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Senkevich K, Liu L, Alvarado CX, Leonard HL, Nalls MA, Gan-Or Z. Lack of genetic evidence for NLRP3 inflammasome involvement in Parkinson's disease pathogenesis. NPJ Parkinsons Dis 2024; 10:145. [PMID: 39103393 DOI: 10.1038/s41531-024-00744-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 06/26/2024] [Indexed: 08/07/2024] Open
Abstract
Activation of the NLRP3 inflammasome has been implicated in Parkinson's disease (PD) based on in vitro and in vivo studies. Clinical trials targeting the NLRP3 inflammasome in PD are ongoing. However, the evidence supporting NLRP3's involvement in PD from human genetics data is limited. We analyzed common and rare variants in NLRP3 inflammasome-related genes in PD cohorts, performed pathway-specific polygenic risk score (PRS) analyses, and studied causal associations using Mendelian randomization (MR) with the NLRP3 components and the cytokines IL-1β and IL-18. Our findings showed no associations of common or rare variants, nor of the pathway PRS with PD. MR suggests that altering the expression of the NLRP3 inflammasome, IL-1β, or IL-18, does not affect PD risk or progression. Therefore, our results do not support a role for the NLRP3 inflammasome in PD pathogenesis or as a target for drug development.
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Affiliation(s)
- Konstantin Senkevich
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada
- Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada
| | - Lang Liu
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada
- Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Chelsea X Alvarado
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20814, USA
- Data Tecnica, Washington, DC, 200373, USA
| | - Hampton L Leonard
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20814, USA
- Data Tecnica, Washington, DC, 200373, USA
- DZNE Tübingen, Tübingen, Germany
| | - Mike A Nalls
- Center for Alzheimer's and Related Dementias (CARD), National Institute on Aging and National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20814, USA
- Data Tecnica, Washington, DC, 200373, USA
| | - Ziv Gan-Or
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, QC, Canada.
- Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada.
- Department of Human Genetics, McGill University, Montréal, QC, Canada.
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Yin K, Chen T, Gu X, Su W, Jiang Z, Lu S, Cao B, Chi L, Gao X, Chen Y. Systematic druggable genome-wide Mendelian randomization identifies therapeutic targets for sarcopenia. J Cachexia Sarcopenia Muscle 2024; 15:1324-1334. [PMID: 38644354 PMCID: PMC11294052 DOI: 10.1002/jcsm.13479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 02/27/2024] [Accepted: 03/07/2024] [Indexed: 04/23/2024] Open
Abstract
BACKGROUND There are no effective pharmacological treatments for sarcopenia. We aim to identify potential therapeutic targets for sarcopenia by integrating various publicly available datasets. METHODS We integrated druggable genome data, cis-eQTL/cis-pQTL from human blood and skeletal muscle tissue, and GWAS summary data of sarcopenia-related traits to analyse the potential causal relationships between drug target genes and sarcopenia using the Mendelian Randomization (MR) method. Sensitivity analyses and Bayesian colocalization were employed to validate the causal relationships. We also assessed the side effects or additional indications of the identified drug targets using a phenome-wide MR (Phe-MR) approach and investigated actionable drugs for target genes using available databases. RESULTS MR analysis identified 17 druggable genes with potential causation to sarcopenia in human blood or skeletal muscle tissue. Six of them (HP, HLA-DRA, MAP 3K3, MFGE8, COL15A1, and AURKA) were further confirmed by Bayesian colocalization (PPH4 > 90%). The up-regulation of HP [higher ALM (beta: 0.012, 95% CI: 0.007-0.018, P = 1.2*10-5) and higher grip strength (OR: 0.96, 95% CI: 0.94-0.98, P = 4.2*10-5)], MAP 3K3 [higher ALM (beta: 0.24, 95% CI: 0.21-0.26, P = 1.8*10-94), higher grip strength (OR: 0.82, 95% CI: 0.75-0.90, P = 2.1*10-5), and faster walking pace (beta: 0.03, 95% CI: 0.02-0.05, P = 8.5*10-6)], and MFGE8 [higher ALM (muscle eQTL, beta: 0.09, 95% CI: 0.06-0.11, P = 6.1*10-13; blood pQTL, beta: 0.05, 95% CI: 0.03-0.07, P = 3.8*10-09)], as well as the down-regulation of HLA-DRA [lower ALM (beta: -0.09, 95% CI: -0.11 to -0.08, P = 5.4*10-36) and lower grip strength (OR: 1.13, 95% CI: 1.07-1.20, P = 1.8*10-5)] and COL15A1 [higher ALM (muscle eQTL, beta: -0.07, 95% CI: -0.10 to -0.04, P = 3.4*10-07; blood pQTL, beta: -0.05, 95% CI: -0.06 to -0.03, P = 1.6*10-07)], decreased the risk of sarcopenia. AURKA in blood (beta: -0.16, 95% CI: -0.22 to -0.09, P = 2.1*10-06) and skeletal muscle (beta: 0.03, 95% CI: 0.02 to 0.05, P = 5.3*10-05) tissues showed an inverse relationship with sarcopenia risk. The Phe-MR indicated that the six potential therapeutic targets for sarcopenia had no significant adverse effects. Drug repurposing analysis supported zinc supplementation and collagenase clostridium histolyticum might be potential therapeutics for sarcopenia by activating HP and inhibiting COL15A1, respectively. CONCLUSIONS Our research indicated MAP 3K3, MFGE8, COL15A1, HP, and HLA-DRA may serve as promising targets for sarcopenia, while the effectiveness of zinc supplementation and collagenase clostridium histolyticum for sarcopenia requires further validation.
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Affiliation(s)
- Kang‐Fu Yin
- Department of Neurology, West China HospitalSichuan UniversityChengduChina
- Institute of Brain Science and Brain‐Inspired Technology, West China HospitalSichuan UniversityChengduChina
| | - Ting Chen
- Department of Neurology, West China HospitalSichuan UniversityChengduChina
- Institute of Brain Science and Brain‐Inspired Technology, West China HospitalSichuan UniversityChengduChina
| | - Xiao‐Jing Gu
- Mental Health Center, West China HospitalSichuan UniversityChengduChina
| | - Wei‐Ming Su
- Department of Neurology, West China HospitalSichuan UniversityChengduChina
- Institute of Brain Science and Brain‐Inspired Technology, West China HospitalSichuan UniversityChengduChina
| | - Zheng Jiang
- Department of Neurology, West China HospitalSichuan UniversityChengduChina
- Institute of Brain Science and Brain‐Inspired Technology, West China HospitalSichuan UniversityChengduChina
| | - Si‐Jia Lu
- Department of RespiratoryThe Fourth People's Hospital of Chengdu, Mental Health Center of ChengduChengduChina
| | - Bei Cao
- Department of Neurology, West China HospitalSichuan UniversityChengduChina
- Institute of Brain Science and Brain‐Inspired Technology, West China HospitalSichuan UniversityChengduChina
| | - Li‐Yi Chi
- Department of NeurologyFirst Affiliated Hospital of Air Force Military Medical UniversityXi'anChina
| | - Xia Gao
- Department of GeriatricsDazhou Central HospitalDazhouChina
| | - Yong‐Ping Chen
- Department of Neurology, West China HospitalSichuan UniversityChengduChina
- Institute of Brain Science and Brain‐Inspired Technology, West China HospitalSichuan UniversityChengduChina
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3
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Qi T, Song L, Guo Y, Chen C, Yang J. From genetic associations to genes: methods, applications, and challenges. Trends Genet 2024; 40:642-667. [PMID: 38734482 DOI: 10.1016/j.tig.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/13/2024]
Abstract
Genome-wide association studies (GWASs) have identified numerous genetic loci associated with human traits and diseases. However, pinpointing the causal genes remains a challenge, which impedes the translation of GWAS findings into biological insights and medical applications. In this review, we provide an in-depth overview of the methods and technologies used for prioritizing genes from GWAS loci, including gene-based association tests, integrative analysis of GWAS and molecular quantitative trait loci (xQTL) data, linking GWAS variants to target genes through enhancer-gene connection maps, and network-based prioritization. We also outline strategies for generating context-dependent xQTL data and their applications in gene prioritization. We further highlight the potential of gene prioritization in drug repurposing. Lastly, we discuss future challenges and opportunities in this field.
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Affiliation(s)
- Ting Qi
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
| | - Liyang Song
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Yazhou Guo
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Chang Chen
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Jian Yang
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China; School of Life Sciences, Westlake University, Hangzhou 310024, China.
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Krishna C, Chiou J, Sakaue S, Kang JB, Christensen SM, Lee I, Aksit MA, Kim HI, von Schack D, Raychaudhuri S, Ziemek D, Hu X. The influence of HLA genetic variation on plasma protein expression. Nat Commun 2024; 15:6469. [PMID: 39085222 PMCID: PMC11291675 DOI: 10.1038/s41467-024-50583-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 07/15/2024] [Indexed: 08/02/2024] Open
Abstract
Genetic variation in the human leukocyte antigen (HLA) loci is associated with risk of immune-mediated diseases, but the molecular effects of HLA polymorphism are unclear. Here we examined the effects of HLA genetic variation on the expression of 2940 plasma proteins across 45,330 Europeans in the UK Biobank, with replication analyses across multiple ancestry groups. We detected 504 proteins affected by HLA variants (HLA-pQTL), including widespread trans effects by autoimmune disease risk alleles. More than 80% of the HLA-pQTL fine-mapped to amino acid positions in the peptide binding groove. HLA-I and II affected proteins expressed in similar cell types but in different pathways of both adaptive and innate immunity. Finally, we investigated potential HLA-pQTL effects on disease by integrating HLA-pQTL with fine-mapped HLA-disease signals in the UK Biobank. Our data reveal the diverse effects of HLA genetic variation and aid the interpretation of associations between HLA alleles and immune-mediated diseases.
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Affiliation(s)
- Chirag Krishna
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA.
| | - Joshua Chiou
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Joyce B Kang
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Isac Lee
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA
| | | | - Hye In Kim
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - David von Schack
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Daniel Ziemek
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA
| | - Xinli Hu
- Pfizer Research and Development, Pfizer Inc., Cambridge, MA, USA.
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5
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Doostparast Torshizi A, Truong DT, Hou L, Smets B, Whelan CD, Li S. Proteogenomic network analysis reveals dysregulated mechanisms and potential mediators in Parkinson's disease. Nat Commun 2024; 15:6430. [PMID: 39080267 PMCID: PMC11289099 DOI: 10.1038/s41467-024-50718-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 07/18/2024] [Indexed: 08/02/2024] Open
Abstract
Parkinson's disease is highly heterogeneous across disease symptoms, clinical manifestations and progression trajectories, hampering the identification of therapeutic targets. Despite knowledge gleaned from genetics analysis, dysregulated proteome mechanisms stemming from genetic aberrations remain underexplored. In this study, we develop a three-phase system-level proteogenomic analytical framework to characterize disease-associated proteins and dysregulated mechanisms. Proteogenomic analysis identified 577 proteins that enrich for Parkinson's disease-related pathways, such as cytokine receptor interactions and lysosomal function. Converging lines of evidence identified nine proteins, including LGALS3, CSNK2A1, SMPD3, STX4, APOA2, PAFAH1B3, LDLR, HSPB1, BRK1, with potential roles in disease pathogenesis. This study leverages the largest population-scale proteomics dataset, the UK Biobank Pharma Proteomics Project, to characterize genetically-driven protein disturbances associated with Parkinson's disease. Taken together, our work contributes to better understanding of genome-proteome dynamics in Parkinson's disease and sets a paradigm to identify potential indirect mediators connected to GWAS signals for complex neurodegenerative disorders.
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Affiliation(s)
- Abolfazl Doostparast Torshizi
- Population Analytics & Insights, AI/ML, Data Science & Digital Health, Janssen Research & Development, LLC, Spring House, PA, USA.
| | - Dongnhu T Truong
- Population Analytics & Insights, AI/ML, Data Science & Digital Health, Janssen Research & Development, LLC, Spring House, PA, USA
| | - Liping Hou
- Population Analytics & Insights, AI/ML, Data Science & Digital Health, Janssen Research & Development, LLC, Spring House, PA, USA
| | - Bart Smets
- Neuroscience Data Science, Janssen Pharmaceutica NV, Beerse, Belgium
| | - Christopher D Whelan
- Neuroscience Data Science, Janssen Research & Development, LLC, Cambridge, MA, USA
| | - Shuwei Li
- Population Analytics & Insights, AI/ML, Data Science & Digital Health, Janssen Research & Development, LLC, Spring House, PA, USA
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Li MM, Huang Y, Sumathipala M, Liang MQ, Valdeolivas A, Ananthakrishnan AN, Liao K, Marbach D, Zitnik M. Contextual AI models for single-cell protein biology. Nat Methods 2024:10.1038/s41592-024-02341-3. [PMID: 39039335 DOI: 10.1038/s41592-024-02341-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 06/10/2024] [Indexed: 07/24/2024]
Abstract
Understanding protein function and developing molecular therapies require deciphering the cell types in which proteins act as well as the interactions between proteins. However, modeling protein interactions across biological contexts remains challenging for existing algorithms. Here we introduce PINNACLE, a geometric deep learning approach that generates context-aware protein representations. Leveraging a multiorgan single-cell atlas, PINNACLE learns on contextualized protein interaction networks to produce 394,760 protein representations from 156 cell type contexts across 24 tissues. PINNACLE's embedding space reflects cellular and tissue organization, enabling zero-shot retrieval of the tissue hierarchy. Pretrained protein representations can be adapted for downstream tasks: enhancing 3D structure-based representations for resolving immuno-oncological protein interactions, and investigating drugs' effects across cell types. PINNACLE outperforms state-of-the-art models in nominating therapeutic targets for rheumatoid arthritis and inflammatory bowel diseases and pinpoints cell type contexts with higher predictive capability than context-free models. PINNACLE's ability to adjust its outputs on the basis of the context in which it operates paves the way for large-scale context-specific predictions in biology.
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Affiliation(s)
- Michelle M Li
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yepeng Huang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marissa Sumathipala
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Man Qing Liang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Alberto Valdeolivas
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Ashwin N Ananthakrishnan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Katherine Liao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Marbach
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Kempner Institute for the Study of Natural and Artificial Intelligence, Harvard University, Allston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Data Science Initiative, Cambridge, MA, USA.
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Sun X, Chen B, Qi Y, Wei M, Chen W, Wu X, Wang Q, Li J, Lei X, Luo G. Multi-omics Mendelian randomization integrating GWAS, eQTL and pQTL data revealed GSTM4 as a potential drug target for migraine. J Headache Pain 2024; 25:117. [PMID: 39039470 PMCID: PMC11265128 DOI: 10.1186/s10194-024-01828-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Accepted: 07/12/2024] [Indexed: 07/24/2024] Open
Abstract
INTRODUCTION Migraine, as a complex neurological disease, brings heavy burden to patients and society. Despite the availability of established therapies, existing medications have limited efficacy. Thus, we aimed to find the drug targets that improve the prognosis of migraine. METHOD We used Mendelian Randomization (MR) and Summary-data-based MR (SMR) analyses to study possible drug targets of migraine by summary statistics from FinnGen cohorts (nCase = 44,616, nControl = 367,565), with further replication in UK Biobank (nCase = 26,052, nControl = 487,214). Genetic instruments were obtained from eQTLGen and UKB-PPP to verify the drug targets at the gene expression and protein levels. The additional analyses including Bayesian co-localization, the heterogeneity in dependent instruments(HEIDI), Linkage Disequilibrium Score(LDSC), bidirectional MR, multivariate MR(MVMR), heterogeneity test, horizontal pleiotropy test, and Steiger filtering were implemented to consolidate the findings further. Lastly, drug prediction analysis and phenome-wide association study(PheWAS) were employed to imply the possibility of drug targets for future clinical applications. RESULT The MR analysis of eQTL data showed that four drug targets (PROCR, GSTM4, SLC4A1, and TNFRSF10A) were significantly associated with migraine risk in both the FinnGen and UK Biobank cohorts. However, only GSTM4 exhibited consistent effect directions across the two outcomes(Discovery cohort: OR(95%CI) = 0.94(0.93-0.96); p = 2.70e - 10; Replication cohort: OR(95%CI) = 0.93(0.91-0.94); p = 4.21e - 17). Furthermore, GSTM4 passed the SMR at p < 0.05 and HEIDI test at p > 0.05 at both the gene expression and protein levels. The protein-level MR analysis revealed a strong correlation between genetically predicted GSTM4 with a lower incidence of migraine and its subtypes(Overall migraine: OR(95%CI) = 0.91(0.87-0.95); p = 6.98e-05; Migraine with aura(MA): OR(95%CI) = 0.90(0.85-0.96); p = 2.54e-03; Migraine without aura(MO): OR(95%CI) = 0.90(0.83-0.96); p = 2.87e-03), indicating a strong co-localization relationship (PPH4 = 0.86). Further analyses provided additional validation for the possibility of GSTM4 as a migraine treatment target. CONCLUSION This study identifies GSTM4 as a potential druggable gene and promising therapeutic target for migraine.
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Affiliation(s)
- Xinyue Sun
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Bohong Chen
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Yi Qi
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Meng Wei
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Wanying Chen
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xiaoyu Wu
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Qingfan Wang
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Jiahao Li
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xiangyu Lei
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
| | - Guogang Luo
- Department of Neurology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
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Lee PC, Jung IH, Thussu S, Patel V, Wagoner R, Burks KH, Amrute J, Elenbaas JS, Kang CJ, Young EP, Scherer PE, Stitziel NO. Instrumental variable and colocalization analyses identify endotrophin and HTRA1 as potential therapeutic targets for coronary artery disease. iScience 2024; 27:110104. [PMID: 38989470 PMCID: PMC11233907 DOI: 10.1016/j.isci.2024.110104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 03/26/2024] [Accepted: 05/22/2024] [Indexed: 07/12/2024] Open
Abstract
Coronary artery disease (CAD) remains a leading cause of disease burden globally, and there is a persistent need for new therapeutic targets. Instrumental variable (IV) and genetic colocalization analyses can help identify novel therapeutic targets for human disease by nominating causal genes in genome-wide association study (GWAS) loci. We conducted cis-IV analyses for 20,125 genes and 1,746 plasma proteins with CAD using molecular trait quantitative trait loci variant (QTLs) data from three different studies. 19 proteins and 119 genes were significantly associated with CAD risk by IV analyses and demonstrated evidence of genetic colocalization. Notably, our analyses validated well-established targets such as PCSK9 and ANGPTL4 while also identifying HTRA1 and endotrophin (a cleavage product of COL6A3) as proteins whose levels are causally associated with CAD risk. Further experimental studies are needed to confirm the causal role of the genes and proteins identified through our multiomic cis-IV analyses on human disease.
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Affiliation(s)
- Paul C. Lee
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - In-Hyuk Jung
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Shreeya Thussu
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ved Patel
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Ryan Wagoner
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Kendall H. Burks
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Junedh Amrute
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Jared S. Elenbaas
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Chul Joo Kang
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Erica P. Young
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Philipp E. Scherer
- Touchstone Diabetes Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Nathan O. Stitziel
- Center for Cardiovascular Research, Division of Cardiology, Department of Medicine, Washington University School of Medicine, Saint Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University School of Medicine, Saint Louis, MO 63108, USA
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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Zhao QG, Song ZT, Ma XL, Xu Q, Bu F, Li K, Zhang L, Pei YF. Human brain proteome-wide association study provides insights into the genetic components of protein abundance in obesity. Int J Obes (Lond) 2024:10.1038/s41366-024-01592-6. [PMID: 39025989 DOI: 10.1038/s41366-024-01592-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 07/10/2024] [Accepted: 07/10/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUNDS Genome-wide association studies have identified multiple genetic variants associated with obesity. However, most obesity-associated loci were waiting to be translated into new biological insights. Given the critical role of brain in obesity development, we sought to explore whether obesity-associated genetic variants could be mapped to brain protein abundances. METHODS We performed proteome-wide association studies (PWAS) and colocalization analyses to identify genes whose cis-regulated brain protein abundances were associated with obesity-related traits, including body fat percentage, trunk fat percentage, body mass index, visceral adipose tissue, waist circumference, and waist-to-hip ratio. We then assessed the druggability of the identified genes and conducted pathway enrichment analysis to explore their functional relevance. Finally, we evaluated the effects of the significant PWAS genes at the brain transcriptional level. RESULTS By integrating human brain proteomes from discovery (ROSMAP, N = 376) and validation datasets (BANNER, N = 198) with genome-wide summary statistics of obesity-related phenotypes (N ranged from 325,153 to 806,834), we identified 51 genes whose cis-regulated brain protein abundance was associated with obesity. These 51 genes were enriched in 11 metabolic processes, e.g., small molecule metabolic process and metabolic pathways. Fourteen of the 51 genes had high drug repurposing value. Ten of the 51 genes were also associated with obesity at the transcriptome level, suggesting that genetic variants likely confer risk of obesity by regulating mRNA expression and protein abundance of these genes. CONCLUSIONS Our study provides new insights into the genetic component of human brain protein abundance in obesity. The identified proteins represent promising therapeutic targets for future drug development.
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Affiliation(s)
- Qi-Gang Zhao
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Zi-Tong Song
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Xin-Ling Ma
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Qian Xu
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Fan Bu
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Kuan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China
| | - Lei Zhang
- Center for Genetic Epidemiology and Genomics, School of Public Health, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China.
| | - Yu-Fang Pei
- Department of Epidemiology and Biostatistics, School of Public Health, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu, PR China.
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Sun D, Wang R, Du Q, Chen H, Shi Z, Zhang Y, Zhang N, Wang X, Zhou H. Integrating genetic and proteomic data to elucidate the association between immune system and blood-brain barrier dysfunction with multiple sclerosis risk and severity. J Affect Disord 2024; 362:652-660. [PMID: 39029667 DOI: 10.1016/j.jad.2024.07.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 07/21/2024]
Abstract
BACKGROUND Immune system dysfunction and blood-brain barrier (BBB) impairment are implicated in multiple sclerosis (MS) risk and severity. However, the causal relationships and potential therapeutic targets remain unclear. METHODS Leveraging the MRC IEU OpenGWAS data infrastructure, we extracted 1254 peripheral immune systems and 792 BBB biomarkers as genetic instruments for exposure. MS risk data from the International Multiple Sclerosis Genetics Consortium (IMSGC) (47,429 MS cases, 68,374 controls) served as one outcome, replicated in FinnGen (1048 cases, 217,141 controls) and the UK Biobank (1679 cases, 461,254 controls). Genetic associations with MS severity derived from IMSGC and MultipleMS Consortium GWAS data (12,584 cases). Two-sample, bidirectional, and protein drug-target MR analyses were conducted, along with interaction analysis of identified proteins and druggability assessment. RESULTS Causal relationships between 45 immunological markers, 15 BBB markers, and MS risk were strongly supported. In peripheral immunity, the causal associations with MS are predominantly concentrated in CD4+ T cells and CD8+ T cells. Notably, anti-Epstein-Barr virus nuclear antigen (EBNA) IgG levels exhibited the most significant causal effect on MS risk (OR = 225.62, P = 5.63E-208), replicated in the MS severity (OR = 1.11, P = 0.04). Weak causal evidence was found between 62 immunological markers, 35 BBB markers, and MS severity. Reverse MR analysis suggested potential causal effects of MS risk on 8 markers. Drug-targeted MR analysis indicated potential therapeutic benefits in reducing MS risk for CD40 (OR = 0.71, P = 7.24E-13, PPH4 = 97.6 %), AHSG (OR = 0.88, P = 2.91E-05, PPH4 = 94.4 %), and FCRL3 (Sun BB et al.: OR = 0.83, P = 8.93E-09, PPH4 = 94.2 %, Suhre K et al.: OR = 0.88, P = 5.20E-08, PPH4 = 99.2 %). CONCLUSIONS This study provides evidence supporting the causal effects of immune system and BBB dysfunction on MS risk and severity. It emphasizes the significant role of anti-EBNA IgG levels, CD4+ T cells, and CD8+ T cells in MS, and delineates the potential therapeutic benefits of targeting three proteins associated with MS risk: CD40, AHSG, and FCRL3.
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Affiliation(s)
- Dongren Sun
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Rui Wang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Qin Du
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Hongxi Chen
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Ziyan Shi
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Yangyang Zhang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Nana Zhang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China
| | - Xiaofei Wang
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China.
| | - Hongyu Zhou
- Department of Neurology, West China Hospital, Sichuan University, Guo Xuexiang No. 37, Chengdu 610041, China.
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Batistatou N, Kritzer JA. Recent advances in methods for quantifying the cell penetration of macromolecules. Curr Opin Chem Biol 2024; 81:102501. [PMID: 39024686 DOI: 10.1016/j.cbpa.2024.102501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/20/2024]
Abstract
As the landscape of macromolecule therapeutics advances, drug developers are continuing to aim at intracellular targets. To activate, inhibit, or degrade these targets, the macromolecule must be delivered efficiently to intracellular compartments. Quite often, there is a discrepancy between binding affinity in biochemical assays and activity in cell-based assays. Identifying the bottleneck for cell-based activity requires robust assays that quantify total cellular uptake and/or cytosolic delivery. Recognizing this need, chemical biologists have designed a plethora of assays to make this measurement, each with distinct advantages and disadvantages. In this review, we describe the latest and most promising developments in the last 3 to 4 years.
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Affiliation(s)
| | - Joshua A Kritzer
- Department of Chemistry, Tufts University, Medford MA 02155, USA.
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12
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Zhai T. Druggable genome-wide Mendelian randomization for identifying the role of integrated stress response in therapeutic targets of bipolar disorder. J Affect Disord 2024; 362:843-852. [PMID: 39025441 DOI: 10.1016/j.jad.2024.07.043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 06/13/2024] [Accepted: 07/12/2024] [Indexed: 07/20/2024]
Abstract
For bipolar disorder (BD), the inconsistency of treatment guidelines and the long phases of pharmacological adjustment remain major challenges. BD is known to be comorbid with many medical and psychiatric conditions and they may share inflammatory and stress-related aetiologies, which could give rise to this association. The integrated stress response (ISR) responds to various stress conditions that lead to alterations in cellular homeostasis. However, as a causative mechanism underlying cognitive deficits and neurodegeneration in a broad range of brain disorders, the impact of ISR on BD is understudied. Mendelian randomization has been widely used to repurpose licensed drugs and discover novel therapeutic targets. Thus, we aimed to identify novel therapeutic targets for BD and analyze their pathophysiological mechanisms, using the summary data-based Mendelian Randomization (SMR) and Bayesian colocalization (COLOC) methods to integrate the summary-level data of the GWAS on BD and the expression quantitative trait locus (eQTL) study in blood. We utilized the GWAS data including 41,917 BD cases and 371,549 controls from the Psychiatric Genomics Consortium and the eQTL data from 31,684 participants of predominantly European ancestry from the eQTLGen consortium. The SMR analysis identified the EIF2B5 gene that was associated with BD due to no linkage but pleiotropy or causality. The COLOC analysis strongly suggested that EIF2B5 and the trait of BD were affected by shared causal variants, and thus were colocalized. Utilizing data in EpiGraphDB we find other putative causal BD genes (EIF2AK4 and GSK3B) to prioritize potential alternative drug targets.
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Affiliation(s)
- Ting Zhai
- School of Humanities, Southeast University, Nanjing 211189, China; Institute of Child Development and Education, Southeast University, Nanjing 211189, China; Key Laboratory of Child Development and Learning Science (Southeast University), Ministry of Education, Nanjing 211189, China.
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13
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Li MM, Huang Y, Sumathipala M, Liang MQ, Valdeolivas A, Ananthakrishnan AN, Liao K, Marbach D, Zitnik M. Contextual AI models for single-cell protein biology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.18.549602. [PMID: 37503080 PMCID: PMC10370131 DOI: 10.1101/2023.07.18.549602] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Understanding protein function and developing molecular therapies require deciphering the cell types in which proteins act as well as the interactions between proteins. However, modeling protein interactions across biological contexts remains challenging for existing algorithms. Here, we introduce Pinnacle, a geometric deep learning approach that generates context-aware protein representations. Leveraging a multi-organ single-cell atlas, Pinnacle learns on contextualized protein interaction networks to produce 394,760 protein representations from 156 cell type contexts across 24 tissues. Pinnacle's embedding space reflects cellular and tissue organization, enabling zero-shot retrieval of the tissue hierarchy. Pretrained protein representations can be adapted for downstream tasks: enhancing 3D structure-based representations for resolving immuno-oncological protein interactions, and investigating drugs' effects across cell types. Pinnacle outperforms state-of-the-art models in nominating therapeutic targets for rheumatoid arthritis and inflammatory bowel diseases, and pinpoints cell type contexts with higher predictive capability than context-free models. Pinnacle's ability to adjust its outputs based on the context in which it operates paves way for large-scale context-specific predictions in biology.
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Affiliation(s)
- Michelle M. Li
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Yepeng Huang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Marissa Sumathipala
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Man Qing Liang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Alberto Valdeolivas
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Ashwin N. Ananthakrishnan
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA
| | - Katherine Liao
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women’s Hospital, Boston, MA, USA
| | - Daniel Marbach
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Marinka Zitnik
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Kempner Institute for the Study of Natural and Artificial Intelligence, Harvard University, Allston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Data Science Initiative, Cambridge, MA, USA
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14
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Gao Y, Zhou Y, Lin Z, Chen F, Wu H, Peng C, Xie Y. Prioritizing drug targets in systemic lupus erythematosus from a genetic perspective: a druggable genome-wide Mendelian randomization study. Clin Rheumatol 2024:10.1007/s10067-024-07059-3. [PMID: 38997544 DOI: 10.1007/s10067-024-07059-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/05/2024] [Accepted: 07/04/2024] [Indexed: 07/14/2024]
Abstract
OBJECTIVES Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease with an unsatisfactory state of treatment. We aim to explore novel targets for SLE from a genetic standpoint. METHODS Cis-expression quantitative trait loci (eQTLs) for whole blood from 31,684 samples provided by the eQTLGen Consortium as well as two large SLE cohorts were utilized for screening and validating genes causally associated with SLE. Colocalization analysis was employed to further investigate whether changes in the expression of risk genes, as indicated by GWAS signals, influence the occurrence and development of SLE. Targets identified for drug development were evaluated for potential side effects using a phenome-wide association study (PheWAS). Based on the multiple databases, we explored the interactions between drugs and genes for drug prediction and the assessment of current medications. RESULTS The analysis comprised 5427 druggable genes in total. The two-sample Mendelian randomization (MR) in the discovery phase identified 20 genes causally associated with SLE and validated 8 genes in the replication phase. Colocalization analysis ultimately identified five genes (BLK, HIST1H3H, HSPA1A, IL12A, NEU1) with PPH4 > 0.8. PheWAS further indicated that drugs acting on BLK and IL12A are less likely to have potential side effects, while HSPA1A and NEU1 were associated with other traits. Four genes (BLK, HSPA1A, IL12A, NEU1) have been targeted for drug development in autoimmune diseases and other conditions. CONCLUSIONS .This study identified five genes as therapeutic targets for SLE. Repurposing and developing drugs targeting these genes is anticipated to improve the existing treatment state for SLE. Key Points • We identified five gene targets of priority for the treatment of SLE, with BLK and IL12A indicating fewer side effects. • Among the existing drugs that target these candidate genes, Ustekinumab, Ebdarokimab, and Briakinumab (targeting the IL12 gene) and CD24FC (targeting HSPA1A) may potentially be repurposed for the treatment of SLE.
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Affiliation(s)
- Yuan Gao
- The First Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Youtao Zhou
- The First Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Zikai Lin
- Nanshan College, Guangzhou Medical University, Guangzhou, China
| | - Fengzhen Chen
- The First Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Haiyang Wu
- The Second Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Chusheng Peng
- The First Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Yingying Xie
- Department of Rheumatology and Immunology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, No. 151, Yanjiang West Road, Yuexiu District, Guangzhou, China.
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15
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Chan A, Haley RM, Najar MA, Gonzalez-Martinez D, Bugaj LJ, Burslem GM, Mitchell MJ, Tsourkas A. Lipid-mediated intracellular delivery of recombinant bioPROTACs for the rapid degradation of undruggable proteins. Nat Commun 2024; 15:5808. [PMID: 38987546 PMCID: PMC11237011 DOI: 10.1038/s41467-024-50235-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 07/04/2024] [Indexed: 07/12/2024] Open
Abstract
Recently, targeted degradation has emerged as a powerful therapeutic modality. Relying on "event-driven" pharmacology, proteolysis targeting chimeras (PROTACs) can degrade targets and are superior to conventional inhibitors against undruggable proteins. Unfortunately, PROTAC discovery is limited by warhead scarcity and laborious optimization campaigns. To address these shortcomings, analogous protein-based heterobifunctional degraders, known as bioPROTACs, have been developed. Compared to small-molecule PROTACs, bioPROTACs have higher success rates and are subject to fewer design constraints. However, the membrane impermeability of proteins severely restricts bioPROTAC deployment as a generalized therapeutic modality. Here, we present an engineered bioPROTAC template able to complex with cationic and ionizable lipids via electrostatic interactions for cytosolic delivery. When delivered by biocompatible lipid nanoparticles, these modified bioPROTACs can rapidly degrade intracellular proteins, exhibiting near-complete elimination (up to 95% clearance) of targets within hours of treatment. Our bioPROTAC format can degrade proteins localized to various subcellular compartments including the mitochondria, nucleus, cytosol, and membrane. Moreover, substrate specificity can be easily reprogrammed, allowing modular design and targeting of clinically-relevant proteins such as Ras, Jnk, and Erk. In summary, this work introduces an inexpensive, flexible, and scalable platform for efficient intracellular degradation of proteins that may elude chemical inhibition.
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Affiliation(s)
- Alexander Chan
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca M Haley
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Mohd Altaf Najar
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David Gonzalez-Martinez
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Lukasz J Bugaj
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - George M Burslem
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Cancer Biology and Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Michael J Mitchell
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew Tsourkas
- Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, PA, USA.
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Ramírez J, van Duijvenboden S, Young WJ, Chen Y, Usman T, Orini M, Lambiase PD, Tinker A, Bell CG, Morris AP, Munroe PB. Fine mapping of candidate effector genes for heart rate. Hum Genet 2024:10.1007/s00439-024-02684-z. [PMID: 38969939 DOI: 10.1007/s00439-024-02684-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 06/19/2024] [Indexed: 07/07/2024]
Abstract
An elevated resting heart rate (RHR) is associated with increased cardiovascular mortality. Genome-wide association studies (GWAS) have identified > 350 loci. Uniquely, in this study we applied genetic fine-mapping leveraging tissue specific chromatin segmentation and colocalization analyses to identify causal variants and candidate effector genes for RHR. We used RHR GWAS summary statistics from 388,237 individuals of European ancestry from UK Biobank and performed fine mapping using publicly available genomic annotation datasets. High-confidence causal variants (accounting for > 75% posterior probability) were identified, and we collated candidate effector genes using a multi-omics approach that combined evidence from colocalisation with molecular quantitative trait loci (QTLs), and long-range chromatin interaction analyses. Finally, we performed druggability analyses to investigate drug repurposing opportunities. The fine mapping pipeline indicated 442 distinct RHR signals. For 90 signals, a single variant was identified as a high-confidence causal variant, of which 22 were annotated as missense. In trait-relevant tissues, 39 signals colocalised with cis-expression QTLs (eQTLs), 3 with cis-protein QTLs (pQTLs), and 75 had promoter interactions via Hi-C. In total, 262 candidate genes were highlighted (79% had promoter interactions, 15% had a colocalised eQTL, 8% had a missense variant and 1% had a colocalised pQTL), and, for the first time, enrichment in nervous system pathways. Druggability analyses highlighted ACHE, CALCRL, MYT1 and TDP1 as potential targets. Our genetic fine-mapping pipeline prioritised 262 candidate genes for RHR that warrant further investigation in functional studies, and we provide potential therapeutic targets to reduce RHR and cardiovascular mortality.
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Affiliation(s)
- Julia Ramírez
- Aragon Institute of Engineering Research, University of Zaragoza, Zaragoza, Spain.
- Centro de Investigación Biomédica en Red - Bioingeniería, Biomateriales y Nanomedicina, Zaragoza, Spain.
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
| | - Stefan van Duijvenboden
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
- Nuffield Department of Population Health, University of Oxford, Old Road Campus, Headington, Oxford, OX3 7LF, UK.
- Institute of Cardiovascular Science, University College London, London, UK.
| | - William J Young
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Barts Heart Centre, St Bartholomew's Hospital, London, EC1A 7BE, UK
| | - Yutang Chen
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | | | - Michele Orini
- Institute of Cardiovascular Science, University College London, London, UK
| | - Pier D Lambiase
- Institute of Cardiovascular Science, University College London, London, UK
- Barts Heart Centre, St Bartholomew's Hospital, London, EC1A 7BE, UK
| | - Andrew Tinker
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
- Barts Cardiovascular Biomedical Research Centre, National Institute of Health and Care Research, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Christopher G Bell
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK
| | - Andrew P Morris
- Centre for Musculoskeletal Research, The University of Manchester, Manchester, UK
- National Institute of Health and Care Research, Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | - Patricia B Munroe
- William Harvey Research Institute, Barts and the London Faculty of Medicine and Dentistry, Queen Mary University of London, London, EC1M 6BQ, UK.
- Khalifa University, Abu Dhabi, United Arab Emirates.
- Barts Cardiovascular Biomedical Research Centre, National Institute of Health and Care Research, Queen Mary University of London, London, EC1M 6BQ, UK.
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17
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Park BS, Jeon H, Kim Y, Kwon H, Choi GE, Chi SG, Park HM, Lee H, Kim T. Polyamine and EIF5A hypusination downstream of c-Myc confers targeted therapy resistance in BRAF mutant melanoma. Mol Cancer 2024; 23:136. [PMID: 38965534 PMCID: PMC11223307 DOI: 10.1186/s12943-024-02031-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/24/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND BRAF inhibitors are widely employed in the treatment of melanoma with the BRAF V600E mutation. However, the development of resistance compromises their therapeutic efficacy. Diverse genomic and transcriptomic alterations are found in BRAF inhibitor resistant melanoma, posing a pressing need for convergent, druggable target that reverse therapy resistant tumor with different resistance mechanisms. METHODS CRISPR-Cas9 screens were performed to identify novel target gene whose inhibition selectively targets A375VR, a BRAF V600E mutant cell line with acquired resistance to vemurafenib. Various in vitro and in vivo assays, including cell competition assay, water soluble tetrazolium (WST) assay, live-dead assay and xenograft assay were performed to confirm synergistic cell death. Liquid Chromatography-Mass Spectrometry analyses quantified polyamine biosynthesis and changes in proteome in vemurafenib resistant melanoma. EIF5A hypusination dependent protein translation and subsequent changes in mitochondrial biogenesis and activity were assayed by O-propargyl-puromycin labeling assay, mitotracker, mitoSOX labeling and seahorse assay. Bioinformatics analyses were used to identify the association of polyamine biosynthesis with BRAF inhibitor resistance and poor prognosis in melanoma patient cohorts. RESULTS We elucidate the role of polyamine biosynthesis and its regulatory mechanisms in promoting BRAF inhibitor resistance. Leveraging CRISPR-Cas9 screens, we identify AMD1 (S-adenosylmethionine decarboxylase 1), a critical enzyme for polyamine biosynthesis, as a druggable target whose inhibition reduces vemurafenib resistance. Metabolomic and proteomic analyses reveal that polyamine biosynthesis is upregulated in vemurafenib-resistant cancer, resulting in enhanced EIF5A hypusination, translation of mitochondrial proteins and oxidative phosphorylation. We also identify that sustained c-Myc levels in vemurafenib-resistant cancer are responsible for elevated polyamine biosynthesis. Inhibition of polyamine biosynthesis or c-Myc reversed vemurafenib resistance both in vitro cell line models and in vivo in a xenograft model. Polyamine biosynthesis signature is associated with poor prognosis and shorter progression free survival after BRAF/MAPK inhibitor treatment in melanoma cohorts, highlighting the clinical relevance of our findings. CONCLUSIONS Our findings delineate the molecular mechanisms involving polyamine-EIF5A hypusination-mitochondrial respiration pathway conferring BRAF inhibitor resistance in melanoma. These targets will serve as effective therapeutic targets that can maximize the therapeutic efficacy of existing BRAF inhibitors.
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Affiliation(s)
- Byung-Sun Park
- Medicinal Materials Research Center, Korea Institute of Science and Technology, 5 Hwarangro-14-Gil, SeongbukGu, Seoul, 02792, Republic of Korea
- Department of Life Sciences, Korea University, 145 AnamRo, SeongbukGu, Seoul, 02841, Republic of Korea
| | - Heeju Jeon
- Medicinal Materials Research Center, Korea Institute of Science and Technology, 5 Hwarangro-14-Gil, SeongbukGu, Seoul, 02792, Republic of Korea
- Department of Life Sciences, Korea University, 145 AnamRo, SeongbukGu, Seoul, 02841, Republic of Korea
| | - Yeonseo Kim
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, 5 Hwarangro- 14-Gil, SeongbukGu, Seoul, 02792, Republic of Korea
| | - Haejin Kwon
- Advanced Analysis and Data Center, Korea Institute of Science and Technology, 5 Hwarangro-14-Gil, SeongbukGu, Seoul, 02792, Republic of Korea
| | - Ga-Eun Choi
- Medicinal Materials Research Center, Korea Institute of Science and Technology, 5 Hwarangro-14-Gil, SeongbukGu, Seoul, 02792, Republic of Korea
| | - Sung-Gil Chi
- Department of Life Sciences, Korea University, 145 AnamRo, SeongbukGu, Seoul, 02841, Republic of Korea
| | - Hyun-Mee Park
- Advanced Analysis and Data Center, Korea Institute of Science and Technology, 5 Hwarangro-14-Gil, SeongbukGu, Seoul, 02792, Republic of Korea
| | - Hyunbeom Lee
- Center for Advanced Biomolecular Recognition, Korea Institute of Science and Technology, 5 Hwarangro- 14-Gil, SeongbukGu, Seoul, 02792, Republic of Korea
| | - Tackhoon Kim
- Medicinal Materials Research Center, Korea Institute of Science and Technology, 5 Hwarangro-14-Gil, SeongbukGu, Seoul, 02792, Republic of Korea.
- Department of Life Sciences, Korea University, 145 AnamRo, SeongbukGu, Seoul, 02841, Republic of Korea.
- Division of Bio-Medical Science and Technology, Korea University of Science and Technology, 217 GajeongRo YuseongGu, Daejeon, 34113, Republic of Korea.
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18
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Luo P, Yu X. ENPP2/Autotaxin: The potential drug target for alcoholic liver disease identified through Mendelian randomization analysis. Liver Int 2024; 44:1624-1633. [PMID: 38517150 DOI: 10.1111/liv.15905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 02/21/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024]
Abstract
BACKGROUND AND AIMS At present, there is still a lack of radical drug targets for intervention in alcoholic liver disease (ALD), and drug discovery through randomized controlled trials is a lengthy, risky, and expensive undertaking, so we aimed to identify effective drug targets based on human genetics. METHODS We used Mendelian randomization (MR) and Bayesian colocalization analysis to investigate 2639 genes encoding druggable proteins and examined the causal effects on ALD (PMID 34737426: 456348 European with 451 cases and 455 897 controls). In addition, we conducted the mediation analysis to explore the potential mechanism using the genome-wide association study (GWAS) data of blood biomarkers as mediators. RESULTS We finally identified the drug target: ENPP2/Autotaxin and genetically proxied ENPP2/Autotaxin was causally associated with the risk of ALD (OR = 2.28, 95% CI: 1.64 to 3.16, p = 7.49E-7). In addition, we found that the effect of ENPP2/Autotaxin on ALD may be partly mediated by effector memory CD8+ T cell (the proportion of mediation effect: 8.49%). CONCLUSIONS Our integrative analysis suggested that genetically determined levels of circulating ENPP2/Autotaxin have a causal effect on ALD risk and are a promising drug target.
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Affiliation(s)
- Peiqiong Luo
- Division of Endocrinology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Branch of National Clinical Research Center for Metabolic Diseases, Wuhan, Hubei, China
| | - Xuefeng Yu
- Division of Endocrinology, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Branch of National Clinical Research Center for Metabolic Diseases, Wuhan, Hubei, China
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19
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Saluja S, Lennon R. Exploring novel therapeutic opportunities for hypertension: a paradigm-shifting approach via integrative multiomic analysis, pioneering the path to precision medicine. J Hypertens 2024; 42:1147-1149. [PMID: 38818837 DOI: 10.1097/hjh.0000000000003738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Affiliation(s)
- Sushant Saluja
- Division of Cardiovascular Sciences, Faculty of Biology, Medicine and Health, The University of Manchester
- Division of Medicine and Manchester Academic Health Science Centre, Manchester University NHS Foundation Trust Manchester
| | - Rachel Lennon
- Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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20
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Qin S, Jiang Y, Ou Y, Zhan Y, Ji L, Xu P, Shao X, Chen H, Chen T, Cheng Y. Mendelian randomization of circulating proteome identifies IFN-γ as a druggable target in aplastic anemia. Ann Hematol 2024; 103:2245-2256. [PMID: 38644415 DOI: 10.1007/s00277-024-05746-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 04/02/2024] [Indexed: 04/23/2024]
Abstract
BACKGROUND Aplastic anemia (AA) is a kind of bone marrow failure (BMF) characterized by pancytopenia with hypoplasia/aplasia of bone marrow. Immunosuppressive therapy and bone marrow transplantation are effective methods to treat severe aplastic anemia. However, the efficacy is limited by complications and the availability of suitable donors. This study aimed to determine whether any circulating druggable protein levels may have causal effects on AA and provide potential novel drug targets for AA. METHODS Genetic variants strongly associated with circulating druggable protein levels to perform Mendelian randomization (MR) analyses were used. The effect of these druggable protein levels on AA risk was measured using the summary statistics from a large-scale proteomic genome-wide association study (GWAS) and FinnGen database ( https://www.finngen.fi/en/access_results ). Multivariable MR analyses were performed to statistically adjust for potential confounders, including platelet counts, reticulocyte counts, neutrophil counts, and proportions of hematopoietic stem cells. RESULTS The data showed that higher level of circulating IFN-γ levels was causally associated with AA susceptibility. The causal effects of circulating IFN-γ levels on the AA were broadly consistent, when adjusted for platelet counts, reticulocyte counts, neutrophil counts and proportions of hematopoietic stem cells. CONCLUSIONS High levels of circulating IFN-γ levels might increase the risk of AA and might provide a potential novel target for AA.
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Affiliation(s)
- Shanshan Qin
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Yingxin Jiang
- Centenary Institute, The University of Sydney, Sydney, NSW, 2050, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Yang Ou
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Yanxia Zhan
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Lili Ji
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Pengcheng Xu
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xia Shao
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China
| | - Hao Chen
- Department of Thoracic Surgery, Zhongshan-Xuhui Hospital, Fudan University, Shanghai, 200237, China
| | - Tong Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Yunfeng Cheng
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- Center for Tumor Diagnosis & Therapy, Jinshan Hospital, Fudan University, Shanghai, 201508, China.
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21
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Kukendrarajah K, Farmaki AE, Lambiase PD, Schilling R, Finan C, Floriaan Schmidt A, Providencia R. Advancing drug development for atrial fibrillation by prioritising findings from human genetic association studies. EBioMedicine 2024; 105:105194. [PMID: 38941956 PMCID: PMC11260865 DOI: 10.1016/j.ebiom.2024.105194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 05/14/2024] [Accepted: 05/28/2024] [Indexed: 06/30/2024] Open
Abstract
BACKGROUND Drug development for atrial fibrillation (AF) has failed to yield new approved compounds. We sought to identify and prioritise potential druggable targets with support from human genetics, by integrating the available evidence with bioinformatics sources relevant for AF drug development. METHODS Genetic hits for AF and related traits were identified through structured search of MEDLINE. Genes derived from each paper were cross-referenced with the OpenTargets platform for drug interactions. Confirmation/validation was demonstrated through structured searches and review of evidence on MEDLINE and ClinialTrials.gov for each drug and its association with AF. FINDINGS 613 unique drugs were identified, with 21 already included in AF Guidelines. Cardiovascular drugs from classes not currently used for AF (e.g. ranolazine and carperitide) and anti-inflammatory drugs (e.g. dexamethasone and mehylprednisolone) had evidence of potential benefit. Further targets were considered druggable but remain open for drug development. INTERPRETATION Our systematic approach, combining evidence from different bioinformatics platforms, identified drug repurposing opportunities and druggable targets for AF. FUNDING KK is supported by Barts Charity grant G-002089 and is mentored on the AFGen 2023-24 Fellowship funded by the AFGen NIH/NHLBI grant R01HL092577. RP is supported by the UCL BHF Research Accelerator AA/18/6/34223 and NIHR grant NIHR129463. AFS is supported by the BHF grants PG/18/5033837, PG/22/10989 and UCL BHF Accelerator AA/18/6/34223 as well as the UK Research and Innovation (UKRI) under the UK government's Horizon Europe funding guarantee EP/Z000211/1 and by the UKRI-NIHR grant MR/V033867/1 for the Multimorbidity Mechanism and Therapeutics Research Collaboration. AF is supported by UCL BHF Accelerator AA/18/6/34223. CF is supported by UCL BHF Accelerator AA/18/6/34223.
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Affiliation(s)
- Kishore Kukendrarajah
- Institute of Health Informatics, University College London, 222 Euston Road, NW1 2DA, United Kingdom; Barts Heart Centre, St Bartholomew's Hospital, West Smithfield, EC1A 7BE, United Kingdom.
| | - Aliki-Eleni Farmaki
- Institute of Health Informatics, University College London, 222 Euston Road, NW1 2DA, United Kingdom
| | - Pier D Lambiase
- Barts Heart Centre, St Bartholomew's Hospital, West Smithfield, EC1A 7BE, United Kingdom; Institute of Cardiovascular Science, University College London, Gower Street, WC1E 6HX, United Kingdom
| | - Richard Schilling
- Barts Heart Centre, St Bartholomew's Hospital, West Smithfield, EC1A 7BE, United Kingdom
| | - Chris Finan
- Institute of Cardiovascular Science, University College London, Gower Street, WC1E 6HX, United Kingdom; UCL British Heart Foundation Research Accelerator, United Kingdom; Division Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, the Netherlands
| | - Amand Floriaan Schmidt
- Institute of Cardiovascular Science, University College London, Gower Street, WC1E 6HX, United Kingdom; UCL British Heart Foundation Research Accelerator, United Kingdom; Division Heart and Lungs, Department of Cardiology, University Medical Center Utrecht, Utrecht University, the Netherlands; Department of Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centres, University of Amsterdam, the Netherlands
| | - Rui Providencia
- Institute of Health Informatics, University College London, 222 Euston Road, NW1 2DA, United Kingdom; Barts Heart Centre, St Bartholomew's Hospital, West Smithfield, EC1A 7BE, United Kingdom
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22
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Feng T, Wang Y, Zhang W, Cai T, Tian X, Su J, Zhang Z, Zheng S, Ye S, Dai B, Wang Z, Zhu Y, Zhang H, Chang K, Ye D. Machine Learning-based Framework Develops a Tumor Thrombus Coagulation Signature in Multicenter Cohorts for Renal Cancer. Int J Biol Sci 2024; 20:3590-3620. [PMID: 38993563 PMCID: PMC11234220 DOI: 10.7150/ijbs.94555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 05/17/2024] [Indexed: 07/13/2024] Open
Abstract
Background: Renal cell carcinoma (RCC) is frequently accompanied by tumor thrombus in the venous system with an extremely dismal prognosis. The current Tumor Node Metastasis (TNM) stage and Mayo clinical classification do not appropriately identify preference-sensitive treatment. Therefore, there is an urgent need to develop a better ideal model for precision medicine. Methods: In this study, we developed a coagulation tumor thrombus signature for RCC with 10 machine-learning algorithms (101 combinations) based on a novel computational framework using multiple independent cohorts. Results: The established tumor thrombus coagulation-related risk stratification (TTCRRS) signature comprises 10 prognostic coagulation-related genes (CRGs). This signature could predict survival outcomes in public and in-house protein cohorts and showed high performance compared to 129 published signatures. Additionally, the TTCRRS signature was significantly related to some immune landscapes, immunotherapy response, and chemotherapy. Furthermore, we also screened out hub genes, transcription factors, and small compounds based on the TTCRRS signature. Meanwhile, CYP51A1 can regulate the proliferation and migration properties of RCC. Conclusions: The TTCRRS signature can complement the traditional anatomic TNM staging system and Mayo clinical stratification and provide clinicians with more therapeutic options.
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Affiliation(s)
- Tao Feng
- Qingdao Institute, School of Life Medicine, Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Qingdao, 266500, China
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Yue Wang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Wei Zhang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Tingting Cai
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Xi Tian
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Jiaqi Su
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Zihao Zhang
- Qingdao Institute, School of Life Medicine, Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Qingdao, 266500, China
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Shengfeng Zheng
- Qingdao Institute, School of Life Medicine, Department of Urology, Fudan University Shanghai Cancer Center, Fudan University, Qingdao, 266500, China
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Shiqi Ye
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Bo Dai
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Ziliang Wang
- Central Laboratory, Shanghai Municipal Hospital of Traditional Chinese Medicine, Shanghai University of Traditional Chinese Medicine, 274 Middle Zhijiang Road, Shanghai 200071, China
| | - Yiping Zhu
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Hailiang Zhang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Kun Chang
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
| | - Dingwei Ye
- Department of Urology, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200433, China
- Department of Urology, Fudan University Shanghai Cancer Center, No. 270 Dong'an Road, Shanghai, 200032, People's Republic of China
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23
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Brennan RJ, Jenkinson S, Brown A, Delaunois A, Dumotier B, Pannirselvam M, Rao M, Ribeiro LR, Schmidt F, Sibony A, Timsit Y, Sales VT, Armstrong D, Lagrutta A, Mittlestadt SW, Naven R, Peri R, Roberts S, Vergis JM, Valentin JP. The state of the art in secondary pharmacology and its impact on the safety of new medicines. Nat Rev Drug Discov 2024; 23:525-545. [PMID: 38773351 DOI: 10.1038/s41573-024-00942-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2024] [Indexed: 05/23/2024]
Abstract
Secondary pharmacology screening of investigational small-molecule drugs for potentially adverse off-target activities has become standard practice in pharmaceutical research and development, and regulatory agencies are increasingly requesting data on activity against targets with recognized adverse effect relationships. However, the screening strategies and target panels used by pharmaceutical companies may vary substantially. To help identify commonalities and differences, as well as to highlight opportunities for further optimization of secondary pharmacology assessment, we conducted a broad-ranging survey across 18 companies under the auspices of the DruSafe leadership group of the International Consortium for Innovation and Quality in Pharmaceutical Development. Based on our analysis of this survey and discussions and additional research within the group, we present here an overview of the current state of the art in secondary pharmacology screening. We discuss best practices, including additional safety-associated targets not covered by most current screening panels, and present approaches for interpreting and reporting off-target activities. We also provide an assessment of the safety impact of secondary pharmacology screening, and a perspective on opportunities and challenges in this rapidly developing field.
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Affiliation(s)
| | | | | | | | | | | | - Mohan Rao
- Janssen Research & Development, San Diego, CA, USA
- Neurocrine Biosciences, San Diego, CA, USA
| | - Lyn Rosenbrier Ribeiro
- UCB Biopharma, Braine-l'Alleud, Belgium
- AstraZeneca, Cambridge, UK
- Grunenthal, Berkshire, UK
| | | | | | - Yoav Timsit
- Novartis Biomedical Research, Cambridge, MA, USA
- Blueprint Medicines, Cambridge, MA, USA
| | | | - Duncan Armstrong
- Novartis Biomedical Research, Cambridge, MA, USA
- Armstrong Pharmacology, Macclesfield, UK
| | | | | | - Russell Naven
- Takeda Pharmaceuticals, Cambridge, MA, USA
- Novartis Biomedical Research, Cambridge, MA, USA
| | - Ravikumar Peri
- Takeda Pharmaceuticals, Cambridge, MA, USA
- Alexion Pharmaceuticals, Wilmington, DE, USA
| | - Sonia Roberts
- Roche Pharma Research and Early Development, Roche Innovation Center, Basel, Switzerland
| | - James M Vergis
- Faegre Drinker Biddle and Reath, LLP, Washington, DC, USA
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24
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Zhu Y, Li M, Wang H, Yang F, Du R, Pang X, Bai J, Huang X. Mendelian Randomization Identifies Genetically Supported Drug Targets for Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Mol Neurobiol 2024; 61:3809-3818. [PMID: 38019415 DOI: 10.1007/s12035-023-03817-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 11/18/2023] [Indexed: 11/30/2023]
Abstract
Currently, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) have no effective treatments. Drug repurposing offers a rapid method to meet therapeutic need for ALS and FTD. To identify therapeutic targets associated with ALS and FTD, Mendelian randomization (MR) analysis and colocalization were performed. Genetic instruments were based on transcriptomic and proteomic data for 422 actionable proteins targeted by approved drugs or clinical drug candidates. The publicly available ALS GWAS summary data (including a total of 20,806 ALS cases and 59,804 controls) and FTD GWAS summary data (including a total of 2154 patients with FTD and 4308 controls) were used. Using cis-expression quantitative trait loci and cis-protein quantitative trait loci genetic instruments, we identified several drug targets for repurposing (ALS: MARK3, false-discovery rate (FDR) = 0.043; LTBR, FDR = 0.068) (FTD: HLA-DRB1, FDR = 0.083; ADH5, FDR = 0.056). Our MR study analyzed the actionable druggable proteins and provided potential therapeutic targets for ALS and FTD. Future studies should further elucidate the underlying mechanism of corresponding drug targets in the pathogenesis of ALS and FTD.
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Affiliation(s)
- Yahui Zhu
- Medical School of Chinese PLA, Beijing, China
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Mao Li
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hongfen Wang
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Fei Yang
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - RongRong Du
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- College of Medicine, Nankai University, Tianjin, China
| | - Xinyuan Pang
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- College of Medicine, Nankai University, Tianjin, China
| | - Jiongming Bai
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- College of Medicine, Nankai University, Tianjin, China
| | - Xusheng Huang
- Medical School of Chinese PLA, Beijing, China.
- Department of Neurology, the First Medical Center, Chinese PLA General Hospital, Beijing, China.
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25
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Lin H, Bei Y, Shen Z, Wei T, Ge Y, Yu L, Xu H, He W, Dai Y, Yao D, Dai H. HDAC9 Deficiency Upregulates cGMP-dependent Kinase II to Mitigate Neuronal Apoptosis in Ischemic Stroke. Transl Stroke Res 2024:10.1007/s12975-024-01272-7. [PMID: 38940872 DOI: 10.1007/s12975-024-01272-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/05/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024]
Abstract
Histone deacetylase 9 (HDAC9) is implicated in ischemic stroke by genome-wide association studies. We conducted a series of experiments using a mouse model of ischemic stroke (middle cerebral artery occlusion followed by reperfusion) to examine the potential role of HDAC9. Briefly, HDAC9 was upregulated in the penumbra. Deletion of HDAC9 from neurons reduced infarction volume, inhibited neuronal apoptosis in the penumbra, and improved neurological outcomes. HDAC9 knockout from neurons in the penumbra upregulated cGMP-dependent kinase II (cGK II), blocking which abrogated the protective effects of HDAC9 deletion. Mechanistically, HDAC9 interacts with the transcription factor MEF2, thereby inhibiting MEF2's binding to the promoter region of the cGK II gene, which results in the suppression of cGK II expression. Inhibiting the interaction between HDAC9 and MEF2 by BML210 upregulated cGK II and attenuated ischemic injury in mice. These results encourage targeting the HDAC9-MEF2 interaction in developing novel therapy against ischemic stroke.
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Affiliation(s)
- Haoran Lin
- Department of Pharmacy, the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, China
| | - Yun Bei
- Department of Pharmacy, the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, China
| | - Zexu Shen
- Department of Pharmacy, the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, China
| | - Taofeng Wei
- Department of Pharmacy, the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, China
| | - Yuyang Ge
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Lingyan Yu
- Department of Pharmacy, the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, China
| | - Huimin Xu
- Department of Pharmacy, the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, China
| | - Wei He
- Department of Pharmacy, the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, China
| | - Yunjian Dai
- Department of Pharmacy, the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, China
| | - Difei Yao
- Department of Pharmacy, the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, China
| | - Haibin Dai
- Department of Pharmacy, the Second Affiliated Hospital, Zhejiang University School of Medicine, No. 88 Jiefang Road, Hangzhou, 310009, China.
- Clinical Pharmacy Research Center, Zhejiang University, Hangzhou, 310058, China.
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26
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Chen X, Shen R, Zhu D, Luo S, You G, Li R, Hong X, Li R, Wu J, Huang Y, Lin T. Drug repurposing opportunities for chronic kidney disease. iScience 2024; 27:109953. [PMID: 38947510 PMCID: PMC11214293 DOI: 10.1016/j.isci.2024.109953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 02/08/2024] [Accepted: 05/08/2024] [Indexed: 07/02/2024] Open
Abstract
The development of targeted drugs for the early prevention and management of chronic kidney disease (CKD) is of great importance. However, the success rates and cost-effectiveness of traditional drug development approaches are extremely low. Utilizing large sample genome-wide association study data for drug repurposing has shown promise in many diseases but has not yet been explored in CKD. Herein, we investigated actionable druggable targets to improve renal function using large-scale Mendelian randomization and colocalization analyses. We combined two population-scale independent genetic datasets and validated findings with cell-type-dependent eQTL data of kidney tubular and glomerular samples. We ultimately prioritized two drug targets, opioid receptor-like 1 and F12, with potential genetic support for restoring renal function and subsequent treatment of CKD. Our findings explore the potential pathological mechanisms of CKD, bridge the gap between the molecular mechanisms of pathogenesis and clinical intervention, and provide new strategies in future clinical trials of CKD.
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Affiliation(s)
- Xiong Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Runnan Shen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Dongxi Zhu
- School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Shulu Luo
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
| | - Guochang You
- School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Ruijie Li
- School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Xiaosi Hong
- Department of Endocrinology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ruijun Li
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
| | - Jihao Wu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-sen University, Guangzhou, P.R. China
| | - Yinong Huang
- Faculty of Medicine, Macau University of Science and Technology, Macau, China
| | - Tianxin Lin
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Clinical Research Center for Urological Diseases, Guangzhou, Guangdong, China
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Wang F, Zhu L, Cui H, Guo S, Wu J, Li A, Wang Z. Renshen Yangrong decoction for secondary malaise and fatigue: network pharmacology and Mendelian randomization study. Front Nutr 2024; 11:1404123. [PMID: 38966421 PMCID: PMC11222649 DOI: 10.3389/fnut.2024.1404123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 06/13/2024] [Indexed: 07/06/2024] Open
Abstract
Background Renshen Yangrong decoction (RSYRD) has been shown therapeutic effects on secondary malaise and fatigue (SMF). However, to date, its bioactive ingredients and potential targets remain unclear. Purpose The purpose of this study is to assess the potential ingredients and targets of RSYRD on SMF through a comprehensive strategy integrating network pharmacology, Mendelian randomization as well as molecular docking verification. Methods Search for potential active ingredients and corresponding protein targets of RSYRD on TCMSP and BATMAN-TCM for network pharmacology analysis. Mendelian randomization (MR) was performed to find therapeutic targets for SMF. The eQTLGen Consortium (sample sizes: 31,684) provided data on cis-expression quantitative trait loci (cis-eQTL, exposure). The summary data on SMF (outcome) from genome-wide association studies (GWAS) were gathered from the MRC-IEU Consortium (sample sizes: 463,010). We built a target interaction network between the probable active ingredient targets of RSYRD and the therapeutic targets of SMF. We next used drug prediction and molecular docking to confirm the therapeutic value of the therapeutic targets. Results In RSYRD, network pharmacology investigations revealed 193 possible active compounds and 234 associated protein targets. The genetically predicted amounts of 176 proteins were related to SMF risk in the MR analysis. Thirty-seven overlapping targets for RSYRD in treating SMF, among which six (NOS3, GAA, IMPA1, P4HTM, RB1, and SLC16A1) were prioritized with the most convincing evidence. Finally, the 14 active ingredients of RSYRD were identified as potential drug molecules. The strong affinity between active components and putative protein targets was established by molecular docking. Conclusion This study revealed several active components and possible RSYRD protein targets for the therapy of SMF and provided novel insights into the feasibility of using Mendelian randomization for causal inference between Chinese medical formula and disease.
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Affiliation(s)
- Fanghan Wang
- Department of Medical Oncology, The Fourth People’s Hospital of Zibo, Zibo, China
| | - Liping Zhu
- Department of Medical Oncology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Haiyan Cui
- Department of Pathology, The Fourth People’s Hospital of Zibo, Zibo, China
| | - Shanchun Guo
- RCMI Cancer Research Center, Xavier University of Louisiana, New Orleans, LA, United States
| | - Jingliang Wu
- Medical School, Weifang University of Science and Technology, Shouguang, China
| | - Aixiang Li
- Department of Medical Oncology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
| | - Zhiqiang Wang
- Department of Urology, Shouguang Hospital of Traditional Chinese Medicine, Shouguang, China
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Song Y, Cui J, Zhu J, Kim B, Kuo ML, Potts PR. RNATACs: Multispecific small molecules targeting RNA by induced proximity. Cell Chem Biol 2024; 31:1101-1117. [PMID: 38876100 DOI: 10.1016/j.chembiol.2024.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/09/2024] [Accepted: 05/22/2024] [Indexed: 06/16/2024]
Abstract
RNA-targeting small molecules (rSMs) have become an attractive modality to tackle traditionally undruggable proteins and expand the druggable space. Among many innovative concepts, RNA-targeting chimeras (RNATACs) represent a new class of multispecific, induced proximity small molecules that act by chemically bringing RNA targets into proximity with an endogenous RNA effector, such as a ribonuclease (RNase). Depending on the RNA effector, RNATACs can alter the stability, localization, translation, or splicing of the target RNA. Although still in its infancy, this new modality has the potential for broad applications in the future to treat diseases with high unmet need. In this review, we discuss potential advantages of RNATACs, recent progress in the field, and challenges to this cutting-edge technology.
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Affiliation(s)
- Yan Song
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA.
| | - Jia Cui
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Jiaqiang Zhu
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Boseon Kim
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Mei-Ling Kuo
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA.
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Sun H, Li L, Yan J, Huang T. Prioritization of drug targets for thyroid cancer: a multi-omics Mendelian randomization study. Endocrine 2024:10.1007/s12020-024-03933-x. [PMID: 38896366 DOI: 10.1007/s12020-024-03933-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
OBJECTIVES Recurrence or tumor metastasis and drug resistance remain the major challenge in the treatment of thyroid cancer. It is needed to identify novel drug targets for thyroid cancer. METHODS Summary data-based Mendelian randomization (SMR) and colocalization analysis were performed to evaluate the associations between gene methylation, expression, protein levels with thyroid cancer. We additionally performed protein-protein interaction (PPI) network, gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) analyses to further explore the potential roles of identified genes in thyroid cancer. RESULTS SDCCAG8 and VCAM1 genes were associated with risk of thyroid cancer with tier 1 evidence, while TCN2 gene was with tier 3 evidence. SDCCAG8 gene was associated with risk of papillary thyroid cancer with tier 1 evidence. At the level of circulating proteins, genetically predicted higher levels of SDCCAG8 (OR = 0.46, 95% CI 0.34-0.64) and VCAM1 (OR = 0.21, 95% CI 0.10-0.45) were inversely associated with thyroid cancer risk; higher level of TCN2 was associated with an increased risk of thyroid cancer (OR = 1.30, 95% CI 1.15-1.47); and the higher level of SDCCAG8 (OR = 0.40, 95% CI 0.28-0.58) was associated with a decreased risk of papillary thyroid cancer. The bioinformatics analysis showed that SDCCAG8, VCAM1 and TCN2 might play roles in immune-related pathways. CONCLUSION SDCCAG8, VCAM1 and TCN2 genes were associated with thyroid cancer risk with evidence at multi-omics levels. There were potential roles of SDCCAG8, VCAM1 and TCN2 in immune-related pathways. Our findings might improve the understanding of the pathogenesis of thyroid cancer and discovery of novel potential drug targets for this disease.
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Affiliation(s)
- Hong Sun
- Department of Pharmacy, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Ling Li
- Department of Pharmacy, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Jingchao Yan
- Department of Pharmacy, Eye & ENT Hospital, Fudan University, Shanghai, China.
| | - Taomin Huang
- Department of Pharmacy, Eye & ENT Hospital, Fudan University, Shanghai, China.
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Si S, Liu H, Xu L, Zhan S. Identification of novel therapeutic targets for chronic kidney disease and kidney function by integrating multi-omics proteome with transcriptome. Genome Med 2024; 16:84. [PMID: 38898508 PMCID: PMC11186236 DOI: 10.1186/s13073-024-01356-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 06/05/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is a progressive disease for which there is no effective cure. We aimed to identify potential drug targets for CKD and kidney function by integrating plasma proteome and transcriptome. METHODS We designed a comprehensive analysis pipeline involving two-sample Mendelian randomization (MR) (for proteins), summary-based MR (SMR) (for mRNA), and colocalization (for coding genes) to identify potential multi-omics biomarkers for CKD and combined the protein-protein interaction, Gene Ontology (GO), and single-cell annotation to explore the potential biological roles. The outcomes included CKD, extensive kidney function phenotypes, and different CKD clinical types (IgA nephropathy, chronic glomerulonephritis, chronic tubulointerstitial nephritis, membranous nephropathy, nephrotic syndrome, and diabetic nephropathy). RESULTS Leveraging pQTLs of 3032 proteins from 3 large-scale GWASs and corresponding blood- and tissue-specific eQTLs, we identified 32 proteins associated with CKD, which were validated across diverse CKD datasets, kidney function indicators, and clinical types. Notably, 12 proteins with prior MR support, including fibroblast growth factor 5 (FGF5), isopentenyl-diphosphate delta-isomerase 2 (IDI2), inhibin beta C chain (INHBC), butyrophilin subfamily 3 member A2 (BTN3A2), BTN3A3, uromodulin (UMOD), complement component 4A (C4a), C4b, centrosomal protein of 170 kDa (CEP170), serologically defined colon cancer antigen 8 (SDCCAG8), MHC class I polypeptide-related sequence B (MICB), and liver-expressed antimicrobial peptide 2 (LEAP2), were confirmed. To our knowledge, 20 novel causal proteins have not been previously reported. Five novel proteins, namely, GCKR (OR 1.17, 95% CI 1.10-1.24), IGFBP-5 (OR 0.43, 95% CI 0.29-0.62), sRAGE (OR 1.14, 95% CI 1.07-1.22), GNPTG (OR 0.90, 95% CI 0.86-0.95), and YOD1 (OR 1.39, 95% CI 1.18-1.64,) passed the MR, SMR, and colocalization analysis. The other 15 proteins were also candidate targets (GATM, AIF1L, DQA2, PFKFB2, NFATC1, activin AC, Apo A-IV, MFAP4, DJC10, C2CD2L, TCEA2, HLA-E, PLD3, AIF1, and GMPR1). These proteins interact with each other, and their coding genes were mainly enrichment in immunity-related pathways or presented specificity across tissues, kidney-related tissue cells, and kidney single cells. CONCLUSIONS Our integrated analysis of plasma proteome and transcriptome data identifies 32 potential therapeutic targets for CKD, kidney function, and specific CKD clinical types, offering potential targets for the development of novel immunotherapies, combination therapies, or targeted interventions.
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Affiliation(s)
- Shucheng Si
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Hongyan Liu
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Lu Xu
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China
- Peking University Health Science Center, Beijing, 100191, China
| | - Siyan Zhan
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, 100191, China.
- Peking University Health Science Center, Beijing, 100191, China.
- Key Laboratory of Epidemiology of Major Diseases (Peking University), Ministry of Education, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China.
- Institute for Artificial Intelligence, Peking University, Beijing, 100871, China.
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Rosoff DB, Hamandi AM, Bell AS, Mavromatis LA, Park LM, Jung J, Wagner J, Lohoff FW. Major Psychiatric Disorders, Substance Use Behaviors, and Longevity. JAMA Psychiatry 2024:2820199. [PMID: 38888899 PMCID: PMC11195603 DOI: 10.1001/jamapsychiatry.2024.1429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/04/2024] [Indexed: 06/20/2024]
Abstract
Importance Observational studies suggest that major psychiatric disorders and substance use behaviors reduce longevity, making it difficult to disentangle their relationships with aging-related outcomes. Objective To evaluate the associations between the genetic liabilities for major psychiatric disorders, substance use behaviors (smoking and alcohol consumption), and longevity. Design, Settings, and Participants This 2-sample mendelian randomization (MR) study assessed associations between psychiatric disorders, substance use behaviors, and longevity using single-variable and multivariable models. Multiomics analyses were performed elucidating transcriptomic underpinnings of the MR associations and identifying potential proteomic therapeutic targets. This study sourced summary-level genome-wide association study (GWAS) data, gene expression, and proteomic data from cohorts of European ancestry. Analyses were performed from May 2022 to November 2023. Exposures Genetic susceptibility for major depression (n = 500 199), bipolar disorder (n = 413 466), schizophrenia (n = 127 906), problematic alcohol use (n = 435 563), weekly alcohol consumption (n = 666 978), and lifetime smoking index (n = 462 690). Main Outcomes and Measures The main outcome encompassed aspects of health span, lifespan, and exceptional longevity. Additional outcomes were epigenetic age acceleration (EAA) clocks. Results Findings from multivariable MR models simultaneously assessing psychiatric disorders and substance use behaviorsm suggest a negative association between smoking and longevity in cohorts of European ancestry (n = 709 709; 431 503 [60.8%] female; β, -0.33; 95% CI, -0.38 to -0.28; P = 4.59 × 10-34) and with increased EAA (n = 34 449; 18 017 [52.3%] female; eg, PhenoAge: β, 1.76; 95% CI, 0.72 to 2.79; P = 8.83 × 10-4). Transcriptomic imputation and colocalization identified 249 genes associated with smoking, including 36 novel genes not captured by the original smoking GWAS. Enriched pathways included chromatin remodeling and telomere assembly and maintenance. The transcriptome-wide signature of smoking was inversely associated with longevity, and estimates of individual smoking-associated genes, eg, XRCC3 and PRMT6, aligned with the smoking-longevity MR analyses, suggesting underlying transcriptomic mediators. Cis-instrument MR prioritized brain proteins associated with smoking behavior, including LY6H (β, 0.02; 95% CI, 0.01 to 0.03; P = 2.37 × 10-6) and RIT2 (β, 0.02; 95% CI, 0.01 to 0.03; P = 1.05 × 10-5), which had favorable adverse-effect profiles across 367 traits evaluated in phenome-wide MR. Conclusions The findings suggest that the genetic liability of smoking, but not of psychiatric disorders, is associated with longevity. Transcriptomic associations offer insights into smoking-related pathways, and identified proteomic targets may inform therapeutic development for smoking cessation strategies.
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Affiliation(s)
- Daniel B. Rosoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
- Radcliffe Department of Medicine, NIH-Oxford-Cambridge Scholars Program, University of Oxford, United Kingdom
| | - Ali M. Hamandi
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Andrew S. Bell
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Lucas A. Mavromatis
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Lauren M. Park
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Jeesun Jung
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Josephin Wagner
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
| | - Falk W. Lohoff
- Section on Clinical Genomics and Experimental Therapeutics, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, Maryland
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Savage SR, Yi X, Lei JT, Wen B, Zhao H, Liao Y, Jaehnig EJ, Somes LK, Shafer PW, Lee TD, Fu Z, Dou Y, Shi Z, Gao D, Hoyos V, Gao Q, Zhang B. Pan-cancer proteogenomics expands the landscape of therapeutic targets. Cell 2024:S0092-8674(24)00583-X. [PMID: 38917788 DOI: 10.1016/j.cell.2024.05.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 04/03/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024]
Abstract
Fewer than 200 proteins are targeted by cancer drugs approved by the Food and Drug Administration (FDA). We integrate Clinical Proteomic Tumor Analysis Consortium (CPTAC) proteogenomics data from 1,043 patients across 10 cancer types with additional public datasets to identify potential therapeutic targets. Pan-cancer analysis of 2,863 druggable proteins reveals a wide abundance range and identifies biological factors that affect mRNA-protein correlation. Integration of proteomic data from tumors and genetic screen data from cell lines identifies protein overexpression- or hyperactivation-driven druggable dependencies, enabling accurate predictions of effective drug targets. Proteogenomic identification of synthetic lethality provides a strategy to target tumor suppressor gene loss. Combining proteogenomic analysis and MHC binding prediction prioritizes mutant KRAS peptides as promising public neoantigens. Computational identification of shared tumor-associated antigens followed by experimental confirmation nominates peptides as immunotherapy targets. These analyses, summarized at https://targets.linkedomics.org, form a comprehensive landscape of protein and peptide targets for companion diagnostics, drug repurposing, and therapy development.
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Affiliation(s)
- Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hongwei Zhao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of the Ministry of China, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lauren K Somes
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Paul W Shafer
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tobie D Lee
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zile Fu
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of the Ministry of China, Fudan University, 180 Fenglin Road, Shanghai 200032, China
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Daming Gao
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Valentina Hoyos
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of the Ministry of China, Fudan University, 180 Fenglin Road, Shanghai 200032, China.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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Xiong Y, Wang T, Wang W, Zhang Y, Zhang F, Yuan J, Qin F, Wang X. Plasma proteome analysis implicates novel proteins as potential therapeutic targets for chronic kidney disease: A proteome-wide association study. Heliyon 2024; 10:e31704. [PMID: 38828357 PMCID: PMC11140797 DOI: 10.1016/j.heliyon.2024.e31704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 05/13/2024] [Accepted: 05/21/2024] [Indexed: 06/05/2024] Open
Abstract
Chronic kidney disease (CKD) is prevalent globally with limited therapeutic drugs available. To systemically identify novel proteins involved in the pathogenesis of CKD and possible therapeutic targets, we integrated human plasma proteomes with the genome-wide association studies (GWASs) of CKD, estimated glomerular filtration rate (eGFR) and blood urea nitrogen (BUN) to perform proteome-wide association study (PWAS), Mendelian Randomization and Bayesian colocalization analyses. The single-cell RNA sequencing data of healthy human and mouse kidneys were analyzed to explore the cell-type specificity of identified genes. Functional enrichment analysis was conducted to investigate the involved signaling pathways. The PWAS identified 22 plasma proteins significantly associated with CKD. Of them, the significant associations of three proteins (INHBC, LMAN2, and SNUPN) were replicated in the GWASs of eGFR, and BUN. Mendelian Randomization analyses showed that INHBC and SNUPN were causally associated with CKD, eGFR, and BUN. The Bayesian colocalization analysis identified shared causal variants for INHBC in CKD, eGFR, and BUN (all PP4 > 0.75). The single-cell RNA sequencing revealed that the INHBC gene was sparsely scattered within the kidney cells. This proteomic study revealed that INHBC, LMAN2, and SNUPN may be involved in the pathogenesis of CKD, which represent novel therapeutic targets and warrant further exploration in future research.
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Affiliation(s)
- Yang Xiong
- Department of Urology and Andrology Laboratory, West China Hospital, Sichuan University, Sichuan, 610041, China
| | - Tianhong Wang
- Department of Anesthesiology, West China Hospital, Sichuan University, Sichuan, 610041, China
| | - Wei Wang
- Department of Urology and Andrology Laboratory, West China Hospital, Sichuan University, Sichuan, 610041, China
| | - Yangchang Zhang
- Department of Public Health, Capital Medical University, Beijing, 100000, China
| | - Fuxun Zhang
- Department of Urology, Tangdu Hospital, The Air Force Medical University, Xi'an, Shaanxi, 710000, China
| | - Jiuhong Yuan
- Department of Urology and Andrology Laboratory, West China Hospital, Sichuan University, Sichuan, 610041, China
| | - Feng Qin
- Department of Urology and Andrology Laboratory, West China Hospital, Sichuan University, Sichuan, 610041, China
| | - Xianding Wang
- Department of Urology and Andrology Laboratory, West China Hospital, Sichuan University, Sichuan, 610041, China
- Kidney Transplant Center, Transplant Center, West China Hospital, Sichuan University, Sichuan, 610041, China
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Klocker EV, Hasenleithner S, Bartsch R, Gampenrieder SP, Egle D, Singer CF, Rinnerthaler G, Hubalek M, Schmitz K, Bago-Horvath Z, Petzer A, Heibl S, Heitzer E, Balic M, Gnant M. Clinical applications of next-generation sequencing-based ctDNA analyses in breast cancer: defining treatment targets and dynamic changes during disease progression. Mol Oncol 2024. [PMID: 38867388 DOI: 10.1002/1878-0261.13671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/03/2024] [Accepted: 05/17/2024] [Indexed: 06/14/2024] Open
Abstract
The advancements in the detection and characterization of circulating tumor DNA (ctDNA) have revolutionized precision medicine and are likely to transform standard clinical practice. The non-invasive nature of this approach allows for molecular profiling of the entire tumor entity, while also enabling real-time monitoring of the effectiveness of cancer therapies as well as the identification of resistance mechanisms to guide targeted therapy. Although the field of ctDNA studies offers a wide range of applications, including in early disease, in this review we mainly focus on the role of ctDNA in the dynamic molecular characterization of unresectable locally advanced and metastatic BC (mBC). Here, we provide clinical practice guidance for the rapidly evolving field of molecular profiling of mBC, outlining the current landscape of liquid biopsy applications and how to choose the right ctDNA assay. Additionally, we underline the importance of exploring the clinical relevance of novel molecular alterations that potentially represent therapeutic targets in mBC, along with mutations where targeted therapy is already approved. Finally, we present a potential roadmap for integrating ctDNA analysis into clinical practice.
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Affiliation(s)
- Eva Valentina Klocker
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Samantha Hasenleithner
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Austria
| | - Rupert Bartsch
- Division of Oncology, Department of Medicine I, Medical University of Vienna, Austria
| | - Simon P Gampenrieder
- Third Medical Department with Hematology and Medical Oncology, Hemostaseology, Rheumatology and Infectious Diseases, Oncologic Center, Paracelsus Medical University Salzburg, Austria
| | - Daniel Egle
- Department of Gynecology, Breast Cancer Center Tirol, Medical University of Innsbruck, Austria
| | - Christian F Singer
- Department of Gynecology, Breast Cancer Center Vienna, Medical University of Vienna, Austria
| | - Gabriel Rinnerthaler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Michael Hubalek
- Department of Gynecology, Breast Health Center Schwaz, Austria
| | - Katja Schmitz
- Institute of Pathology, University Medical Center Göttingen, Germany
- Tyrolpath Obrist Brunhuber GmbH and Krankenhaus St. Vinzenz, Zams, Austria
| | | | - Andreas Petzer
- Department of Internal Medicine I for Hematology with Stem Cell Transplantation, Hemostaseology and Medical Oncology, Barmherzige Schwestern, Elisabethinen, Ordensklinikum Linz GmbH, Austria
| | - Sonja Heibl
- Department of Internal Medicine IV, Klinikum Wels-Grieskirchen GmbH, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Christian Doppler Laboratory for Liquid Biopsies for early Detection of Cancer, Medical University of Graz, Austria
| | - Marija Balic
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
- Division of Hematology and Medical Oncology, University of Pittsburgh School of Medicine, PA, USA
| | - Michael Gnant
- Comprehensive Cancer Center, Medical University of Vienna, Austria
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35
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Zhang C, He Y, Liu L. Identifying therapeutic target genes for migraine by systematic druggable genome-wide Mendelian randomization. J Headache Pain 2024; 25:100. [PMID: 38867170 PMCID: PMC11167905 DOI: 10.1186/s10194-024-01805-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Accepted: 06/05/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Currently, the treatment and prevention of migraine remain highly challenging. Mendelian randomization (MR) has been widely used to explore novel therapeutic targets. Therefore, we performed a systematic druggable genome-wide MR to explore the potential therapeutic targets for migraine. METHODS We obtained data on druggable genes and screened for genes within brain expression quantitative trait locis (eQTLs) and blood eQTLs, which were then subjected to two-sample MR analysis and colocalization analysis with migraine genome-wide association studies data to identify genes highly associated with migraine. In addition, phenome-wide research, enrichment analysis, protein network construction, drug prediction, and molecular docking were performed to provide valuable guidance for the development of more effective and targeted therapeutic drugs. RESULTS We identified 21 druggable genes significantly associated with migraine (BRPF3, CBFB, CDK4, CHD4, DDIT4, EP300, EPHA5, FGFRL1, FXN, HMGCR, HVCN1, KCNK5, MRGPRE, NLGN2, NR1D1, PLXNB1, TGFB1, TGFB3, THRA, TLN1 and TP53), two of which were significant in both blood and brain (HMGCR and TGFB3). The results of phenome-wide research showed that HMGCR was highly correlated with low-density lipoprotein, and TGFB3 was primarily associated with insulin-like growth factor 1 levels. CONCLUSIONS This study utilized MR and colocalization analysis to identify 21 potential drug targets for migraine, two of which were significant in both blood and brain. These findings provide promising leads for more effective migraine treatments, potentially reducing drug development costs.
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Affiliation(s)
- Chengcheng Zhang
- Department of Acupuncture and Moxibustion, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing Key Laboratory of Acupuncture Neuromodulation, No. 23, Meishuguan Houjie, Beijing, 100010, China
| | - Yiwei He
- State Key Laboratory of Networking and Switching Technology, Beijing University of Posts and Telecommunications, Beijing, 100876, China
| | - Lu Liu
- Department of Acupuncture and Moxibustion, Beijing Hospital of Traditional Chinese Medicine, Capital Medical University, Beijing Key Laboratory of Acupuncture Neuromodulation, No. 23, Meishuguan Houjie, Beijing, 100010, China.
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Li H, Li W, Li D, Yuan L, Xu Y, Su P, Wu L, Zhang Z. Based on systematic druggable genome-wide Mendelian randomization identifies therapeutic targets for diabetes. Front Endocrinol (Lausanne) 2024; 15:1366290. [PMID: 38915894 PMCID: PMC11194396 DOI: 10.3389/fendo.2024.1366290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 05/28/2024] [Indexed: 06/26/2024] Open
Abstract
Purpose Diabetes and its complications cause a heavy burden of disease worldwide. In recent years, Mendelian randomization (MR) has been widely used to discover the pathogenesis and epidemiology of diseases, as well as to discover new therapeutic targets. Therefore, based on systematic "druggable" genomics, we aim to identify new therapeutic targets for diabetes and analyze its pathophysiological mechanisms to promote its new therapeutic strategies. Material and method We used double sample MR to integrate the identified druggable genomics to evaluate the causal effect of quantitative trait loci (eQTLs) expressed by druggable genes in blood on type 1 and 2 diabetes (T1DM and T2DM). Repeat the study using different data sources on diabetes and its complications to verify the identified genes. Not only that, we also use Bayesian co-localization analysis to evaluate the posterior probabilities of different causal variations, shared causal variations, and co-localization probabilities to examine the possibility of genetic confounding. Finally, using diabetes markers with available genome-wide association studies data, we evaluated the causal relationship between established diabetes markers to explore possible mechanisms. Result Overall, a total of 4,477 unique druggable genes have been gathered. After filtering using methods such as Bonferroni significance (P<1.90e-05), the MR Steiger directionality test, Bayesian co-localization analysis, and validation with different datasets, Finally, 7 potential druggable genes that may affect the results of T1DM and 7 potential druggable genes that may affect the results of T2DM were identified. Reverse MR suggests that C4B may play a bidirectional role in the pathogenesis of T1DM, and none of the other 13 target genes have a reverse causal relationship. And the 7 target genes in T2DM may each affect the biomarkers of T2DM to mediate the pathogenesis of T2DM. Conclusion This study provides genetic evidence supporting the potential therapeutic benefits of targeting seven druggable genes, namely MAP3K13, KCNJ11, REG4, KIF11, CCNE2, PEAK1, and NRBP1, for T2DM treatment. Similarly, targeting seven druggable genes, namely ERBB3, C4B, CD69, PTPN22, IL27, ATP2A1, and LT-β, has The potential therapeutic benefits of T1DM treatment. This will provide new ideas for the treatment of diabetes and also help to determine the priority of drug development for diabetes.
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Affiliation(s)
- Hu Li
- Emergency Department, Binzhou Medical University Hospital, Binzhou, China
| | - Wei Li
- Urology Department, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Dongyang Li
- Internal Medicine-Neurology, Binzhou Medical University Hospital, Binzhou, China
| | - Lijuan Yuan
- Emergency Department, Binzhou Medical University Hospital, Binzhou, China
| | - Yucheng Xu
- Department of Critical Care Medicine, Jinan Central Hospital, Jinan, China
| | - Pengtao Su
- Emergency Department, Binzhou Medical University Hospital, Binzhou, China
| | - Liqiang Wu
- Emergency Department, Binzhou Medical University Hospital, Binzhou, China
| | - Zhiqiang Zhang
- Emergency Department, Binzhou Medical University Hospital, Binzhou, China
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Ma J, Fu L, Lu Z, Sun Y. Evaluating the Causal Effects of Circulating Proteome on the Risk of Sepsis and Related Outcomes. ACS OMEGA 2024; 9:23864-23872. [PMID: 38854583 PMCID: PMC11154893 DOI: 10.1021/acsomega.4c01934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/09/2024] [Accepted: 05/17/2024] [Indexed: 06/11/2024]
Abstract
The current investigation deployed Mendelian randomization (MR) to elucidate the causal relationship between circulating proteins and sepsis. A rigorous two-sample MR analysis evaluated the effect of plasma proteins on the sepsis susceptibility. To affirm the integrity of MR findings, a suite of supplementary analyses, including Bayesian colocalization, Steiger filtering, the assessment of protein-altering polymorphisms, and the correlation between expression quantitative trait loci and protein quantitative trait loci (pQTLs), was employed. The study further integrated the examination of protein-protein interactions and pathway enrichment, along with the identification of pharmacologically actionable targets, to advance our comprehension and outline potential sepsis therapies. Subsequent analyses leveraging cis-pQTLs within MR studies unveiled noteworthy relationships: 94 specific proteins exhibited significant links with sepsis-related 28 day mortality, while 96 distinct proteins correlated with survival outcomes in sepsis. Furthermore, incorporating both cis- and trans-pQTLs in MR investigations revealed more comprehensive findings, associating 201 unique proteins with sepsis-related 28 day mortality and 199 distinct proteins with survival outcomes in sepsis. Markedly, colocalization analyses confirmed that eight of these proteins exhibited prominent evidence for colocalization, emphasizing their potential criticality in sepsis pathophysiology. Further in silico analyses were conducted to delineate putative regulatory networks and to highlight prospective drug targets among these proteins. Employing the MR methodology has shed light on plasma proteins implicated in the etiopathogenesis of sepsis. This novel approach unveiled numerous biomarkers and targets, providing a scientific rationale for the development of new therapeutic strategies and prophylactic measures against sepsis.
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Affiliation(s)
- Jiawei Ma
- The
First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
- Department
of Critical Care Medicine, Wuxi No. 2 People’s
Hospital, Wuxi 214002, China
- Department
of Critical Care Medicine, Aheqi County
People’s Hospital, Xinjiang 843599, China
| | - Lu Fu
- The
First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| | - Zhonghua Lu
- The
First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
| | - Yun Sun
- The
First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, China
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38
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Song W, Li Y, Yao Y, Sun S, Guan X, Wang B. Systematic druggable genome-wide Mendelian randomization identifies therapeutic targets for lung cancer. BMC Cancer 2024; 24:680. [PMID: 38834983 DOI: 10.1186/s12885-024-12449-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 05/29/2024] [Indexed: 06/06/2024] Open
Abstract
BACKGROUND Drug repurposing provides a cost-effective approach to address the need for lung cancer prevention and therapeutics. We aimed to identify actionable druggable targets using Mendelian randomization (MR). METHODS Summary-level data of gene expression quantitative trait loci (eQTLs) were sourced from the eQTLGen resource. We procured genetic associations with lung cancer and its subtypes from the TRICL, ILCCO studies (discovery) and the FinnGen study (replication). We implemented Summary-data-based Mendelian Randomization analysis to identify potential therapeutic targets for lung cancer. Colocalization analysis was further conducted to assess whether the identified signal pairs shared a causal genetic variant. FINDINGS In the main analysis dataset, we identified 55 genes that demonstrate a causal relationship with lung cancer and its subtypes. However, in the replication cohort, only three genes were found to have such a causal association with lung cancer and its subtypes, and of these, HYKK (also known as AGPHD1) was consistently present in both the primary analysis dataset and the replication cohort. Following HEIDI tests and colocalization analyses, it was revealed that HYKK (AGPHD1) is associated with an increased risk of squamous cell carcinoma of the lung, with an odds ratio and confidence interval of OR = 1.28,95%CI = 1.24 to 1.33. INTERPRETATION We have found that the HYKK (AGPHD1) gene is associated with an increased risk of squamous cell carcinoma of the lung, suggesting that this gene may represent a potential therapeutic target for both the prevention and treatment of lung squamous cell carcinoma.
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Affiliation(s)
- Wenfu Song
- Department of Hematology and Oncology, the First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China
- The First Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China
| | - Yingying Li
- Department of Hematology and Oncology, the First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China
- The First Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China
| | - Yaxuan Yao
- The First Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China
| | - Shiling Sun
- Department of Hematology and Oncology, the First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China.
- The First Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China.
| | - Xutao Guan
- Department of Hematology and Oncology, the First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China
- The First Clinical Medical College of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China
| | - Bing Wang
- Department of Hematology and Oncology, the First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan Province, China
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Nam H, Lee E, Yang H, Lee K, Kwak T, Kim D, Kim H, Yang M, Yang Y, Son S, Nam YH, Minn I. PROMER technology: A new real-time PCR tool enabling multiplex detection of point mutation with high specificity and sensitivity. Biol Methods Protoc 2024; 9:bpae041. [PMID: 38938409 PMCID: PMC11208725 DOI: 10.1093/biomethods/bpae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/21/2024] [Accepted: 06/02/2024] [Indexed: 06/29/2024] Open
Abstract
Real-time polymerase chain reaction (real-time PCR) is a powerful tool for the precise quantification of nucleic acids in various applications. In cancer management, the monitoring of circulating tumor DNA (ctDNA) from liquid biopsies can provide valuable information for precision care, including treatment selection and monitoring, prognosis, and early detection. However, the rare and heterogeneous nature of ctDNA has made its precise detection and quantification challenging, particularly for ctDNA containing hotspot mutations. We have developed a new real-time PCR tool, PROMER technology, which enables the precise and sensitive detection of ctDNA containing cancer-driven single-point mutations. The PROMER functions as both a PRObe and priMER, providing enhanced detection specificity. We validated PROMER technology using synthetic templates with known KRAS point mutations and demonstrated its sensitivity and linearity of quantification. Using genomic DNA from human cancer cells with mutant and wild-type KRAS, we confirmed that PROMER PCR can detect mutant DNA. Furthermore, we demonstrated the ability of PROMER technology to efficiently detect mutation-carrying ctDNA from the plasma of mice with human cancers. Our results suggest that PROMER technology represents a promising new tool for the precise detection and quantification of DNA containing point mutations in the presence of a large excess of wild-type counterpart.
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Affiliation(s)
- Hwanhee Nam
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Esder Lee
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Hichang Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Kyeyoon Lee
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Taeho Kwak
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Dain Kim
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Hyemin Kim
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Mihwa Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Younjoo Yang
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Seungwan Son
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Young-Hyean Nam
- NuriBio Co., Ltd, Anyang-si, Gyeonggi-Do, 14058, Republic of Korea
| | - Il Minn
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, United States
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins Medical Institutions, Baltimore, MD 21287, United States
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40
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Lin YL, Yao T, Wang YW, Zhou ZX, Hong ZC, Shen Y, Yan Y, Li YC, Lin JF. Potential drug targets for gastroesophageal reflux disease and Barrett's esophagus identified through Mendelian randomization analysis. J Hum Genet 2024; 69:245-253. [PMID: 38429412 DOI: 10.1038/s10038-024-01234-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 03/03/2024]
Abstract
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.
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Affiliation(s)
- Yun-Lu Lin
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Tao Yao
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Ying-Wei Wang
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Zhi-Xiang Zhou
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Ze-Chao Hong
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yu Shen
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yu Yan
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China
| | - Yue-Chun Li
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
| | - Jia-Feng Lin
- The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, 325000, Zhejiang, China.
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Schormair B, Zhao C, Bell S, Didriksen M, Nawaz MS, Schandra N, Stefani A, Högl B, Dauvilliers Y, Bachmann CG, Kemlink D, Sonka K, Paulus W, Trenkwalder C, Oertel WH, Hornyak M, Teder-Laving M, Metspalu A, Hadjigeorgiou GM, Polo O, Fietze I, Ross OA, Wszolek ZK, Ibrahim A, Bergmann M, Kittke V, Harrer P, Dowsett J, Chenini S, Ostrowski SR, Sørensen E, Erikstrup C, Pedersen OB, Topholm Bruun M, Nielsen KR, Butterworth AS, Soranzo N, Ouwehand WH, Roberts DJ, Danesh J, Burchell B, Furlotte NA, Nandakumar P, Earley CJ, Ondo WG, Xiong L, Desautels A, Perola M, Vodicka P, Dina C, Stoll M, Franke A, Lieb W, Stewart AFR, Shah SH, Gieger C, Peters A, Rye DB, Rouleau GA, Berger K, Stefansson H, Ullum H, Stefansson K, Hinds DA, Di Angelantonio E, Oexle K, Winkelmann J. Genome-wide meta-analyses of restless legs syndrome yield insights into genetic architecture, disease biology and risk prediction. Nat Genet 2024; 56:1090-1099. [PMID: 38839884 PMCID: PMC11176086 DOI: 10.1038/s41588-024-01763-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/19/2024] [Indexed: 06/07/2024]
Abstract
Restless legs syndrome (RLS) affects up to 10% of older adults. Their healthcare is impeded by delayed diagnosis and insufficient treatment. To advance disease prediction and find new entry points for therapy, we performed meta-analyses of genome-wide association studies in 116,647 individuals with RLS (cases) and 1,546,466 controls of European ancestry. The pooled analysis increased the number of risk loci eightfold to 164, including three on chromosome X. Sex-specific meta-analyses revealed largely overlapping genetic predispositions of the sexes (rg = 0.96). Locus annotation prioritized druggable genes such as glutamate receptors 1 and 4, and Mendelian randomization indicated RLS as a causal risk factor for diabetes. Machine learning approaches combining genetic and nongenetic information performed best in risk prediction (area under the curve (AUC) = 0.82-0.91). In summary, we identified targets for drug development and repurposing, prioritized potential causal relationships between RLS and relevant comorbidities and risk factors for follow-up and provided evidence that nonlinear interactions are likely relevant to RLS risk prediction.
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Affiliation(s)
- Barbara Schormair
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.
- Institute of Human Genetics, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany.
| | - Chen Zhao
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Steven Bell
- Department of Oncology, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Maria Didriksen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Neuroscience, University of Copenhagen, Copenhagen, Denmark
| | | | - Nathalie Schandra
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Ambra Stefani
- Sleep Disorders Clinic, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Birgit Högl
- Sleep Disorders Clinic, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Yves Dauvilliers
- Sleep-Wake Disorders Center, Department of Neurology, Hôpital Gui-de-Chauliac, CHU Montpellier, Institut des Neurosciences de Montpellier, INSERM, Université de Montpellier, Montpellier, France
| | - Cornelius G Bachmann
- SomnoDiagnostics, Osnabrück, Germany
- Department of Neurology, University Medical Center Göttingen, Göttingen, Germany
| | - David Kemlink
- Department of Neurology and Centre of Clinical Neuroscience, Charles University, First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Karel Sonka
- Department of Neurology and Centre of Clinical Neuroscience, Charles University, First Faculty of Medicine and General University Hospital, Prague, Czech Republic
| | - Walter Paulus
- Department of Neurology, Ludwig Maximilians University Munich, Munich, Germany
| | - Claudia Trenkwalder
- Paracelsus-Elena-Klinik, Kassel, Germany
- Department of Neurosurgery, University Medical Center Göttingen, Göttingen, Germany
| | - Wolfgang H Oertel
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Neurology, Philipps-University Marburg, Marburg, Germany
| | | | - Maris Teder-Laving
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Andres Metspalu
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Georgios M Hadjigeorgiou
- Department of Neurology, Nicosia General Hospital Medical School, University of Cyprus, Nicosia, Cyprus
| | - Olli Polo
- Bragée ME/CFS Center, Stockholm, Sweden
| | - Ingo Fietze
- Department of Pulmonology, Center of Sleep Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, FL, USA
| | | | - Abubaker Ibrahim
- Sleep Disorders Clinic, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Melanie Bergmann
- Sleep Disorders Clinic, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Volker Kittke
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Philip Harrer
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Joseph Dowsett
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Sofiene Chenini
- Sleep-Wake Disorders Center, Department of Neurology, Hôpital Gui-de-Chauliac, CHU Montpellier, Institut des Neurosciences de Montpellier, INSERM, Université de Montpellier, Montpellier, France
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Christian Erikstrup
- Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Ole B Pedersen
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Mie Topholm Bruun
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Kaspar R Nielsen
- Department of Clinical Immunology, Aalborg University Hospital, Aalborg, Denmark
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Nicole Soranzo
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
- Department of Human Genetics, the Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - Willem H Ouwehand
- Department of Haematology, University of Cambridge, Cambridge, UK
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
- Department of Haematology, University College London Hospitals, London, UK
| | - David J Roberts
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Radcliffe Department of Medicine and National Health Service Blood and Transplant, Oxford, UK
- Department of Haematology and BRC Haematology Theme, Churchill Hospital, Headington, Oxford, UK
| | - John Danesh
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Department of Human Genetics, the Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | | | | | | | - Christopher J Earley
- Center for Restless Legs Syndrome, Department of Neurology, Johns Hopkins University, Baltimore, MD, USA
| | - William G Ondo
- Department of Neurology, Methodist Neurological Institute, Weill Cornell Medical School, Houston, TX, USA
| | - Lan Xiong
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Alex Desautels
- Centre d'Études Avancées en Médecine du Sommeil, Hôpital du Sacré-Cœur de Montréal, Montreal, Quebec, Canada
- Department of Neurosciences, Université de Montréal, Montreal, Quebec, Canada
| | - Markus Perola
- Clinical and Molecular Metabolism Research Program (CAMM), Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Public Health and Welfare, National Institute for Health and Welfare, Helsinki, Finland
| | - Pavel Vodicka
- Department of Molecular Biology of Cancer, Institute of Experimental Medicine, Academy of Science of Czech Republic, Prague, Czech Republic
- First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Christian Dina
- L'institut du thorax, CNRS, INSERM, Nantes Université, Nantes, France
| | - Monika Stoll
- Department of Genetic Epidemiology, Institute for Human Genetics, University of Münster, Münster, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Kiel, Germany
| | - Wolfgang Lieb
- PopGen Biobank and Institute of Epidemiology, Christian Albrechts University Kiel, Kiel, Germany
| | - Alexandre F R Stewart
- John and Jennifer Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Svati H Shah
- Department of Medicine, Duke University School of Medicine, Durham, NC, USA
- Duke Clinical Research Institute, Duke University School of Medicine, Durham, NC, USA
| | - Christian Gieger
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- German Research Center for Cardiovascular Disease (DZHK), partner site Munich Heart Alliance, Hannover, Germany
- Chair of Epidemiology, Institute for Medical Information Processing, Biometry and Epidemiology, Medical Faculty, Ludwig-Maximilians-Universität München, Munich, Germany
| | - David B Rye
- Department of Neurology, Emory University, Atlanta, GA, USA
| | - Guy A Rouleau
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Klaus Berger
- Institute of Epidemiology and Social Medicine, University of Münster, Münster, Germany
| | | | | | | | | | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK
- National Institute for Health and Care Research Blood and Transplant Research Unit in Donor Health and Behaviour, University of Cambridge, Cambridge, UK
- Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
- Victor Phillip Dahdaleh Heart and Lung Research Institute, University of Cambridge, Cambridge, UK
- Health Data Science Research Centre, Fondazione Human Technopole, Milan, Italy
| | - Konrad Oexle
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Neurogenetic Systems Analysis Group, Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Human Genetics, TUM School of Medicine and Health, Technical University of Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
- German Center for Mental Health (DZPG), partner site Munich-Augsburg, Munich-Augsburg, Germany
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Li Q, Song Q, Chen Z, Choi J, Moreno V, Ping J, Wen W, Li C, Shu X, Yan J, Shu XO, Cai Q, Long J, Huyghe JR, Pai R, Gruber SB, Casey G, Wang X, Toriola AT, Li L, Singh B, Lau KS, Zhou L, Wu C, Peters U, Zheng W, Long Q, Yin Z, Guo X. Large-scale integration of omics and electronic health records to identify potential risk protein biomarkers and therapeutic drugs for cancer prevention and intervention. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.29.24308170. [PMID: 38853880 PMCID: PMC11160851 DOI: 10.1101/2024.05.29.24308170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Identifying risk protein targets and their therapeutic drugs is crucial for effective cancer prevention. Here, we conduct integrative and fine-mapping analyses of large genome-wide association studies data for breast, colorectal, lung, ovarian, pancreatic, and prostate cancers, and characterize 710 lead variants independently associated with cancer risk. Through mapping protein quantitative trait loci (pQTL) for these variants using plasma proteomics data from over 75,000 participants, we identify 365 proteins associated with cancer risk. Subsequent colocalization analysis identifies 101 proteins, including 74 not reported in previous studies. We further characterize 36 potential druggable proteins for cancers or other disease indications. Analyzing >3.5 million electronic health records, we uncover five drugs (Haloperidol, Trazodone, Tranexamic Acid, Haloperidol, and Captopril) associated with increased cancer risk and two drugs (Caffeine and Acetazolamide) linked to reduced colorectal cancer risk. This study offers novel insights into therapeutic drugs targeting risk proteins for cancer prevention and intervention.
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Lu YQ, Wang Y. Multi-Omic Analysis Reveals Genetic Determinants and Therapeutic Targets of Chronic Kidney Disease and Kidney Function. Int J Mol Sci 2024; 25:6033. [PMID: 38892221 PMCID: PMC11172763 DOI: 10.3390/ijms25116033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/20/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Chronic kidney disease (CKD) presents a significant global health challenge, characterized by complex pathophysiology. This study utilized a multi-omic approach, integrating genomic data from the CKDGen consortium alongside transcriptomic, metabolomic, and proteomic data to elucidate the genetic underpinnings and identify therapeutic targets for CKD and kidney function. We employed a range of analytical methods including cross-tissue transcriptome-wide association studies (TWASs), Mendelian randomization (MR), summary-based MR (SMR), and molecular docking. These analyses collectively identified 146 cross-tissue genetic associations with CKD and kidney function. Key Golgi apparatus-related genes (GARGs) and 41 potential drug targets were highlighted, with MAP3K11 emerging as a significant gene from the TWAS and MR data, underscoring its potential as a therapeutic target. Capsaicin displayed promising drug-target interactions in molecular docking analyses. Additionally, metabolome- and proteome-wide MR (PWMR) analyses revealed 33 unique metabolites and critical inflammatory proteins such as FGF5 that are significantly linked to and colocalized with CKD and kidney function. These insights deepen our understanding of CKD pathogenesis and highlight novel targets for treatment and prevention.
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Affiliation(s)
| | - Yirong Wang
- School of Biology & Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China;
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Senkevich K, Liu L, Alvarado CX, Leonard HL, Nalls MA, Gan-Or Z. Lack of genetic evidence for NLRP3-inflammasome involvement in Parkinson's disease pathogenesis. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.09.20.23295790. [PMID: 37886468 PMCID: PMC10602039 DOI: 10.1101/2023.09.20.23295790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Activation of the NLRP3-inflammasome has been implicated in Parkinson's disease based on in vitro and in vivo studies. Clinical trials targeting the NLRP3-inflammasome in Parkinson's disease are ongoing. However, the evidence supporting NLRP3's involvement in Parkinson's disease from human genetics data is limited. In this study, we conducted analyses of common and rare variants in NLRP3-inflammasome related genes in Parkinson's disease cohorts. We performed pathway-specific analyses using polygenic risk scores and studied potential causal associations using Mendelian randomization with the NLRP3 components and the cytokines IL-1β and IL-18. Our findings showed no associations of common or rare variants, nor of the pathway polygenic risk score with Parkinson's disease. Mendelian randomization suggests that altering the expression of the NLRP3-inflammasome, IL-1β or IL-18, does not affect Parkinson's disease risk or progression. Therefore, our results do not support a role for the NLRP3-inflammasome in Parkinson's disease pathogenesis or as a target for drug development.
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45
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Jiang D, Zheng S, Xu X, Yue H, Liang W, Wu Z. Uncovering Druggable Targets in Aortic Dissection: An Association Study Integrating Mendelian Randomization, pQTL, and Protein-Protein Interaction Network. Biomedicines 2024; 12:1204. [PMID: 38927411 PMCID: PMC11200553 DOI: 10.3390/biomedicines12061204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/16/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Aortic dissection (AD) is a life-threatening acute aortic syndrome. There are limitations and challenges in the discovery and application of biomarkers and drug targets for AD. Mendelian randomization (MR) analysis is a reliable analytical method to identify effective therapeutic targets. We aimed to identify novel therapeutic targets for AD and investigate their potential side-effects based on MR analysis. Data from protein quantitative trait loci (pQTLs) were used for MR analyses to identify potential therapeutic targets. We probed druggable proteins involved in the pathogenesis of aortic dissection from deCODE. In this study, a two-sample MR analysis was conducted, with druggable proteins as the exposure factor and data on genome-wide association studies (GWAS) of AD as the outcome. After conducting a two-sample MR, summary data-based Mendelian randomization (SMR) analysis and colocalization analysis were performed. A protein-protein interaction (PPI) network was also constructed to delve into the interactions between identified proteins. After MR analysis and the Steiger test, we identified five proteins as potential therapeutic targets for AD. SMR analysis and colocalization analysis also confirmed our findings. Finally, we identified ASPN (OR = 1.36, 95% CI: 1.20, 1.54, p = 4.22 × 10-5) and SPOCK2 (OR = 0.57, 95% CI: 0.41, 0.78, p = 4.52 × 10-4) as the core therapeutic targets. Through PPI network analysis, we identified six druggable targets, enabling the subsequent identification of six promising drugs from DrugBank for treating AD. This discovery of specific proteins as novel therapeutic targets represents a significant advancement in AD treatment. These findings provide more effective treatment options for AD.
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Affiliation(s)
| | | | | | | | | | - Zhong Wu
- Department of Cardiovascular Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Road, Wuhou District, Chengdu 610041, China; (D.J.)
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Dai L, Ye Y, Mugaany J, Hu Z, Huang J, Lu C. Leveraging pQTL-based Mendelian randomization to identify new treatment prospects for primary biliary cholangitis and primary sclerosing cholangitis. Aging (Albany NY) 2024; 16:9228-9250. [PMID: 38809509 PMCID: PMC11164478 DOI: 10.18632/aging.205867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 04/15/2024] [Indexed: 05/30/2024]
Abstract
Primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) are autoimmune disorders characterized by progressive and chronic damage to the bile ducts, presenting clinicians with significant challenges. The objective of this study is to identify potential druggable targets to offer new avenues for treatment. A Mendelian randomization analysis was performed to identify druggable targets for PBC and PSC. This involved obtaining Cis-protein quantitative trait loci (Cis-pQTL) data from the deCODE database to serve as exposure. Outcome data for PBC (557 cases and 281,127 controls) and PSC (1,715 cases and 330,903 controls) were obtained from the FINNGEN database. Colocalization analysis was conducted to determine whether these features share the same associated SNPs. Validation of the expression level of druggable targets was done using the GSE119600 dataset and immunohistochemistry for clinical samples. Lastly, the DRUGBANK database was used to predict potential drugs. The MR analysis identified eight druggable targets each for PBC and PSC. Subsequent summary-data-based MR and colocalization analyses showed that LEFTY2 had strong evidence as a therapeutic candidate for PBC, while HSPB1 had moderate evidence. For PSC, only FCGR3B showed strong evidence as a therapeutic candidate. Additionally, upregulated expression of these genes was validated in PBC and PSC groups by GEO dataset and clinical samples. This study identifies two novel druggable targets with strong evidence for therapeutic candidates for PBC (LEFTY2 and HSPB1) and one for PSC (FCGR3B). These targets offer new therapeutic opportunities to address the challenging nature of PBC and PSC treatment.
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Affiliation(s)
- Lei Dai
- Department of Hepato-Pancreato-Biliary Surgery, Ningbo Medical Centre Lihuili Hospital, The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315040, China
| | - Yunyan Ye
- Department of Ophthalmology, Ningbo Medical Centre Lihuili Hospital, The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315040, China
| | - Joseph Mugaany
- Department of Hepato-Pancreato-Biliary Surgery, Ningbo Medical Centre Lihuili Hospital, The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315040, China
- Health Science Center, Ningbo University, Ningbo 315211, China
| | - Zetong Hu
- Department of Hepato-Pancreato-Biliary Surgery, Ningbo Medical Centre Lihuili Hospital, The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315040, China
- Health Science Center, Ningbo University, Ningbo 315211, China
| | - Jing Huang
- Department of Hepato-Pancreato-Biliary Surgery, Ningbo Medical Centre Lihuili Hospital, The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315040, China
| | - Changjiang Lu
- Department of Hepato-Pancreato-Biliary Surgery, Ningbo Medical Centre Lihuili Hospital, The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315040, China
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Wang Y, Wang X, Yuan Z, Liu F, Luo X, Yang J. Identifying Potential Drug Targets for Keloid: A Mendelian Randomization Study. J Invest Dermatol 2024:S0022-202X(24)00388-9. [PMID: 38797322 DOI: 10.1016/j.jid.2024.04.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 04/03/2024] [Accepted: 04/19/2024] [Indexed: 05/29/2024]
Abstract
Keloids are a skin fibrosis disease characterized by troublesome symptoms, a varying degree of recurrence and inevitable side effects from treatments. Thus, identifying their drug targets is necessary. A 2-sample Mendelian randomization analysis was conducted using proteins from the intersection of the deCODE database and "The Druggable Genome and Support for Target Identification and Validation in Drug Development" as the exposure variable. The outcome variable was based on recently published GWAS of keloids. Summary data-based Mendelian randomization and colocalization analysis was employed to distinguish pleiotropy from linkage. Candidate targets underwent drug target analysis. The primary findings were validated through single-cell RNA-sequencing data, Western Blot and immunofluorescence staining on keloids. Seven proteins were identified as potential drug targets for keloids. Among these proteins, Hedgehog-interacting protein, neurotrimin [NTM], KLKB1, and CRIPTO showed positive correlations with keloids, while PLXNC1, SCG3 and PDGFD exhibited negative correlations. Combined with the single-cell RNA-sequencing data, NTM, PLXNC1, and PDGFD were found highly expressed in the fibroblasts. NTM showed a significant increase in keloids as compared to normal scars. In accordance with the analysis, higher levels of protein expression of NTM in keloids compared to normal skin was observed. The identified proteins may be appealing drug targets for keloids treatment with a special emphasis on NTM.
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Affiliation(s)
- Yinmin Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiuxia Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaoqi Yuan
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Liu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; The First People's Hospital of the Lancang Lahu Autonomous County, Yunnan, China
| | - Xusong Luo
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Jun Yang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Liu Z, Peng Z, Lin H, Zhou K, Liang L, Cao J, Huang Z, Mei J. Identifying potential drug targets for idiopathic pulmonary fibrosis: a mendelian randomization study based on the druggable genes. Respir Res 2024; 25:217. [PMID: 38783236 PMCID: PMC11118997 DOI: 10.1186/s12931-024-02848-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/13/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Idiopathic pulmonary fibrosis (IPF) is a chronic fibrotic interstitial lung disease characterized by progressive dyspnea and decreased lung function, yet its exact etiology remains unclear. It is of great significance to discover new drug targets for IPF. METHODS We obtained the cis-expression quantitative trait locus (cis-eQTL) of druggable genes from eQTLGen Consortium as exposure and the genome wide association study (GWAS) of IPF from the International IPF Genetics Consortium as outcomes to simulate the effects of drugs on IPF by employing mendelian randomization analysis. Then colocalization analysis was performed to calculate the probability of both cis-eQTL of druggable genes and IPF sharing a causal variant. For further validation, we conducted protein quantitative trait locus (pQTL) analysis to reaffirm our findings. RESULTS The expression of 45 druggable genes was significantly associated with IPF susceptibility at FDR < 0.05. The expression of 23 and 15 druggable genes was significantly associated with decreased forced vital capacity (FVC) and diffusing capacity of the lungs for carbon monoxide (DLco) in IPF patients, respectively. IPF susceptibility and two significant genes (IL-7 and ABCB2) were likely to share a causal variant. The results of the pQTL analysis demonstrated that high levels of IL-7 in plasma are associated with a reduced risk of IPF (OR = 0.67, 95%CI: 0.47-0.97). CONCLUSION IL-7 stands out as the most promising potential drug target to mitigate the risk of IPF. Our study not only sheds light on potential drug targets but also provides a direction for future drug development in IPF.
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Affiliation(s)
- Zetao Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Zhiyu Peng
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Huahang Lin
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Ke Zhou
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Linchuan Liang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Jie Cao
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Zhaokang Huang
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China
| | - Jiandong Mei
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Western China Collaborative Innovation Center for Early Diagnosis and Multidisciplinary Therapy of Lung Cancer, Sichuan University, Chengdu, China.
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Kraft J, Braun A, Awasthi S, Panagiotaropoulou G, Schipper M, Bell N, Posthuma D, Pardiñas AF, Ripke S, Heilbron K. Identifying drug targets for schizophrenia through gene prioritization. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.15.24307423. [PMID: 38798390 PMCID: PMC11118622 DOI: 10.1101/2024.05.15.24307423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Background Schizophrenia genome-wide association studies (GWASes) have identified >250 significant loci and prioritized >100 disease-related genes. However, gene prioritization efforts have mostly been restricted to locus-based methods that ignore information from the rest of the genome. Methods To more accurately characterize genes involved in schizophrenia etiology, we applied a combination of highly-predictive tools to a published GWAS of 67,390 schizophrenia cases and 94,015 controls. We combined both locus-based methods (fine-mapped coding variants, distance to GWAS signals) and genome-wide methods (PoPS, MAGMA, ultra-rare coding variant burden tests). To validate our findings, we compared them with previous prioritization efforts, known neurodevelopmental genes, and results from the PsyOPS tool. Results We prioritized 62 schizophrenia genes, 41 of which were also highlighted by our validation methods. In addition to DRD2, the principal target of antipsychotics, we prioritized 9 genes that are targeted by approved or investigational drugs. These included drugs targeting glutamatergic receptors (GRIN2A and GRM3), calcium channels (CACNA1C and CACNB2), and GABAB receptor (GABBR2). These also included genes in loci that are shared with an addiction GWAS (e.g. PDE4B and VRK2). Conclusions We curated a high-quality list of 62 genes that likely play a role in the development of schizophrenia. Developing or repurposing drugs that target these genes may lead to a new generation of schizophrenia therapies. Rodent models of addiction more closely resemble the human disorder than rodent models of schizophrenia. As such, genes prioritized for both disorders could be explored in rodent addiction models, potentially facilitating drug development.
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Affiliation(s)
- Julia Kraft
- Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- German Center for Mental Health (DZPG), partner site Berlin/Potsdam, Berlin, Germany
| | - Alice Braun
- Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- German Center for Mental Health (DZPG), partner site Berlin/Potsdam, Berlin, Germany
| | - Swapnil Awasthi
- Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- German Center for Mental Health (DZPG), partner site Berlin/Potsdam, Berlin, Germany
| | - Georgia Panagiotaropoulou
- Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- German Center for Mental Health (DZPG), partner site Berlin/Potsdam, Berlin, Germany
| | | | - Nathaniel Bell
- Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Danielle Posthuma
- Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Child and Adolescent Psychiatry and Pediatric Psychology, Section Complex Trait Genetics, Amsterdam Neuroscience, Vrije Universiteit Medical Center, Amsterdam, The Netherlands
| | - Antonio F. Pardiñas
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | | | - Stephan Ripke
- Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- German Center for Mental Health (DZPG), partner site Berlin/Potsdam, Berlin, Germany
| | - Karl Heilbron
- Department of Psychiatry and Psychotherapy, Charité – Universitätsmedizin Berlin, Berlin, Germany
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- German Center for Mental Health (DZPG), partner site Berlin/Potsdam, Berlin, Germany
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50
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Salgueiro VC, Passemar C, Vázquez-Iniesta L, Lerma L, Floto A, Prados-Rosales R. Extracellular vesicles in mycobacteria: new findings in biogenesis, host-pathogen interactions, and diagnostics. mBio 2024; 15:e0255223. [PMID: 38567992 PMCID: PMC11077946 DOI: 10.1128/mbio.02552-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2024] Open
Abstract
Since the discovery of extracellular vesicles (EVs) in mycobacterial species 15 years back, we have learned that this phenomenon is conserved in the Mycobacterium genus and has critical roles in bacterial physiology and host-pathogen interactions. Mycobacterium tuberculosis (Mtb), the tuberculosis (TB) causative agent, produces EVs both in vitro and in vivo including a diverse set of biomolecules with demonstrated immunomodulatory effects. Moreover, Mtb EVs (MEVs) have been shown to possess vaccine properties and carry biomarkers with diagnostic capacity. Although information on MEV biogenesis relative to other bacterial species is scarce, recent studies have shed light on how MEVs originate and are released to the extracellular space. In this minireview, we discuss past and new information about the vesiculogenesis phenomenon in Mtb, including biogenesis, MEV cargo, aspects in the context of host-pathogen interactions, and applications that could help to develop effective tools to tackle the disease.
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Affiliation(s)
- Vivian C. Salgueiro
- Department of Preventive Medicine, Public Health, and Microbiology. School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Charlotte Passemar
- Cambridge Center for Lung Infection, Royal Papworth Hospital NHS Trust, Cambridge, United Kingdom
| | - Lucía Vázquez-Iniesta
- Department of Preventive Medicine, Public Health, and Microbiology. School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Laura Lerma
- Department of Preventive Medicine, Public Health, and Microbiology. School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
| | - Andrés Floto
- Cambridge Center for Lung Infection, Royal Papworth Hospital NHS Trust, Cambridge, United Kingdom
| | - Rafael Prados-Rosales
- Department of Preventive Medicine, Public Health, and Microbiology. School of Medicine, Universidad Autónoma de Madrid, Madrid, Spain
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