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Sayers I, John C, Chen J, Hall IP. Genetics of chronic respiratory disease. Nat Rev Genet 2024; 25:534-547. [PMID: 38448562 DOI: 10.1038/s41576-024-00695-0] [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: 01/19/2024] [Indexed: 03/08/2024]
Abstract
Chronic respiratory diseases, such as chronic obstructive pulmonary disease (COPD), asthma and interstitial lung diseases are frequently occurring disorders with a polygenic basis that account for a large global burden of morbidity and mortality. Recent large-scale genetic epidemiology studies have identified associations between genetic variation and individual respiratory diseases and linked specific genetic variants to quantitative traits related to lung function. These associations have improved our understanding of the genetic basis and mechanisms underlying common lung diseases. Moreover, examining the overlap between genetic associations of different respiratory conditions, along with evidence for gene-environment interactions, has yielded additional biological insights into affected molecular pathways. This genetic information could inform the assessment of respiratory disease risk and contribute to stratified treatment approaches.
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Affiliation(s)
- Ian Sayers
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, University Park, Nottingham, UK
- Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, UK
| | - Catherine John
- University of Leicester, Leicester, UK
- University Hospitals of Leicester, Leicester, UK
| | - Jing Chen
- University of Leicester, Leicester, UK
| | - Ian P Hall
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, University Park, Nottingham, UK.
- Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, UK.
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2
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Lin L, Wu Z, Zhong A, Luo H, Xu W, Luo W. Causal effects of genetically determined blood metabolites on asthma: a bidirectional Mendelian randomization study. J Asthma 2024:1-11. [PMID: 39087774 DOI: 10.1080/02770903.2024.2380515] [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: 04/18/2024] [Revised: 07/07/2024] [Accepted: 07/10/2024] [Indexed: 08/02/2024]
Abstract
OBJECTIVE The observational association between blood metabolites and asthma has been extensively studied. However, it is still unclear whether this association is causal. In this study, we aimed to investigate the causal relationship between blood metabolites and asthma using a bidirectional Mendelian randomization (MR) analysis. Additionally, we aimed to explore the potential mechanisms underlying this relationship. METHODS The study design involved the use of genetic instruments as instrumental variables (IVs) to fulfill the assumptions of MR analysis. The data on 1,091 metabolites and 309 metabolite ratios were obtained from the Canadian Longitudinal Study on Aging (CLSA), while the data on asthma were obtained from the Integrative Epidemiology Unit (IEU) Open GWAS Project. Utilizing the inverse variance-weighted (IVW) method as the primary MR analysis approach, sensitivity tests were conducted to assess the reliability of the findings, which involved employing Cochran's Q and the MR-Egger intercept. Furthermore, Bayesian weighted MR was used to further test the robustness of the results. Additionally, pathway analysis was conducted to explore the metabolic explanations underlying asthma. RESULT In our study, a comprehensive MR Analysis identified 10 metabolites and 6 metabolite ratios significantly associated with the development of asthma (FDR < 0.05). The metabolites included glycerophosphocholines(GPCs), glycerophosphoethanolamines(GPEs), and an unknown metabolite. Of these, 1-arachidonoyl-GPC, 1-myristoyl-2-arachidonoyl-GPC, 1-palmitoyl-2-arachidonoyl-GPC, and 1-(1-enyl-palmitoyl)-2-arachidonoyl-GPC were associated with an increased risk of asthma, whereas 1,2-dilinoleoyl-GPC, 1-palmitoyl-2-linoleoyl-GPC, 1,2-dilinoleoyl-GPE, 1 - oleoyl - 2 - linoleoyl - GPE, 1-palmitoyl-2-linoleoyl-GPE, and X-21470 were found to have a protective effect. No heterogeneity and pleiotropy were observed in the significant metabolites (p > 0.05), and each metabolite exhibited a consistent effect direction across all five methods. BWMR analysis results confirmed the significance and direction of effects across exposures, except for Cholesterol to linoleoyl-arachidonoyl-glycerol ratio(p = 0.673). Pathway analysis suggests that glycerophospholipid metabolism may potentially be a mechanism underlying the development of asthma. CONCLUSION Our MR findings suggest that the identified metabolites and pathways can serve as biomarkers for clinical asthma screening and prevention, while also providing new insights for future mechanistic exploration and drug target selection.
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Affiliation(s)
- Liyu Lin
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zilun Wu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Anqi Zhong
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Haocheng Luo
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wenjie Xu
- The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Wen Luo
- The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou, China
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3
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Zhou S, Xiao H, Gao M, Wang M, He W, Shu Y, Wang X. Causal role of immune cells in asthma: a Mendelian randomization study. J Asthma 2024:1-18. [PMID: 39087928 DOI: 10.1080/02770903.2024.2387758] [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: 04/05/2024] [Revised: 07/16/2024] [Accepted: 07/30/2024] [Indexed: 08/02/2024]
Abstract
BackgroundImmune cells may have a significant role in the pathophysiology of asthma, according to increasing evidence, although it is yet unclear how immune cells cause asthma. Therefore, we aimed to use Mendelian randomization (MR) methods to investigate this causal relationship.Methods:This study explored the causal effects between immune cells and asthma using a two-sample Mendelian randomization technique. Using publicly available genetic data, the causal connection between asthma risk and 731 immune cell phenotypes was investigated. Sensitivity analysis guaranteed the results' stability. To further evaluate the existence of reverse causality, we employed reverse MR analysis.Results:According to the inverse-variance weighted (IVW) method, five immune cell phenotypes were found to be statistically significantly associated with asthma risk (p < 0.001). Among them, TCRgd %T cell (OR = 0.968,95%CI = 0.951-0.986), TCRgd %lymphocyte (OR = 0.978,95%CI = 0.965-0.991), HLA DR + NK AC (OR = 0.966,95% CI = 0.947-0.986) and CD3 on CD4 Treg (OR = 0.956,95%CI= 0.931-0.981), four phenotypes that resulted in a decreased risk of asthma.CD25 on transitional (OR = 1.033, 95%CI = 1.014-1.052) resulted in an increased risk of asthma. Reverse MR analysis revealed that asthma increases HLA DR + NK AC levels (p < 0.05).Conclusion:The results of MR analysis showed a causal relationship between immune cell phenotype and asthma risk, which provides a direction for future asthma treatment.
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Affiliation(s)
- Siding Zhou
- Department of Medical College of Yangzhou University, Yangzhou, 225000, China
| | - Hongbi Xiao
- Department of Medical College of Yangzhou University, Yangzhou, 225000, China
| | - Mingjun Gao
- Department of Dalian Medical University, Dalian, 116000, China
| | - Mengmeng Wang
- Department of Dalian Medical University, Dalian, 116000, China
| | - Wenbo He
- Department of Medical College of Yangzhou University, Yangzhou, 225000, China
| | - Yusheng Shu
- Department of Thoracic Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, 225000, China
| | - Xiaolin Wang
- Department of Thoracic Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Yangzhou, 225000, China
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Han X, Wu TQ, Bian Y, Chen L, Feng X. Asthma and risk of adverse pregnancy outcomes: A Mendelian randomization study. Heliyon 2024; 10:e33857. [PMID: 39044964 PMCID: PMC11263667 DOI: 10.1016/j.heliyon.2024.e33857] [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: 03/13/2024] [Revised: 06/26/2024] [Accepted: 06/27/2024] [Indexed: 07/25/2024] Open
Abstract
Background Multiple empirical investigations have indicated a connection between asthma and adverse pregnancy outcomes (APOs). Nevertheless, the effects of asthma on APOs remain uncertain. Methods We performed bi-directional Univariable Mendelian randomization (UVMR) analyses using combined information obtained from genome-wide association studies (GWAS) data that is publicly accessible. The principal approach used to analyze the causal association between asthma or age when diagnosed and APOs was the inverse variance weighted (IVW) method. The two types of data regarding exposure originate from the IEU Open GWAS project, which includes 56,167 and 47,222 European asthma patients, respectively. The data of four APOs were acquired via the GWAS dataset of the FinnGen collaboration. In addition, we implemented multivariable Mendelian randomization (MVMR), controlling for confounding factors such as smoking status, frequent drinking, body mass index (BMI), and live birth quantity. Furthermore, we executed several meticulous sensitivity studies to ascertain the reliability of our MR results. Results Following the implementation of the Bonferroni adjustment, the UVMR assessment revealed that in the IVW model, asthma was significantly linked to an elevated risk of spontaneous abortion (SA) (odds ratio [OR]: 1.115; 95 % confidence interval [CI]: 1.031-1.206; P = 0.006) and gestational diabetes mellitus (GDM) (OR: 1.125; 95 % CI: 1.037-1.220; P = 0.005). However, there was no causal correlation between asthma and preterm birth (PTB) (OR: 0.979; 95 % CI: 0.897-1.068; P = 0.629) or preeclampsia (PE) (OR: 1.059; 95 % CI: 0.951-1.179; P = 0.297). After adjusting for confounding factors, including smoking status, frequent drinking, BMI, and live birth quantity, the MVMR analysis shows a statistically significant causal relationship between asthma and SA or GDM. Furthermore, our investigation's findings did not reveal a substantial correlation between the age of asthma onset based on genetics and the likelihood of SA or GDM. The inverse MR outcomes indicate a lack of causal connection linking APOs to the incidence of asthma. The validity of these findings were verified by sensitivity analyses. Conclusions The evidence provided by this study proves that genetically determined asthma is linked to a higher likelihood of SA and GDM. Further research is required to examine potential pathways. However, no conclusive evidence has been found to support the increased risk of SA and GDM in early asthma diagnosis or the interaction between asthma and PTB or PE, indicating that confounding factors may affect the results of previous observational studies.
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Affiliation(s)
- Xinyu Han
- Department of First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Tian qiang Wu
- Department of First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yuanyuan Bian
- Department of First Clinical Medical College, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Lu Chen
- Department of Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiaoling Feng
- Department of Gynecology, The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
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Panganiban RA, Nadeau KC, Lu Q. Pyroptosis, gasdermins and allergic diseases. Allergy 2024. [PMID: 39003568 DOI: 10.1111/all.16236] [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: 03/05/2024] [Revised: 07/01/2024] [Accepted: 07/04/2024] [Indexed: 07/15/2024]
Abstract
Pyroptosis is an inflammatory form of programmed cell death that is distinct from necrosis and apoptosis. Pyroptosis is primarily mediated by the gasdermin family of proteins (GSDMA-E and PVJK), which, when activated by proteolytic cleavage, form pores in the plasma membrane, leading to cell death. While much of the past research on pyroptosis has focused on its role in cancer, metabolic disorders, and infectious diseases, recent experimental and observational studies have begun to implicate pyroptosis in allergic diseases. These studies suggest that gasdermin-mediated pyroptosis contributes to the development of allergic conditions and could offer novel targets for therapy. Here, we review our current understanding of pyroptosis with an emphasis on the role of gasdermins as executioners of pyroptosis and potential mediators to allergic disease. We highlight new discoveries that establish a mechanistic link between the biochemical actions of gasdermins and the onset of allergic diseases. Additionally, we discuss how pyroptosis and gasdermins might contribute to the dysfunction of epithelial barrier, a key factor believed to initiate the progression of various allergic diseases.
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Affiliation(s)
- Ronald Allan Panganiban
- Division of Asthma Research, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Kari C Nadeau
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
- Division of Allergy and Inflammation, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA
| | - Quan Lu
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
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Chen X, Cheng Z, Xu J, Wang Q, Zhao Z, Jiang Q. Causal effects of autoimmune diseases on temporomandibular disorders and the mediating pathways: a Mendelian randomization study. Front Immunol 2024; 15:1390516. [PMID: 39044823 PMCID: PMC11263080 DOI: 10.3389/fimmu.2024.1390516] [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: 02/23/2024] [Accepted: 06/28/2024] [Indexed: 07/25/2024] Open
Abstract
Background The role of autoimmune diseases (ADs) in temporomandibular disorders (TMDs) has been emphasized in observational studies. However, whether the causation exists is unclear, and controversy remains about which specific disorder is destructive in TMDs. This Mendelian randomization (MR) study aims to estimate the causal effect of common ADs on TMDs. Methods Genetic data from published genome-wide association studies for fourteen common ADs, specifically multiple sclerosis (MS, N = 15,283), ankylosing spondylitis (AS, N = 22,647), asthma (N = 408,422), celiac disease (N = 15,283), Graves' disease (N = 458,620), Hashimoto thyroiditis (N = 395,640), primary biliary cirrhosis (PBC, N = 11,375), primary sclerosing cholangitis (PSC, N = 14,890), psoriasis vulgaris (N = 483,174), rheumatoid arthritis (RA, N = 417,256), systemic lupus erythematosus (SLE, N = 23,210), Type 1 diabetes (T1D, N = 520,580), inflammatory bowel disease (IBD, N = 34,652), and Sjogren's syndrome (SS, N = 407,746) were collected. Additionally, the latest summary-level data for TMDs (N = 228,812) were extracted from the FinnGen database. The overall effects of each immune traits were assessed via inverse-variance weighted (IVW), weighted median, and MR-Egger methods, and performed extensive sensitivity analyses. Finally, 731 immune cell phenotypes (N = 3,757) were analyzed for their mediating role in the significant causality. Results Univariable MR analyses revealed that genetically predicted RA (IVW OR: 1.12, 95% CI: 1.05-1.19, p < 0.001) and MS (IVW OR: 1.06, 95% CI: 1.03-1.10, p = 0.001) were associated with increased risk of TMDs. Two out of 731 immune cell phenotypes were identified as causal mediators in the associations of RA with TMDs, including "CD25++ CD8+ T cell % CD8+ T cell" (mediation proportion: 6.2%) and "CD3 on activated CD4 regulatory T cell" (5.4%). Additionally, "CD127 on granulocyte" mediated 10.6% of the total effect of MS on TMDs. No reverse directions, heterogeneity, and pleiotropy were detected in the analyses (p > 0.05). Conclusion This MR study provides new evidence regarding the causal impact of genetic predisposition to RA or MS on the increased risk of TMDs, potentially mediated by the modulation of immune cells. These findings highlight the importance for clinicians to pay more attention to patients with RA or MS when consulting for temporomandibular discomfort. The mediating role of specific immune cells is proposed but needs further investigation.
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Affiliation(s)
- Xin Chen
- Department of Oral and Maxillofacial Surgery, Jiangyin People’s Hospital Affiliated to Nantong University, Jiangyin, China
| | - Zheng Cheng
- Department of Oral and Maxillofacial Surgery, Jiangyin People’s Hospital Affiliated to Nantong University, Jiangyin, China
| | - Junyu Xu
- Department of Oral and Maxillofacial Surgery, Jiangyin People’s Hospital Affiliated to Nantong University, Jiangyin, China
| | - Qianyi Wang
- Department of Cardiology, Jiangyin People’s Hospital Affiliated to Nantong University, Jiangyin, China
| | - Zhibai Zhao
- Department of Oral Mucosal Diseases, The Affiliated Stomatological Hospital of Nanjing Medical University, Nanjing, China
| | - Qianglin Jiang
- Department of Oral and Maxillofacial Surgery, Jiangyin People’s Hospital Affiliated to Nantong University, Jiangyin, China
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Plender EG, Prodanov T, Hsieh P, Nizamis E, Harvey WT, Sulovari A, Munson KM, Kaufman EJ, O'Neal WK, Valdmanis PN, Marschall T, Bloom JD, Eichler EE. Structural and genetic diversity in the secreted mucins MUC5AC and MUC5B. Am J Hum Genet 2024:S0002-9297(24)00213-1. [PMID: 38991590 DOI: 10.1016/j.ajhg.2024.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 07/13/2024] Open
Abstract
The secreted mucins MUC5AC and MUC5B are large glycoproteins that play critical defensive roles in pathogen entrapment and mucociliary clearance. Their respective genes contain polymorphic and degenerate protein-coding variable number tandem repeats (VNTRs) that make the loci difficult to investigate with short reads. We characterize the structural diversity of MUC5AC and MUC5B by long-read sequencing and assembly of 206 human and 20 nonhuman primate (NHP) haplotypes. We find that human MUC5B is largely invariant (5,761-5,762 amino acids [aa]); however, seven haplotypes have expanded VNTRs (6,291-7,019 aa). In contrast, 30 allelic variants of MUC5AC encode 16 distinct proteins (5,249-6,325 aa) with cysteine-rich domain and VNTR copy-number variation. We group MUC5AC alleles into three phylogenetic clades: H1 (46%, ∼5,654 aa), H2 (33%, ∼5,742 aa), and H3 (7%, ∼6,325 aa). The two most common human MUC5AC variants are smaller than NHP gene models, suggesting a reduction in protein length during recent human evolution. Linkage disequilibrium and Tajima's D analyses reveal that East Asians carry exceptionally large blocks with an excess of rare variation (p < 0.05) at MUC5AC. To validate this result, we use Locityper for genotyping MUC5AC haplogroups in 2,600 unrelated samples from the 1000 Genomes Project. We observe a signature of positive selection in H1 among East Asians and a depletion of the likely ancestral haplogroup (H3). In Europeans, H3 alleles show an excess of common variation and deviate from Hardy-Weinberg equilibrium (p < 0.05), consistent with heterozygote advantage and balancing selection. This study provides a generalizable strategy to characterize complex protein-coding VNTRs for improved disease associations.
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Affiliation(s)
- Elizabeth G Plender
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Timofey Prodanov
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany; Center for Digital Medicine, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Genetics, Cell Biology, and Development, University of Minnesota Medical School, Minneapolis, MN 55455, USA
| | - Evangelos Nizamis
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Computational Biology, Cajal Neuroscience Inc, Seattle, WA 98102, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Eli J Kaufman
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wanda K O'Neal
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Paul N Valdmanis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany; Center for Digital Medicine, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Jesse D Bloom
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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Xiu Z, Sun L, Liu K, Cao H, Qu HQ, Glessner JT, Ding Z, Zheng G, Wang N, Xia Q, Li J, Li MJ, Hakonarson H, Liu W, Li J. Shared molecular mechanisms and transdiagnostic potential of neurodevelopmental disorders and immune disorders. Brain Behav Immun 2024; 119:767-780. [PMID: 38677625 DOI: 10.1016/j.bbi.2024.04.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 02/27/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024] Open
Abstract
The co-occurrence and familial clustering of neurodevelopmental disorders and immune disorders suggest shared genetic risk factors. Based on genome-wide association summary statistics from five neurodevelopmental disorders and four immune disorders, we conducted genome-wide, local genetic correlation and polygenic overlap analysis. We further performed a cross-trait GWAS meta-analysis. Pleotropic loci shared between the two categories of diseases were mapped to candidate genes using multiple algorithms and approaches. Significant genetic correlations were observed between neurodevelopmental disorders and immune disorders, including both positive and negative correlations. Neurodevelopmental disorders exhibited higher polygenicity compared to immune disorders. Around 50%-90% of genetic variants of the immune disorders were shared with neurodevelopmental disorders. The cross-trait meta-analysis revealed 154 genome-wide significant loci, including 8 novel pleiotropic loci. Significant associations were observed for 30 loci with both types of diseases. Pathway analysis on the candidate genes at these loci revealed common pathways shared by the two types of diseases, including neural signaling, inflammatory response, and PI3K-Akt signaling pathway. In addition, 26 of the 30 lead SNPs were associated with blood cell traits. Neurodevelopmental disorders exhibit complex polygenic architecture, with a subset of individuals being at a heightened genetic risk for both neurodevelopmental and immune disorders. The identification of pleiotropic loci has important implications for exploring opportunities for drug repurposing, enabling more accurate patient stratification, and advancing genomics-informed precision in the medical field of neurodevelopmental disorders.
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Affiliation(s)
- Zhanjie Xiu
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Ling Sun
- Department of Child and Adolescent Psychology, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin, China
| | - Kunlun Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Haiyan Cao
- Department of Child and Adolescent Psychology, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin, China
| | - Hui-Qi Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Joseph T Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, China
| | - Gang Zheng
- National Supercomputer Center in Tianjin (NSCC-TJ), Tianjin, China
| | - Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, China
| | - Qianghua Xia
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jie Li
- Laboratory of Biological Psychiatry, Institute of Mental Health, Tianjin Anding Hospital, Tianjin Medical University, Tianjin, China
| | - Mulin Jun Li
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
| | - Wei Liu
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China; Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China.
| | - Jin Li
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China.
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9
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Li Z, Teng Z, Han Z, Zhang Y, Wang Y. Genetically predicted asthma and the risk of abnormal spermatozoa. Front Genet 2024; 15:1377770. [PMID: 38846962 PMCID: PMC11153665 DOI: 10.3389/fgene.2024.1377770] [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: 01/28/2024] [Accepted: 05/01/2024] [Indexed: 06/09/2024] Open
Abstract
Background Several previous animal and human studies have found a strong association between asthma and spermatozoa quality, but whether these associations are causal or due to bias remains to be elucidated. Methods We performed a two-sample Mendelian randomization (MR) analysis to assess the causal effect of genetically predicted asthma on the risk of abnormal spermatozoa. Asthma, childhood-onset asthma (COA), and adult-onset asthma (AOA) (sample sizes ranging from 327,670 to 408,442) were included as the exposures. Genetic information for abnormal spermatozoa was obtained from a genome-wide association study (GWAS) comprising 209,921 participants. In univariable MR (UVMR) analysis, the inverse variance weighted (IVW) method was conducted as the primary method, with the MR Egger and weighted median used as supplementary methods for causal inference. Sensitivity analyses, including the Cochran Q test, Egger intercept test, MR-PRESSO, and leave-one-out analysis, were performed to verify the robustness of the MR results. Multivariable MR (MVMR) was conducted to evaluate the direct causal effects of asthma on abnormal spermatozoa risk. Results UVMR detected causal associations between genetically predicted asthma and an increased risk of abnormal spermatozoa (OR: 1.270, 95% CI: 1.045-1.545, p = 0.017). Moreover, we found that AOA (OR: 1.46, 95% CI: 1.051, 2.018, p = 0.024) has positive causal effects on the risk of abnormal spermatozoa rather than COA (p = 0.558). Sensitivity analysis found little evidence of bias in the current study (p > 0.05). MVMR further confirmed that asthma directly affected the risk of abnormal spermatozoa. Conclusion Our MR study suggested that genetically predicted asthma could be associated with an increased risk of abnormal spermatozoa, and similar results were obtained in AOA. Further studies are warranted to explain the underlying mechanisms of this association and may provide new avenues for prevention and treatment.
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Affiliation(s)
| | | | | | | | - Yaxuan Wang
- Department of Urology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
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10
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Yang J, Lin W, Ma Y, Song H, Mu C, Wu Q, Han C, Zhang J, Liu X. Investigation of the causal association between Parkinson's disease and autoimmune disorders: a bidirectional Mendelian randomization study. Front Immunol 2024; 15:1370831. [PMID: 38774879 PMCID: PMC11106379 DOI: 10.3389/fimmu.2024.1370831] [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: 01/15/2024] [Accepted: 04/24/2024] [Indexed: 05/24/2024] Open
Abstract
Background To date, an increasing number of epidemiological evidence has pointed to potential relationships between Parkinson's disease (PD) and various autoimmune diseases (AIDs), however, no definitive conclusions has been drawn about whether PD is causally related to AIDs risk. Methods By employing summary statistics from the latest and most extensive genome-wide association studies (GWAS), we performed a bidirectional two-sample Mendelian randomization (MR) analysis to investigate the causal associations between PD and a variety of 17 AIDs, encompassing multiple sclerosis, neuromyelitis optica spectrum disorder, myasthenia gravis, asthma, inflammatory bowel disease, Crohn's disease, ulcerative colitis, irritable bowel syndrome, celiac disease, primary biliary cirrhosis, primary sclerosing cholangitis, type 1 diabetes, ankylosing spondylitis, rheumatoid arthritis, systemic lupus erythematosus, psoriasis and vitiligo. Inverse-variance weighted (IVW) was adopted as the main statistical approach to obtain the causal estimates of PD on different AIDs, supplemented by a series of complementary analyses (weighted median, MR Egger regression, and MR-PRESSO) for further strengthening the robustness of results. Results Our MR findings suggested that genetically predicted higher liability to PD was causally associated with a decreased risk of irritable bowel syndrome (OR = 0.98; 95% CI: 0.96-0.99; P = 0.032). On the contrary, IVW analysis showed a potential positive correlation between genetically determined PD and the incidence of type 1 diabetes (OR = 1.10; 95%CI: 1.02-1.19; P = 0.010). Subsequent MR tests ended up in similar results, confirming our findings were reliable. Additionally, in the reverse MR analyses, we did not identify any evidence to support the causal relationship of genetic predisposition to AIDs with PD susceptibility. Conclusion In general, a bifunctional role that PD exerted on the risk of developing AIDs was detected in our studies, both protecting against irritable bowel syndrome occurrence and raising the incidence of type 1 diabetes. Future studies, including population-based observational studies and molecular experiments in vitro and in vivo, are warranted to validate the results of our MR analyses and refine the underlying pathological mechanisms involved in PD-AIDs associations.
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Affiliation(s)
- Junyi Yang
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Weiran Lin
- Department of Cell Biology, Key Laboratory of Cell Biology, National Health Commission of the People's Republic of China, China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of the People's Republic of China, China Medical University, Shenyang, Liaoning, China
- Department of Laboratory Medicine, General Hospital of Northern Theater Command, Shenyang, Liaoning, China
| | - Yumei Ma
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Hui Song
- Department of Cell Biology, Key Laboratory of Cell Biology, National Health Commission of the People's Republic of China, China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of the People's Republic of China, China Medical University, Shenyang, Liaoning, China
| | - Changqing Mu
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Qian Wu
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chen Han
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jian Zhang
- Department of Cell Biology, Key Laboratory of Cell Biology, National Health Commission of the People's Republic of China, China Medical University, Shenyang, Liaoning, China
- Key Laboratory of Medical Cell Biology, Ministry of Education of the People's Republic of China, China Medical University, Shenyang, Liaoning, China
| | - Xu Liu
- Department of Neurology, First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
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11
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Wang J, Song M, Cao M. The causal role of multiple psycho-emotional disorders in gastroesophageal reflux disease: A two-sample Mendelian randomized study. PLoS One 2024; 19:e0302469. [PMID: 38709755 PMCID: PMC11073702 DOI: 10.1371/journal.pone.0302469] [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: 10/04/2023] [Accepted: 04/04/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND Observational studies have previously shown a potential link between psycho-emotional disorders, such as mood swings, highly strung, anxious feelings, and gastroesophageal reflux disease (GERD). However, the credibility of these associations could be influenced by various confounding factors. Consequently, our study sought to employ a Mendelian randomization (MR) approach to elucidate a potential causal relationship between psycho-emotional disorders and GERD. METHOD Information on independent genetic variants linked to mood swings, highly strung, and anxious feelings was gathered from European populations participating in the IEU Open GWAS research. The FinnGen Consortium provided the genome-wide association study (GWAS) summary statistics for GERD. Our analysis employed the inverse variance weighted (IVW) method under the random effects model as the main analytical method. To further bolster our findings, we employed the weighted median and MR Egger methods. In addition, we conducted a series of sensitivity analyses. RESULTS Our study supports the existence of a causal relationship between psycho-emotional disorders and GERD. Mood swings, highly strung, and anxious feelings adversely affected GERD risk (mood swings: OR 2.21, 95% CI 1.19-5.59, p = 3.09 × 10-2; highly strung: OR 5.63, 95% CI 1.77-17.94, p = 3.42 × 10-3; anxious feelings: OR 2.48, 95% CI 1.08-4.33, p = 2.89 × 10-2). CONCLUSION This Mendelian randomization study provides robust support for the notion that mood swings, highly strung and anxious feelings, are associated with an increased risk of developing GERD.
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Affiliation(s)
- Jing Wang
- Department of Gastroenterology, People’s Hospital of Zhengzhou University, Henan Zhengzhou, China
| | - Meng Song
- Cancer Center, People’s Hospital of Zhengzhou University, Henan Zhengzhou, China
| | - Mingbo Cao
- Department of Gastroenterology, People’s Hospital of Zhengzhou University, Henan Zhengzhou, China
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12
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Risemberg EL, Smeekens JM, Cruz Cisneros MC, Hampton BK, Hock P, Linnertz CL, Miller DR, Orgel K, Shaw GD, de Villena FPM, Burks AW, Valdar W, Kulis MD, Ferris MT. A mutation in Themis contributes to anaphylaxis severity following oral peanut challenge in CC027 mice. J Allergy Clin Immunol 2024:S0091-6749(24)00411-1. [PMID: 38670234 DOI: 10.1016/j.jaci.2024.03.027] [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: 09/07/2023] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND The development of peanut allergy is due to a combination of genetic and environmental factors, although specific genes have proven difficult to identify. Previously, we reported that peanut-sensitized Collaborative Cross strain CC027/GeniUnc (CC027) mice develop anaphylaxis upon oral challenge to peanut, in contrast to C3H/HeJ (C3H) mice. OBJECTIVE This study aimed to determine the genetic basis of orally induced anaphylaxis to peanut in CC027 mice. METHODS A genetic mapping population between CC027 and C3H mice was designed to identify the genetic factors that drive oral anaphylaxis. A total of 356 CC027xC3H backcrossed mice were generated, sensitized to peanut, then challenged to peanut by oral gavage. Anaphylaxis and peanut-specific IgE were quantified for all mice. T-cell phenotyping was conducted on CC027 mice and 5 additional Collaborative Cross strains. RESULTS Anaphylaxis to peanut was absent in 77% of backcrossed mice, with 19% showing moderate anaphylaxis and 4% having severe anaphylaxis. There were 8 genetic loci associated with variation in response to peanut challenge-6 associated with anaphylaxis (temperature decrease) and 2 associated with peanut-specific IgE levels. There were 2 major loci that impacted multiple aspects of the severity of acute anaphylaxis, at which the CC027 allele was associated with worse outcome. At one of these loci, CC027 has a private genetic variant in the Themis gene. Consistent with described functions of Themis, we found that CC027 mice have more immature T cells with fewer CD8+, CD4+, and CD4+CD25+CD127- regulatory T cells. CONCLUSIONS Our results demonstrate a key role for Themis in the orally reactive CC027 mouse model of peanut allergy.
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Affiliation(s)
- Ellen L Risemberg
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Johanna M Smeekens
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Marta C Cruz Cisneros
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Brea K Hampton
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Pablo Hock
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Colton L Linnertz
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Darla R Miller
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kelly Orgel
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Ginger D Shaw
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Fernando Pardo Manuel de Villena
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - A Wesley Burks
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - William Valdar
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Michael D Kulis
- Division of Allergy and Immunology, Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC.
| | - Martin T Ferris
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC.
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13
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Ding M, Chen K, Yang Y, Zhao H. Prioritizing genomic variants pathogenicity via DNA, RNA, and protein-level features based on extreme gradient boosting. Hum Genet 2024:10.1007/s00439-024-02667-0. [PMID: 38575818 DOI: 10.1007/s00439-024-02667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 03/05/2024] [Indexed: 04/06/2024]
Abstract
Genetic diseases are mostly implicated with genetic variants, including missense, synonymous, non-sense, and copy number variants. These different kinds of variants are indicated to affect phenotypes in various ways from previous studies. It remains essential but challenging to understand the functional consequences of these genetic variants, especially the noncoding ones, due to the lack of corresponding annotations. While many computational methods have been proposed to identify the risk variants. Most of them have only curated DNA-level and protein-level annotations to predict the pathogenicity of the variants, and others have been restricted to missense variants exclusively. In this study, we have curated DNA-, RNA-, and protein-level features to discriminate disease-causing variants in both coding and noncoding regions, where the features of protein sequences and protein structures have been shown essential for analyzing missense variants in coding regions while the features related to RNA-splicing and RBP binding are significant for variants in noncoding regions and synonymous variants in coding regions. Through the integration of these features, we have formulated the Multi-level feature Genomic Variants Predictor (ML-GVP) using the gradient boosting tree. The method has been trained on more than 400,000 variants in the Sherloc-training set from the 6th critical assessment of genome interpretation with superior performance. The method is one of the two best-performing predictors on the blind test in the Sherloc assessment, and is further confirmed by another independent test dataset of de novo variants.
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Affiliation(s)
- Maolin Ding
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Ken Chen
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Yuedong Yang
- School of Data and Computer Science, Sun Yat-Sen University, Guangzhou, 510000, China.
- Key Laboratory of Machine Intelligence and Advanced Computing (Sun Yat-Sen University), Ministry of Education, Guangzhou, China.
| | - Huiying Zhao
- Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510000, China.
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14
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Pietzner M, Uluvar B, Kolnes KJ, Jeppesen PB, Frivold SV, Skattebo Ø, Johansen EI, Skålhegg BS, Wojtaszewski JFP, Kolnes AJ, Yeo GSH, O'Rahilly S, Jensen J, Langenberg C. Systemic proteome adaptions to 7-day complete caloric restriction in humans. Nat Metab 2024; 6:764-777. [PMID: 38429390 DOI: 10.1038/s42255-024-01008-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024]
Abstract
Surviving long periods without food has shaped human evolution. In ancient and modern societies, prolonged fasting was/is practiced by billions of people globally for religious purposes, used to treat diseases such as epilepsy, and recently gained popularity as weight loss intervention, but we still have a very limited understanding of the systemic adaptions in humans to extreme caloric restriction of different durations. Here we show that a 7-day water-only fast leads to an average weight loss of 5.7 kg (±0.8 kg) among 12 volunteers (5 women, 7 men). We demonstrate nine distinct proteomic response profiles, with systemic changes evident only after 3 days of complete calorie restriction based on in-depth characterization of the temporal trajectories of ~3,000 plasma proteins measured before, daily during, and after fasting. The multi-organ response to complete caloric restriction shows distinct effects of fasting duration and weight loss and is remarkably conserved across volunteers with >1,000 significantly responding proteins. The fasting signature is strongly enriched for extracellular matrix proteins from various body sites, demonstrating profound non-metabolic adaptions, including extreme changes in the brain-specific extracellular matrix protein tenascin-R. Using proteogenomic approaches, we estimate the health consequences for 212 proteins that change during fasting across ~500 outcomes and identified putative beneficial (SWAP70 and rheumatoid arthritis or HYOU1 and heart disease), as well as adverse effects. Our results advance our understanding of prolonged fasting in humans beyond a merely energy-centric adaptions towards a systemic response that can inform targeted therapeutic modulation.
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Affiliation(s)
- Maik Pietzner
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK.
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
| | - Burulça Uluvar
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kristoffer J Kolnes
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
- Steno Diabetes Center Odense, Odense University Hospital, Odense, Denmark
| | - Per B Jeppesen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - S Victoria Frivold
- Institute of Health and Society, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Øyvind Skattebo
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Egil I Johansen
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Bjørn S Skålhegg
- Department of Nutrition, Division for Molecular Nutrition, University of Oslo, Oslo, Norway
| | - Jørgen F P Wojtaszewski
- August Krogh Section for Molecular Physiology, Department of Nutrition, Exercise and Sports, University of Copenhagen, Copenhagen, Denmark
| | - Anders J Kolnes
- Section of Specialized Endocrinology, Department of Endocrinology, Oslo University Hospital, Oslo, Norway
| | - Giles S H Yeo
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Stephen O'Rahilly
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Jørgen Jensen
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway
| | - Claudia Langenberg
- Computational Medicine, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany.
- Precision Healthcare University Research Institute, Queen Mary University of London, London, UK.
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK.
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15
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Yuan W, Li X, Wang G, Qu B, Zhao F. Association of autoimmune and allergic diseases with senile cataract: a bidirectional two-sample Mendelian randomization study. Front Immunol 2024; 15:1325868. [PMID: 38585265 PMCID: PMC10995295 DOI: 10.3389/fimmu.2024.1325868] [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: 10/22/2023] [Accepted: 02/19/2024] [Indexed: 04/09/2024] Open
Abstract
Background Many observational studies have been reported that patients with autoimmune or allergic diseases seem to have a higher risk of developing senile cataract, but the views are not consistent. In order to minimize the influence of reverse causality and potential confounding factors, we performed Mendelian Randomization (MR) analysis to investigate the genetic causal associations between autoimmune, allergic diseases and senile cataract. Methods Single nucleotide polymorphisms associated with ten common autoimmune and allergic diseases were obtained from the IEU Open genome-wide association studies (GWAS) database. Summary-level GWAS statistics for clinically diagnosed senile cataract were obtained from the FinnGen research project GWAS, which consisted of 59,522 individuals with senile cataracts and 312,864 control individuals. MR analysis was conducted using mainly inverse variance weighted (IVW) method and further sensitivity analysis was performed to test robustness. Results As for ten diseases, IVW results confirmed that type 1 diabetes (OR = 1.06; 95% CI = 1.05-1.08; p = 2.24×10-12), rheumatoid arthritis (OR = 1.05; 95% CI = 1.02-1.08; p = 1.83×10-4), hypothyroidism (OR = 2.4; 95% CI = 1.42-4.06; p = 1.12×10-3), systemic lupus erythematosus (OR = 1.02; 95% CI = 1.01-1.03; p = 2.27×10-3), asthma (OR = 1.02; 95% CI = 1.01-1.03; p = 1.2×10-3) and allergic rhinitis (OR = 1.07; 95% CI = 1.02-1.11; p = 2.15×10-3) were correlated with the risk of senile cataract. Celiac disease (OR = 1.04; 95% CI = 1.01-1.08; P = 0.0437) and atopic dermatitis (OR = 1.05; 95% CI = 1.01-1.10; P = 0.0426) exhibited a suggestive connection with senile cataract after Bonferroni correction. These associations are consistent across weighted median and MR Egger methods, with similar causal estimates in direction and magnitude. Sensitivity analysis further proved that these associations were reliable. Conclusions The results of the MR analysis showed that there were causal relationships between type 1 diabetes, rheumatoid arthritis, hypothyroidism, systemic lupus erythematosus, asthma, allergic rhinitis and senile cataract. To clarify the possible role of autoimmune and allergy in the pathophysiology of senile cataract, further studies are needed.
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Affiliation(s)
- Weichen Yuan
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Xiangrui Li
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Guan Wang
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Bo Qu
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
| | - Fangkun Zhao
- Department of Ophthalmology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
- Key Lens Research Laboratory of Liaoning Province, Shenyang, China
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16
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Plender EG, Prodanov T, Hsieh P, Nizamis E, Harvey WT, Sulovari A, Munson KM, Kaufman EJ, O’Neal WK, Valdmanis PN, Marschall T, Bloom JD, Eichler EE. Structural and genetic diversity in the secreted mucins, MUC5AC and MUC5B. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585560. [PMID: 38562829 PMCID: PMC10983947 DOI: 10.1101/2024.03.18.585560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The secreted mucins MUC5AC and MUC5B play critical defensive roles in airway pathogen entrapment and mucociliary clearance by encoding large glycoproteins with variable number tandem repeats (VNTRs). These polymorphic and degenerate protein coding VNTRs make the loci difficult to investigate with short reads. We characterize the structural diversity of MUC5AC and MUC5B by long-read sequencing and assembly of 206 human and 20 nonhuman primate (NHP) haplotypes. We find that human MUC5B is largely invariant (5761-5762aa); however, seven haplotypes have expanded VNTRs (6291-7019aa). In contrast, 30 allelic variants of MUC5AC encode 16 distinct proteins (5249-6325aa) with cysteine-rich domain and VNTR copy number variation. We grouped MUC5AC alleles into three phylogenetic clades: H1 (46%, ~5654aa), H2 (33%, ~5742aa), and H3 (7%, ~6325aa). The two most common human MUC5AC variants are smaller than NHP gene models, suggesting a reduction in protein length during recent human evolution. Linkage disequilibrium (LD) and Tajima's D analyses reveal that East Asians carry exceptionally large MUC5AC LD blocks with an excess of rare variation (p<0.05). To validate this result, we used Locityper for genotyping MUC5AC haplogroups in 2,600 unrelated samples from the 1000 Genomes Project. We observed signatures of positive selection in H1 and H2 among East Asians and a depletion of the likely ancestral haplogroup (H3). In Africans and Europeans, H3 alleles show an excess of common variation and deviate from Hardy-Weinberg equilibrium, consistent with heterozygote advantage and balancing selection. This study provides a generalizable strategy to characterize complex protein coding VNTRs for improved disease associations.
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Affiliation(s)
- Elizabeth G. Plender
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Timofey Prodanov
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - PingHsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evangelos Nizamis
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - William T. Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Eli J. Kaufman
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wanda K. O’Neal
- Marsico Lung Institute/UNC CF Research Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, 27599, North Carolina, USA
| | - Paul N. Valdmanis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tobias Marschall
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany
- Center for Digital Medicine, Heinrich Heine University, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Jesse D. Bloom
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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17
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Lan G, Xie M, Lan J, Huang Z, Xie X, Liang M, Chen Z, Jiang X, Lu X, Ye X, Xu T, Zeng Y, Xie X. Association and mediation between educational attainment and respiratory diseases: a Mendelian randomization study. Respir Res 2024; 25:115. [PMID: 38448970 PMCID: PMC10918882 DOI: 10.1186/s12931-024-02722-4] [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: 01/05/2024] [Accepted: 02/08/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Respiratory diseases are a major health burden, and educational inequalities may influence disease prevalence. We aim to evaluate the causal link between educational attainment and respiratory disease, and to determine the mediating influence of several known modifiable risk factors. METHODS We conducted a two-step, two-sample Mendelian randomization (MR) analysis using summary statistics from genome-wide association studies (GWAS) and single nucleotide polymorphisms (SNPs) as instrumental variables for educational attainment and respiratory diseases. Additionally, we performed a multivariable MR analysis to estimate the direct causal effect of each exposure variable included in the analysis on the outcome, conditional on the other exposure variables included in the model. The mediating roles of body mass index (BMI), physical activity, and smoking were also assessed. FINDINGS MR analyses provide evidence of genetically predicted educational attainment on the risk of FEV1 (β = 0.10, 95% CI 0.06, 0.14), FVC (β = 0.12, 95% CI 0.07, 0.16), FEV1/FVC (β = - 0.005, 95% CI - 0.05, 0.04), lung cancer (OR = 0.54, 95% CI 0.45, 0.65) and asthma (OR = 0.86, 95% CI 0.78, 0.94). Multivariable MR dicated the effect of educational attainment on FEV1 (β = 0.10, 95% CI 0.04, 0.16), FVC (β = 0.07, 95% CI 0.01, 0.12), FEV1/FVC (β = 0.07, 95% CI 0.01, 0.01), lung cancer (OR = 0.55, 95% CI 0.42, 0.71) and asthma (OR = 0.88, 95% CI 0.78, 0.99) persisted after adjusting BMI and cigarettes per day. Of the 23 potential risk factors, BMI, smoking may partially mediate the relationship between education and lung disease. CONCLUSION High levels of educational attainment have a potential causal protective effect on respiratory diseases. Reducing smoking and adiposity may be a target for the prevention of respiratory diseases attributable to low educational attainment.
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Affiliation(s)
- Guohui Lan
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Mengying Xie
- The Second Clinical Medical School, Nanchang University, Nanchang, China
| | - Jieli Lan
- Clinical Research Unit, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China
| | - Zelin Huang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Xiaowei Xie
- The First Clinical Medical School, Shanxi Medical University, Taiyuan, China
| | - Mengdan Liang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Zhehui Chen
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Xiannuan Jiang
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Xiaoli Lu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Xiaoying Ye
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Tingting Xu
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China
| | - Yiming Zeng
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine of Fujian Province, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
| | - Xiaoxu Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Fujian Medical University, Fuzhou, China.
- Clinical Research Unit, The Second Affiliated Hospital, Fujian Medical University, Quanzhou, China.
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine of Fujian Province, The Second Affiliated Hospital of Fujian Medical University, Quanzhou, China.
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18
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Peh HY, Brüggemann TR, Duvall MG, Nshimiyimana R, Nijmeh J, Cinelli MA, Israel E, Serhan CN, Levy BD. Resolvin D2 regulates type 2 inflammatory responses and promotes resolution of mouse allergic inflammation. Allergy 2024; 79:739-743. [PMID: 37888888 PMCID: PMC10922258 DOI: 10.1111/all.15920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/27/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023]
Affiliation(s)
- Hong Yong Peh
- Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Thayse R. Brüggemann
- Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Melody G. Duvall
- Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Robert Nshimiyimana
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Julie Nijmeh
- Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria A. Cinelli
- Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Elliot Israel
- Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Charles N. Serhan
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Bruce D. Levy
- Pulmonary and Critical Care Medicine Division, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
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Wu Z, Jiao M, Shu C, Li C, Zhu Y. Tea intake and lung diseases: a Mendelian randomization study. Front Immunol 2024; 15:1328933. [PMID: 38375474 PMCID: PMC10875148 DOI: 10.3389/fimmu.2024.1328933] [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: 10/27/2023] [Accepted: 01/19/2024] [Indexed: 02/21/2024] Open
Abstract
Background Existing studies on the relationship between tea intake and lung diseases have yielded inconsistent results, leading to an ongoing dispute on this issue. The impact of tea consumption on the respiratory system remained elucidating. Materials and methods We conducted a two-sample Mendelian randomization (MR) study to evaluate the associations between five distinct tea intake phenotypes and 15 different respiratory outcomes using open Genome-wide association study (GWAS) data. The inverse variance weighted (IVW) was used for preliminary screening and a variety of complementary methods were used as sensitivity analysis to validate the robustness of MR estimates. Pathway enrichment analysis was used to explore possible mechanisms. Results IVW found evidence for a causal effect of standard tea intake on an increased risk of lung squamous cell cancer (LSCC) (OR = 1.004; 95% CI = 1.001-1.007; P = 0.00299). No heterogeneity or pleiotropy was detected. After adjustment for potential mediators, including smoking, educational attainment, and time spent watching television, the association was still robust in multivariable MR. KEGG and GO enrichment predicted proliferation and activation of B lymphocytes may play a role in this causal relation. No causalities were observed when evaluating the effect of other kinds of tea intake on various pulmonary diseases. Conclusion Our MR estimates provide causal evidence of the independent effect of standard tea intake (black tea intake) on LSCC, which may be mediated by B lymphocytes. The results implied that the population preferring black tea intake should be wary of a higher risk of LSCC.
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Affiliation(s)
- Zhengyan Wu
- Department of Health Management Center, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Min Jiao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chenying Shu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Chang Li
- Department of Pulmonary and Critical Care Medicine, Chongzhou People's Hospital, Chongzhou, China
| | - Yehan Zhu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
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20
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Huang Q, Huang Y, Xu S, Yuan X, Liu X, Chen Z. Association of asthma and lung cancer risk: A pool of cohort studies and Mendelian randomization analysis. Medicine (Baltimore) 2024; 103:e35060. [PMID: 38306564 PMCID: PMC10843492 DOI: 10.1097/md.0000000000035060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 02/04/2024] Open
Abstract
BACKGROUND Over the past 2 decades, population-based studies have shown an increased association between asthma and the risk of lung cancer. However, the causal links between these 2 conditions remain poorly understood. METHODS We conducted a comprehensive search of various databases, including PubMed, Embase, Web of Science, and Cochrane Library, up until May 04, 2023. Only articles published in English were included in our study. We performed a meta-analysis using random-effects models to calculate the odds ratio (OR) and corresponding 95% confidence interval (CI). Subgroup analyses were conducted based on study design, gender, and histologic types. We also conducted a 2-sample Mendelian randomization (MR) using the genome-wide association study pooled data (408,422 people) published by the UK Biobank to explore further the potential causal relationship between asthma and lung cancer. RESULTS Our meta-analysis reviewed 24 population-based cohort studies involving 1072,502 patients, revealing that asthma is significantly associated with an increased risk of lung cancer (OR = 1.29, 95% CI 1.19-1.38) in all individuals. Subgroup analysis showed a significantly higher risk of lung cancer in females with asthma (OR = 1.23, 95% CI 1.01-1.49). We found no significant association between asthma and lung adenocarcinoma (LUAD) (OR = 0.76, 95% CI 0.54-1.05), lung squamous carcinomas (LUSC) (OR = 1.09, 95% CI 0.79-1.50), or small-cell lung cancer (SCLC) (OR = 1.00, 95% CI 0.68-1.49). Interestingly, our MR analysis supported an increasing causality between asthma and lung cancer (OR = 1.11, 95% CI 1.04-1.17, P = .0008), specifically in those who ever smoker (OR = 1.09, 95% CI 1.01-1.16, P = .0173) and LUSC pathological type (OR = 1.15, 95% CI 1.05-1.26, P = .0038). CONCLUSION Through meta-analysis, our study confirms that patients with asthma have a higher risk of developing lung cancer. Our MR study further support an increasing causal relationship between asthma and the risk of lung cancer, particularly in smokers and LUSC. Future studies examining the link between asthma and the risk of developing lung cancer should consider the bias of controlled and uncontrolled asthma.
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Affiliation(s)
- Qinyao Huang
- Department of Respiratory and Critical Care Medicine, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
- The Sixth Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Yunxia Huang
- Department of Respiratory and Critical Care Medicine, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
- The Sixth Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Senkai Xu
- Department of Respiratory and Critical Care Medicine, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
- The Sixth Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Xiaojun Yuan
- Department of Respiratory and Critical Care Medicine, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
- The Sixth Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Xinqi Liu
- Department of Respiratory and Critical Care Medicine, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
- The Sixth Clinical College, Guangzhou Medical University, Guangzhou, China
| | - Zisheng Chen
- Department of Respiratory and Critical Care Medicine, the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People’s Hospital, Qingyuan, China
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Haque TT, Weissler KA, Schmiechen Z, Laky K, Schwartz DM, Li J, Locci M, Turfkruyer M, Yao C, Schaughency P, Leak L, Lack J, Kanno Y, O'Shea J, Frischmeyer-Guerrerio PA. TGFβ prevents IgE-mediated allergic disease by restraining T follicular helper 2 differentiation. Sci Immunol 2024; 9:eadg8691. [PMID: 38241399 DOI: 10.1126/sciimmunol.adg8691] [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: 01/26/2023] [Accepted: 11/15/2023] [Indexed: 01/21/2024]
Abstract
Allergic diseases are common, affecting more than 20% of the population. Genetic variants in the TGFβ pathway are strongly associated with atopy. To interrogate the mechanisms underlying this association, we examined patients and mice with Loeys-Dietz syndrome (LDS) who harbor missense mutations in the kinase domain of TGFΒR1/2. We demonstrate that LDS mutations lead to reduced TGFβ signaling and elevated total and allergen-specific IgE, despite the presence of wild-type T regulatory cells in a chimera model. Germinal center activity was enhanced in LDS and characterized by a selective increase in type 2 follicular helper T cells (TFH2). Expression of Pik3cg was increased in LDS TFH cells and associated with reduced levels of the transcriptional repressor SnoN. PI3Kγ/mTOR signaling in LDS naïve CD4+ T cells was elevated after T cell receptor cross-linking, and pharmacologic inhibition of PI3Kγ or mTOR prevented exaggerated TFH2 and antigen-specific IgE responses after oral antigen exposure in an adoptive transfer model. Naïve CD4+ T cells from nonsyndromic allergic individuals also displayed decreased TGFβ signaling, suggesting that our mechanistic discoveries may be broadly relevant to allergic patients in general. Thus, TGFβ plays a conserved, T cell-intrinsic, and nonredundant role in restraining TFH2 development via the PI3Kγ/mTOR pathway and thereby protects against allergic disease.
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Affiliation(s)
- Tamara T Haque
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Katherine A Weissler
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Zoe Schmiechen
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Karen Laky
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daniella M Schwartz
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jenny Li
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Michela Locci
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mathilde Turfkruyer
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Chen Yao
- Laboratory of Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Paul Schaughency
- Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Lashawna Leak
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Justin Lack
- Collaborative Bioinformatics Resource, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Yuka Kanno
- Laboratory of Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John O'Shea
- Laboratory of Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Pamela A Frischmeyer-Guerrerio
- Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
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22
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Wang K, Zhao L, Luo H, Deng C, Gong L, Chen Z. Association of serum vitamin C levels with Asthma in adults: results of NHANES 2003-2006 and mendelian randomization study. BMC Pulm Med 2024; 24:4. [PMID: 38166915 PMCID: PMC10759650 DOI: 10.1186/s12890-023-02821-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: 09/19/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The protective effect of vitamin C as an antioxidant against asthma in adults remains controversial. This study used an observational study and Mendelian randomization (MR) analysis to investigate the association between adult asthma and serum vitamin C levels. METHODS Using information from the National Health and Nutrition Examination Survey (NHANES) 2003-2006, we carried out an observational study. A multivariate logistic regression model was employed to examine the connection between adult asthma and serum vitamin C levels. We used the inverse-variance weighted (IVW) method of MR analysis as the primary method to analyze the causal effect of serum vitamin C levels on asthma in adults. RESULTS A total of 8,504 participants were included in the observational study, including 639 in the asthma group and 7,865 in the non-asthma group. Before sample weighting, serum vitamin C was associated with a reduced risk of asthma in adults (OR = 0.798, 95% CI: 0.673-0.945, P = 0.009). After sample weighting, serum vitamin C was not associated with adult asthma risk (OR = 0.829, 95% CI: 0.660 ~ 1.042, P = 0.104). MR analysis showed no causal relationship between serum vitamin C and adult asthma in either the UK Biobank (OR = 0.957, 95% CI: 0.871 ~ 1.053, P = 0.370) or FinnGen (OR = 0.973, 95% CI: 0.824 ~ 1.149, P = 0.750) cohorts. CONCLUSION Our study did not support a causal association between serum vitamin C levels and adult asthma risk. The relationship between serum vitamin C and adult asthma requires further research.
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Affiliation(s)
- Kang Wang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of the Army Medical University, No. 30 Gaotanyanzheng Road, Shapingba District, Chongqing, 400038, China
| | - Lintao Zhao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of the Army Medical University, No. 30 Gaotanyanzheng Road, Shapingba District, Chongqing, 400038, China
| | - Hu Luo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of the Army Medical University, No. 30 Gaotanyanzheng Road, Shapingba District, Chongqing, 400038, China
| | - Caixia Deng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of the Army Medical University, No. 30 Gaotanyanzheng Road, Shapingba District, Chongqing, 400038, China
| | - Liang Gong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of the Army Medical University, No. 30 Gaotanyanzheng Road, Shapingba District, Chongqing, 400038, China.
| | - Zhujun Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of the Army Medical University, No. 30 Gaotanyanzheng Road, Shapingba District, Chongqing, 400038, China.
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23
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Lai J, Fang B, Luo L, Xie W, Xu Y, Li J. Causal relationship between asthma and inflammatory bowel disease : A two-sample bidirectional mendelian randomization analysis. Heart Lung 2024; 63:108-113. [PMID: 37844535 DOI: 10.1016/j.hrtlng.2023.10.004] [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: 07/29/2023] [Revised: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/18/2023]
Abstract
BACKGROUND Based on the findings of current observational studies, asthma and inflammatory bowel disease (including Crohn's disease and ulcerative colitis) are associated; however, their causal association cannot be established due to methodological limitations. OBJECTIVES we use two-sample bidirectional mendelian randomization (MR) to overcome the confounding factors and explore the causal link between asthma and inflammatory bowel disease. METHODS After selecting asthma and IBD-related genome-wide association studies (GWAS) data and screening single nucleotide polymorphisms (SNPs), MR analysis was performed by four methods: inverse variance weighted (IVW), MR-Egger, maximum likelihood, and weighted median (WM), while Cochran's Q test was used to detect heterogeneity and MR-Egger intercept to detect horizontal pleiotropy. Finally, we used the leave-one-out method and funnel plot to perform sensitivity analysis. RESULTS We screened 57, 59, and 60 SNPs in the association analysis of asthma and IBD, CD, and UC, respectively. The results of MR analysis showed that asthma only increased the risk of CD (IVW: OR = 1.1712, 95% CI = 1.0418-1.3167, P value = 0.0082; maximum likelihood: OR = 1.1739, 95% CI = 1.0428-1.3215, P value = 0.0080). Neither forward nor reverse MR analysis revealed heterogeneity or horizontal pleiotropy. Similarly, we did not find potential directional pleiotropy by funnel plot, and the leave-one-out method did not suggest a significant effect of a single SNP on the overall results. CONCLUSIONS we found a negative correlation between asthma and Crohn's disease, but more research is needed to confirm this.
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Affiliation(s)
- Jianxiong Lai
- Department of General Surgery, The Third Hospital of Mianyang (Sichuan Mental Health Center), Mianyang 621054, Sichuan Province, China
| | - Bin Fang
- Department of General Surgery, The Third Hospital of Mianyang (Sichuan Mental Health Center), Mianyang 621054, Sichuan Province, China
| | - Lirong Luo
- Department of General Surgery, The Third Hospital of Mianyang (Sichuan Mental Health Center), Mianyang 621054, Sichuan Province, China
| | - Wenjie Xie
- Department of General Surgery, The Third Hospital of Mianyang (Sichuan Mental Health Center), Mianyang 621054, Sichuan Province, China
| | - Yuanhui Xu
- Department of General Surgery, The Third Hospital of Mianyang (Sichuan Mental Health Center), Mianyang 621054, Sichuan Province, China
| | - Jian Li
- Department of General Surgery, The Third Hospital of Mianyang (Sichuan Mental Health Center), Mianyang 621054, Sichuan Province, China.
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24
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Tutino M, Hankinson J, Murray C, Lowe L, Kerry G, Rattray M, Custovic A, Johnston SL, Shi C, Orozco G, Eyre S, Martin P, Simpson A, Curtin JA. Identification of differences in CD4 + T-cell gene expression between people with asthma and healthy controls. Sci Rep 2023; 13:22796. [PMID: 38129444 PMCID: PMC10739740 DOI: 10.1038/s41598-023-49135-9] [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: 03/23/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
Functional enrichment analysis of genome-wide association study (GWAS)-summary statistics has suggested that CD4+ T-cells play an important role in asthma pathogenesis. Despite this, CD4+ T-cells are under-represented in asthma transcriptome studies. To fill the gap, 3'-RNA-Seq was used to generate gene expression data on CD4+ T-cells (isolated within 2 h from collection) from peripheral blood from participants with well-controlled asthma (n = 32) and healthy controls (n = 11). Weighted Gene Co-expression Network Analysis (WGCNA) was used to identify sets of co-expressed genes (modules) associated with the asthma phenotype. We identified three modules associated with asthma, which are strongly enriched for GWAS-identified asthma genes, antigen processing/presentation and immune response to viral infections. Through integration of publicly available eQTL and GWAS summary statistics (colocalisation), and protein-protein interaction (PPI) data, we identified PTPRC, a potential druggable target, as a putative master regulator of the asthma gene-expression profiles. Using a co-expression network approach, with integration of external genetic and PPI data, we showed that CD4+ T-cells from peripheral blood from asthmatics have different expression profiles, albeit small in magnitude, compared to healthy controls, for sets of genes involved in immune response to viral infections (upregulated) and antigen processing/presentation (downregulated).
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Affiliation(s)
- Mauro Tutino
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK.
| | - Jenny Hankinson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - Clare Murray
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Lesley Lowe
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gina Kerry
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
- Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
| | - Magnus Rattray
- Division of Informatics, Imaging and Data Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Adnan Custovic
- National Heart and Lung Institute, Asthma UK Centre in Allergic Mechanisms of Asthma, Imperial College London, London, UK
| | - Sebastian L Johnston
- National Heart and Lung Institute, Asthma UK Centre in Allergic Mechanisms of Asthma, Imperial College London, London, UK
| | - Chenfu Shi
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Gisela Orozco
- Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Stephen Eyre
- Manchester Biomedical Research Centre, Manchester University NHS Foundation Trust, Manchester, UK
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Paul Martin
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- The Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
| | - John A Curtin
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, M13 9PL, UK
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25
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Li Y, Zhang J, Wen J, Liu M, Liu W, Li Y. Large-scale genome-wide association study to identify causal relationships and potential mediators between education and autoimmune diseases. Front Immunol 2023; 14:1249017. [PMID: 38146362 PMCID: PMC10749315 DOI: 10.3389/fimmu.2023.1249017] [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: 06/28/2023] [Accepted: 11/08/2023] [Indexed: 12/27/2023] Open
Abstract
Objectives Epidemiological studies suggested a potential connection between education and autoimmune disorders. This study investigated the possible cause-and-effect relationship using a Mendelian randomization approach. Methods We explored the causality between four education traits (n = 257,841~1,131,881) and 22 autoimmune diseases. The mediating role of smoking (632,802 individuals), BMI (681,275 individuals), alcohol (335,394 individuals), and income (397,751 individuals) was also investigated. Transcriptome-wide association study (TWAS) and enriched signaling pathways analysis were used to investigate the underlying biological mechanisms. Results Especially, higher cognitive performance was protective for psoriasis (odds ratio (OR) = 0.69, 95% confidence interval (CI) = 0.60-0.79, p = 6.12×10-8), rheumatoid arthritis (RA) (OR = 0.75, 95% CI = 0.67-0.83, p = 4.62×10-6), and hypothyroidism (OR = 0.83, 95% CI = 0.77-0.90, p = 9.82×10-6). Higher levels of educational attainment decreased risks of psoriasis (OR = 0.61, 95% CI = 0.52-0.72, p = 1.12×10-9), RA (OR = 0.68, 95% CI = 0.59-0.79, p = 1.56×10-7), and hypothyroidism (OR = 0.80, 95% CI = 0.72-0.88, p = 5.00×10-6). The completion of highest-level math class genetically downregulates the incidence of psoriasis (OR = 0.66, 95% CI = 0.58-0.76, p = 2.47×10-9), RA (OR = 0.71, 95% CI = 0.63-0.81, p = 5.28×10-8), and hypothyroidism (OR = 0.85, 95% CI = 0.79-0.92, p = 8.88×10-5). Higher self-reported math ability showed protective effects on Crohn's disease (CD) (OR = 0.67, 95% CI = 0.55-0.81, p = 4.96×10-5), RA (OR = 0.76, 95% CI = 0.67-0.87, p = 5.21×10-5), and psoriasis (OR = 0.76, 95% CI = 0.65-0.88, p = 4.08×10-4). Protein modification and localization, response to arsenic-containing substances may participate in the genetic association of cognitive performance on UC, RA, psoriasis, and hypothyroidism. According to mediation analyses, BMI, smoking, and income served as significant mediators in the causal connection between educational traits and autoimmune diseases. Conclusion Higher levels of education-related factors have a protective effect on the risk of several autoimmune disorders. Reducing smoking and BMI and promoting income equality can mitigate health risks associated with low education levels.
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Affiliation(s)
- Yingjie Li
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, China
- The Institution of Hepatology, Central South University, Changsha, China
| | - Jingwei Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jie Wen
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Mingren Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hypothalamic Pituitary Research Center, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Wanyao Liu
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yongzhen Li
- Department of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China
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Donovan C, Barnes JL, Kim RY. Back to the Eosinophil: Resolvin Spatiotemporal Regulation. Am J Respir Cell Mol Biol 2023; 69:608-609. [PMID: 37703390 DOI: 10.1165/rcmb.2023-0261ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/13/2023] [Indexed: 09/15/2023] Open
Affiliation(s)
- Chantal Donovan
- School of Life Sciences University of Technology Sydney Ultimo, New South Wales, Australia
- Hunter Medical Research Institute The University of Newcastle Callaghan, New South Wales, Australia
| | - Jessica L Barnes
- Hunter Medical Research Institute The University of Newcastle Callaghan, New South Wales, Australia
| | - Richard Y Kim
- School of Life Sciences University of Technology Sydney Ultimo, New South Wales, Australia
- Hunter Medical Research Institute The University of Newcastle Callaghan, New South Wales, Australia
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Brüggemann TR, Peh HY, Tavares LP, Nijmeh J, Shay AE, Rezende RM, Lanser TB, Serhan CN, Levy BD. Eosinophil Phenotypes Are Functionally Regulated by Resolvin D2 during Allergic Lung Inflammation. Am J Respir Cell Mol Biol 2023; 69:666-677. [PMID: 37552821 DOI: 10.1165/rcmb.2023-0121oc] [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: 03/28/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023] Open
Abstract
Eosinophils (Eos) reside in multiple organs during homeostasis and respond rapidly to an inflammatory challenge. Although Eos share chemical staining properties, they also demonstrate phenotypic and functional plasticity that is not fully understood. Here, we used a murine model of allergic lung inflammation to characterize Eos subsets and determine their spatiotemporal and functional regulation during inflammation and its resolution in response to resolvin D2 (RvD2), a potent specialized proresolving mediator. Two Eos subsets were identified by CD101 expression with distinct anatomic localization and transcriptional signatures at baseline and during inflammation. CD101low Eos were predominantly located in a lung vascular niche and responded to allergen challenge by moving into the lung interstitium. CD101high Eos were predominantly located in bronchoalveolar lavage (BAL) and extravascular lung, only present during inflammation, and had transcriptional evidence for cell activation. RvD2 reduced total Eos numbers and changed their phenotype and activation by at least two distinct mechanisms: decreasing interleukin 5-dependent recruitment of CD101low Eos and decreasing conversion of CD101low Eos to CD101high Eos. Collectively, these findings indicate that Eos are a heterogeneous pool of cells with distinct activation states and spatiotemporal regulation during resolution of inflammation and that RvD2 is a potent proresolving mediator for Eos recruitment and activation.
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Affiliation(s)
| | - Hong Yong Peh
- Pulmonary and Critical Care Medicine, Department of Internal Medicine
| | - Luciana P Tavares
- Pulmonary and Critical Care Medicine, Department of Internal Medicine
| | - Julie Nijmeh
- Pulmonary and Critical Care Medicine, Department of Internal Medicine
| | - Ashley E Shay
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, and
| | - Rafael M Rezende
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Toby B Lanser
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Charles N Serhan
- Center for Experimental Therapeutics and Reperfusion Injury, Department of Anesthesiology, Perioperative and Pain Medicine, and
| | - Bruce D Levy
- Pulmonary and Critical Care Medicine, Department of Internal Medicine
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Kronzer VL, Hayashi K, Crowson CS, Davis JM, McDermott GC, Cui J, Losina E, Juge PA, Cerhan JR, Sparks JA. Gene-respiratory disease interactions for rheumatoid arthritis risk. Semin Arthritis Rheum 2023; 63:152254. [PMID: 37595508 PMCID: PMC10840753 DOI: 10.1016/j.semarthrit.2023.152254] [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: 04/19/2023] [Revised: 06/30/2023] [Accepted: 08/07/2023] [Indexed: 08/20/2023]
Abstract
OBJECTIVE We aimed to identify gene by respiratory tract disease interactions that increase RA risk. METHODS In this case-control study using the Mass General Brigham Biobank, we matched incident RA cases, confirmed by ACR/EULAR criteria, to four controls on age, sex, and electronic health record history. Genetic exposures included a validated overall genetic risk score (GRS) for RA, a Human Leukocyte Antigen (HLA) GRS for RA, and the MUC5B promoter variant, an established risk factor for RA-associated interstitial lung disease (ILD). Preceding respiratory tract diseases came from diagnosis codes (positive predictive value 86%). We estimated attributable proportions (AP) and multiplicative odds ratios (OR) with 95% confidence intervals (CI) for RA for each genetic and respiratory exposure using conditional logistic regression models, adjusting for potential confounders. RESULTS We identified 653 incident RA cases and 2,607 matched controls (mean 54 years, 76% female). The highest tertile of the overall GRS and the HLA GRS were both associated with increased RA risk (OR 2.28, 95% CI 1.89,2.74; OR 2.02, 95% CI 1.67-2.45). ILD and the HLA GRS exhibited a synergistic relationship for RA risk (OR for both exposures 4.30, 95% CI 1.28,14.38; AP 0.51, 95% CI-0.16,1.18). Asthma and the MUC5B promoter variant also exhibited a synergistic interaction for seropositive RA (OR for both exposures 2.58, 95% CI 1.10,6.07; AP 0.62, 95% CI 0.24,1.00). CONCLUSION ILD-HLA GRS and asthma-MUC5B promoter variant showed synergistic interactions for RA risk. Such interactions may prove useful for RA prevention and screening.
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Affiliation(s)
| | - Keigo Hayashi
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital; Harvard Medical School, Boston, USA.
| | - Cynthia S Crowson
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA; Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA.
| | - John M Davis
- Division of Rheumatology, Mayo Clinic, Rochester, MN, USA.
| | - Gregory C McDermott
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital; Harvard Medical School, Boston, USA.
| | - Jing Cui
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, USA.
| | - Elena Losina
- Department of Orthopedic Surgery, Brigham and Women's Hospital, Boston, USA.
| | - Pierre-Antoine Juge
- Dept of Rheumatology, DMU Locomotion, INSERM UMR1152, Hôpital Bichat-Claude Bernard, APHP, Université de Paris, Paris, France.
| | - James R Cerhan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA.
| | - Jeffrey A Sparks
- Division of Rheumatology, Inflammation, and Immunity, Brigham and Women's Hospital; Harvard Medical School, Boston, USA.
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Wang X, Huang Y, Li X, He Y, Liu X. The associations between asthma and common comorbidities: a comprehensive Mendelian randomization study. Front Med (Lausanne) 2023; 10:1251827. [PMID: 38034531 PMCID: PMC10684927 DOI: 10.3389/fmed.2023.1251827] [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: 07/08/2023] [Accepted: 10/31/2023] [Indexed: 12/02/2023] Open
Abstract
Background Asthma is a chronic respiratory disease and is often associated with multiple comorbidities. The causal relationship between asthma and these comorbidities is still unclear. This study aimed to investigate the association between genetically predicted asthma and common comorbidities. Methods After searching PubMed and GWAS summary statistics, we identified 26 comorbidities of asthma. The causal relationship between asthma and comorbidities was assessed in two independent GWASs by bidirectional Mendelian randomization, followed by validation of the results using a multivariate Mendelian randomization analysis and several sensitivity analyses. Results In the bidirectional Mendelian randomization analysis, chronic sinusitis [odds ratio (OR) = 1.54, p = 1.40 × 10-5], atopic dermatitis (OR = 1.36, p = 9.37 × 10-21), allergic conjunctivitis (OR = 2.07, p = 4.32 × 10-6), and allergic rhinitis (OR = 1.53, p = 5.20 × 10-6) were significantly associated with increased asthma risk. Hyperthyroidism (OR = 1.12, p = 0.04) had a potential increased risk for asthma. For the reverse direction, asthma showed significant associations with an increased risk of chronic obstructive pulmonary disease (OR = 1.24, p = 2.25 × 10-9), chronic sinusitis (OR = 1.61, p = 5.25 × 10-21), atopic dermatitis (OR = 2.11, p = 1.24 × 10-24), allergic conjunctivitis (OR = 1.65, p = 6.66 × 10-35), allergic rhinitis (OR = 1.90, p = 2.38 × 10-57), and a potential higher risk of allergic urticaria (OR = 1.25, p = 0.003). Conclusion This study suggested a significant bidirectional association of chronic sinusitis, atopic dermatitis, allergic conjunctivitis, and allergic rhinitis with asthma. In addition, hyperthyroidism was associated with an increased risk of asthma and asthma increased the risk of chronic obstructive pulmonary disease and allergic urticaria.
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Affiliation(s)
- Xuezhao Wang
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Pulmonary Diseases of National Health Commission, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yuchen Huang
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Pulmonary Diseases of National Health Commission, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Xiaochen Li
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Pulmonary Diseases of National Health Commission, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yuanzhou He
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Pulmonary Diseases of National Health Commission, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Xiansheng Liu
- Department of Pulmonary and Critical Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Pulmonary Diseases of National Health Commission, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
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Valencia-Hernández CA, Del Greco M F, Sundaram V, Portas L, Minelli C, Bloom CI. Asthma and incident coronary heart disease: an observational and Mendelian randomisation study. Eur Respir J 2023; 62:2301788. [PMID: 37945032 PMCID: PMC10695770 DOI: 10.1183/13993003.01788-2023] [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: 09/01/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Observational studies suggest asthma is a risk factor for coronary heart disease (CHD) and sex modifies the risk, but they may suffer from methodological limitations. To overcome these, we applied a "triangulation approach", where different methodologies, with different potential biases, were leveraged to enhance confidence in findings. METHODS First, we conducted an observational study using UK medical records to match asthma patients 1:1, by age, sex and general practitioner (GP) practice, to the general population. We measured the association between asthma and incident CHD (myocardial infarction: hospitalisation/death) by applying minimal sufficient adjustment: model 1, smoking, body mass index, oral corticosteroids, atopy and deprivation; model 2, additionally adjusting for healthcare behaviour (GP consultation frequency). Second, we conducted a Mendelian randomisation (MR) study using data from the UK Biobank, Trans-National Asthma Genetic Consortium (TAGC) and Coronary Artery Disease Genome-wide Replication and Meta-analysis consortium (CARDIoGRAM). Using 64 asthma single nucleotide polymorphisms, the effect of asthma on CHD was estimated with inverse variance-weighted meta-analysis and methods that adjust for pleiotropy. RESULTS In our observational study (n=1 522 910), we found asthma was associated with 6% increased risk of CHD (model 1: HR 1.06, 95% CI 1.01-1.13); after accounting for healthcare behaviour, we found no association (model 2: HR 0.99, 95% CI 0.94-1.05). Asthma severity did not modify the association, but sex did (females: HR 1.11, 95% CI 1.01-1.21; males: HR 0.91, 95% CI 0.84-0.98). Our MR study (n=589 875) found no association between asthma and CHD (OR 1.01, 95% CI 0.98-1.04) and no modification by sex. CONCLUSIONS Our findings suggest that asthma is not a risk factor for CHD. Previous studies may have suffered from detection bias or residual confounding.
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Affiliation(s)
| | | | - Varun Sundaram
- Louis Stokes Cleveland Medical Center, Case Western Reserve University, Cleveland, OH, USA
| | - Laura Portas
- National Heart and Lung Institute, Imperial College London, London, UK
- Oxford Big Data Institute, University of Oxford, Oxford, UK
| | - Cosetta Minelli
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Chloe I Bloom
- National Heart and Lung Institute, Imperial College London, London, UK
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Pandey R, Bakay M, Hakonarson H. SOCS-JAK-STAT inhibitors and SOCS mimetics as treatment options for autoimmune uveitis, psoriasis, lupus, and autoimmune encephalitis. Front Immunol 2023; 14:1271102. [PMID: 38022642 PMCID: PMC10643230 DOI: 10.3389/fimmu.2023.1271102] [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: 08/01/2023] [Accepted: 10/02/2023] [Indexed: 12/01/2023] Open
Abstract
Autoimmune diseases arise from atypical immune responses that attack self-tissue epitopes, and their development is intricately connected to the disruption of the JAK-STAT signaling pathway, where SOCS proteins play crucial roles. Conditions such as autoimmune uveitis, psoriasis, lupus, and autoimmune encephalitis exhibit immune system dysfunctions associated with JAK-STAT signaling dysregulation. Emerging therapeutic strategies utilize JAK-STAT inhibitors and SOCS mimetics to modulate immune responses and alleviate autoimmune manifestations. Although more research and clinical studies are required to assess their effectiveness, safety profiles, and potential for personalized therapeutic approaches in autoimmune conditions, JAK-STAT inhibitors and SOCS mimetics show promise as potential treatment options. This review explores the action, effectiveness, safety profiles, and future prospects of JAK inhibitors and SOCS mimetics as therapeutic agents for psoriasis, autoimmune uveitis, systemic lupus erythematosus, and autoimmune encephalitis. The findings underscore the importance of investigating these targeted therapies to advance treatment options for individuals suffering from autoimmune diseases.
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Affiliation(s)
- Rahul Pandey
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Marina Bakay
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, The University of Pennsylvania School of Medicine, Philadelphia, PA, United States
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Li X, Li H, Christenson SA, Castro M, Denlinger LC, Erzurum SC, Fahy JV, Gaston BM, Israel E, Jarjour NN, Levy BD, Mauger DT, Moore WC, Zein J, Kaminski N, Wenzel SE, Woodruff PG, Bleecker ER, Meyers DA. Genetic analyses of chr11p15.5 region identify MUC5AC- MUC5B associated with asthma-related phenotypes. J Asthma 2023; 60:1824-1835. [PMID: 36946148 PMCID: PMC10524756 DOI: 10.1080/02770903.2023.2193631] [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: 01/30/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023]
Abstract
OBJECTIVE Genome-wide association studies (GWASs) have identified single nucleotide polymorphisms (SNPs) in chr11p15.5 region associated with asthma and idiopathic interstitial pneumonias (IIPs). We sought to identify functional genes for asthma by combining SNPs and mRNA expression in bronchial epithelial cells (BEC) in the Severe Asthma Research Program (SARP). METHODS Correlation analyses of mRNA expression of six candidate genes (AP2A2, MUC6, MUC2, MUC5AC, MUC5B, and TOLLIP) and asthma phenotypes were performed in the longitudinal cohort (n = 156) with RNAseq in BEC, and replicated in the cross-sectional cohort (n = 155). eQTL (n = 114) and genetic association analysis of asthma severity (426 severe vs. 531 non-severe asthma) were performed, and compared with previously published GWASs of IIPs and asthma. RESULTS Higher expression of AP2A2 and MUC5AC and lower expression of MUC5B in BEC were correlated with asthma, asthma exacerbations, and T2 biomarkers (P < 0.01). SNPs associated with asthma and IIPs in previous GWASs were eQTL SNPs for MUC5AC, MUC5B, or TOLLIP, however, they were not in strong linkage disequilibrium. The risk alleles for asthma or protective alleles for IIPs were associated with higher expression of MUC5AC and lower expression of MUC5B. rs11603634, rs12788104, and rs28415845 associated with moderate-to-severe asthma or adult onset asthma in previous GWASs were not associated with asthma severity (P > 0.8). CONCLUSIONS SNPs associated with asthma in chr11p15.5 region are not associated with asthma severity neither with IIPs. Higher expression of MUC5AC and lower expression of MUC5B are risk for asthma but protective for IIPs.
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Affiliation(s)
- Xingnan Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Huashi Li
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Stephanie A. Christenson
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Mario Castro
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Loren C. Denlinger
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Serpil C. Erzurum
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - John V. Fahy
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Benjamin M. Gaston
- Wells Center for Pediatric Research and Riley Hospital for Children, Indiana University, Indianapolis, Indiana, USA
| | - Elliot Israel
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Nizar N. Jarjour
- Department of Medicine, University of Wisconsin School of Medicine & Public Health, Madison, Wisconsin, USA
| | - Bruce D. Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - David T Mauger
- Department of Public Health Sciences, College of Medicine, Penn State University, Hershey, Pennsylvania, USA
| | - Wendy C. Moore
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Joe Zein
- Lerner Research Institute and the Respiratory Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Naftali Kaminski
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Sally E. Wenzel
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Prescott G. Woodruff
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of California at San Francisco, San Francisco, California, USA
| | - Eugene R. Bleecker
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
| | - Deborah A. Meyers
- Division of Genetics, Genomics and Precision Medicine, Department of Medicine, University of Arizona, Tucson, Arizona, USA
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Frey A, Lunding LP, Wegmann M. The Dual Role of the Airway Epithelium in Asthma: Active Barrier and Regulator of Inflammation. Cells 2023; 12:2208. [PMID: 37759430 PMCID: PMC10526792 DOI: 10.3390/cells12182208] [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: 07/13/2023] [Revised: 09/01/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
Chronic airway inflammation is the cornerstone on which bronchial asthma arises, and in turn, chronic inflammation arises from a complex interplay between environmental factors such as allergens and pathogens and immune cells as well as structural cells constituting the airway mucosa. Airway epithelial cells (AECs) are at the center of these processes. On the one hand, they represent the borderline separating the body from its environment in order to keep inner homeostasis. The airway epithelium forms a multi-tiered, self-cleaning barrier that involves an unstirred, discontinuous mucous layer, the dense and rigid mesh of the glycocalyx, and the cellular layer itself, consisting of multiple, densely interconnected cell types. On the other hand, the airway epithelium represents an immunologically highly active tissue once its barrier has been penetrated: AECs play a pivotal role in releasing protective immunoglobulin A. They express a broad spectrum of pattern recognition receptors, enabling them to react to environmental stressors that overcome the mucosal barrier. By releasing alarmins-proinflammatory and regulatory cytokines-AECs play an active role in the formation, strategic orientation, and control of the subsequent defense reaction. Consequently, the airway epithelium is of vital importance to chronic inflammatory diseases, such as asthma.
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Affiliation(s)
- Andreas Frey
- Division of Mucosal Immunology and Diagnostics, Research Center Borstel, 23845 Borstel, Germany;
- Airway Research Center North (ARCN), German Center for Lung Research (DZL), 22927 Großhansdorf, Germany;
| | - Lars P. Lunding
- Airway Research Center North (ARCN), German Center for Lung Research (DZL), 22927 Großhansdorf, Germany;
- Division of Lung Immunology, Research Center Borstel, 23845 Borstel, Germany
| | - Michael Wegmann
- Airway Research Center North (ARCN), German Center for Lung Research (DZL), 22927 Großhansdorf, Germany;
- Division of Lung Immunology, Research Center Borstel, 23845 Borstel, Germany
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Mai J, Lu M, Gao Q, Zeng J, Xiao J. Transcriptome-wide association studies: recent advances in methods, applications and available databases. Commun Biol 2023; 6:899. [PMID: 37658226 PMCID: PMC10474133 DOI: 10.1038/s42003-023-05279-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Genome-wide association study has identified fruitful variants impacting heritable traits. Nevertheless, identifying critical genes underlying those significant variants has been a great task. Transcriptome-wide association study (TWAS) is an instrumental post-analysis to detect significant gene-trait associations focusing on modeling transcription-level regulations, which has made numerous progresses in recent years. Leveraging from expression quantitative loci (eQTL) regulation information, TWAS has advantages in detecting functioning genes regulated by disease-associated variants, thus providing insight into mechanisms of diseases and other phenotypes. Considering its vast potential, this review article comprehensively summarizes TWAS, including the methodology, applications and available resources.
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Affiliation(s)
- Jialin Mai
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingming Lu
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qianwen Gao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingyao Zeng
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
| | - Jingfa Xiao
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Li YK, Wang HY, Chen Y, Shi XQ, Zhang XX, Li K, Fu WP, Sun C. Single‑nucleotide polymorphism rs6592645 confers asthma risk through regulating LRRC32 expression. Exp Ther Med 2023; 26:451. [PMID: 37614425 PMCID: PMC10443064 DOI: 10.3892/etm.2023.12150] [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: 01/31/2023] [Accepted: 06/23/2023] [Indexed: 08/25/2023] Open
Abstract
Asthma is a complex disease, often with evident genetic predisposition; for example, the single-nucleotide polymorphism (SNP) rs7130588 was significantly associated with asthma by genome-wide association study (GWAS). Analysis of 1000 Genomes Project data suggests that there is another SNP, rs6592645, in complete linkage disequilibrium with rs7130588 and should present the same signal in GWAS. However, the causal SNP and the mechanism for the association between rs7130588 and asthma remain to be elucidated. In the presents study, results from dual-luciferase assays indicated that the A/G alleles of rs7130588 failed to present significantly different reporter gene expression. By contrast, A allele of rs6592645 presented a significant increase in relative luciferase activity than G allele, thus suggesting that rs6592645 may be a causal SNP. Using chromosome conformation capture, the enhancer region containing rs6592645 was observed to interact with promoter region of leucine-rich repeat-containing 32 (LRRC32). Gene expression quantification suggested that LRRC32 expression is significantly increased in lung tissue of patients with asthma and is dependent on the genotype of this locus, thus verifying that LRRC32 may be involved in asthma onset and that rs6592645 can regulate LRRC32 expression. Through chromatin immunoprecipitation, transcription factor 3 (TCF3) was identified to bind to rs6592645 surrounding region and the interaction between TCF3 and rs6592645 surrounding region was investigated. Results from the present study may improve our understanding of the mechanism by which the genetic variation in this locus might influence asthma susceptibility.
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Affiliation(s)
- Yi-Kun Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Hong-Yan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Ying Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Xiao-Qian Shi
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Xin-Xin Zhang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Ke Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Wei-Ping Fu
- Department of Respiratory Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650032, P.R. China
| | - Chang Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
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Recto K, Kachroo P, Huan T, Van Den Berg D, Lee GY, Bui H, Lee DH, Gereige J, Yao C, Hwang SJ, Joehanes R, Weiss ST, O'Connor GT, Levy D, DeMeo DL. Epigenome-wide DNA methylation association study of circulating IgE levels identifies novel targets for asthma. EBioMedicine 2023; 95:104758. [PMID: 37598461 PMCID: PMC10462855 DOI: 10.1016/j.ebiom.2023.104758] [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: 03/14/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/22/2023] Open
Abstract
BACKGROUND Identifying novel epigenetic signatures associated with serum immunoglobulin E (IgE) may improve our understanding of molecular mechanisms underlying asthma and IgE-mediated diseases. METHODS We performed an epigenome-wide association study using whole blood from Framingham Heart Study (FHS; n = 3,471, 46% females) participants and validated results using the Childhood Asthma Management Program (CAMP; n = 674, 39% females) and the Genetic Epidemiology of Asthma in Costa Rica Study (CRA; n = 787, 41% females). Using the closest gene to each IgE-associated CpG, we highlighted biologically plausible pathways underlying IgE regulation and analyzed the transcription patterns linked to IgE-associated CpGs (expression quantitative trait methylation loci; eQTMs). Using prior UK Biobank summary data from genome-wide association studies of asthma and allergy, we performed Mendelian randomization (MR) for causal inference testing using the IgE-associated CpGs from FHS with methylation quantitative trait loci (mQTLs) as instrumental variables. FINDINGS We identified 490 statistically significant differentially methylated CpGs associated with IgE in FHS, of which 193 (39.3%) replicated in CAMP and CRA (FDR < 0.05). Gene ontology analysis revealed enrichment in pathways related to transcription factor binding, asthma, and other immunological processes. eQTM analysis identified 124 cis-eQTMs for 106 expressed genes (FDR < 0.05). MR in combination with drug-target analysis revealed CTSB and USP20 as putatively causal regulators of IgE levels (Bonferroni adjusted P < 7.94E-04) that can be explored as potential therapeutic targets. INTERPRETATION By integrating eQTM and MR analyses in general and clinical asthma populations, our findings provide a deeper understanding of the multidimensional inter-relations of DNA methylation, gene expression, and IgE levels. FUNDING US NIH/NHLBI grants: P01HL132825, K99HL159234. N01-HC-25195 and HHSN268201500001I.
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Affiliation(s)
- Kathryn Recto
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Priyadarshini Kachroo
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA 02115, USA
| | - Tianxiao Huan
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - David Van Den Berg
- University of Southern California Methylation Characterization Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Gha Young Lee
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Helena Bui
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Dong Heon Lee
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Jessica Gereige
- Boston University School of Medicine, Pulmonary Center, Boston, MA 02118, USA
| | - Chen Yao
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Shih-Jen Hwang
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Roby Joehanes
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA
| | - Scott T Weiss
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA 02115, USA
| | - George T O'Connor
- The Framingham Heart Study, Framingham, MA 01702, USA; Boston University School of Medicine, Pulmonary Center, Boston, MA 02118, USA
| | - Daniel Levy
- The Population Sciences Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA; The Framingham Heart Study, Framingham, MA 01702, USA.
| | - Dawn L DeMeo
- Brigham and Women's Hospital, Channing Division of Network Medicine, Boston, MA 02115, USA.
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Li Y, Wang W, Zhou D, Lu Q, Li L, Zhang B. Mendelian randomization study shows a causal effect of asthma on chronic obstructive pulmonary disease risk. PLoS One 2023; 18:e0291102. [PMID: 37656706 PMCID: PMC10473539 DOI: 10.1371/journal.pone.0291102] [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: 05/19/2023] [Accepted: 08/22/2023] [Indexed: 09/03/2023] Open
Abstract
BACKGROUND This study was performed to explore the causal association between asthma and chronic obstructive pulmonary disease(COPD). METHODS We obtained summary statistics for asthma from 408,442 Europeans in an open genome-wide association study (GWAS) from the UK Biobank to select strongly associated single nucleotide polymorphisms that could serve as instrumental variables for asthma (P < 5×10-8). Additional summary statistics for COPD were obtained from 193,638 individuals of European ancestry in the GWAS published by FinnGen. Univariable Mendelian randomization(UVMR) analysis was performed using inverse variance weighted (IVW) as the primary method of analysis. The reliability of the results was verified by multivariable MR(MVMR), reverse and replication MR analysis, and sensitivity analysis. RESULTS In the UVMR analysis, asthma increased the risk of COPD, with an odds ratio (OR) of 1.27 (95% confidence interval (CI) = 1.16-1.39, P = 5.44×10-7). Estimates were consistent in MVMR analyses by the adjustments of smoking initiation, age of smoking initiation, cigarettes per day, PM 2.5, and the combination of the above factors. In the reverse MR analysis, there was no evidence of a causal effect of COPD on asthma risk(OR = 1.02, 95% CI = 0.97-1.07, P = 0.3643). In the replication MR analysis, asthma still increased the risk of COPD. Sensitivity analyses validated the robustness of the above associations. CONCLUSIONS We found that genetically predicted asthma was positively associated with the risk of COPD. Additionally, there was no evidence that COPD increases the risk of asthma. Further clarification of this link and underlying mechanisms is needed to identify feasible measures to promote COPD prevention.
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Affiliation(s)
- Yuanyuan Li
- Department of Respiratory and Critical Care Medicine, Wuhan Fourth Hospital, Wuhan, Hubei Province, China
| | - Weina Wang
- Department of Respiratory and Critical Care Medicine, Wuhan Fourth Hospital, Wuhan, Hubei Province, China
| | - Dengfeng Zhou
- Department of Respiratory and Critical Care Medicine, Wuhan Fourth Hospital, Wuhan, Hubei Province, China
| | - Qiaofa Lu
- Department of Respiratory and Critical Care Medicine, Wuhan Fourth Hospital, Wuhan, Hubei Province, China
| | - Lili Li
- Department of Gastroenterology, Wuhan Fourth Hospital, Wuhan, Hubei Province, China
| | - Bo Zhang
- Department of Respiratory and Critical Care Medicine, Wuhan Fourth Hospital, Wuhan, Hubei Province, China
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Zaied RE, Fadason T, O'Sullivan JM. De novo identification of complex traits associated with asthma. Front Immunol 2023; 14:1231492. [PMID: 37680636 PMCID: PMC10480836 DOI: 10.3389/fimmu.2023.1231492] [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: 05/30/2023] [Accepted: 08/02/2023] [Indexed: 09/09/2023] Open
Abstract
Introduction Asthma is a heterogeneous inflammatory disease often associated with other complex phenotypes. Identifying asthma-associated diseases and uncovering the molecular mechanisms mediating their interaction can help detangle the heterogeneity of asthma. Network analysis is a powerful approach for untangling such inter-disease relationships. Methods Here, we integrated information on physical contacts between common single nucleotide polymorphisms (SNPs) and gene expression with expression quantitative trait loci (eQTL) data from the lung and whole blood to construct two tissue-specific spatial gene regulatory networks (GRN). We then located the asthma GRN (level 0) within each tissue-specific GRN by identifying the genes that are functionally affected by asthma-associated spatial eQTLs. Curated protein interaction partners were subsequently identified up to four edges or levels away from the asthma GRN. The eQTLs spatially regulating genes on levels 0-4 were queried against the GWAS Catalog to identify the traits enriched (hypergeometric test; FDR ≤ 0.05) in each level. Results We identified 80 and 82 traits significantly enriched in the lung and blood GRNs, respectively. All identified traits were previously reported to be comorbid or associated (positively or negatively) with asthma (e.g., depressive symptoms and lung cancer), except 8 traits whose association with asthma is yet to be confirmed (e.g., reticulocyte count). Our analysis additionally pinpoints the variants and genes that link asthma to the identified asthma-associated traits, a subset of which was replicated in a comorbidity analysis using health records of 26,781 asthma patients in New Zealand. Discussion Our discovery approach identifies enriched traits in the regulatory space proximal to asthma, in the tissue of interest, without a priori selection of the interacting traits. The predictions it makes expand our understanding of possible shared molecular interactions and therapeutic targets for asthma, where no cure is currently available.
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Affiliation(s)
- Roan E Zaied
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Tayaza Fadason
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Justin M O'Sullivan
- The Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Medical Research Council (MRC) Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore
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Xie W, Li J, Du H, Xia J. Causal relationship between PCSK9 inhibitor and autoimmune diseases: a drug target Mendelian randomization study. Arthritis Res Ther 2023; 25:148. [PMID: 37580807 PMCID: PMC10424393 DOI: 10.1186/s13075-023-03122-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/19/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND In addition to decreasing the level of cholesterol, proprotein convertase subtilis kexin 9 (PCSK9) inhibitor has pleiotropic effects, including immune regulation. However, the impact of PCSK9 on autoimmune diseases is controversial. Therefore, we used drug target Mendelian randomization (MR) analysis to investigate the effect of PCSK9 inhibitor on different autoimmune diseases. METHODS We collected single nucleotide polymorphisms (SNPs) of PCSK9 from published genome-wide association studies statistics and conducted drug target MR analysis to detect the causal relationship between PCSK9 inhibitor and the risk of autoimmune diseases. 3-Hydroxy-3-methylglutaryl-assisted enzyme A reductase (HMGCR) inhibitor, the drug target of statin, was used to compare the effect with that of PCSK9 inhibitor. With the risk of coronary heart disease as a positive control, primary outcomes included the risk of systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), myasthenia gravis (MG), multiple sclerosis (MS), asthma, Crohn's disease (CD), ulcerative colitis (UC), and type 1 diabetes (T1D). RESULTS PCSK9 inhibitor significantly reduced the risk of SLE (OR [95%CI] = 0.47 [0.30 to 0.76], p = 1.74 × 10-3) but increased the risk of asthma (OR [95%CI] = 1.15 [1.03 to 1.29], p = 1.68 × 10-2) and CD (OR [95%CI] = 1.38 [1.05 to 1.83], p = 2.28 × 10-2). In contrast, HMGCR inhibitor increased the risk of RA (OR [95%CI] = 1.58 [1.19 to 2.11], p = 1.67 × 10-3), asthma (OR [95%CI] = 1.21 [1.04 to 1.40], p = 1.17 × 10-2), and CD (OR [95%CI] = 1.60 [1.08 to 2.39], p = 2.04 × 10-2). CONCLUSIONS PCSK9 inhibitor significantly reduced the risk of SLE but increased the risk of asthma and CD. In contrast, HMGCR inhibitor may be a risk factor for RA, asthma, and CD.
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Affiliation(s)
- Weijia Xie
- Department of Neurology, Xiangya Hospital, Central South University, 87# Xiangya Road, Changsha, Hunan, China
| | - Jiaxin Li
- Department of Neurology, Xiangya Hospital, Central South University, 87# Xiangya Road, Changsha, Hunan, China
| | - Hao Du
- Department of Neurology, Xiangya Hospital, Central South University, 87# Xiangya Road, Changsha, Hunan, China
| | - Jian Xia
- Department of Neurology, Xiangya Hospital, Central South University, 87# Xiangya Road, Changsha, Hunan, China.
- Clinical Research Center for Cerebrovascular Disease of Hunan Province, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
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Jeong Y, Song J, Lee Y, Choi E, Won Y, Kim B, Jang W. A Transcriptome-Wide Analysis of Psoriasis: Identifying the Potential Causal Genes and Drug Candidates. Int J Mol Sci 2023; 24:11717. [PMID: 37511476 PMCID: PMC10380797 DOI: 10.3390/ijms241411717] [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: 05/31/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Psoriasis is a chronic inflammatory skin disease characterized by cutaneous eruptions and pruritus. Because the genetic backgrounds of psoriasis are only partially revealed, an integrative and rigorous study is necessary. We conducted a transcriptome-wide association study (TWAS) with the new Genotype-Tissue Expression version 8 reference panels, including some tissue and multi-tissue panels that were not used previously. We performed tissue-specific heritability analyses on genome-wide association study data to prioritize the tissue panels for TWAS analysis. TWAS and colocalization (COLOC) analyses were performed with eight tissues from the single-tissue panels and the multi-tissue panels of context-specific genetics (CONTENT) to increase tissue specificity and statistical power. From TWAS, we identified the significant associations of 101 genes in the single-tissue panels and 64 genes in the multi-tissue panels, of which 26 genes were replicated in the COLOC. Functional annotation and network analyses identified that the genes were associated with psoriasis and/or immune responses. We also suggested drug candidates that interact with jointly significant genes through a conditional and joint analysis. Together, our findings may contribute to revealing the underlying genetic mechanisms and provide new insights into treatments for psoriasis.
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Affiliation(s)
- Yeonbin Jeong
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Jaeseung Song
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Yubin Lee
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Eunyoung Choi
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Youngtae Won
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Byunghyuk Kim
- Department of Life Sciences, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Wonhee Jang
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
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41
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Cheng X, Shi J, Zhang D, Li C, Xu H, He J, Liang W. Assessing the genetic relationship between gastroesophageal reflux disease and chronic respiratory diseases: a mendelian randomization study. BMC Pulm Med 2023; 23:243. [PMID: 37403021 DOI: 10.1186/s12890-023-02502-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/31/2023] [Indexed: 07/06/2023] Open
Abstract
BACKGROUND Previous observational studies have found an association between gastroesophageal reflux disease (GERD) and chronic respiratory diseases, but it remains uncertain whether GERD causally influences these diseases. In this study, we aimed to estimate the causal associations between GERD and 5 chronic respiratory diseases. METHODS 88 GERD-associated single nucleotide polymorphisms (SNPs) identified by the latest genome-wide association study were included as instrumental variables. Individual-level genetic summary data of participants were obtained from corresponding studies and the FinnGen consortium. We applied the inverse-variance weighted method to estimate the causality between genetically predicted GERD and 5 chronic respiratory diseases. Furthermore, the associations between GERD and common risk factors were investigated, and mediation analyses were conducted using multivariable MR. Various sensitivity analyses were also performed to verify the robustness of the findings. RESULTS Our study demonstrated that genetically predicted GERD was causally associated with an increased risk of asthma (OR 1.39, 95%CI 1.25-1.56, P < 0.001), idiopathic pulmonary fibrosis (IPF) (OR 1.43, 95%CI 1.05-1.95, P = 0.022), chronic obstructive disease (COPD) (OR 1.64, 95%CI 1.41-1.93, P < 0.001), chronic bronchitis (OR 1.77, 95%CI 1.15-2.74, P = 0.009), while no correlation was observed for bronchiectasis (OR 0.93, 95%CI 0.68-1.27, P = 0.645). Additionally, GERD was associated with 12 common risk factors for chronic respiratory diseases. Nevertheless, no significant mediators were discovered. CONCLUSIONS Our study suggested that GERD was a causal factor in the development of asthma, IPF, COPD and chronic bronchitis, indicating that GERD-associated micro-aspiration of gastric contents process might play a role in the development of pulmonary fibrosis in these diseases.
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Affiliation(s)
- Xiaoxue Cheng
- Nanshan School, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jiang Shi
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
- State Key Laboratory of Respiratory Disease, Guangzhou, 510120, China
- National Clinical Research Center for Respiratory Disease, Guangzhou, 510120, China
| | - Ding Zhang
- Department of Gastroenterology, Maoming Hospital of Guangzhou University of Chinese Medicine, Maoming, China
| | - Caichen Li
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
- State Key Laboratory of Respiratory Disease, Guangzhou, 510120, China
- National Clinical Research Center for Respiratory Disease, Guangzhou, 510120, China
| | - Haoxiang Xu
- The Second Affiliated Hospital, Guangdong Provincial Hospital of Chinese Medicine) of Guangzhou University of Chinese Medicine, Guangzhou, 510120, China
| | - Jianxing He
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China
- State Key Laboratory of Respiratory Disease, Guangzhou, 510120, China
- National Clinical Research Center for Respiratory Disease, Guangzhou, 510120, China
| | - Wenhua Liang
- Department of Thoracic Surgery and Oncology, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, China.
- State Key Laboratory of Respiratory Disease, Guangzhou, 510120, China.
- National Clinical Research Center for Respiratory Disease, Guangzhou, 510120, China.
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Chung CJ, Hermes BM, Gupta Y, Ibrahim S, Belheouane M, Baines JF. Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling. Anim Microbiome 2023; 5:31. [PMID: 37264412 DOI: 10.1186/s42523-023-00250-y] [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: 11/22/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Mammalian lungs comprise a complex microbial ecosystem that interacts with host physiology. Previous research demonstrates that the environment significantly contributes to bacterial community structure in the upper and lower respiratory tract. However, the influence of host genetics on the makeup of lung microbiota remains ambiguous, largely due to technical difficulties related to sampling, as well as challenges inherent to investigating low biomass communities. Thus, innovative approaches are warranted to clarify host-microbe interactions in the mammalian lung. RESULTS Here, we aimed to characterize host genomic regions associated with lung bacterial traits in an advanced intercross mouse line (AIL). By performing quantitative microbial profiling (QMP) using the highly precise method of droplet digital PCR (ddPCR), we refined 16S rRNA gene amplicon-based traits to identify and map candidate lung-resident taxa using a QTL mapping approach. In addition, the two abundant core taxa Lactobacillus and Pelomonas were chosen for independent microbial phenotyping using genus-specific primers. In total, this revealed seven significant loci involving eight bacterial traits. The narrow confidence intervals afforded by the AIL population allowed us to identify several promising candidate genes related to immune and inflammatory responses, cell apoptosis, DNA repair, and lung functioning and disease susceptibility. Interestingly, one genomic region associated with Lactobacillus abundance contains the well-known anti-inflammatory cytokine Il10, which we confirmed through the analysis of Il10 knockout mice. CONCLUSIONS Our study provides the first evidence for a role of host genetic variation contributing to variation in the lung microbiota. This was in large part made possible through the careful curation of 16S rRNA gene amplicon data and the incorporation of a QMP-based methods. This approach to evaluating the low biomass lung environment opens new avenues for advancing lung microbiome research using animal models.
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Affiliation(s)
- C J Chung
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - B M Hermes
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - Y Gupta
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - S Ibrahim
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Meriem Belheouane
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
- Research Center Borstel, Evolution of the Resistome, Leibniz Lung Center, Parkallee 1-40, 23845, Borstel, Germany.
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
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Huang T, Long Y, Ou Y, Li J, Huang Y, Gao J. Association between circulating fatty acid metabolites and asthma risk: a two-sample bidirectional Mendelian randomization study. BMC Med Genomics 2023; 16:112. [PMID: 37221513 DOI: 10.1186/s12920-023-01545-4] [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: 10/11/2022] [Accepted: 05/13/2023] [Indexed: 05/25/2023] Open
Abstract
BACKGROUND Fatty acids are involved in a wide range of immunological responses in humans. Supplementation of polyunsaturated fatty acids has been reported to help alleviate symptoms and airway inflammation in asthma patients, whereas the effects of fatty acids on the actual risk of asthma remain controversial. This study comprehensively investigated the causal effects of serum fatty acids on asthma risk using two-sample bidirectional Mendelian Randomization (MR) analysis. METHODS Genetic variants strongly associated with 123 circulating fatty acid metabolites were extracted as instrumental variables, and a large GWAS data of asthma was used to test effects of the metabolites on this outcome. The inverse-variance weighted method was used for primary MR analysis. The weighted median, MR-Egger regression, MR-PRESSO, and leave-one-out analyses were utilized to evaluate heterogeneity and pleiotropy. Potential confounders were adjusted by performing multivariable MR analyses. Reverse MR analysis was also conducted to estimate the causal effect of asthma on candidate fatty acid metabolites. Further, we performed colocalization analysis to examine the pleiotropy of variants within the fatty acid desaturase 1 (FADS1) locus between the significant metabolite traits and the risk of asthma. Cis-eQTL-MR and colocalization analysis were also performed to determine the association between RNA expression of FADS1 and asthma. RESULTS Genetically instrumented higher average number of methylene groups was causally associated with a lower risk of asthma in primary MR analysis, while inversely, the higher ratio of bis-allylic groups to double bonds and the higher ratio of bis-allylic groups to total fatty acids, were associated with higher probabilities of asthma. Consistent results were obtained in multivariable MR when adjusted for potential confounders. However, these effects were completely eliminated after SNPs correlated with the FADS1 gene were excluded. The reverse MR also found no causal association. The colocalization analysis suggested that the three candidate metabolite traits and asthma likely share causal variants within the FADS1 locus. In addition, the cis-eQTL-MR and colocalization analyses demonstrated a causal association and shared causal variants between FADS1 expression and asthma. CONCLUSIONS Our study supports a negative association between several PUFA traits and the risk of asthma. However, this association is largely attributed to the influence of FADS1 polymorphisms. The results of this MR study should be carefully interpreted given the pleiotropy of SNPs associated with FADS1.
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Affiliation(s)
- Tingting Huang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yichen Long
- Department of Epidemiology, School of Public Health, Southeast University, Jiangsu, Nanjing, China
| | - Yang Ou
- Center for Tumor Diagnosis and Therapy, Jinshan Hospital, Fudan University, Shanghai, China
| | - Jia Li
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yilin Huang
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jinming Gao
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
- Department of Respiratory and Critical Care Medicine, Peking Union Medical College Hospital, Beijing, China.
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Meadows AM, Han K, Singh K, Murgia A, McNally BD, West JA, Huffstutler RD, Powell-Wiley TM, Baumer Y, Griffin JL, Sack MN. N-arachidonylglycine is a caloric state-dependent circulating metabolite which regulates human CD4 +T cell responsiveness. iScience 2023; 26:106578. [PMID: 37128607 PMCID: PMC10148119 DOI: 10.1016/j.isci.2023.106578] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/29/2023] [Accepted: 03/29/2023] [Indexed: 05/03/2023] Open
Abstract
Caloric deprivation interventions such as intermittent fasting and caloric restriction ameliorate metabolic and inflammatory disease. As a human model of caloric deprivation, a 24-h fast blunts innate and adaptive immune cell responsiveness relative to the refed state. Isolated serum at these time points confers these same immunomodulatory effects on transformed cell lines. To identify serum mediators orchestrating this, metabolomic and lipidomic analysis was performed on serum extracted after a 24-h fast and re-feeding. Bioinformatic integration with concurrent peripheral blood mononuclear cells RNA-seq analysis implicated key metabolite-sensing GPCRs in fasting-mediated immunomodulation. The putative GPR18 ligand N-arachidonylglycine (NAGly) was elevated during fasting and attenuated CD4+T cell responsiveness via GPR18 MTORC1 signaling. In parallel, NAGly reduced inflammatory Th1 and Th17 cytokines levels in CD4+T cells isolated from obese subjects, identifying a fasting-responsive metabolic intermediate that may contribute to the regulation of nutrient-level dependent inflammation associated with metabolic disease.
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Affiliation(s)
- Allison M. Meadows
- Laboratory of Mitochondrial Biology and Metabolism, NHLBI, NIH, Bethesda, MD, USA
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Kim Han
- Laboratory of Mitochondrial Biology and Metabolism, NHLBI, NIH, Bethesda, MD, USA
| | - Komudi Singh
- Laboratory of Mitochondrial Biology and Metabolism, NHLBI, NIH, Bethesda, MD, USA
| | - Antonio Murgia
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - Ben D. McNally
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | - James A. West
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
| | | | - Tiffany M. Powell-Wiley
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, NHLBI, NIH, Bethesda, MD, USA
| | - Yvonne Baumer
- Social Determinants of Obesity and Cardiovascular Risk Laboratory, NHLBI, NIH, Bethesda, MD, USA
| | - Julian L. Griffin
- Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge, UK
- The Rowett Institute, School of Medicine, Medical Sciences and Nutrition, Foresterhill Campus, Aberdeen, UK
| | - Michael N. Sack
- Laboratory of Mitochondrial Biology and Metabolism, NHLBI, NIH, Bethesda, MD, USA
- Cardiovascular Branch, NHLBI, NIH, Bethesda, MD, USA
- Corresponding author
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Pandey R, Bakay M, Hakonarson H. CLEC16A-An Emerging Master Regulator of Autoimmunity and Neurodegeneration. Int J Mol Sci 2023; 24:ijms24098224. [PMID: 37175930 PMCID: PMC10179542 DOI: 10.3390/ijms24098224] [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: 03/30/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
CLEC16A is emerging as an important genetic risk factor for several autoimmune disorders and for Parkinson disease (PD), opening new avenues for translational research and therapeutic development. While the exact role of CLEC16A in health and disease is still being elucidated, the gene plays a critical role in the regulation of autophagy, mitophagy, endocytosis, intracellular trafficking, immune function, and in biological processes such as insulin secretion and others that are important to cellular homeostasis. As shown in both human and animal modeling studies, CLEC16A hypofunction predisposes to both autoinflammatory phenotype and neurodegeneration. While the two are clearly related, further functional studies are needed to fully understand the mechanisms involved for optimized therapeutic interventions. Based on recent data, mitophagy-inducing drugs may be warranted, and such therapy should be tested in clinical trials as these drugs would tackle the underlying pathogenic mechanism (s) and could treat or prevent symptoms of autoimmunity and neurodegeneration in individuals with CLEC16A risk variants. Accordingly, interventions directed at reversing the dysregulated mitophagy and the consequences of loss of function of CLEC16A without activating other detrimental cellular pathways could present an effective therapy. This review presents the emerging role of CLEC16A in health and disease and provides an update on the disease processes that are attributed to variants located in the CLEC16A gene, which are responsible for autoimmune disorders and neurodegeneration with emphasis on how this information is being translated into practical and effective applications in the clinic.
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Affiliation(s)
- Rahul Pandey
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
| | - Marina Bakay
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, 3615 Civic Center Boulevard, Philadelphia, PA 19104-4318, USA
- Department of Pediatrics, The University of Pennsylvania School of Medicine, Philadelphia, PA 19104-4318, USA
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Sharma M, Leung D, Momenilandi M, Jones LC, Pacillo L, James AE, Murrell JR, Delafontaine S, Maimaris J, Vaseghi-Shanjani M, Del Bel KL, Lu HY, Chua GT, Di Cesare S, Fornes O, Liu Z, Di Matteo G, Fu MP, Amodio D, Tam IYS, Chan GSW, Sharma AA, Dalmann J, van der Lee R, Blanchard-Rohner G, Lin S, Philippot Q, Richmond PA, Lee JJ, Matthews A, Seear M, Turvey AK, Philips RL, Brown-Whitehorn TF, Gray CJ, Izumi K, Treat JR, Wood KH, Lack J, Khleborodova A, Niemela JE, Yang X, Liang R, Kui L, Wong CSM, Poon GWK, Hoischen A, van der Made CI, Yang J, Chan KW, Rosa Duque JSD, Lee PPW, Ho MHK, Chung BHY, Le HTM, Yang W, Rohani P, Fouladvand A, Rokni-Zadeh H, Changi-Ashtiani M, Miryounesi M, Puel A, Shahrooei M, Finocchi A, Rossi P, Rivalta B, Cifaldi C, Novelli A, Passarelli C, Arasi S, Bullens D, Sauer K, Claeys T, Biggs CM, Morris EC, Rosenzweig SD, O’Shea JJ, Wasserman WW, Bedford HM, van Karnebeek CD, Palma P, Burns SO, Meyts I, Casanova JL, Lyons JJ, Parvaneh N, Nguyen ATV, Cancrini C, Heimall J, Ahmed H, McKinnon ML, Lau YL, Béziat V, Turvey SE. Human germline heterozygous gain-of-function STAT6 variants cause severe allergic disease. J Exp Med 2023; 220:e20221755. [PMID: 36884218 PMCID: PMC10037107 DOI: 10.1084/jem.20221755] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/12/2022] [Accepted: 02/09/2023] [Indexed: 03/09/2023] Open
Abstract
STAT6 (signal transducer and activator of transcription 6) is a transcription factor that plays a central role in the pathophysiology of allergic inflammation. We have identified 16 patients from 10 families spanning three continents with a profound phenotype of early-life onset allergic immune dysregulation, widespread treatment-resistant atopic dermatitis, hypereosinophilia with esosinophilic gastrointestinal disease, asthma, elevated serum IgE, IgE-mediated food allergies, and anaphylaxis. The cases were either sporadic (seven kindreds) or followed an autosomal dominant inheritance pattern (three kindreds). All patients carried monoallelic rare variants in STAT6 and functional studies established their gain-of-function (GOF) phenotype with sustained STAT6 phosphorylation, increased STAT6 target gene expression, and TH2 skewing. Precision treatment with the anti-IL-4Rα antibody, dupilumab, was highly effective improving both clinical manifestations and immunological biomarkers. This study identifies heterozygous GOF variants in STAT6 as a novel autosomal dominant allergic disorder. We anticipate that our discovery of multiple kindreds with germline STAT6 GOF variants will facilitate the recognition of more affected individuals and the full definition of this new primary atopic disorder.
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Affiliation(s)
- Mehul Sharma
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Daniel Leung
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Mana Momenilandi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris-Cité, Paris, France
| | - Lauren C.W. Jones
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Lucia Pacillo
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Academic Dept. of Pediatrics (DPUO), Unit of Clinical Immunology and Vaccinology, IRCCS Bambin Gesù Children Hospital, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Alyssa E. James
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jill R. Murrell
- Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Selket Delafontaine
- Dept. of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Pediatric Immunodeficiencies Division, University Hospitals Leuven, Leuven, Belgium
| | - Jesmeen Maimaris
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- Dept. of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Maryam Vaseghi-Shanjani
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Kate L. Del Bel
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Henry Y. Lu
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
- Dept. of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Gilbert T. Chua
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
- Allergy Centre, Union Hospital, Hong Kong, China
| | - Silvia Di Cesare
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Oriol Fornes
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
- Dept. of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Zhongyi Liu
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Gigliola Di Matteo
- Academic Dept. of Pediatrics (DPUO), Unit of Clinical Immunology and Vaccinology, IRCCS Bambin Gesù Children Hospital, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Maggie P. Fu
- Dept. of Medical Genetics, The University of British Columbia, Vancouver, Canada
- Genome Science and Technology Program, Faculty of Science, The University of British Columbia, Vancouver, Canada
| | - Donato Amodio
- Academic Dept. of Pediatrics (DPUO), Unit of Clinical Immunology and Vaccinology, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Issan Yee San Tam
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | | | | | - Joshua Dalmann
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Robin van der Lee
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
- Dept. of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Géraldine Blanchard-Rohner
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
- Unit of Immunology and Vaccinology, Division of General Pediatrics, Dept. of Woman, Child, and Adolescent Medicine, Geneva University Hospitals and Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Susan Lin
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Quentin Philippot
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris-Cité, Paris, France
| | - Phillip A. Richmond
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
| | - Jessica J. Lee
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
- Genome Science and Technology Graduate Program, University of British Columbia, Vancouver, Canada
| | - Allison Matthews
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
- Dept. of Paediatrics, University of Toronto, Toronto, Canada
| | - Michael Seear
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Alexandra K. Turvey
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Rachael L. Philips
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Terri F. Brown-Whitehorn
- Dept. of Pediatrics, Division of Allergy and Immunology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Christopher J. Gray
- Pediatrics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kosuke Izumi
- Pediatrics, Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - James R. Treat
- Pediatrics, Division of Pediatric Dermatology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathleen H. Wood
- Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, MD, USA
| | - Asya Khleborodova
- NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, MD, USA
| | | | - Xingtian Yang
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Rui Liang
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Lin Kui
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
- Dept. of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Christina Sze Man Wong
- Dept. of Medicine, Divison of Dermatology, The University of Hong Kong, Hong Kong, China
| | - Grace Wing Kit Poon
- Dept. of Paediatrics and Adolescent Medicine, Queen Mary Hospital, Hong Kong, China
| | - Alexander Hoischen
- Dept. of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Jing Yang
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Koon Wing Chan
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Jaime Sou Da Rosa Duque
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Pamela Pui Wah Lee
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Marco Hok Kung Ho
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
- Virtus Medical, Hong Kong, China
| | - Brian Hon Yin Chung
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Huong Thi Minh Le
- Pediatric Center, Vinmec Times City International General Hospital, Hanoi, Vietnam
| | - Wanling Yang
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Pejman Rohani
- Pediatrics, Pediatric Gastroenterology and Hepatology Research Center, Pediatrics Centre of Excellence, Children’s Medical Center, University of Medical Sciences, Tehran, Iran
| | - Ali Fouladvand
- Pediatrics, Allergy and Clinical Immunology, Lorestan University of Medical Sciences, Khoramabad, Iran
| | - Hassan Rokni-Zadeh
- Dept. of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | | | - Mohammad Miryounesi
- Dept. of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris-Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Mohammad Shahrooei
- Microbiology and Immunology, Laboratory of Clinical Bacteriology and Mycology, KU Leuven, Leuven, Belgium
| | - Andrea Finocchi
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Paolo Rossi
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- DPUO, Research Unit of Infectivology and Pediatrics Drugs Development, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Beatrice Rivalta
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Academic Dept. of Pediatrics (DPUO), Unit of Clinical Immunology and Vaccinology, IRCCS Bambin Gesù Children Hospital, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Cristina Cifaldi
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Chiara Passarelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital IRCCS, Rome, Italy
| | - Stefania Arasi
- Allergy Unit, Area of Translational Research in Pediatric Specialities, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Dominique Bullens
- Dept. of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Pediatric Allergy Division, University Hospitals Leuven, Leuven, Belgium
| | - Kate Sauer
- Dept. of Pediatrics, Pediatric Pulmonology Division, AZ Sint-Jan Brugge, Brugge, Belgium
- Dept. of Pediatrics, Pediatric Pulmonology Division, University Hospitals Leuven, Leuven, Belgium
| | - Tania Claeys
- Dept. of Pediatrics, Pediatric Gastroenterology Division, AZ Sint-Jan Brugge, Brugge, Belgium
| | - Catherine M. Biggs
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
| | - Emma C. Morris
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- Dept. of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | | | - John J. O’Shea
- Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, USA
| | - Wyeth W. Wasserman
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
| | - H. Melanie Bedford
- Dept. of Paediatrics, University of Toronto, Toronto, Canada
- Genetics Program, North York General Hospital, Toronto, Canada
| | - Clara D.M. van Karnebeek
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Vancouver, Canada
- Depts. of Pediatrics and Clinical Genetics, Amsterdam University Medical Centers, Amsterdam, Netherlands
| | - Paolo Palma
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Academic Dept. of Pediatrics (DPUO), Unit of Clinical Immunology and Vaccinology, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Siobhan O. Burns
- Institute of Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
- Dept. of Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Isabelle Meyts
- Dept. of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium
- Dept. of Pediatrics, Pediatric Immunodeficiencies Division, University Hospitals Leuven, Leuven, Belgium
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris-Cité, Paris, France
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
- Department of Pediatrics, Necker Hospital for Sick Children, AP-HP, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Jonathan J. Lyons
- Translational Allergic Immunopathology Unit, Laboratory of Allergic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nima Parvaneh
- Department of Pediatrics, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Anh Thi Van Nguyen
- Dept. of Immunology, Allergy and Rheumatology, Division of Primary Immunodeficiency, Vietnam National Children’s Hospital, Hanoi, Vietnam
| | - Caterina Cancrini
- Dept. of System Medicine, Pediatric Chair, University of Tor Vergata, Rome, Italy
- Research Unit of Primary Immunodeficiency, IRCCS Bambin Gesù Children Hospital, Rome, Italy
| | - Jennifer Heimall
- Dept. of Pediatrics, Division of Allergy and Immunology, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Hanan Ahmed
- Faculty of Health Sciences, McMaster University, Hamilton, Canada
| | | | - Yu Lung Lau
- Dept. of Paediatrics and Adolescent Medicine, School of Clinical Medicine, The University of Hong Kong, Hong Kong, China
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, Necker Hospital for Sick Children, Paris, France
- Imagine Institute, University of Paris-Cité, Paris, France
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA
| | - Stuart E. Turvey
- Dept. of Pediatrics, BC Children’s Hospital, University of British Columbia, Vancouver, Canada
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Murty DVPS, Song S, Surampudi SG, Pessoa L. Threat and Reward Imminence Processing in the Human Brain. J Neurosci 2023; 43:2973-2987. [PMID: 36927571 PMCID: PMC10124955 DOI: 10.1523/jneurosci.1778-22.2023] [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: 09/17/2022] [Revised: 03/03/2023] [Accepted: 03/12/2023] [Indexed: 03/18/2023] Open
Abstract
In the human brain, aversive and appetitive processing have been studied with controlled stimuli in rather static settings. In addition, the extent to which aversive-related and appetitive-related processing engage distinct or overlapping circuits remains poorly understood. Here, we sought to investigate the dynamics of aversive and appetitive processing while male and female participants engaged in comparable trials involving threat avoidance or reward seeking. A central goal was to characterize the temporal evolution of responses during periods of threat or reward imminence. For example, in the aversive domain, we predicted that the bed nucleus of the stria terminalis (BST), but not the amygdala, would exhibit anticipatory responses given the role of the former in anxious apprehension. We also predicted that the periaqueductal gray (PAG) would exhibit threat-proximity responses based on its involvement in proximal-threat processes, and that the ventral striatum would exhibit threat-imminence responses given its role in threat escape in rodents. Overall, we uncovered imminence-related temporally increasing ("ramping") responses in multiple brain regions, including the BST, PAG, and ventral striatum, subcortically, and dorsal anterior insula and anterior midcingulate, cortically. Whereas the ventral striatum generated anticipatory responses in the proximity of reward as expected, it also exhibited threat-related imminence responses. In fact, across multiple brain regions, we observed a main effect of arousal. In other words, we uncovered extensive temporally evolving, imminence-related processing in both the aversive and appetitive domain, suggesting that distributed brain circuits are dynamically engaged during the processing of biologically relevant information regardless of valence, findings further supported by network analysis.SIGNIFICANCE STATEMENT In the human brain, aversive and appetitive processing have been studied with controlled stimuli in rather static settings. Here, we sought to investigate the dynamics of aversive/appetitive processing while participants engaged in trials involving threat avoidance or reward seeking. A central goal was to characterize the temporal evolution of responses during periods of threat or reward imminence. We uncovered imminence-related temporally increasing ("ramping") responses in multiple brain regions, including the bed nucleus of the stria terminalis, periaqueductal gray, and ventral striatum, subcortically, and dorsal anterior insula and anterior midcingulate, cortically. Overall, we uncovered extensive temporally evolving, imminence-related processing in both the aversive and appetitive domain, suggesting that distributed brain circuits are dynamically engaged during the processing of biologically relevant information regardless of valence.
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Affiliation(s)
| | - Songtao Song
- Department of Psychology, University of Maryland, College Park, Maryland 20742
| | | | - Luiz Pessoa
- Department of Psychology, University of Maryland, College Park, Maryland 20742
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48
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Hamilton F, Mentzer AJ, Parks T, Baillie JK, Smith GD, Ghazal P, Timpson NJ. Variation in ERAP2 has opposing effects on severe respiratory infection and autoimmune disease. Am J Hum Genet 2023; 110:691-702. [PMID: 36889308 PMCID: PMC10119032 DOI: 10.1016/j.ajhg.2023.02.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/06/2023] [Indexed: 03/09/2023] Open
Abstract
ERAP2 is an aminopeptidase involved in immunological antigen presentation. Genotype data in human samples from before and after the Black Death, an epidemic due to Yersinia pestis, have marked changes in allele frequency of the single-nucleotide polymorphism (SNP) rs2549794, with the T allele suggested to be deleterious during this period, while ERAP2 is also implicated in autoimmune diseases. This study explored the association between variation at ERAP2 and (1) infection, (2) autoimmune disease, and (3) parental longevity. Genome-wide association studies (GWASs) of these outcomes were identified in contemporary cohorts (UK Biobank, FinnGen, and GenOMICC). Effect estimates were extracted for rs2549794 and rs2248374, a haplotype tagging SNP. Additionally, cis expression and protein quantitative trait loci (QTLs) for ERAP2 were used in Mendelian randomization (MR) analyses. Consistent with decreased survival in the Black Death, the T allele of rs2549794 showed evidence of association with respiratory infection (odds ratio; OR for pneumonia 1.03; 95% CI 1.01-1.05). Effect estimates were larger for more severe phenotypes (OR for critical care admission with pneumonia 1.08; 95% CI 1.02-1.14). In contrast, opposing effects were identified for Crohn disease (OR 0.86; 95% CI 0.82-0.90). This allele was shown to associate with decreased ERAP2 expression and protein levels, independent of haplotype. MR analyses suggest that ERAP2 expression may be mediating disease associations. Decreased ERAP2 expression is associated with severe respiratory infection with an opposing association with autoimmune diseases. These data support the hypothesis of balancing selection at this locus driven by autoimmune and infectious disease.
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Affiliation(s)
- Fergus Hamilton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Infection Science, North Bristol NHS Trust, Bristol, UK.
| | | | - Tom Parks
- Wellcome Centre For Human Genetics, University of Oxford, Oxford, UK; Department of Infectious Disease, Imperial College London, London, UK
| | - J Kenneth Baillie
- Baillie Gifford Pandemic Science Hub, Centre for Inflammation Research, University of Edinburgh, Edinburgh, UK; Roslin Institute, University of Edinburgh, Edinburgh, UK; Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, UK
| | | | | | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
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49
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Gupta S, Nerli S, Kandy SK, Mersky GL, Sgourakis NG. HLA3DB: comprehensive annotation of peptide/HLA complexes enables blind structure prediction of T cell epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533510. [PMID: 36993660 PMCID: PMC10055217 DOI: 10.1101/2023.03.20.533510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
The class I proteins of the major histocompatibility complex (MHC-I) display epitopic peptides derived from endogenous proteins on the cell surface for immune surveillance. Accurate modeling of peptide/HLA (pHLA, the human MHC) structures has been mired by conformational diversity of the central peptide residues, which are critical for recognition by T cell receptors. Here, analysis of X-ray crystal structures within a curated database (HLA3DB) shows that pHLA complexes encompassing multiple HLA allotypes present a discrete set of peptide backbone conformations. Leveraging these representative backbones, we employ a regression model trained on terms of a physically relevant energy function to develop a comparative modeling approach for nonamer peptide/HLA structures named RepPred. Our method outperforms the top pHLA modeling approach by up to 19% in terms of structural accuracy, and consistently predicts blind targets not included in our training set. Insights from our work provide a framework for linking conformational diversity with antigen immunogenicity and receptor cross-reactivity.
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Mihaljevic M, Lam M, Ayala-Grosso C, Davis-Batt F, Schretlen DJ, Ishizuka K, Yang K, Sawa A. Olfactory neuronal cells as a promising tool to realize the "druggable genome" approach for drug discovery in neuropsychiatric disorders. Front Neurosci 2023; 16:1081124. [PMID: 36967982 PMCID: PMC10038100 DOI: 10.3389/fnins.2022.1081124] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/26/2022] [Indexed: 03/12/2023] Open
Abstract
"Druggable genome" is a novel concept that emphasizes the importance of using the information of genome-wide genetic studies for drug discovery and development. Successful precedents of "druggable genome" have recently emerged for some disorders by combining genomic and gene expression profiles with medical and pharmacological knowledge. One of the key premises for the success is the good access to disease-relevant tissues from "living" patients in which we may observe molecular expression changes in association with symptomatic alteration. Thus, given brain biopsies are ethically and practically difficult, the application of the "druggable genome" approach is challenging for neuropsychiatric disorders. Here, to fill this gap, we propose the use of olfactory neuronal cells (ONCs) biopsied and established via nasal biopsy from living subjects. By using candidate genes that were proposed in a study in which genetic information, postmortem brain expression profiles, and pharmacological knowledge were considered for cognition in the general population, we addressed the utility of ONCs in the "druggable genome" approach by using the clinical and cell resources of an established psychosis cohort in our group. Through this pilot effort, we underscored the chloride voltage-gated channel 2 (CLCN2) gene as a possible druggable candidate for early-stage psychosis. The CLCN2 gene expression was associated with verbal memory, but not with other dimensions in cognition, nor psychiatric manifestations (positive and negative symptoms). The association between this candidate molecule and verbal memory was also confirmed at the protein level. By using ONCs from living subjects, we now provide more specific information regarding molecular expression and clinical phenotypes. The use of ONCs also provides the opportunity of validating the relationship not only at the RNA level but also protein level, leading to the potential of functional assays in the future. Taken together, we now provide evidence that supports the utility of ONCs as a tool for the "druggable genome" approach in translational psychiatry.
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Affiliation(s)
- Marina Mihaljevic
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Max Lam
- IMH Neuropsychiatric Genomics Laboratory, Institute of Mental Health, Singapore, Singapore
- Population and Global Health, LKC Medicine, Nanyang Technological University, Singapore, Singapore
- Neurogenomic Biomarkers Laboratory, Zucker Hillside Hospital, Glen Oaks, NY, United States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Carlos Ayala-Grosso
- Unit of Cellular Therapy, Centre of Experimental Medicine, Instituto Venezolano de Investigaciones Cientificas IVIC, Caracas, Venezuela
| | - Finn Davis-Batt
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David J. Schretlen
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Koko Ishizuka
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kun Yang
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Akira Sawa
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
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