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Tan M, Liu X, Wang L, Jiang N, Bai Y, Guo Z. Differential Expression of mRNA in Peripheral Blood Mononuclear Cells May Predict Postoperative Atrial Fibrillation in Coronary Artery Bypass Surgery Patients. J Cardiovasc Transl Res 2024:10.1007/s12265-024-10524-8. [PMID: 39009943 DOI: 10.1007/s12265-024-10524-8] [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: 12/27/2023] [Accepted: 05/16/2024] [Indexed: 07/17/2024]
Abstract
Postoperative Atrial Fibrillation (POAF) frequently follows Coronary Artery Bypass Grafting (CABG) surgery. This prospective study investigates genes linked to POAF in CABG patients, aiming to create a predictive model. Employing differential gene and methylation analyses, the study identified four genes (WARS2, CKAP2, CHI3L1, HSD17B6) associated with POAF. Preoperative plasma samples and clinical data were collected from 139 CABG patients, categorized into POAF (+) (43) and POAF (-) (96). Real-time quantitative PCR assessed gene expression, and a predictive model using the LASSO method demonstrated robust performance, with AUC values of 0.8895 in the training set and 0.7840 in the test set. This pioneering study integrates genomics and clinical data, suggesting WARS2, CKAP2, and CHI3L1 as potential indicators for POAF prediction.
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Affiliation(s)
- Mingqi Tan
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China
| | - Xiankun Liu
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China
- Tianjin Institute of Cardiovascular Diseases, Chest Hospital, Tianjin University, Tianjin, China
| | - Lianqun Wang
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China
| | - Nan Jiang
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China
| | - Yunpeng Bai
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China.
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China.
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, China.
| | - Zhigang Guo
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China.
- Department of Cardiac Surgery, Chest Hospital, Tianjin University, Tianjin, China.
- Clinical School of Thoracic, Tianjin Medical University, Tianjin, China.
- Tianjin Key Laboratory of Cardiovascular Emergency and Critical Care, Tianjin Municipal Science and Technology Bureau, Tianjin, China.
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Tao T, Mo X, Zhao L. Identifying novel potential drug targets for endometriosis via plasma proteome screening. Front Endocrinol (Lausanne) 2024; 15:1416978. [PMID: 39036049 PMCID: PMC11257892 DOI: 10.3389/fendo.2024.1416978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Background Endometriosis (EM) is a chronic painful condition that predominantly affects women of reproductive age. Currently, surgery or medication can only provide limited symptom relief. This study used a comprehensive genetic analytical approach to explore potential drug targets for EM in the plasma proteome. Methods In this study, 2,923 plasma proteins were selected as exposure and EM as outcome for two-sample Mendelian randomization (MR) analyses. The plasma proteomic data were derived from the UK Biobank Pharmaceutical Proteomics Project (UKB-PPP), while the EM dataset from the FinnGen consortium R10 release data. Several sensitivity analyses were performed, including summary-data-based MR (SMR) analyses, heterogeneity in dependent instruments (HEIDI) test, reverse MR analyses, steiger detection test, and bayesian co-localization analyses. Furthermore, proteome-wide association study (PWAS) and single-cell transcriptomic analyses were also conducted to validate the findings. Results Six significant (p < 3.06 × 10-5) plasma protein-EM pairs were identified by MR analyses. These included EPHB4 (OR = 1.40, 95% CI: 1.20 - 1.63), FSHB (OR = 3.91, 95% CI: 3.13 - 4.87), RSPO3 (OR = 1.60, 95% CI: 1.38 - 1.86), SEZ6L2 (OR = 1.44, 95% CI: 1.23 - 1.68) and WASHC3 (OR = 2.00, 95% CI: 1.54 - 2.59) were identified as risk factors, whereas KDR (OR = 0.80, 95% CI: 0.75 - 0.90) was found to be a protective factor. All six plasma proteins passed the SMR test (P < 8.33 × 10-3), but only four plasma proteins passed the HEIDI heterogeneity test (PHEIDI > 0.05), namely FSHB, RSPO3, SEZ6L2 and EPHB4. These four proteins showed strong evidence of co-localization (PPH4 > 0.7). In particular, RSPO3 and EPHB4 were replicated in the validated PWAS. Single-cell analyses revealed high expression of SEZ6L2 and EPHB4 in stromal and epithelial cells within EM lesions, while RSPO3 exhibited elevated expression in stromal cells and fibroblasts. Conclusion Our study identified FSHB, RSPO3, SEZ6L2, and EPHB4 as potential drug targets for EM and highlighted the critical role of stromal and epithelial cells in disease development. These findings provide new insights into the diagnosis and treatment of EM.
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Affiliation(s)
- Tian Tao
- Department of Nephrology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoyu Mo
- Department of Gynaecology and Obstetrics, West China Second Hospital, Sichuan University, Chengdu, China
| | - Liangbin Zhao
- Department of Nephrology, Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
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Gou L, Li H, Jiang Y, Liu Y, Gu H, Xu Z, Jin W, Li L, Shi Y, Zhang J, Fang Z, Meng X, Jiang Y, Li H, Wang Y, Cheng S. Non-O blood types are associated with a greater risk of large artery atherosclerosis stroke and dysregulation of cholesterol metabolism: an observational study. Lipids Health Dis 2024; 23:211. [PMID: 38965603 PMCID: PMC11223365 DOI: 10.1186/s12944-024-02199-6] [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: 04/01/2024] [Accepted: 06/26/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Previous research on ABO blood types and stroke has been controversial, predominantly suggesting heightened risk of stroke in non-O blood types. Nonetheless, investigations into the correlation and underlying mechanisms between ABO blood groups and stroke subtypes, especially within Chinese cohorts, remain limited. METHODS The ABO blood types of 9,542 ischaemic stroke (IS) patients were inferred using two ABO gene loci (c.261G > del; c.802G > A). The healthy population was derived from the 1000 Genomes Project. Patients were classified by the causative classification system (CCS). Volcano plot and gene ontology (GO) analysis were employed to explore protein differential expression among blood types. Additionally, HT29 and SW480 cell lines with downregulated ABO expression were generated to evaluate its impact on cholesterol uptake and efflux. RESULTS A greater proportion of stroke patients had non-O blood types (70.46%) than did healthy individuals (61.54%). Notable differences in blood type distributions were observed among stroke subtypes, with non-O blood type patients mainly classified as having large artery atherosclerosis (LAA). Clinical baseline characteristics, such as the low-density lipoprotein cholesterol level, activated partial thromboplastin time and thrombin time, varied significantly among blood types. A volcano plot revealed 17 upregulated and 42 downregulated proteins in the O blood type. GO term analysis indicated that downregulated proteins were primarily associated with lipid metabolism pathways. In vitro experiments revealed that reducing ABO gene expression decreased cholesterol uptake and increased cholesterol efflux. CONCLUSIONS This study revealed that the non-O blood type increased the risk of LAA stroke through cholesterol metabolism.
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Affiliation(s)
- Lan Gou
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Haowen Li
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yingyu Jiang
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yang Liu
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hongqiu Gu
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhe Xu
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Weina Jin
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lanxin Li
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanfeng Shi
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jie Zhang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | | | - Xia Meng
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yong Jiang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Hao Li
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yongjun Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- Changping Laboratory, Beijing, China.
- Clinical Center for Precision Medicine in Stroke, Capital Medical University, Beijing, China.
| | - Si Cheng
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
- Changping Laboratory, Beijing, China.
- Clinical Center for Precision Medicine in Stroke, Capital Medical University, Beijing, China.
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Zhao H, Liu Y, Zhang X, Liao Y, Zhang H, Han X, Guo L, Fan B, Wang W, Lu C. Identifying novel proteins for suicide attempt by integrating proteomes from brain and blood with genome-wide association data. Neuropsychopharmacology 2024; 49:1255-1265. [PMID: 38317018 PMCID: PMC11224332 DOI: 10.1038/s41386-024-01807-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/28/2023] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
Genome-wide association studies (GWASs) have identified risk loci for suicide attempt (SA), but deciphering how they confer risk for SA remains largely unknown. This study aims to identify the key proteins and gain insights into SA pathogenesis. We integrated data from the brain proteome (N = 376) and blood proteome (N = 35,559) and combined it with the largest SA GWAS summary statistics to date (N = 518,612). A comprehensive set of methods was employed, including Mendelian randomization (MR), Steiger filtering, Bayesian colocalization, proteome‑wide association studies (PWAS), transcript-levels, cell-type specificity, correlation, and protein-protein interaction (PPI) network analysis. Validation was performed using other protein datasets and the SA dataset from FinnGen study. We identified ten proteins (GLRX5, GMPPB, B3GALTL, FUCA2, TTLL12, ADCK1, MMAA, HIBADH, ACP1, DOC2A) associated with SA in brain proteomics. GLRX5, GMPPB, and FUCA2 showed strong colocalization evidence and were supported by PWAS and transcript-level analysis, and were predominantly expressed in glutamatergic neuronal cells. In blood proteomics, one significant protein (PEAR1) and three near-significant proteins (NDE1, EVA1C, B4GALT2) were identified, but lacked colocalization evidence. Moreover, despite the limited correlation between the same protein in brain and blood, the PPI network analysis provided new insights into the interaction between brain and blood in SA. Furthermore, GLRX5 was associated with the GSTP1, the target of Clozapine. The comprehensive analysis provides strong evidence supporting a causal association between three genetically determined brain proteins (GLRX5, GMPPB, and FUCA2) with SA. These findings offer valuable insights into SA's underlying mechanisms and potential therapeutic approaches.
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Affiliation(s)
- Hao Zhao
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou, China
| | - Yifeng Liu
- Department of Psychiatry, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Xuening Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yuhua Liao
- Department of Psychiatry, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Huimin Zhang
- Department of Psychiatry, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Xue Han
- Department of Psychiatry, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Lan Guo
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou, China
| | - Beifang Fan
- Department of Psychiatry, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China.
| | - Wanxin Wang
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China.
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou, China.
| | - Ciyong Lu
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, Guangzhou, China
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Seo Y, Bae H, Lee C. Bayesian colocalization of GWAS and eQTL signals reveals cell type-specific genes and regulatory variants for susceptibility to subtypes of ischemic stroke. Comput Biol Chem 2024; 110:108086. [PMID: 38744227 DOI: 10.1016/j.compbiolchem.2024.108086] [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: 02/14/2024] [Revised: 04/09/2024] [Accepted: 04/23/2024] [Indexed: 05/16/2024]
Abstract
A colocalization analysis of genome-wide association study (GWAS) signals and expression quantitative trait loci (eQTL) was conducted to pinpoint target genes and their regulatory nucleotide variants for subtypes of ischemic stroke. We utilized GWAS data from prominent meta-analysis consortia (MEGASTROKE and GIGASTROKE) and single-cell eQTL data in brain and blood tissues to enhance accuracy and minimize noise inherent in bulk RNA-seq. Employing Bayesian colocalization methods, we identified ten shared loci between GWAS and eQTL signals, targeting five eGenes. Specifically, RAPH1 and ICA1L were discovered for small vessel stroke (SVS), whereas SCYL3, CAV1, and CAV2 were for cardioembolic stroke (CS). However, no findings have been made for large artery stroke. The exploration and subsequent functional analysis of causal variants within the colocalized regions revealed their regulatory roles, particularly as enhancer variants (e.g., rs144505847 and rs72932755 targeting ICA1L; rs629234 targeting SCYL3; rs3807989 targeting CAV1 and CAV2). Notably, our study unveiled that all eQTL for CS were identified in oligodendrocytes, while those for SVS were across excitatory neurons, astrocytes, and oligodendrocyte precursor cells. This underscores the heterogeneous tissue-specific genetic factors by subtypes of ischemic stroke. The study emphasizes the need for intensive research efforts to discover causative genes and variants, unravelling the cell type-specific genetic architecture of ischemic stroke subtypes. This knowledge is crucial for advancing our understanding of the underlying pathophysiology and paving the way for precision neurology applications.
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Affiliation(s)
- Yunji Seo
- Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, South Korea
| | - Hojin Bae
- Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, South Korea
| | - Chaeyoung Lee
- Department of Bioinformatics and Life Science, Soongsil University, 369 Sangdo-ro, Dongjak-gu, Seoul 06978, South Korea.
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Zhou Q, Ma J, Liu Q, Wu C, Yang Z, Yang T, Chen Q, Yue Y, Shang J. Traditional Chinese Medicine formula, Sanwujiao granule, attenuates ischemic stroke by promoting angiogenesis through early administration. JOURNAL OF ETHNOPHARMACOLOGY 2024; 321:117418. [PMID: 37979814 DOI: 10.1016/j.jep.2023.117418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/24/2023] [Accepted: 11/10/2023] [Indexed: 11/20/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Ischemic stroke (IS) is one of the most lethal diseases with the insufficient pharmacology therapeutic approach. Sanwujiao granule (SW) is widely used for IS in China with little known about its underlying mechanism. AIM OF THE STUDY To investigate the characteristics of therapeutic effects and potential mechanisms of SW against IS. MATERIALS AND METHODS The fingerprint of SW was applied by high-performance liquid chromatography-mass spectrometry (HPLC-MS). Three different drug treatment strategies, including prophylactic administration, early administration and delayed administration, were applied in rats' permanent middle cerebral occlusion (pMCAO) model. The Garcia neurological deficit test, adhesive removal test, rotarod test, TTC and TUNEL staining were performed to evaluate the pathological changes. The transcriptomic analysis was used to predict the potential mechanism of SW. The vascular deficiency model of Tg(kdrl:eGFP) zebrafish larvae and oxygen-glucose deprivation model on bEnd.3 cells were used to verify SW's pharmacological effect. qRT-PCR, immunofluorescent staining and Western Blot were applied to detect the expression of genes and proteins. The network pharmacology approach was applied to discover the potential bioactive compounds in SW that contribute to its pharmacological effect. RESULTS SW early and delayed administration attenuated cerebral infarction, neurological deficit and cell apoptosis. The transcriptomic analysis revealed that SW activated angiogenesis-associated biological processes specifically by early administration. CD31 immunofluorescent staining further confirmed the microvessel intensity in peri-infarct regions was significantly elevated after SW early treatment. Additionally, on the vascular deficiency model of zebrafish larvae, SW showed the angiogenesis effect. Next, the cell migration and tube formation were also observed in the bEnd.3 cells with the oxygen-glucose deprivation induced cell injury. It's worth noting that both mRNA and protein levels of angiogenesis factor, insulin-like growth factor 1, were significantly elevated in the pMCAO rats' brains treated with SW. The network pharmacology approach was applied and chasmanine, karacoline, talatisamine, etc. were probably the main active compounds of SW in IS treatment as they affected the angiogenesis-associated targets. CONCLUSIONS These results demonstrate that SW plays a critical role in anti-IS via promoting angiogenesis through early administration, indicating that SW is a candidate herbal complex for further investigation in treating IS in the clinical.
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Affiliation(s)
- Qinyang Zhou
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Ji Ma
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Qiuyan Liu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Changyue Wu
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Ziwei Yang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Tingting Yang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Qimeng Chen
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China
| | - Yunyun Yue
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China.
| | - Jing Shang
- School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, 211198, China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Jiangsu Key Laboratory of TCM Evaluation and Translational Research, China Pharmaceutical University, Nanjing, 210009, China; NMPA Key Laboratory for Research and Evaluation of Cosmetics, National Institutes for Food and Drug Control, Beijing, 100050, China.
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Ruscu M, Capitanescu B, Rupek P, Dandekar T, Radu E, Hermann DM, Popa-Wagner A. The post-stroke young adult brain has limited capacity to re-express the gene expression patterns seen during early postnatal brain development. Brain Pathol 2024:e13232. [PMID: 38198833 DOI: 10.1111/bpa.13232] [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: 06/07/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
The developmental origins of the brain's response to injury can play an important role in recovery after a brain lesion. In this study, we investigated whether the ischemic young adult brain can re-express brain plasticity genes that were active during early postnatal development. Differentially expressed genes in the cortex of juvenile post-natal day 3 and the peri-infarcted cortical areas of young, 3-month-old post-stroke rats were identified using fixed-effects modeling within an empirical Bayes framework through condition-specific comparison. To further analyze potential biological processes, upregulated and downregulated genes were assessed for enrichment using GSEA software. The genes showing the highest expression changes were subsequently verified through RT-PCR. Our findings indicate that the adult brain partially recapitulates the gene expression profile observed in the juvenile brain but fails to upregulate many genes and pathways necessary for brain plasticity. Of the upregulated genes in post-stroke brains, specific roles have not been assigned to Apobec1, Cenpf, Ect2, Folr2, Glipr1, Myo1f, and Pttg1. New genes that failed to upregulate in the adult post-stroke brain include Bex4, Cd24, Klhl1/Mrp2, Trim67, and St8sia2. Among the upregulated pathways, the largest change was observed in the KEGG pathway "One carbon pool of folate," which is necessary for cellular proliferation, followed by the KEGG pathway "Antifolate resistance," whose genes mainly encode the family of ABC transporters responsible for the efflux of drugs that have entered the brain. We also noted three less-described downregulated KEGG pathways in experimental models: glycolipid biosynthesis, oxytocin, and cortisol pathways, which could be relevant as therapeutic targets. The limited brain plasticity of the adult brain is illustrated through molecular and histological analysis of the axonal growth factor, KIF4. Collectively, these results strongly suggest that further research is needed to decipher the complex genetic mechanisms that prevent the re-expression of brain plasticity-associated genes in the adult brain.
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Affiliation(s)
- Mihai Ruscu
- Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
- University of Medicine and Pharmacy Craiova, Craiova, Romania
| | | | - Paul Rupek
- Chair of Bioinformatics, University of Würzburg, Wuerzburg, Germany
| | - Thomas Dandekar
- Chair of Bioinformatics, University of Würzburg, Wuerzburg, Germany
| | - Eugen Radu
- University of Medicine and Pharmacy Carol Davila, Bucharest, Romania
| | - Dirk M Hermann
- Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
- University of Medicine and Pharmacy Craiova, Craiova, Romania
| | - Aurel Popa-Wagner
- Vascular Neurology and Dementia, Department of Neurology, University Hospital Essen, Essen, Germany
- University of Medicine and Pharmacy Craiova, Craiova, Romania
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Jung J, Lu Z, de Smith A, Mancuso N. Novel insight into the etiology of ischemic stroke gained by integrative multiome-wide association study. Hum Mol Genet 2024; 33:170-181. [PMID: 37824084 PMCID: PMC10772041 DOI: 10.1093/hmg/ddad174] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 09/14/2023] [Accepted: 10/09/2023] [Indexed: 10/13/2023] Open
Abstract
Stroke, characterized by sudden neurological deficits, is the second leading cause of death worldwide. Although genome-wide association studies (GWAS) have successfully identified many genomic regions associated with ischemic stroke (IS), the genes underlying risk and their regulatory mechanisms remain elusive. Here, we integrate a large-scale GWAS (N = 1 296 908) for IS together with molecular QTLs data, including mRNA, splicing, enhancer RNA (eRNA), and protein expression data from up to 50 tissues (total N = 11 588). We identify 136 genes/eRNA/proteins associated with IS risk across 60 independent genomic regions and find IS risk is most enriched for eQTLs in arterial and brain-related tissues. Focusing on IS-relevant tissues, we prioritize 9 genes/proteins using probabilistic fine-mapping TWAS analyses. In addition, we discover that blood cell traits, particularly reticulocyte cells, have shared genetic contributions with IS using TWAS-based pheWAS and genetic correlation analysis. Lastly, we integrate our findings with a large-scale pharmacological database and identify a secondary bile acid, deoxycholic acid, as a potential therapeutic component. Our work highlights IS risk genes/splicing-sites/enhancer activity/proteins with their phenotypic consequences using relevant tissues as well as identify potential therapeutic candidates for IS.
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Affiliation(s)
- Junghyun Jung
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, United States
| | - Zeyun Lu
- Biostatistics Division, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, 2001 North Soto Street, Los Angeles, CA 90033, United States
| | - Adam de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, United States
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, 1450 Biggy Street, Los Angeles, CA 90033, United States
- Biostatistics Division, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, 2001 North Soto Street, Los Angeles, CA 90033, United States
- Department of Quantitative and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089, United States
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9
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Li H, Zhang Z, Qiu Y, Weng H, Yuan S, Zhang Y, Zhang Y, Xi L, Xu F, Ji X, Hao R, Yang P, Chen G, Zuo X, Zhai Z, Wang C. Proteome-wide mendelian randomization identifies causal plasma proteins in venous thromboembolism development. J Hum Genet 2023; 68:805-812. [PMID: 37537391 PMCID: PMC10678328 DOI: 10.1038/s10038-023-01186-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/19/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023]
Abstract
Genome-wide association studies (GWAS) have identified numerous risk loci for venous thromboembolism (VTE), but it is challenging to decipher the underlying mechanisms. We employed an integrative analytical pipeline to transform genetic associations to identify novel plasma proteins for VTE. Proteome-wide association studies (PWAS) were determined by functional summary-based imputation leveraging data from a genome-wide association analysis (14,429 VTE patients, 267,037 controls), blood proteomes (1348 cases), followed by Mendelian randomization, Bayesian colocalization, protein-protein interaction, and pathway enrichment analysis. Twenty genetically regulated circulating protein abundances (F2, F11, ABO, PLCG2, LRP4, PLEK, KLKB1, PROC, KNG1, THBS2, SERPINA1, RARRES2, CEL, GP6, SERPINE2, SERPINA10, OBP2B, EFEMP1, F5, and MSR1) were associated with VTE. Of these 13 proteins demonstrated Mendelian randomized correlations. Six proteins (F2, F11, PLEK, SERPINA1, RARRES2, and SERPINE2) had strong support in colocalization analysis. Utilizing multidimensional data, this study suggests PLEK, SERPINA1, and SERPINE2 as compelling proteins that may provide key hints for future research and possible diagnostic and therapeutic targets for VTE.
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Affiliation(s)
- Haobo Li
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Zhu Zhang
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China.
| | - Yuting Qiu
- Capital Medical University, Beijing, China
| | - Haoyi Weng
- WeGene, Shenzhen, China; Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Shuai Yuan
- Unit of Cardiovascular and Nutritional Epidemiology, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Yunxia Zhang
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Yu Zhang
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Capital Medical University, Beijing, China
| | - Linfeng Xi
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Capital Medical University, Beijing, China
| | - Feiya Xu
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Capital Medical University, Beijing, China
| | - Xiaofan Ji
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Risheng Hao
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Capital Medical University, Beijing, China
| | - Peiran Yang
- State Key Laboratory of Respiratory Health and Multimorbidity, Department of Physiology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College; National Center for Respiratory Medicine; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; National Clinical Research Center for Respiratory Diseases, Beijing, China
| | - Gang Chen
- WeGene, Shenzhen, China; Hunan Provincial Key Lab on Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Xianbo Zuo
- Department of Pharmacy, China-Japan Friendship Hospital, Beijing, China
| | - Zhenguo Zhai
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China.
| | - Chen Wang
- National Center for Respiratory Medicine; State Key Laboratory of Respiratory Health and Multimorbidity; National Clinical Research Center for Respiratory Diseases; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences; Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China.
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10
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Wang Y, Wang J, Yan Z, Liu S, Xu W. Potential drug targets for asthma identified in the plasma and brain through Mendelian randomization analysis. Front Immunol 2023; 14:1240517. [PMID: 37809092 PMCID: PMC10551444 DOI: 10.3389/fimmu.2023.1240517] [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: 06/15/2023] [Accepted: 08/31/2023] [Indexed: 10/10/2023] Open
Abstract
Background Asthma is a heterogeneous disease, and the involvement of neurogenic inflammation is crucial in its development. The standardized treatments focus on alleviating symptoms. Despite the availability of medications for asthma, they have proven to be inadequate in controlling relapses and halting the progression of the disease. Therefore, there is a need for novel drug targets to prevent asthma. Methods We utilized Mendelian randomization to investigate potential drug targets for asthma. We analyzed summary statistics from the UK Biobank and then replicated our findings in GWAS data by Demenais et al. and the FinnGen cohort. We obtained genetic instruments for 734 plasma and 73 brain proteins from recently reported GWAS. Next, we utilized reverse causal relationship analysis, Bayesian co-localization, and phenotype scanning as part of our sensitivity analysis. Furthermore, we performed a comparison and protein-protein interaction analysis to identify causal proteins. We also analyzed the possible consequences of our discoveries by the given existing asthma drugs and their targets. Results Using Mendelian randomization analysis, we identified five protein-asthma pairs that were significant at the Bonferroni level (P < 6.35 × 10-5). Specifically, in plasma, we found that an increase of one standard deviation in IL1R1 and ECM1 was associated with an increased risk of asthma, while an increase in ADAM19 was found to be protective. The corresponding odds ratios were 1.03 (95% CI, 1.02-1.04), 1.00 (95% CI, 1.00-1.01), and 0.99 (95% CI, 0.98-0.99), respectively. In the brain, per 10-fold increase in ECM1 (OR, 1.05; 95% CI, 1.03-1.08) and PDLIM4 (OR, 1.05; 95% CI, 1.04-1.07) increased the risk of asthma. Bayesian co-localization found that ECM1 in the plasma (coloc.abf-PPH4 = 0.965) and in the brain (coloc.abf-PPH4 = 0.931) shared the same mutation with asthma. The target proteins of current asthma medications were found to interact with IL1R1. IL1R1 and PDLIM4 were validated in two replication cohorts. Conclusion Our integrative analysis revealed that asthma risk is causally affected by the levels of IL1R1, ECM1, and PDLIM4. The results suggest that these three proteins have the potential to be used as drug targets for asthma, and further investigation through clinical trials is needed.
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Affiliation(s)
- Yuting Wang
- Department of Otorhinolaryngology, Dongfang Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
| | - Jiaxi Wang
- Department of Otorhinolaryngology, Dongfang Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
| | - Zhanfeng Yan
- Department of Otorhinolaryngology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
| | - Siming Liu
- Department of Otorhinolaryngology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
| | - Wenlong Xu
- Department of Otorhinolaryngology, Dongzhimen Hospital Affiliated to Beijing University of Chinese Medicine, Beijing, China
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11
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Lu M, Feng R, Zhang C, Xiao Y, Yin C. Identifying Novel Drug Targets for Epilepsy Through a Brain Transcriptome-Wide Association Study and Protein-Wide Association Study with Chemical-Gene-Interaction Analysis. Mol Neurobiol 2023; 60:5055-5066. [PMID: 37246165 PMCID: PMC10415436 DOI: 10.1007/s12035-023-03382-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/04/2023] [Indexed: 05/30/2023]
Abstract
Epilepsy is a severe neurological condition affecting 50-65 million individuals worldwide that can lead to brain damage. Nevertheless, the etiology of epilepsy remains poorly understood. Meta-analyses of genome-wide association studies involving 15,212 epilepsy cases and 29,677 controls of the ILAE Consortium cohort were used to conduct transcriptome-wide association studies (TWAS) and protein-wide association studies (PWAS). Furthermore, a protein-protein interaction (PPI) network was generated using the STRING database, and significant epilepsy-susceptible genes were verified using chip data. Chemical-related gene set enrichment analysis (CGSEA) was performed to determine novel drug targets for epilepsy. TWAS analysis identified 21,170 genes, of which 58 were significant (TWASfdr < 0.05) in ten brain regions, and 16 differentially expressed genes were verified based on mRNA expression profiles. The PWAS identified 2249 genes, of which 2 were significant (PWASfdr < 0.05). Through chemical-gene set enrichment analysis, 287 environmental chemicals associated with epilepsy were identified. We identified five significant genes (WIPF1, IQSEC1, JAM2, ICAM3, and ZNF143) that had causal relationships with epilepsy. CGSEA identified 159 chemicals that were significantly correlated with epilepsy (Pcgsea < 0.05), such as pentobarbital, ketone bodies, and polychlorinated biphenyl. In summary, we performed TWAS, PWAS (for genetic factors), and CGSEA (for environmental factors) analyses and identified several epilepsy-associated genes and chemicals. The results of this study will contribute to our understanding of genetic and environmental factors for epilepsy and may predict novel drug targets.
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Affiliation(s)
- Mengnan Lu
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China
| | - Ruoyang Feng
- Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China
| | - Chenglin Zhang
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China
| | - Yanfeng Xiao
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China.
| | - Chunyan Yin
- Department of Pediatrics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710054, Shanxi, China.
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12
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Zhang D, Gao B, Feng Q, Manichaikul A, Peloso GM, Tracy RP, Durda P, Taylor KD, Liu Y, Johnson WC, Gabriel S, Gupta N, Smith JD, Aguet F, Ardlie KG, Blackwell TW, Gerszten RE, Rich SS, Rotter JI, Scott LJ, Zhou X, Lee S. Proteome-Wide Association Studies for Blood Lipids and Comparison with Transcriptome-Wide Association Studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.17.553749. [PMID: 37662416 PMCID: PMC10473643 DOI: 10.1101/2023.08.17.553749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Blood lipid traits are treatable and heritable risk factors for heart disease, a leading cause of mortality worldwide. Although genome-wide association studies (GWAS) have discovered hundreds of variants associated with lipids in humans, most of the causal mechanisms of lipids remain unknown. To better understand the biological processes underlying lipid metabolism, we investigated the associations of plasma protein levels with total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL), and low-density lipoprotein cholesterol (LDL) in blood. We trained protein prediction models based on samples in the Multi-Ethnic Study of Atherosclerosis (MESA) and applied them to conduct proteome-wide association studies (PWAS) for lipids using the Global Lipids Genetics Consortium (GLGC) data. Of the 749 proteins tested, 42 were significantly associated with at least one lipid trait. Furthermore, we performed transcriptome-wide association studies (TWAS) for lipids using 9,714 gene expression prediction models trained on samples from peripheral blood mononuclear cells (PBMCs) in MESA and 49 tissues in the Genotype-Tissue Expression (GTEx) project. We found that although PWAS and TWAS can show different directions of associations in an individual gene, 40 out of 49 tissues showed a positive correlation between PWAS and TWAS signed p-values across all the genes, which suggests a high-level consistency between proteome-lipid associations and transcriptome-lipid associations.
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Affiliation(s)
- Daiwei Zhang
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| | - Boran Gao
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| | - Qidi Feng
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine, and Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT USA
| | - Peter Durda
- Departments of Pathology & Laboratory Medicine, Larner College of Medicine, The University of Vermont, Burlington, VT USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Yongmei Liu
- Department of Medicine, Divisions of Cardiology and Neurology, Duke University Medical Center, Durham, NC USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA USA
| | - Stacey Gabriel
- Genomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Namrata Gupta
- Genomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Joshua D Smith
- Department of Genome Sciences, Human Genetics and Translational Genomics, The University of Washington, Seattle, WA, USA
| | - Francois Aguet
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Kristin G Ardlie
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Thomas W Blackwell
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO USA
| | - Robert E Gerszten
- Genomics Platform, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA USA
| | - Laura J Scott
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| | - Xiang Zhou
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
| | - Seunggeun Lee
- Graduate School of Data Science, Seoul National University, Seoul, Republic of Korea
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI USA
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13
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Zhao Q, Liu R, Chen H, Yang X, Dong J, Bai M, Lu Y, Leng Y. Transcriptome-wide association study reveals novel susceptibility genes for coronary atherosclerosis. Front Cardiovasc Med 2023; 10:1149113. [PMID: 37351287 PMCID: PMC10282549 DOI: 10.3389/fcvm.2023.1149113] [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: 01/21/2023] [Accepted: 05/23/2023] [Indexed: 06/24/2023] Open
Abstract
Background Genetic risk factors substantially contributed to the development of coronary atherosclerosis. Genome-wide association study (GWAS) has identified many risk loci for coronary atherosclerosis, but the translation of these loci into therapeutic targets is limited for their location in non-coding regions. Here, we aimed to screen the potential coronary atherosclerosis pathogenic genes expressed though TWAS (transcriptome wide association study) and explore the underlying mechanism association. Methods Four TWAS approaches (PrediXcan, JTI, UTMOST, and FUSION) were used to screen genes associated with coronary atherosclerosis. Enrichment analysis of TWAS-identified genes was applied through the Metascape website. The summary-data-based Mendelian randomization (SMR) analysis was conducted to provide the evidence of causal relationship between the candidate genes and coronary atherosclerosis. At last, the cell type-specific expression of the intersection genes was examined by using human coronary artery single-cell RNA-seq, interrogating the immune microenvironment of human coronary atherosclerotic plaque at different stages of maturity. Results We identified 19 genes by at least three approaches and 1 gene (NBEAL1) by four approaches. Enrichment analysis enriching the genes identified at least by two TWAS approaches, suggesting that these genes were markedly enriched in asthma and leukocyte mediated immunity reaction. Further, the summary-data-based Mendelian randomization (SMR) analysis provided the evidence of causal relationship between NBEAL1 gene and coronary atherosclerosis, confirming the protecting effects of NBEAL1 gene and coronary atherosclerosis. At last, the single cell cluster analysis demonstrated that NBEAL1 gene has differential expressions in macrophages, plasma cells and endothelial cells. Conclusion Our study identified the novel genes associated with coronary atherosclerosis and suggested the potential biological function for these genes, providing insightful guidance for further biological investigation and therapeutic approaches development in atherosclerosis-related diseases.
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Affiliation(s)
- Qiuping Zhao
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Rongmei Liu
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Hui Chen
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Xiaomo Yang
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Jiajia Dong
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Minfu Bai
- Heart Center of Henan Provincial People’s Hospital, Fuwai Central China Cardiovascular Hospital, Zhengzhou, China
| | - Yao Lu
- School of Life Course Sciences, King’s College London, London, United Kingdom
| | - Yiming Leng
- Clinical Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
- Department of Cardiology, The Third Xiangya Hospital, Central South University, Changsha, China
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14
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Jung J, Lu Z, de Smith A, Mancuso N. Novel insight into the etiology of ischemic stroke gained by integrative transcriptome-wide association study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.30.23287918. [PMID: 37034585 PMCID: PMC10081428 DOI: 10.1101/2023.03.30.23287918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Stroke, characterized by sudden neurological deficits, is the second leading cause of death worldwide. Although genome-wide association studies (GWAS) have successfully identified many genomic regions associated with ischemic stroke (IS), the genes underlying risk and their regulatory mechanisms remain elusive. Here, we integrate a large-scale GWAS (N=1,296,908) for IS together with mRNA, splicing, enhancer RNA (eRNA) and protein expression data (N=11,588) from 50 tissues. We identify 136 genes/eRNA/proteins associated with IS risk across 54 independent genomic regions and find IS risk is most enriched for eQTLs in arterial and brain-related tissues. Focusing on IS-relevant tissues, we prioritize 9 genes/proteins using probabilistic fine-mapping TWAS analyses. In addition, we discover that blood cell traits, particularly reticulocyte cells, have shared genetic contributions with IS using TWAS-based pheWAS and genetic correlation analysis. Lastly, we integrate our findings with a large-scale pharmacological database and identify a secondary bile acid, deoxycholic acid, as a potential therapeutic component. Our work highlights IS risk genes/splicing-sites/enhancer activity/proteins with their phenotypic consequences using relevant tissues as well as identify potential therapeutic candidates for IS.
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Affiliation(s)
- Junghyun Jung
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Zeyun Lu
- Biostatistics Division, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Adam de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Nicholas Mancuso
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Biostatistics Division, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
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