Target Discovery for Drug Development Using Mendelian Randomization

Association between lipid-lowering drug targets and the risk of cystic kidney disease: a drug-target Mendelian randomization analysis

BACKGROUND

Evidence regarding the causal relationship between lipid-lowering drugs and cystic kidney disease, including polycystic kidney disease (PKD), was limited. This study aimed to evaluate the causal relationship between lipid phenotypes mediated by lipid-lowering drug targets-3-hydroxy-3-methyl glutaryl coenzyme A reductase (HMGCR), proprotein convertase subtilisin/kexin type-9 (PCSK9), and Niemann-Pick C1-like 1 (NPC1L1)-and the risk of cystic kidney disease and PKD.

METHODS

Genetic variants encoding lipid-lowering drug targets-HMGCR, PCSK9, and NPC1L1-from published genome-wide association study (GWAS) statistics were collected to perform drug target Mendelian randomization (MR) analysis. Summary statistics for the GWAS of cystic kidney disease and PKD were obtained from the FinnGen consortium and the European Bioinformatics Institute. Inverse variance weighting (IVW) was used as the primary MR analysis method, with sensitivity analyses conducted to ensure the robustness of the results.

RESULTS

Increased gene expression of HMGCR was associated with an elevated risk of cystic kidney disease (IVW-MR: odds ratio [OR] = 3.05, 95% confidence interval [CI] = 1.19-7.84, p = 0.02) and PKD (IVW-MR: OR = 2.13, 95% CI = 1.01-4.46; p = 0.045). There was no evidence of causal effects of PCSK9 and NPC1L1 targets on cystic kidney disease and PKD. Cochran's Q test, MR-PRESSO, and MR-Egger intercept tests showed no heterogeneity or horizontal pleiotropy among the instrumental variables.

CONCLUSIONS

This study supported that increased HMGCR expression was associated with an increased risk of cystic kidney disease and PKD, suggesting potential benefits of statin therapy for cystic kidney disease and PKD. Further research is necessary to elucidate specific mechanisms and potential therapeutic applications of HMGCR inhibitors.

Identification of Novel Therapeutic Targets for Hypertension

BACKGROUND

Persistently high blood pressure remains the leading risk factor for mortality worldwide. This study aims to identify potential drug targets for hypertension.

METHODS

Mendelian randomization was used to identify therapeutic targets for hypertension. Genome-wide association study summary statistics were obtained from the UK Biobank and FinnGen study. Cis-expression quantitative trait loci from the eQTLGen Consortium served as genetic instruments. Colocalization analysis evaluated the likelihood of shared causal variants between single-nucleotide polymorphisms influencing hypertension and gene expression. Survival analysis of UK Biobank data assessed hypertension and mortality risks across participants with different gene alleles.

RESULTS

Mendelian randomization analysis identified 190 drug targets in the discovery cohort and 65 in the replication cohort after multiple testing correction. Colocalization analysis identified 14 hypertension-related drug targets, including ACE, AIMP1, CDC25A, EHMT2, FES, GPX1, GRK4, HSD3B7, NEK4, PTPN12, SIK2, SLC22A4, SLC2A4, and TNFSF12. Survival analysis revealed individuals with the A allele at rs4308 in the ACE gene had a higher incidence of hypertension, while those with the T allele at rs11242109 in the SLC22A4 gene showed a lower hypertension-specific mortality rate.

CONCLUSIONS

Drug target Mendelian randomization studies offer new directions for hypertension treatment, providing insights into its mechanisms and robust targets for developing antihypertensive drugs.

Genetic variation in targets of antihyperglycemic drugs and inflammatory bowel disease' risk: A mendelian randomization study

AIM

Antihyperglycemic drugs have potential therapeutic benefits for inflammatory bowel disease (IBD). We aimed to investigate the association between genetic variations in gene-targeted antihyperglycemic drugs and the risk of IBD.

METHODS

Summary statistics for HbA1c data were from the UK Biobank including 344,182 participants. Statistics of IBD were obtained from UK Inflammatory Bowel Disease Genetics. Two Mendelian randomization methods were employed to derive the main findings.

RESULTS

In the SMR analysis, increased expression of genetic variations in SGLT2 inhibitor targets (gene: SLC5A2) was linked to a higher risk of CD (OR: 1.97, P = 0.048). Genetic variation in brain cerebellum tissue of sulfonylurea targets (gene: ABCC8) expression was positively associated with IBD (OR = 1.11, P = 0.000). The genetic variation in the GLP-1RA targets (gene: GLP1R) expression was positively correlated with IBD (OR: 1.45, P = 0.039). The IVW-MR analysis suggested reduced IBD and CD risk with expression of increased genetic variation in the thiazolidinediones targets (gene: PPARG).

CONCLUSION

Genetic variations in SGLT2 inhibitor targets might be associated with an increased risk of CD. The ABCC8 gene might be linked to IBD, CD, and UC. There might be a positive correlation between genetic variation in the GLP-1RA targets expression and IBD occurrence.

Identification of Potential Therapeutic Targets for Sensorineural Hearing Loss and Evaluation of Drug Development Potential Using Mendelian Randomization Analysis

Background: Sensorineural hearing loss (SNHL) is a major contributor to hearing impairment, yet effective therapeutic options remain elusive. Mendelian randomization (MR) has proven valuable for drug repurposing and identifying new therapeutic targets. This study aims to pinpoint novel treatment targets for SNHL, exploring their pathophysiological roles and potential adverse effects. Methods: This research utilized the UKB-PPP database to access cis-protein quantitative trait locus (cis-pQTL) data, with SNHL data sourced from the FinnGen database as the endpoint for the MR causal analysis of drug targets. Colocalization analysis was employed to determine whether SNHL risk and protein expression share common SNPs. A phenotype-wide association analysis was conducted to assess the potential side effects of these targets. Drug prediction and molecular docking were subsequently used to evaluate the therapeutic potential of the identified targets. Results: Four drug target proteins significantly associated with sensorineural hearing loss (SNHL) were determined by Mendelian randomization (MR) analysis and co-localization analysis. These drug targets include LATS1, TEF, LMNB2, and OGFR and were shown to have fewer potential side effects when acting on these target proteins by phenotype-wide association analysis. Genes associated with sensorineural hearing loss are primarily implicated in the Hippo signaling pathway, cell-cell adhesion, and various binding regulatory activities and are involved in the regulation of cell proliferation and apoptosis. Next, drugs for the treatment of SNHL were screened by the DsigDB database and molecular docking, and the top 10 drugs were selected based on p-value. Among them, atrazine CTD 00005450 was identified as the most likely therapeutic target, followed by ampyrone HL60 DOWN and genistein CTD 00007324. In addition, LMNB2, LATS1, and OGFR could be intervened in by multiple drugs; however, fewer drugs intervened in TEF. Conclusion: This study has successfully identified four promising drug targets for SNHL, which are likely to be effective in clinical trials with minimal side effects. These findings could significantly streamline drug development for SNHL, potentially reducing the costs and time associated with pharmaceutical research and development.

Genetic association analysis of lipid-lowering drug target genes in chronic kidney disease

Objective

The impact of lipid-lowering medications on chronic kidney disease (CKD) remains a subject of debate. This Mendelian randomization (MR) study aims to elucidate the potential effects of lipid-lowering drug targets on CKD development.

Methods

We extracted 11 genetic variants encoding targets of lipid-lowering drugs from published genome-wide association study (GWAS) summary statistics, encompassing LDLR, HMGCR, PCSK9, NPC1L1, APOB, ABCG5/ABCG8, LPL, APOC3, ANGPTL3, and PPARA. A Mendelian randomization analysis was conducted targeting these drug-related genes. CKD risk was designated as the primary outcome, while estimated glomerular filtration rate (eGFR) and blood urea nitrogen (BUN) were assessed as secondary outcomes. Additionally, mediation analysis was performed utilizing 731 immune cell phenotypes to identify potential mediators.

Results

The meta-analysis revealed a significant association between ANGPTL3 inhibitors and a reduced risk of CKD (OR [95% CI] = 0.85 [0.75-0.96]). Conversely, LDLR agonists were significantly linked to an increased risk of CKD (OR [95% CI] = 1.11 [1.02-1.22]). Regarding secondary outcomes, lipid-lowering drugs did not significantly affect eGFR and BUN levels. Mediation analysis indicated that the reduction in CKD risk by ANGPTL3 inhibitors was mediated through modulation of the immune cell phenotype, specifically HLA-DR on CD14+ CD16+ monocytes (Mediated proportion: 4.69%; Mediated effect: -0.00899).

Conclusion

Through drug-targeted MR analysis, we identified a causal relationship between lipid-lowering drug targets and CKD. ANGPTL3 and LDLR may represent promising candidate drug targets for CKD treatment.

The Role of Genetics in Managing Peripheral Arterial Disease

BACKGROUND

Genome wide association studies (GWAS) have allowed for a rapid increase in our understanding of the underlying genetics and biology of many diseases. By capitalizing on common genetic variation between individuals, GWAS can identify DNA variants associated with diseases of interest. A variety of statistical methods can be applied to GWAS results which allows for risk factor identification, stratification, and to identify potential treatments. Peripheral artery disease (PAD) is a common vascular disease that has been shown to have a strong genetic component. This article provides a review of the modern literature and our current understanding of the role of genetics in PAD.

METHODS

All available GWAS studies on PAD were reviewed. A literature search involving these studies was conducted and relevant articles applying the available GWAS data were summarized to provide a comprehensive review of our current understanding of the genetic component in PAD.

RESULTS

The largest available GWAS on PAD has identified 19 genome wide significant loci, with factor V Leiden and genes responsible for circulating lipoproteins being implicated in the development of PAD. Mendelian randomization (MR) studies have identified risk factors and causal associations with smoking, diabetes, and obesity and many other traits; protein-based MR has also identified circulating lipid and clotting factor levels associated with the incidence of PAD. Polygenic risk scores may allow for improved prediction of disease incidence and allow for early identification of at-risk patients but more work needs to be done to validate this approach.

CONCLUSIONS

Genetic epidemiology has allowed for an increased understanding of PAD in the past decade. Genome-wide association studies have led to improved detection of genetic contributions to PAD, and further genetic analyses have validated risk factors and may provide options for improved screening in at-risk populations. Ongoing biobank studies of chronic limb threatening ischemia patients and the increasing ancestral diversity in biobank enrollment will allow for even further exploration into the pathogenesis and progression of PAD.

Current perspectives and trend of computer-aided drug design: a review and bibliometric analysis

AIM

Computer-aided drug design (CADD) is a drug design technique for computing ligand-receptor interactions and is involved in various stages of drug development. To better grasp the frontiers and hotspots of CADD, we conducted a review analysis through bibliometrics.

METHODS

A systematic review of studies published between 2000 and 20 July 2023 was conducted following the PRISMA guidelines. Literature on CADD was selected from the Web of Science Core Collection. General information, publications, output trends, countries/regions, institutions, journals, keywords, and influential authors were visually analyzed using software such as Excel, VOSviewer, RStudio, and CiteSpace.

RESULTS

A total of 2031 publications were included. These publications primarily originated from 99 countries or regions led by the U.S. and China. Among the contributors, MacKerell AD had the highest number of articles and the greatest influence. The Journal of Medicinal Chemistry was the most cited journal, whereas the Journal of Chemical Information and Modeling had the highest number of publications.

CONCLUSIONS

Influential authors in the field were identified. Current research shows active collaboration between countries, institutions, and companies. CADD technologies such as homology modeling, pharmacophore modeling, quantitative conformational relationships, molecular docking, molecular dynamics simulation, binding free energy prediction, and high-throughput virtual screening can effectively improve the efficiency of new drug discovery. Artificial intelligence-assisted drug design and screening based on CADD represent key topics that will influence future development. Furthermore, this paper will be helpful in better understanding the frontiers and hotspots of CADD.

Identification of potential therapeutic targets for breast cancer using Mendelian randomization analysis and drug target prediction

Breast cancer stands as the foremost cause of cancer-related mortality among women, presenting a substantial economic impact on society. The limitations in current therapeutic options, coupled with poor patient tolerance, underscore the urgent need for novel treatments. Our study embarked on a genomic association exploration of breast cancer, leveraging whole-genome sequencing data from the Finngen database, complemented by expression quantitative trait loci (eQTL) insights from the eQTLGen and GTEx Consortiums. An initial investigation was conducted through summary-based Mendelian randomization (MR) to pinpoint primary eQTLs. Analysis of blood specimens revealed 103 eQTLs significantly correlated with breast cancer. Focusing our efforts, we identified 19 candidates with potential therapeutic significance. Further scrutiny via two-sample MR pinpointed UROD, LMO4, HORMAD1, and ZSWIM5 as promising targets for breast cancer therapy. Our research sheds light on new avenues for the treatment of breast cancer, highlighting the potential of genomic association studies in uncovering viable therapeutic targets.

Genetic association of lipid-lowering drug target genes with erectile dysfunction and male reproductive health

Objective

The effect of hypolipidemic drugs on male erectile function is still controversial. This Mendelian randomization (MR) study aimed to explore the potential impact of lipid-lowering drug targets on ED.

Methods

We collected seven genetic variants encoding lipid-lowering drug targets (LDLR, HMGCR, NPC1L1, PCSK9, APOB, APOC3 and LPL) from published genome-wide association study (GWAS) statistics, and performed drug target MR analysis. The risk of ED was defined as the primary outcome, sex hormone levels and other diseases as the secondary outcomes. Mediation analyses were performed to explore potential mediating factors.

Results

The results showed that LDLR, LPL agonists and APOC3 inhibitors were significantly associated with a reduced risk of ED occurrence. APOB inhibitors were associated with an increased risk of ED occurrence. In terms of sex hormone levels, LDLR and LPL agonists were significantly associated with increased TT levels, and HMGCR was associated with decreased TT and BT levels significantly. In terms of male-related disease, MR results showed that LDLR agonists and PCSK9 inhibitors were significantly associated with an elevated risk of PH; HMGCR, NPC1L1 inhibitors were associated with a reduced risk of PCa; and LDLR agonists were significantly associated with a reduced risk of AS and MI; in addition, HMGCR inhibitors were associated with a reduced risk of PCa.

Conclusion

After performing drug-targeted MR analysis, we found that that there was a causal relationship between lipid-lowering drug targets and ED. APOC3, APOB, LDLR and LPL may be new candidate drug targets for the treatment of ED.

Causal effects of lipid-lowering therapies on aging-related outcomes and risk of cancers: a drug-target Mendelian randomization study

BACKGROUND

Despite the widespread use of statins, newer lipid-lowering drugs have been emerging. It remains unclear how the long-term use of novel lipid-lowering drugs affects the occurrence of cancers and age-related diseases.

METHODS

A drug-target Mendelian randomization study was performed. Genetic variants of nine lipid-lowering drug-target genes (HMGCR, PCKS9, NPC1L1, LDLR, APOB, CETP, LPL, APOC3, and ANGPTL3) were extracted as exposures from the summary data of Global Lipids Genetics Consortium Genome-Wide Association Studies (GWAS). GWAS summary data of cancers and noncancerous diseases were used as outcomes. The inverse-variance weighted method was applied as the main statistical approach. Sensitivity tests were conducted to evaluate the robustness, pleiotropy, and heterogeneity of the results.

RESULTS

In addition to marked effects on decreased risks of atherosclerotic cardiovascular diseases, genetically proxied lipid-lowering variants of PCKS9, CETP, LPL, LDLR, and APOC3 were associated with longer human lifespans (q<0.05). Lipid-lowering variants of ANGPTL3 and LDLR were associated with reduced risks of colorectal cancer, and ANGPTL3 was also associated with lower risks of gastric cancer (q<0.05). Lipid-lowering LPL variants were associated with decreased risks of hypertension, type 2 diabetes, nonalcoholic fatty liver disease, and bladder cancer (q<0.05). Lipid-lowering variants of PCKS9 and HMGCR were associated with decreased risks of osteoporosis (q<0.05). Lipid-lowering APOB variants were associated with a decreased risk of thyroid cancer (q<0.05).

CONCLUSIONS

Our study provides genetic evidence that newer nonstatin lipid-lowering agents have causal effects on decreased risks of several common cancers and cardiometabolic diseases. These data provide genetic insights into the potential benefits of newer nonstatin therapies.

Genetic insights into the association of statin and newer nonstatin drug target genes with human longevity: a Mendelian randomization analysis

BACKGROUND

It remains controversial whether the long-term use of statins or newer nonstatin drugs has a positive effect on human longevity. Therefore, this study aimed to investigate the genetic associations between different lipid-lowering therapeutic gene targets and human longevity.

METHODS

Two-sample Mendelian randomization analyses were conducted. The exposures comprised genetic variants that proxy nine drug target genes mimicking lipid-lowering effects (LDLR, HMGCR, PCKS9, NPC1L1, APOB, CETP, LPL, APOC3, and ANGPTL3). Two large-scale genome-wide association study (GWAS) summary datasets of human lifespan, including up to 500,193 European individuals, were used as outcomes. The inverse-variance weighting method was applied as the main approach. Sensitivity tests were conducted to evaluate the robustness, heterogeneity, and pleiotropy of the results. Causal effects were further validated using expression quantitative trait locus (eQTL) data.

RESULTS

Genetically proxied LDLR variants, which mimic the effects of lowering low-density lipoprotein cholesterol (LDL-C), were associated with extended lifespan. This association was replicated in the validation set and was further confirmed in the eQTL summary data of blood and liver tissues. Mediation analysis revealed that the genetic mimicry of LDLR enhancement extended lifespan by reducing the risk of major coronary heart disease, accounting for 22.8% of the mediation effect. The genetically proxied CETP and APOC3 inhibitions also showed causal effects on increased life expectancy in both outcome datasets. The lipid-lowering variants of HMGCR, PCKS9, LPL, and APOB were associated with longer lifespans but did not causally increase extreme longevity. No statistical evidence was detected to support an association between NPC1L1 and lifespan.

CONCLUSION

This study suggests that LDLR is a promising genetic target for human longevity. Lipid-related gene targets, such as PCSK9, CETP, and APOC3, might potentially regulate human lifespan, thus offering promising prospects for developing newer nonstatin therapies.

Genetic and Gene Expression Resources for Osteoporosis and Bone Biology Research

PURPOSE OF REVIEW

The integration of data from multiple genomic assays from humans and non-human model organisms is an effective approach to identify genes involved in skeletal fragility and fracture risk due to osteoporosis and other conditions. This review summarizes genome-wide genetic variation and gene expression data resources relevant to the discovery of genes contributing to skeletal fragility and fracture risk.

RECENT FINDINGS

Genome-wide association studies (GWAS) of osteoporosis-related traits are summarized, in addition to gene expression in bone tissues in humans and non-human organisms, with a focus on rodent models related to skeletal fragility and fracture risk. Gene discovery approaches using these genomic data resources are described. We also describe the Musculoskeletal Knowledge Portal (MSKKP) that integrates much of the available genomic data relevant to fracture risk. The available genomic resources provide a wealth of knowledge and can be analyzed to identify genes related to fracture risk. Genomic resources that would fill particular scientific gaps are discussed.