology. Proteomic remodeling may also play an important role in the structural, electrical, ion channel, and interactome dysfunctions associated with AF pathogenesis. Different devices for processing RNA and proteomic samples vary from RNA sequencing and microarray to a wide range of mass spectrometry techniques such as Orbitrap, Quadrupole, LC-MS, and hybrid systems. Since AF atrial tissue samples require a more invasive approach to be retrieved and analyzed, blood plasma biomarkers were also considered. A range of different sample preprocessing techniques and bioinformatic methods across studies were examined. The objective of this descriptive review is to examine the most recent developments of transcriptomics, proteomics, and bioinformatics in atrial fibrillation.

Causal inference in the field of arrhythmia: An introduction to mendelian randomization

Mendelian randomization (MR) uses genetic variants associated with an exposure (eg, high blood pressure) as instrumental variables to test causal effects on an outcome (eg, atrial fibrillation [AF]). By leveraging the random assortment of genetic variants during gamete formation, MR reduces biases like confounding and reverse causation. We screened 391 papers, examining 277 that applied MR to investigate arrhythmia and, in others, cardiovascular traits, lifestyle, behavioral traits, and body composition. Our analysis focused on MR studies of arrhythmia and cardiovascular traits. Key findings highlight high systolic blood pressure, low resting heart rate, elevated cardiac troponin I levels, coronary artery disease, and heart failure as risk factors for AF, whereas AF itself increases heart failure risk. As genetic data become more accessible, MR's relevance grows. Sensitivity analyses and integrating MR with other methodologies in a triangulation framework enhance the robustness of causal inferences by navigating different biases.

Fibroblast growth factor 5 as a target for atrial fibrillation treatment: Evidence from mendelian randomization

BACKGROUND

Previous studies have found that inflammatory proteins are involved in the pathogenesis of atrial fibrillation (AF). We used mendelian randomization to explore the potential pathogenic inflammatory proteins of AF.

METHODS

This study adopts a Mendelian randomization design to primarily assess causal associations using the Wald ratio and the inverse variance weighting method. It leverages protein quantitative trait locus (pQTL) data encompassing 91 types of inflammatory proteins from 14,824 participants of European ancestry. The primary analysis phase utilizes AF GWAS data from 55,106 participants, with an additional 237,690 participants included in the validation stage. Sensitivity analyses, including reverse causality analysis, Bayesian colocalization analysis, and phenotype scanning, were conducted. Finally, the study explores potential targeted drugs.

RESULTS

The findings highlight a causal link between 7 inflammatory proteins and AF, with 2 showing positive correlations and 5 exhibiting negative correlations. Among these, fibroblast growth factor 5 (FGF5) emerges as particularly robust in sensitivity analysis. Colocalization analysis indicates a shared genetic variation between FGF5 and AF, supporting its potential as a targeted therapy for AF. Importantly, this causal relationship remains unaffected by reverse causality. Furthermore, significant pleiotropic effects were observed in phenotype scanning. Finally, the causal association between FGF5 and AF was successfully replicated during the validation phase.

CONCLUSION

FGF5 may become an intervention target for AF targeted therapy.

Plasma Proteomic Insights for Identification of Novel Predictors and Potential Drug Targets in Atrial Fibrillation: A Prospective Cohort Study and Mendelian Randomization Analysis

BACKGROUND

Currently, there are no reliable methods for predicting and preventing atrial fibrillation (AF) in its early stages. This study aimed to identify plasma proteins associated with AF to discover biomarkers and potential drug targets.

METHODS

The UK Biobank Pharma Proteomics Project examined 2923 circulating proteins using the Olink platform, forming the basis of this prospective cohort study. The UK Biobank Pharma Proteomics Project included a randomly selected discovery cohort and the consortium-selected replication cohort. The study's end point was incident AF, identified using International Classification of Diseases, Tenth Revision codes. The association between plasma proteins and incident AF was evaluated using Cox proportional hazard models in both cohorts. Proteins present in both cohorts underwent Mendelian randomization analysis to delineate causal connections, utilizing cis-protein quantitative trait loci as genetic tools. The predictive efficacy of the identified proteins for AF was assessed using the area under the receiver operating characteristic curve, and their druggability was explored.

RESULTS

Data from 38 784 participants were included in this study. Incident AF cases were identified in the discovery cohort (1894; 5.5%) within a median follow-up of 14.5 years and in the replication cohort (451; 10.6%) within a median follow-up of 14.4 years. Twenty-one proteins linked to AF were identified in both cohorts. Specifically, COL4A1 (collagen IV α-1; odds ratio, 1.11 [95% CI, 1.04-1.19]; false discovery rate, 0.016) and RET (proto-oncogene tyrosine-protein kinase receptor Ret; odds ratio, 0.96 [95% CI, 0.94-0.98]; false discovery rate, 0.013) demonstrated a causal link with AF, and RET is druggable. COL4A1 improved the short- and long-term predictive performance of established AF models, as evidenced by significant enhancements in the area under the receiver operating characteristic, integrated discrimination improvement, and net reclassification index, all with P values below 0.05.

CONCLUSIONS

COL4A1 and RET are associated with the development of AF. RET is identified as a potential drug target for AF prevention, while COL4A1 serves as a biomarker for AF prediction. Future studies are needed to evaluate the effectiveness of targeting these proteins to reduce AF risk.

Ancestrally diverse genome-wide association analysis highlights ancestry-specific differences in genetic regulation of plasma protein levels

Fully characterizing the genetic architecture of circulating proteins in multi-ancestry populations provides an unprecedented opportunity to gain insights into the etiology of complex diseases. We characterized and contrasted the genetic associations of plasma proteomes in 9,455 participants of European and African (19.8%) ancestry from the Atherosclerosis Risk in Communities Study. Of 4,651 proteins, 1,408 and 2,565 proteins had protein-quantitative trait loci (pQTLs) identified in African and European ancestry respectively, and twelve unreported potentially causal protein-disease relationships were identified. Shared pQTLs across the two ancestries were detected in 1,113 aptamer-region pairs pQTLs, where 53 of them were not previously reported (all trans pQTLs). Sixteen unique protein-cardiovascular trait pairs were colocalized in both European and African ancestry with the same candidate causal variants. Our systematic cross-ancestry comparison provided a reliable set of pQTLs, highlighted the shared and distinct genetic architecture of proteome in two ancestries, and demonstrated possible biological mechanisms underlying complex diseases.

New Insights on the Therapeutic Potential of Runt-Related Transcription Factor 2 for Osteoarthritis: Evidence from Mendelian Randomization

INTRODUCTION

Research has highlighted the role of runt-related transcription factor 2 (Runx2) in the development of osteoarthritis (OA); however, its causal association remains unclear. This study aimed to explore whether Runx2 expression is causally associated with OA and assess its therapeutic potential for OA.

METHODS

Genetic proxy instruments for Runx2 expression were obtained from gene expression quantitative trait locus (eQTLs) study of eQTLGen Consortium (n = 31,684). Aggregated genome-wide association study (GWAS) data for OA (including all OA [177,517 cases and 649,173 controls], knee OA (KOA) [62,497 cases and 333,557 controls], and hip OA (HOA) [36,445 cases and 316,943 controls]) were extracted from the Genetics of Osteoarthritis Consortium. We integrated eQTLs data with OA GWAS data to estimate their causal association and to estimate the potential of Runx2 as a drug target in the treatment of OA using summary data-based Mendelian randomization (SMR) analysis. Furthermore, different OA GWAS data (including all OA [77,052 cases and 378,169 controls], KOA [24,955 cases and 378,169 controls], and HOA [15,704 cases and 378,169 controls]) derived from the GWAS Catalog database were used for replication study.

RESULTS

SMR analysis showed that high expression levels of Runx2 were associated with an increased risk of all OA [odds ratio (OR) 1.044, 95% confidence interval (CI) 1.023-1.067; P = 5.03 × 10-5], KOA (OR 1.040, 95% CI 1.006-1.075; P = 0.021), and HOA (OR 1.067, 95% CI 1.022-1.113; P = 0.003). This suggests that Runx2 inhibitors may have promising potential for the treatment of OA. Notably, the causal effects of Runx2 with all OA (OR 1.053, 95% CI 1.027-1.079; P = 3.95 × 10-5) and KOA (OR 1.043, 95% CI 1.001-1.087; P = 0.045) were repeated in the replication study, but limited evidence supported the association of Runx2 expression levels with HOA (OR 1.045, 95% CI 0.993-1.101; P = 0.094).

CONCLUSIONS

Our analyses indicate a positive correlation between Runx2 expression and OA risk across all three phenotypes, suggesting the potential of Runx2 inhibitors in the treatment of OA and providing evidence from a genetic perspective.

Circulating Proteins and IgA Nephropathy: A Multiancestry Proteome-Wide Mendelian Randomization Study

Key Points

Background

The therapeutic options for IgA nephropathy are rapidly evolving, but early diagnosis and targeted treatment remain challenging. We aimed to identify circulating plasma proteins associated with IgA nephropathy by proteome-wide Mendelian randomization studies across multiple ancestry populations.

Methods

In this study, we applied Mendelian randomization and colocalization analyses to estimate the putative causal effects of 2615 proteins on IgA nephropathy in Europeans and 235 proteins in East Asians. Following two-stage network Mendelian randomization, multitrait colocalization analysis and protein-altering variant annotation were performed to strengthen the reliability of the results. A protein–protein interaction network was constructed to investigate the interactions between the identified proteins and the targets of existing medications.

Results

Putative causal effects of 184 and 13 protein–disease pairs in European and East Asian ancestries were identified, respectively. Two protein–disease pairs showed shared causal effects across them (CFHR1 and FCRL2). Supported by the evidence from colocalization analysis, potential therapeutic targets were prioritized and four drug-repurposing opportunities were suggested. The protein–protein interaction network further provided strong evidence for existing medications and pathways that are known to be therapeutically important.

Conclusions

Our study identified a number of circulating proteins associated with IgA nephropathy and prioritized several potential drug targets that require further investigation.

Causal gene identification using mitochondria-associated genome-wide mendelian randomization in atrial fibrillation

Background: Mitochondrial dysfunction is one of the important patho-mechanisms in the development of atrial fibrillation (AF) with underidentified genetic pathophysiology. Methods: Summarized data of methylation, expression and protein abundance levels of mitochondria-related genes were obtained from corresponding studies, respectively. Genes related to mitochondria dysfunction in associations with AF were obtained from the UK Biobank (discovery), and the FinnGen study (replication). Summary-data-based Mendelian randomization analysis (SMR) was performed to assess potential causal relationships between mitochondria-related genes related to the molecular features of AF. Colocalization analysis was further conducted to assess whether the identified signal pairs shared causal genetic variants. Results: Five mitochondria-related genes were found to have causal effects with AF in the sensitivity and the colocalization analyses. Strong associations with increased risk of AF were identified with increased expression level of 4 mitochondria-related genes, including PCCB (OR 1.09, 95% CI 1.05-1.12; PPH4 = 0.95), COX18 (OR 1.83, 95% CI 1.29-2.60; PPH4 = 0.83), SLC25A15 (OR 1.34, 95% CI 1.14-1.58; PPH4 = 0.85), and STX17 (OR 1.16, 95% CI 1.08-1.24; PPH4 = 0.76). Conversely, genetically predicted higher levels expression of UQCC1 (OR 0.94, 95% CI 0.91-0.97) were associated with decreased risk of AF. After further tissue-specific validation, genetically predicted expression levels of PCCB (OR 1.12, 95%, CI 1.01-1.24, p = 0.025) and STX17 (OR 1.13, 95%, CI 1.04-1.23, p = 0.006) in atrial appendage were strongly associated with the increased risk of AF. Conclusion: Mitochondria-related genes are involved either positively (PCCB, COX18, SLC25A15 and STX17) or negatively (UQCCI) in the pathogenesis and the development of AF. These candidate genes may serve as targets for potential development of agents in the prevention and treatment of AF.

The Strong Activation of p53 Tumor Suppressor Drives the Synthesis of the Enigmatic Isoform of DUSP13 Protein

The p53 tumor suppressor protein activates various sets of genes depending on its covalent modifications, which are controlled by the nature and intensity of cellular stress. We observed that actinomycin D and nutlin-3a (A + N) collaborate in inducing activating phosphorylation of p53. Our recent transcriptomic data demonstrated that these substances strongly synergize in the upregulation of DUSP13, a gene with an unusual pattern of expression, coding for obscure phosphatase having two isoforms, one expressed in the testes and the other in skeletal muscles. In cancer cells exposed to A + N, DUSP13 is expressed from an alternative promoter in the intron, resulting in the expression of an isoform named TMDP-L1. Luciferase reporter tests demonstrated that this promoter is activated by both endogenous and ectopically expressed p53. We demonstrated for the first time that mRNA expressed from this promoter actually produces the protein, which can be detected with Western blotting, in all examined cancer cell lines with wild-type p53 exposed to A + N. In some cell lines, it is also induced by clinically relevant camptothecin, by nutlin-3a acting alone, or by a combination of actinomycin D and other antagonists of p53-MDM2 interaction-idasanutlin or RG7112. This isoform, fused with green fluorescent protein, localizes in the perinuclear region of cells.

Potential drug targets for gastroesophageal reflux disease and Barrett's esophagus identified through Mendelian randomization analysis

Gastroesophageal reflux disease (GERD) is a prevalent chronic ailment, and present therapeutic approaches are not always effective. This study aimed to find new drug targets for GERD and Barrett's esophagus (BE). We obtained genetic instruments for GERD, BE, and 2004 plasma proteins from recently published genome-wide association studies (GWAS), and Mendelian randomization (MR) was employed to explore potential drug targets. We further winnowed down MR-prioritized proteins through replication, reverse causality testing, colocalization analysis, phenotype scanning, and Phenome-wide MR. Furthermore, we constructed a protein-protein interaction network, unveiling potential associations among candidate proteins. Simultaneously, we acquired mRNA expression quantitative trait loci (eQTL) data from another GWAS encompassing four different tissues to identify additional drug targets. Meanwhile, we searched drug databases to evaluate these targets. Under Bonferroni correction (P < 4.8 × 10-5), we identified 11 plasma proteins significantly associated with GERD. Among these, 7 are protective proteins (MSP, GPX1, ERBB3, BT3A3, ANTR2, CCM2, and DECR2), while 4 are detrimental proteins (TMEM106B, DUSP13, C1-INH, and LINGO1). Ultimately, C1-INH and DECR2 successfully passed the screening process and exhibited similar directional causal effects on BE. Further analysis of eQTLs highlighted 4 potential drug targets, including EDEM3, PBX3, MEIS1-AS3, and NME7. The search of drug databases further supported our conclusions. Our study indicated that the plasma proteins C1-INH and DECR2, along with 4 genes (EDEM3, PBX3, MEIS1-AS3, and NME7), may represent potential drug targets for GERD and BE, warranting further investigation.

Genetic insight into putative causes of xanthelasma palpebrarum: a Mendelian randomization study

Xanthelasma palpebrarum (XP) is the most common form of cutaneous xanthoma, with a prevalence of 1.1%~4.4% in the population. However, the cause of XP remains largely unknown. In the present study, we used Mendelian randomization to assess the genetic association between plasma lipids, metabolic traits, and circulating protein with XP, leveraging summary statistics from large genome-wide association studies (GWAS). Genetically predicted plasma cholesterol and LDL-C, but not HDL-C or triglyceride, were significantly associated with XP. Metabolic traits, including BMI, fasting glucose, type 2 diabetes, systolic and diastolic blood pressure, were not significantly associated with XP. Furthermore, we found genetically predicted 12 circulating proteins were associated with XP, including FN1, NTM, FCN2, GOLM1, ICAM5, PDE5A, C5, CLEC11A, CXCL1, CCL2, CCL11, CCL13. In conclusion, this study identified plasma cholesterol, LDL-C, and 12 circulating proteins to be putative causal factors for XP, highlighting the role of plasma cholesterol and inflammatory response in XP development.

Low-Salt Diet Regulates the Metabolic and Signal Transduction Genomic Fabrics, and Remodels the Cardiac Normal and Chronic Pathological Pathways

Low-salt diet (LSD) is a constant recommendation to hypertensive patients, but the genomic mechanisms through which it improves cardiac pathophysiology are still not fully understood. Our publicly accessible transcriptomic dataset of the left ventricle myocardium of adult male mice subjected to prolonged LSD or normal diet was analyzed from the perspective of the Genomic Fabric Paradigm. We found that LSD shifted the metabolic priorities by increasing the transcription control for fatty acids biosynthesis while decreasing it for steroid hormone biosynthesis. Moreover, LSD remodeled pathways responsible for cardiac muscle contraction (CMC), chronic Chagas (CHA), diabetic (DIA), dilated (DIL), and hypertrophic (HCM) cardiomyopathies, and their interplays with the glycolysis/glucogenesis (GLY), oxidative phosphorylation (OXP), and adrenergic signaling in cardiomyocytes (ASC). For instance, the statistically (p < 0.05) significant coupling between GLY and ASC was reduced by LSD from 13.82% to 2.91% (i.e., -4.75×), and that of ASC with HCM from 10.50% to 2.83% (-3.71×). The substantial up-regulation of the CMC, ASC, and OXP genes, and the significant weakening of the synchronization of the expression of the HCM, CHA, DIA, and DIL genes within their respective fabrics justify the benefits of the LSD recommendation.

A proteomic analysis of atrial fibrillation in a prospective longitudinal cohort (AGES-Reykjavik study)

AIMS

Atrial fibrillation (AF) is associated with high risk of comorbidities and mortality. Our aim was to examine causal and predictive relationships between 4137 serum proteins and incident AF in the prospective population-based Age, Gene/Environment Susceptibility-Reykjavik (AGES-Reykjavik) study.

METHODS AND RESULTS

The study included 4765 participants, of whom 1172 developed AF. Cox proportional hazards regression models were fitted for 4137 baseline protein measurements adjusting for known risk factors. Protein associations were tested for replication in the Cardiovascular Health Study (CHS). Causal relationships were examined in a bidirectional, two-sample Mendelian randomization analysis. The time-dependent area under the receiver operating characteristic curve (AUC)-statistic was examined as protein levels and an AF-polygenic risk score (PRS) were added to clinical risk models. The proteomic signature of incident AF consisted of 76 proteins, of which 63 (83%) were novel and 29 (38%) were replicated in CHS. The signature included both N-terminal prohormone of brain natriuretic peptide (NT-proBNP)-dependent (e.g. CHST15, ATP1B1, and SVEP1) and independent components (e.g. ASPN, AKR1B, and LAMA1/LAMB1/LAMC1). Nine causal candidates were identified (TAGLN, WARS, CHST15, CHMP3, COL15A1, DUSP13, MANBA, QSOX2, and SRL). The reverse causal analysis suggested that most AF-associated proteins were affected by the genetic liability to AF. N-terminal prohormone of brain natriuretic peptide improved the prediction of incident AF events close to baseline with further improvements gained by the AF-PRS at all time points.

CONCLUSION

The AF proteomic signature includes biologically relevant proteins, some of which may be causal. It mainly reflects an NT-proBNP-dependent consequence of the genetic liability to AF. N-terminal prohormone of brain natriuretic peptide is a promising marker for incident AF in the short term, but risk assessment incorporating a PRS may improve long-term risk assessment.

The FCGR2A Is Associated with the Presence of Atherosclerotic Plaques in the Carotid Arteries-A Case-Control Study

BACKGROUND

Atherosclerotic plaques in carotid arteries (APCA) are a prevalent condition with severe potential complications. Studies continuously search for innovative biomarkers for APCA, including those participating in cellular metabolic processes, cell adhesion, immune response, and complement activation. This study aimed to assess the relationship between APCA presence and a broad range of cardiometabolic biomarkers in the general population.

METHODS

The study group consisted of consecutive participants of the population study Bialystok PLUS. The proximity extension assay (PEA) technique from the Olink Laboratory (Uppsala, Sweden) was used to measure the levels of 92 cardiometabolic biomarkers.

RESULTS

The study comprised 693 participants (mean age 48.78 ± 15.27 years, 43.4% males, N = 301). APCA was identified in 46.2% of the participants (N = 320). Of the 92 biomarkers that were investigated, 54 were found to be significantly linked to the diagnosis of APCA. After adjusting for the traditional risk factors for atherosclerosis in multivariate analysis, the only biomarker that remained significantly associated with APCA was FCGR2A.

CONCLUSION

In the general population, the prevalence of APCA is very high. A range of biomarkers are linked with APCA. Nonetheless, the majority of these associations are explained by traditional risk factors for atherosclerosis. The only biomarker that was independently associated with APCA was the FCGR2A.