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Seo J, Gaddis NC, Patchen BK, Xu J, Barr RG, O'Connor G, Manichaikul AW, Gharib SA, Dupuis J, North KE, Cassano PA, Hancock DB. Exploiting meta-analysis of genome-wide interaction with serum 25-hydroxyvitamin D to identify novel genetic loci associated with pulmonary function. Am J Clin Nutr 2024; 119:1227-1237. [PMID: 38484975 PMCID: PMC11130669 DOI: 10.1016/j.ajcnut.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 02/12/2024] [Accepted: 03/07/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Higher 25-hydroxyvitamin D (25(OH)D) concentrations in serum has a positive association with pulmonary function. Investigating genome-wide interactions with 25(OH)D may reveal new biological insights into pulmonary function. OBJECTIVES We aimed to identify novel genetic variants associated with pulmonary function by accounting for 25(OH)D interactions. METHODS We included 211,264 participants from the observational United Kingdom Biobank study with pulmonary function tests (PFTs), genome-wide genotypes, and 25(OH)D concentrations from 4 ancestral backgrounds-European, African, East Asian, and South Asian. Among PFTs, we focused on forced expiratory volume in the first second (FEV1) and forced vital capacity (FVC) because both were previously associated with 25(OH)D. We performed genome-wide association study (GWAS) analyses that accounted for variant×25(OH)D interaction using the joint 2 degree-of-freedom (2df) method, stratified by participants' smoking history and ancestry, and meta-analyzed results. We evaluated interaction effects to determine how variant-PFT associations were modified by 25(OH)D concentrations and conducted pathway enrichment analysis to examine the biological relevance of our findings. RESULTS Our GWAS meta-analyses, accounting for interaction with 25(OH)D, revealed 30 genetic variants significantly associated with FEV1 or FVC (P2df <5.00×10-8) that were not previously reported for PFT-related traits. These novel variant signals were enriched in lung function-relevant pathways, including the p38 MAPK pathway. Among variants with genome-wide-significant 2df results, smoking-stratified meta-analyses identified 5 variants with 25(OH)D interactions that influenced FEV1 in both smoking groups (never smokers P1df interaction<2.65×10-4; ever smokers P1df interaction<1.71×10-5); rs3130553, rs2894186, rs79277477, and rs3130929 associations were only evident in never smokers, and the rs4678408 association was only found in ever smokers. CONCLUSION Genetic variant associations with lung function can be modified by 25(OH)D, and smoking history can further modify variant×25(OH)D interactions. These results expand the known genetic architecture of pulmonary function and add evidence that gene-environment interactions, including with 25(OH)D and smoking, influence lung function.
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Affiliation(s)
- Jungkyun Seo
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Nathan C Gaddis
- RTI International, Research Triangle Park, NC, United States
| | - Bonnie K Patchen
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States
| | - Jiayi Xu
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States
| | - R Graham Barr
- Divisions of Pulmonary, Allergy, and Critical Care Medicine, Columbia University Medical Center, New York, NY, United States
| | - George O'Connor
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, United States
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, United States; Division of Pulmonary, Critical Care and Sleep Medicine, Computational Medicine Core, Center for Lung Biology, University of Washington, Seattle, WA, United States
| | - Josée Dupuis
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Kari E North
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States
| | - Patricia A Cassano
- Division of Nutritional Sciences, Cornell University, Ithaca, NY, United States; Division of Epidemiology, Department of Population Health Sciences, Weill Cornell Medicine, NY, United States
| | - Dana B Hancock
- RTI International, Research Triangle Park, NC, United States.
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Werder RB, Zhou X, Cho MH, Wilson AA. Breathing new life into the study of COPD with genes identified from genome-wide association studies. Eur Respir Rev 2024; 33:240019. [PMID: 38811034 PMCID: PMC11134200 DOI: 10.1183/16000617.0019-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 05/31/2024] Open
Abstract
COPD is a major cause of morbidity and mortality globally. While the significance of environmental exposures in disease pathogenesis is well established, the functional contribution of genetic factors has only in recent years drawn attention. Notably, many genes associated with COPD risk are also linked with lung function. Because reduced lung function precedes COPD onset, this association is consistent with the possibility that derangements leading to COPD could arise during lung development. In this review, we summarise the role of leading genes (HHIP, FAM13A, DSP, AGER and TGFB2) identified by genome-wide association studies in lung development and COPD. Because many COPD genome-wide association study genes are enriched in lung epithelial cells, we focus on the role of these genes in the lung epithelium in development, homeostasis and injury.
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Affiliation(s)
- Rhiannon B Werder
- Murdoch Children's Research Institute, Melbourne, Australia
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA, USA
- The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA, USA
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3
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Gao J, Yang Y, Xiang X, Zheng H, Yi X, Wang F, Liang Z, Chen D, Shi W, Wang L, Wu D, Feng S, Huang Q, Li X, Shu W, Chen R, Zhong N, Wang Z. Human genetic associations of the airway microbiome in chronic obstructive pulmonary disease. Respir Res 2024; 25:165. [PMID: 38622589 DOI: 10.1186/s12931-024-02805-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Little is known about the relationships between human genetics and the airway microbiome. Deeply sequenced airway metagenomics, by simultaneously characterizing the microbiome and host genetics, provide a unique opportunity to assess the microbiome-host genetic associations. Here we performed a co-profiling of microbiome and host genetics with the identification of over 5 million single nucleotide polymorphisms (SNPs) through deep metagenomic sequencing in sputum of 99 chronic obstructive pulmonary disease (COPD) and 36 healthy individuals. Host genetic variation was the most significant factor associated with the microbiome except for geography and disease status, with its top 5 principal components accounting for 12.11% of the microbiome variability. Within COPD individuals, 113 SNPs mapped to candidate genes reported as genetically associated with COPD exhibited associations with 29 microbial species and 48 functional modules (P < 1 × 10-5), where Streptococcus salivarius exhibits the strongest association to SNP rs6917641 in TBC1D32 (P = 9.54 × 10-8). Integration of concurrent host transcriptomic data identified correlations between the expression of host genes and their genetically-linked microbiome features, including NUDT1, MAD1L1 and Veillonella parvula, TTLL9 and Stenotrophomonas maltophilia, and LTA4H and Haemophilus influenzae. Mendelian randomization analyses revealed a potential causal link between PARK7 expression and microbial type III secretion system, and a genetically-mediated association between COPD and increased relative abundance of airway Streptococcus intermedius. These results suggest a previously underappreciated role of host genetics in shaping the airway microbiome and provide fresh hypotheses for genetic-based host-microbiome interactions in COPD.
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Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Yuqiong Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xiaopeng Xiang
- The Hong Kong Polytechnic University, Hong Kong, Hung Hom Kowloon, China
| | - Huimin Zheng
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Fengyan Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zhenyu Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Dandan Chen
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Weijuan Shi
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Lingwei Wang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Di Wu
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shengchuan Feng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Qiaoyun Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xueping Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Wensheng Shu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China.
| | - Rongchang Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China.
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China.
| | - Zhang Wang
- Institute of Ecological Sciences, Biomedical Research Center, School of Life Sciences, State Key Laboratory of Respiratory Disease, South China Normal University, Guangzhou, Guangdong Province, China.
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4
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Wang Z, Li S, Cai G, Gao Y, Yang H, Li Y, Liang J, Zhang S, Hu J, Zheng J. Mendelian randomization analysis identifies druggable genes and drugs repurposing for chronic obstructive pulmonary disease. Front Cell Infect Microbiol 2024; 14:1386506. [PMID: 38660492 PMCID: PMC11039854 DOI: 10.3389/fcimb.2024.1386506] [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: 02/15/2024] [Accepted: 03/22/2024] [Indexed: 04/26/2024] Open
Abstract
Background Chronic obstructive pulmonary disease (COPD) is a prevalent condition that significantly impacts public health. Unfortunately, there are few effective treatment options available. Mendelian randomization (MR) has been utilized to repurpose existing drugs and identify new therapeutic targets. The objective of this study is to identify novel therapeutic targets for COPD. Methods Cis-expression quantitative trait loci (cis-eQTL) were extracted for 4,317 identified druggable genes from genomics and proteomics data of whole blood (eQTLGen) and lung tissue (GTEx Consortium). Genome-wide association studies (GWAS) data for doctor-diagnosed COPD, spirometry-defined COPD (Forced Expiratory Volume in one second [FEV1]/Forced Vital Capacity [FVC] <0.7), and FEV1 were obtained from the cohort of FinnGen, UK Biobank and SpiroMeta consortium. We employed Summary-data-based Mendelian Randomization (SMR), HEIDI test, and colocalization analysis to assess the causal effects of druggable gene expression on COPD and lung function. The reliability of these druggable genes was confirmed by eQTL two-sample MR and protein quantitative trait loci (pQTL) SMR, respectively. The potential effects of druggable genes were assessed through the phenome-wide association study (PheWAS). Information on drug repurposing for COPD was collected from multiple databases. Results A total of 31 potential druggable genes associated with doctor-diagnosed COPD, spirometry-defined COPD, and FEV1 were identified through SMR, HEIDI test, and colocalization analysis. Among them, 22 genes (e.g., MMP15, PSMA4, ERBB3, and LMCD1) were further confirmed by eQTL two-sample MR and protein SMR analyses. Gene-level PheWAS revealed that ERBB3 expression might reduce inflammation, while GP9 and MRC2 were associated with other traits. The drugs Montelukast (targeting the MMP15 gene) and MARIZOMIB (targeting the PSMA4 gene) may reduce the risk of spirometry-defined COPD. Additionally, an existing small molecule inhibitor of the APH1A gene has the potential to increase FEV1. Conclusions Our findings identified 22 potential drug targets for COPD and lung function. Prioritizing clinical trials that target these identified druggable genes with existing drugs or novel medications will be beneficial for the development of COPD treatments.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jinping Zheng
- National Center for Respiratory Medicine, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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5
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Li H, House J, Nichols C, Gruzdev A, Ward J, Li JL, Wyss A, Haque E, Edin M, Elmore S, Mahler B, Degraff L, Shi M, Zeldin D, London S. Adam19 Deficiency Impacts Pulmonary Function: Human GWAS Follow-up in Mouse. RESEARCH SQUARE 2024:rs.3.rs-4207678. [PMID: 38659817 PMCID: PMC11042436 DOI: 10.21203/rs.3.rs-4207678/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Purpose Over 550 loci have been associated with human pulmonary function in genome-wide association studies (GWAS); however, the causal role of most remains uncertain. Single nucleotide polymorphisms in a disintegrin and metalloprotease domain 19 (ADAM19) are consistently related to pulmonary function in GWAS. Thus, we used a mouse model to investigate the causal link between Adam19 and pulmonary function. Methods We created an Adam19 knockout (KO) mouse model and validated the gene targeting using RNA-Seq and RT-qPCR. Contrary to prior publications, the KO was not neonatal lethal. Thus, we phenotyped the Adam19 KO. Results KO mice had lower body weight and shorter tibial length than wild type (WT). Dual-energy X-ray Absorptiometry indicated lower soft weight, fat weight, and bone mineral content in KO mice. In lung function analyses using flexiVent, compared to WT, Adam19 KO had decreased baseline respiratory system elastance, minute work of breathing, tissue damping, tissue elastance, and forced expiratory flow at 50% forced vital capacity but higher FEV0.1 and FVC. Adam19 KO had attenuated tissue damping and tissue elastance in response to methacholine following LPS exposure. Adam19 KO also exhibited attenuated neutrophil extravasation into the airway after LPS administration compared to WT. RNA-Seq analysis of KO and WT lungs identified several differentially expressed genes (Cd300lg, Kpna2, and Pttg1) implicated in lung biology and pathogenesis. Gene set enrichment analysis identified negative enrichment for TNF pathways. Conclusion Our murine findings support a causal role of ADAM19, implicated in human GWAS, in regulating pulmonary function.
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Affiliation(s)
- Huiling Li
- National Institute of Environmental Health Sciences
| | - John House
- National Institute of Environmental Health Sciences
| | | | | | - James Ward
- National Institute of Environmental Health Sciences
| | | | | | - Ezazul Haque
- National Institute of Environmental Health Sciences
| | - Matthew Edin
- National Institute of Environmental Health Sciences
| | - Susan Elmore
- National Institute of Environmental Health Sciences
| | - Beth Mahler
- National Institute of Environmental Health Sciences
| | | | - Min Shi
- National Institute of Environmental Health Sciences
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6
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Kato A, Pipil S, Ota C, Kusakabe M, Watanabe T, Nagashima A, Chen AP, Islam Z, Hayashi N, Wong MKS, Komada M, Romero MF, Takei Y. Convergent gene losses and pseudogenizations in multiple lineages of stomachless fishes. Commun Biol 2024; 7:408. [PMID: 38570609 PMCID: PMC10991444 DOI: 10.1038/s42003-024-06103-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 03/25/2024] [Indexed: 04/05/2024] Open
Abstract
The regressive evolution of independent lineages often results in convergent phenotypes. Several teleost groups display secondary loss of the stomach, and four gastric genes, atp4a, atp4b, pgc, and pga2 have been co-deleted in agastric (stomachless) fish. Analyses of genotypic convergence among agastric fishes showed that four genes, slc26a9, kcne2, cldn18a, and vsig1, were co-deleted or pseudogenized in most agastric fishes of the four major groups. kcne2 and vsig1 were also deleted or pseudogenized in the agastric monotreme echidna and platypus, respectively. In the stomachs of sticklebacks, these genes are expressed in gastric gland cells or surface epithelial cells. An ohnolog of cldn18 was retained in some agastric teleosts but exhibited an increased non-synonymous substitution when compared with gastric species. These results revealed novel convergent gene losses at multiple loci among the four major groups of agastric fish, as well as a single gene loss in the echidna and platypus.
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Affiliation(s)
- Akira Kato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan.
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan.
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Japan.
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA.
| | - Supriya Pipil
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Chihiro Ota
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Makoto Kusakabe
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Department of Biological Sciences, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Taro Watanabe
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
| | - Ayumi Nagashima
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - An-Ping Chen
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
| | - Zinia Islam
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | - Naoko Hayashi
- Department of Biological Sciences, Tokyo Institute of Technology, Yokohama, Japan
| | - Marty Kwok-Shing Wong
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
- Department of Biomolecular Science, Toho University, Funabashi, Japan
| | - Masayuki Komada
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Michael F Romero
- Department of Physiology & Biomedical Engineering, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
- Department of Nephrology & Hypertension, Mayo Clinic College of Medicine & Science, Rochester, MN, USA
| | - Yoshio Takei
- Department of Marine Bioscience, Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, Japan
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7
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Sayers I, John C, Chen J, Hall IP. Genetics of chronic respiratory disease. Nat Rev Genet 2024:10.1038/s41576-024-00695-0. [PMID: 38448562 DOI: 10.1038/s41576-024-00695-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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8
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Wang Y, Pan H, Gong X, Wang Z, Qin X, Zhou S, Zhu C, Hu X, Chen S, Liu H, Jin H, Pang Q, Wu W. CDC123 promotes Hepatocellular Carcinoma malignant progression by regulating CDKAL1. Pathol Res Pract 2024; 254:154987. [PMID: 38237400 DOI: 10.1016/j.prp.2023.154987] [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: 06/29/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 02/12/2024]
Abstract
The cell proliferation protein 123 (CDC123) is involved in the synthesis of the eukaryotic initiation factor 2 (eIF2), which regulates eukaryotic translation. Although CDC123 is considered a candidate oncogene in breast cancer, its expression and role in Hepatocellular Carcinoma (HCC) remain unknown. Herein, we obtained the CDC123 RNA-seq and clinical prognostic data from the TCGA database. The mRNA level revealed that CDC123 was highly expressed in HCC patients, and Kaplan-Meier analysis implied better prognoses in HCC patients with low CDC123 expression (P < 0.001). The multivariate Cox analysis revealed that the CDC123 level was an independent prognostic factor (P < 0.001). We further confirmed a high CDC123 expression in HCC cell lines. Additionally, we found that CDC123 knockdown in HCC cell lines significantly inhibited cellular proliferation, invasion, and migration. Moreover, CDC123 was co-expressed with the CDK5 Regulatory Subunit-Associated Protein 1 Like 1 (CDKAL1), whose mRNA level was decreased after silencing CDC123. Therefore, we hypothesized that CDC123 promotes HCC progression by regulating CDKAL1.
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Affiliation(s)
- Yong Wang
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - HongTao Pan
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - XuanKun Gong
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China; Department of Hepatobiliary Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - ZhiCheng Wang
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China; Department of Hepatobiliary Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - XiLiang Qin
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China; Department of Hepatobiliary Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China
| | - Shuai Zhou
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - Chao Zhu
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - XiaoSi Hu
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - ShiLei Chen
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - HuiChun Liu
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - Hao Jin
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China
| | - Qing Pang
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China; Department of Hepatobiliary Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China.
| | - WenYong Wu
- The Clinical College, Anhui No.2 Provincial People's Hospital, Anhui Medical University, Hefei 230041, Anhui, China; Department of Hepatobiliary Surgery, the First Affiliated Hospital of Bengbu Medical College, Bengbu 233000, Anhui, China.
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9
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Werder RB, Berthiaume KA, Merritt C, Gallagher M, Villacorta-Martin C, Wang F, Bawa P, Malik V, Lyons SM, Basil MC, Morrisey EE, Kotton DN, Zhou X, Cho MH, Wilson AA. The COPD GWAS gene ADGRG6 instructs function and injury response in human iPSC-derived type II alveolar epithelial cells. Am J Hum Genet 2023; 110:1735-1749. [PMID: 37734371 PMCID: PMC10577075 DOI: 10.1016/j.ajhg.2023.08.017] [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: 03/31/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/23/2023] Open
Abstract
Emphysema and chronic obstructive pulmonary disease (COPD) most commonly result from the effects of environmental exposures in genetically susceptible individuals. Genome-wide association studies have implicated ADGRG6 in COPD and reduced lung function, and a limited number of studies have examined the role of ADGRG6 in cells representative of the airway. However, the ADGRG6 locus is also associated with DLCO/VA, an indicator of gas exchange efficiency and alveolar function. Here, we sought to evaluate the mechanistic contributions of ADGRG6 to homeostatic function and disease in type 2 alveolar epithelial cells. We applied an inducible CRISPR interference (CRISPRi) human induced pluripotent stem cell (iPSC) platform to explore ADGRG6 function in iPSC-derived AT2s (iAT2s). We demonstrate that ADGRG6 exerts pleiotropic effects on iAT2s including regulation of focal adhesions, cytoskeleton, tight junctions, and proliferation. Moreover, we find that ADGRG6 knockdown in cigarette smoke-exposed iAT2s alters cellular responses to injury, downregulating apical complexes in favor of proliferation. Our work functionally characterizes the COPD GWAS gene ADGRG6 in human alveolar epithelium.
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Affiliation(s)
- Rhiannon B Werder
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Kayleigh A Berthiaume
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Carly Merritt
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marissa Gallagher
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Carlos Villacorta-Martin
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Feiya Wang
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Pushpinder Bawa
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Vidhi Malik
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Shawn M Lyons
- Biochemistry Department, Boston University School of Medicine, Boston, MA 02118, USA
| | - Maria C Basil
- School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Edward E Morrisey
- School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Darrell N Kotton
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew A Wilson
- Center for Regenerative Medicine of Boston University and Boston Medical Center, Boston, MA 02118, USA; The Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA.
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10
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Guyatt A, John C, Williams AT, Shrine N, Reeve NF, Sayers I, Hall I, Wain LV, Sheehan N, Dudbridge F, Tobin MD. Mendelian randomisation of eosinophils and other cell types in relation to lung function and disease. Thorax 2023; 78:496-503. [PMID: 35537820 PMCID: PMC10176352 DOI: 10.1136/thoraxjnl-2021-217993] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/09/2022] [Indexed: 11/04/2022]
Abstract
RATIONALE Eosinophils are associated with airway inflammation in respiratory disease. Eosinophil production and survival is controlled partly by interleukin-5: anti-interleukin-5 agents reduce asthma and response correlates with baseline eosinophil counts. However, whether raised eosinophils are causally related to chronic obstructive pulmonary disease (COPD) and other respiratory phenotypes is not well understood. OBJECTIVES We investigated causality between eosinophils and: lung function, acute exacerbations of COPD, asthma-COPD overlap (ACO), moderate-to-severe asthma and respiratory infections. METHODS We performed Mendelian randomisation (MR) using 151 variants from genome-wide association studies of blood eosinophils in UK Biobank/INTERVAL, and respiratory traits in UK Biobank/SpiroMeta, using methods relying on different assumptions for validity. We performed multivariable analyses using eight cell types where there was possible evidence of causation by eosinophils. MEASUREMENTS AND MAIN RESULTS Causal estimates derived from individual variants were highly heterogeneous, which may arise from pleiotropy. The average effect of raising eosinophils was to increase risk of ACO (weighted median OR per SD eosinophils, 1.44 (95%CI 1.19 to 1.74)), and moderate-severe asthma (weighted median OR 1.50 (95%CI 1.23 to 1.83)), and to reduce forced expiratory volume in 1 s (FEV1)/forced vital capacity (FVC) and FEV1 (weighted median estimator, SD FEV1/FVC: -0.054 (95% CI -0.078 to -0.029), effect only prominent in individuals with asthma). CONCLUSIONS Broad consistency across MR methods may suggest causation by eosinophils (although of uncertain magnitude), yet heterogeneity necessitates caution: other important mechanisms may be responsible for the impairment of respiratory health by these eosinophil-raising variants. These results could suggest that anti-IL5 agents (designed to lower eosinophils) may be valuable in treating other respiratory conditions, including people with overlapping features of asthma and COPD.
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Affiliation(s)
- Anna Guyatt
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Catherine John
- Department of Health Sciences, University of Leicester, Leicester, UK
| | | | - Nick Shrine
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Nicola F Reeve
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Ian Sayers
- Division of Respiratory Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Ian Hall
- Division of Respiratory Medicine, University of Nottingham, Nottingham, UK
- NIHR Nottingham Biomedical Research Centre, University of Nottingham, Nottingham, UK
| | - Louise V Wain
- Department of Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
| | - Nuala Sheehan
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Frank Dudbridge
- Department of Health Sciences, University of Leicester, Leicester, UK
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester, UK
- NIHR Leicester Biomedical Research Centre, University of Leicester, Leicester, UK
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11
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Jiang J, Xu S, Chen Z, Liu W, Zhang L, Li J, Zhu Z, Zhou L. Animal models: An essential tool to dissect the heterogeneity of chronic obstructive pulmonary disease. J Transl Int Med 2023; 11:4-10. [PMID: 37533843 PMCID: PMC10393054 DOI: 10.2478/jtim-2023-0007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2023] Open
Affiliation(s)
- Jingxian Jiang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing210029, Jiangsu Province, China
| | - Shuanglan Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing210029, Jiangsu Province, China
| | - Zi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing210029, Jiangsu Province, China
| | - Weihua Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing210029, Jiangsu Province, China
| | - Liuchao Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing210029, Jiangsu Province, China
| | - Jianmin Li
- Animal Core Facility, Key Laboratory of Model Animal, Nanjing Medical University, Nanjing211166, Jiangsu Province, China
| | - Zhou Zhu
- Department of Pediatrics and Department of Molecular Microbiology and Immunology, Brown University Warren Alpert Medical School, Providence, RI02912, USA
| | - Linfu Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Nanjing Medical University, Nanjing210029, Jiangsu Province, China
- Animal Core Facility, Key Laboratory of Model Animal, Nanjing Medical University, Nanjing211166, Jiangsu Province, China
- Institute of Integrative Medicine, Nanjing Medical University, Nanjing210029, Jiangsu Province, China
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12
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Dapas M, Thompson EE, Wentworth-Sheilds W, Clay S, Visness CM, Calatroni A, Sordillo JE, Gold DR, Wood RA, Makhija M, Khurana Hershey GK, Sherenian MG, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Altman MC, Busse WW, Becker PM, Nicolae D, O’Connor GT, Gern JE, Jackson DJ, Ober C. Multi-omic association study identifies DNA methylation-mediated genotype and smoking exposure effects on lung function in children living in urban settings. PLoS Genet 2023; 19:e1010594. [PMID: 36638096 PMCID: PMC9879483 DOI: 10.1371/journal.pgen.1010594] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 01/26/2023] [Accepted: 12/23/2022] [Indexed: 01/14/2023] Open
Abstract
Impaired lung function in early life is associated with the subsequent development of chronic respiratory disease. Most genetic associations with lung function have been identified in adults of European descent and therefore may not represent those most relevant to pediatric populations and populations of different ancestries. In this study, we performed genome-wide association analyses of lung function in a multiethnic cohort of children (n = 1,035) living in low-income urban neighborhoods. We identified one novel locus at the TDRD9 gene in chromosome 14q32.33 associated with percent predicted forced expiratory volume in one second (FEV1) (p = 2.4x10-9; βz = -0.31, 95% CI = -0.41- -0.21). Mendelian randomization and mediation analyses revealed that this genetic effect on FEV1 was partially mediated by DNA methylation levels at this locus in airway epithelial cells, which were also associated with environmental tobacco smoke exposure (p = 0.015). Promoter-enhancer interactions in airway epithelial cells revealed chromatin interaction loops between FEV1-associated variants in TDRD9 and the promoter region of the PPP1R13B gene, a stimulator of p53-mediated apoptosis. Expression of PPP1R13B in airway epithelial cells was significantly associated the FEV1 risk alleles (p = 1.3x10-5; β = 0.12, 95% CI = 0.06-0.17). These combined results highlight a potential novel mechanism for reduced lung function in urban youth resulting from both genetics and smoking exposure.
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Affiliation(s)
- Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | - Emma E. Thompson
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | - Selene Clay
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
| | | | | | - Joanne E. Sordillo
- Department of Population Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Diane R. Gold
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robert A. Wood
- Department of Pediatrics, Johns Hopkins University Medical Center, Baltimore, Maryland, United States of America
| | - Melanie Makhija
- Division of Allergy and Immunology, Ann & Robert H. Lurie Children’s Hospital, Chicago, Illinois, United States of America
| | - Gurjit K. Khurana Hershey
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Michael G. Sherenian
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio, United States of America
- Division of Asthma Research, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio, United States of America
| | - Rebecca S. Gruchalla
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Michelle A. Gill
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Andrew H. Liu
- Department of Allergy and Immunology, Children’s Hospital Colorado, University of Colorado School of Medicine, Aurora, Colorado, United States of America
| | - Haejin Kim
- Department of Medicine, Henry Ford Health System, Detroit, Michigan, United States of America
| | - Meyer Kattan
- Columbia University College of Physicians and Surgeons, New York, New York, United States of America
| | - Leonard B. Bacharier
- Monroe Carell Jr. Children’s Hospital at Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Deepa Rastogi
- Children’s National Health System, Washington, District of Columbia, United States of America
| | - Matthew C. Altman
- Department of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - William W. Busse
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Patrice M. Becker
- National Institute of Allergy and Infectious Diseases, Bethesda, Maryland, United States of America
| | - Dan Nicolae
- Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
| | - George T. O’Connor
- Pulmonary Center, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - James E. Gern
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Daniel J. Jackson
- Department of Pediatrics and Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago Illinois, United States of America
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13
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The Biology and Function of Tissue Inhibitor of Metalloproteinase 2 in the Lungs. Pulm Med 2022; 2022:3632764. [PMID: 36624735 PMCID: PMC9825218 DOI: 10.1155/2022/3632764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 01/02/2023] Open
Abstract
Tissue inhibitors of matrix metalloproteinases (TIMP) are a family of four endogenous proteins that primarily function to inhibit the activities of proteases such as the matrix metalloproteinases (MMP). Altered MMP/TIMP ratios are frequently observed in several human diseases. During aging and disease progression, the extracellular matrix (ECM) undergoes structural changes in which elastin and collagens serve an essential role. MMPs and TIMPs significantly influence the ECM. Classically, elevated levels of TIMPs are suggested to result in ECM accumulation leading to fibrosis, whereas loss of TIMP responses leads to enhanced matrix proteolysis. Here, we outline the known roles of the most abundant TIMP, TIMP2, in pulmonary diseases but also discuss future perspectives in TIMP2 research that could impact the lungs. TIMP2 directly inhibits MMPs, in particular MMP2, but TIMP2 is also required for the activation of MMP2 through its interaction with MMP14. The protease and antiprotease imbalance of MMPs and TIMPs are extensively studied in diseases but recent discoveries suggest that TIMPs, specifically, TIMP2 could play other roles in aging and inflammation processes.
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14
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Ahmed WUR, Patel MIA, Ng M, McVeigh J, Zondervan K, Wiberg A, Furniss D. Shared genetic architecture of hernias: A genome-wide association study with multivariable meta-analysis of multiple hernia phenotypes. PLoS One 2022; 17:e0272261. [PMID: 36584111 PMCID: PMC9803250 DOI: 10.1371/journal.pone.0272261] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/14/2022] [Indexed: 12/31/2022] Open
Abstract
Abdominal hernias are common and characterised by the abnormal protrusion of a viscus through the wall of the abdominal cavity. The global incidence is 18.5 million annually and there are limited non-surgical treatments. To improve understanding of common hernia aetiopathology, we performed a six-stage genome-wide association study (GWAS) of 62,637 UK Biobank participants with either single or multiple hernia phenotypes including inguinal, femoral, umbilical and hiatus hernia. Additionally, we performed multivariable meta-analysis with metaUSAT, to allow integration of summary data across traits to generate combined effect estimates. On individual hernia analysis, we identified 3404 variants across 38 genome-wide significant (p < 5×10-8) loci of which 11 are previously unreported. Robust evidence for five shared susceptibility loci was discovered: ZC3H11B, EFEMP1, MHC region, WT1 and CALD1. Combined hernia phenotype analyses with additional multivariable meta-analysis of summary statistics in metaUSAT revealed 28 independent (seven previously unreported) shared susceptibility loci. These clustered in functional categories related to connective tissue and elastic fibre homeostasis. Weighted genetic risk scores also correlated with disease severity suggesting a phenotypic-genotypic severity correlation, an important finding to inform future personalised therapeutic approaches to hernia.
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Affiliation(s)
- Waheed Ul-Rahman Ahmed
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Manal I. A. Patel
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Michael Ng
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - James McVeigh
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Krina Zondervan
- Nuffield Department of Women’s & Reproductive Health, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Akira Wiberg
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
- Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Dominic Furniss
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
- Department of Plastic and Reconstructive Surgery, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- * E-mail:
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15
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Wang X, Guo Z, Yan F. RNA Epigenetics in Chronic Lung Diseases. Genes (Basel) 2022; 13:genes13122381. [PMID: 36553648 PMCID: PMC9777603 DOI: 10.3390/genes13122381] [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: 10/07/2022] [Revised: 11/29/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Chronic lung diseases are highly prevalent worldwide and cause significant mortality. Lung cancer is the end stage of many chronic lung diseases. RNA epigenetics can dynamically modulate gene expression and decide cell fate. Recently, studies have confirmed that RNA epigenetics plays a crucial role in the developing of chronic lung diseases. Further exploration of the underlying mechanisms of RNA epigenetics in chronic lung diseases, including lung cancer, may lead to a better understanding of the diseases and promote the development of new biomarkers and therapeutic strategies. This article reviews basic information on RNA modifications, including N6 methylation of adenosine (m6A), N1 methylation of adenosine (m1A), N7-methylguanosine (m7G), 5-methylcytosine (m5C), 2'O-methylation (2'-O-Me or Nm), pseudouridine (5-ribosyl uracil or Ψ), and adenosine to inosine RNA editing (A-to-I editing). We then show how they relate to different types of lung disease. This paper hopes to summarize the mechanisms of RNA modification in chronic lung disease and finds a new way to develop early diagnosis and treatment of chronic lung disease.
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Affiliation(s)
- Xiaorui Wang
- Department of Ophthalmology, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
| | - Zhihou Guo
- Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
| | - Furong Yan
- Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362002, China
- Correspondence:
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16
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Abstract
The assembly and maintenance of most cilia and eukaryotic flagella depends on intraflagellar transport (IFT), the bidirectional movement of multi-megadalton IFT trains along the axonemal microtubules. These IFT trains function as carriers, moving ciliary proteins between the cell body and the organelle. Whereas tubulin, the principal protein of cilia, binds directly to IFT particle proteins, the transport of other ciliary proteins and complexes requires adapters that link them to the trains. Large axonemal substructures, such as radial spokes, outer dynein arms and inner dynein arms, assemble in the cell body before attaching to IFT trains, using the adapters ARMC2, ODA16 and IDA3, respectively. Ciliary import of several membrane proteins involves the putative adapter tubby-like protein 3 (TULP3), whereas membrane protein export involves the BBSome, an octameric complex that co-migrates with IFT particles. Thus, cells employ a variety of adapters, each of which is substoichiometric to the core IFT machinery, to expand the cargo range of the IFT trains. This Review summarizes the individual and shared features of the known cargo adapters and discusses their possible role in regulating the transport capacity of the IFT pathway.
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Affiliation(s)
- Karl Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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17
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Lahmar Z, Ahmed E, Fort A, Vachier I, Bourdin A, Bergougnoux A. Hedgehog pathway and its inhibitors in chronic obstructive pulmonary disease (COPD). Pharmacol Ther 2022; 240:108295. [PMID: 36191777 DOI: 10.1016/j.pharmthera.2022.108295] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 08/22/2022] [Accepted: 09/28/2022] [Indexed: 11/05/2022]
Abstract
COPD affects millions of people and is now ranked as the third leading cause of death worldwide. This largely untreatable chronic airway disease results in irreversible destruction of lung architecture. The small lung hypothesis is now supported by epidemiological, physiological and clinical studies. Accordingly, the early and severe COPD phenotype carries the most dreadful prognosis and finds its roots during lung growth. Pathophysiological mechanisms remain poorly understood and implicate individual susceptibility (genetics), a large part of environmental factors (viral infections, tobacco consumption, air pollution) and the combined effects of those triggers on gene expression. Genetic susceptibility is most likely involved as the disease is severe and starts early in life. The latter observation led to the identification of Mendelian inheritance via disease-causing variants of SERPINA1 - known as the basis for alpha-1 anti-trypsin deficiency, and TERT. In the last two decades multiple genome wide association studies (GWAS) identified many single nucleotide polymorphisms (SNPs) associated with COPD. High significance SNPs are located in 4q31 near HHIP which encodes an evolutionarily highly conserved physiological inhibitor of the Hedgehog signaling pathway (HH). HHIP is critical to several in utero developmental lung processes. It is also implicated in homeostasis, injury response, epithelial-mesenchymal transition and tumor resistance to apoptosis. A few studies have reported decreased HHIP RNA and protein levels in human adult COPD lungs. HHIP+/- murine models led to emphysema. HH pathway inhibitors, such as vismodegib and sonidegib, are already validated in oncology, whereas other drugs have evidenced in vitro effects. Targeting the Hedgehog pathway could lead to a new therapeutic avenue in COPD. In this review, we focused on the early and severe COPD phenotype and the small lung hypothesis by exploring genetic susceptibility traits that are potentially treatable, thus summarizing promising therapeutics for the future.
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Affiliation(s)
- Z Lahmar
- Department of Respiratory Diseases, CHU de Montpellier, Montpellier, France
| | - E Ahmed
- Department of Respiratory Diseases, CHU de Montpellier, Montpellier, France; PhyMedExp, Univ Montpellier, Inserm U1046, CNRS UMR 9214, Montpellier, France
| | - A Fort
- PhyMedExp, Univ Montpellier, Inserm U1046, CNRS UMR 9214, Montpellier, France
| | - I Vachier
- Department of Respiratory Diseases, CHU de Montpellier, Montpellier, France; PhyMedExp, Univ Montpellier, Inserm U1046, CNRS UMR 9214, Montpellier, France
| | - A Bourdin
- Department of Respiratory Diseases, CHU de Montpellier, Montpellier, France; PhyMedExp, Univ Montpellier, Inserm U1046, CNRS UMR 9214, Montpellier, France
| | - A Bergougnoux
- PhyMedExp, Univ Montpellier, Inserm U1046, CNRS UMR 9214, Montpellier, France; Laboratoire de Génétique Moléculaire et de Cytogénomique, CHU de Montpellier, Montpellier, France.
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18
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Caligiuri SPB, Howe WM, Wills L, Smith ACW, Lei Y, Bali P, Heyer MP, Moen JK, Ables JL, Elayouby KS, Williams M, Fillinger C, Oketokoun Z, Lehmann VE, DiFeliceantonio AG, Johnson PM, Beaumont K, Sebra RP, Ibanez-Tallon I, Kenny PJ. Hedgehog-interacting protein acts in the habenula to regulate nicotine intake. Proc Natl Acad Sci U S A 2022; 119:e2209870119. [PMID: 36346845 PMCID: PMC9674224 DOI: 10.1073/pnas.2209870119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/28/2022] [Indexed: 11/10/2023] Open
Abstract
Hedgehog-interacting protein (HHIP) sequesters Hedgehog ligands to repress Smoothened (SMO)-mediated recruitment of the GLI family of transcription factors. Allelic variation in HHIP confers risk of chronic obstructive pulmonary disease and other smoking-related lung diseases, but underlying mechanisms are unclear. Using single-cell and cell-type-specific translational profiling, we show that HHIP expression is highly enriched in medial habenula (MHb) neurons, particularly MHb cholinergic neurons that regulate aversive behavioral responses to nicotine. HHIP deficiency dysregulated the expression of genes involved in cholinergic signaling in the MHb and disrupted the function of nicotinic acetylcholine receptors (nAChRs) through a PTCH-1/cholesterol-dependent mechanism. Further, CRISPR/Cas9-mediated genomic cleavage of the Hhip gene in MHb neurons enhanced the motivational properties of nicotine in mice. These findings suggest that HHIP influences vulnerability to smoking-related lung diseases in part by regulating the actions of nicotine on habenular aversion circuits.
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Affiliation(s)
- Stephanie P B Caligiuri
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - William M Howe
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Lauren Wills
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Alexander C W Smith
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ye Lei
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Purva Bali
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Mary P Heyer
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Janna K Moen
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jessica L Ables
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Karim S Elayouby
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Maya Williams
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Clementine Fillinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Zainab Oketokoun
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Vanessa E Lehmann
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | | | - Paul M Johnson
- Department of Information Technology and Electrical Engineering, ETH Zürich, 8092 Zürich, Switzerland
| | - Kristin Beaumont
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ines Ibanez-Tallon
- Laboratory of Molecular Biology, The Rockefeller University, New York, NY 10065
| | - Paul J Kenny
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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19
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Abbott GW. Kv Channel Ancillary Subunits: Where Do We Go from Here? Physiology (Bethesda) 2022; 37:0. [PMID: 35797055 PMCID: PMC9394777 DOI: 10.1152/physiol.00005.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 01/10/2023] Open
Abstract
Voltage-gated potassium (Kv) channels each comprise four pore-forming α-subunits that orchestrate essential duties such as voltage sensing and K+ selectivity and conductance. In vivo, however, Kv channels also incorporate regulatory subunits-some Kv channel specific, others more general modifiers of protein folding, trafficking, and function. Understanding all the above is essential for a complete picture of the role of Kv channels in physiology and disease.
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Affiliation(s)
- Geoffrey W Abbott
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California
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20
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Zhou Y, Qiu J, Liu S, Wang P, Ma D, Zhang G, Cao Y, Hu L, Wang Z, Wu J, Jiang C. CFDP1 promotes hepatocellular carcinoma progression through activating NEDD4/PTEN/PI3K/AKT signaling pathway. Cancer Med 2022; 12:425-444. [PMID: 35861040 PMCID: PMC9844661 DOI: 10.1002/cam4.4919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/06/2022] [Accepted: 05/24/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND AND AIMS It is being increasingly reported that the Cranio Facial Development Protein 1 (CFDP1) plays a significant role in the onset and progression of tumors. Nonetheless, the underlying mechanisms associated with CFDP1 that contribute to hepatocellular carcinoma (HCC) and the specific biological role of CFDP1 remain vague. METHODS The Gene Expression Omnibus (GEO) database was analyzed to obtain the gene expression profiles as well as the matching clinical data of HCC patients. The gene co-expression network was developed by means of weighted gene co-expression network analysis (WGCNA) to screen for possible biomarkers that could be used for the purpose of predicting prognosis. The Cancer Genome Atlas (TCGA) and Gene Expression Profile Interaction Analysis (GEPIA) databases were used to assess the relationship between survival and expression. In addition, we identified the underlying mechanism associated with CFDP1 by analyzing the KEGG pathway database, applying the GSEA and GeneCards analysis method. We performed a sequence of experiments (in vivo and in vitro) for the purpose of investigating the specific function of CFDP1 in liver cancer. RESULTS The obtained results revealed high expression of CFDP1 in HCC tissues and cell lines. A positive correlation between the overexpression of CFDP1 and the adverse clinicopathological features was observed. Moreover, we observed that the low recurrence-free survival and overall survival were associated with CFDP1 overexpression. In addition, GeneCards and GSEA analysis showed that CFDP1 may interact with NEDD4 and participate in PTEN regulation. Meanwhile, CFDP1 can promote the malignant development of liver cancer in vivo and in vitro. The western blotting technique was also employed so as to examine the samples, and the findings demonstrated that CFDP1 enhanced the malignancy of HCC via the NEDD4-mediated PTEN/PI3K/AKT pathway. CONCLUSION We highlighted that CFDP1 played an oncogenic role in HCC and was identified as a possible clinical prognostic factor and a potential novel therapeutic target for HCC.
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Affiliation(s)
- Yan Zhou
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
| | - Jiannan Qiu
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
| | - Siyuan Liu
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
| | - Peng Wang
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
| | - Ding Ma
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
| | - Guang Zhang
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
- Jinan Microecological Biomedicine Shandong LaboratoryShounuo City Light West BlockJinan CityChina
| | - Yin Cao
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
- Jinan Microecological Biomedicine Shandong LaboratoryShounuo City Light West BlockJinan CityChina
| | - Lili Hu
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
| | - Zhongxia Wang
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
- Jinan Microecological Biomedicine Shandong LaboratoryShounuo City Light West BlockJinan CityChina
| | - Junhua Wu
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
- Jinan Microecological Biomedicine Shandong LaboratoryShounuo City Light West BlockJinan CityChina
| | - Chunping Jiang
- Department of Hepatobiliary SurgeryDrum Tower Clinical College of Nanjing Medical UniversityNanjingChina
- Department of Hepatobiliary SurgeryThe Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjingChina
- Jiangsu Key Laboratory of Molecular MedicineNational Institute of Healthcare Data Science at Nanjing University, Medical School of Nanjing UniversityNanjingChina
- Jinan Microecological Biomedicine Shandong LaboratoryShounuo City Light West BlockJinan CityChina
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21
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Li D, Kim W, An J, Kim S, Lee S, Do A, Kim W, Lee S, Yoon D, Lee K, Ha S, Silverman EK, Cho M, Shin C, Won S. Heritability Analyses Uncover Shared Genetic Effects of Lung Function and Change over Time. Genes (Basel) 2022; 13:genes13071261. [PMID: 35886044 PMCID: PMC9316642 DOI: 10.3390/genes13071261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/05/2022] [Accepted: 07/08/2022] [Indexed: 01/27/2023] Open
Abstract
Genetic influence on lung functions has been identified in previous studies; however, the relative longitudinal effects of genetic factors and their interactions with smoking on lung function remain unclear. Here, we identified the longitudinal effects of genetic variants on lung function by determining single nucleotide polymorphism (SNP) heritability and genetic correlations, and by analyzing interactions with smoking. Subject-specific means and annual change rates were calculated for eight spirometric measures obtained from 6622 Korean adults aged 40−69 years every two years for 14 years, and their heritabilities were estimated separately. Statistically significant (p < 0.05) heritability for the subject-specific means of all spirometric measures (8~32%) and change rates of forced expiratory volume in 1 s to forced vital capacity ratio (FEV1/FVC; 16%) and post-bronchodilator FEV1/FVC (17%) were detected. Significant genetic correlations of the change rate with the subject-specific mean were observed for FEV1/FVC (ρg = 0.64) and post-bronchodilator FEV1/FVC (ρg = 0.47). Furthermore, post-bronchodilator FEV1/FVC showed significant heritability of SNP-by-smoking interaction (hGXS2 = 0.4) for the annual change rate. The GWAS also detected genome-wide significant SNPs for FEV1 (rs4793538), FEV1/FVC (rs2704589, rs62201158, and rs9391733), and post-bronchodilator FEV1/FVC (rs2445936). We found statistically significant evidence of heritability role on the change in lung function, and this was shared with the effects on cross-sectional measurements. We also found some evidence of interaction with smoking for the change of lung function.
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Affiliation(s)
- Donghe Li
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (D.L.); (A.D.)
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, Boston, MA 02118, USA
| | - Woojin Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon 24341, Korea;
| | - Jahoon An
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul 08826, Korea;
| | - Soriul Kim
- Institute for Human Genomic Study, College of Medicine, Korea University, Seoul 136701, Korea; (S.K.); (S.L.)
| | - Seungku Lee
- Institute for Human Genomic Study, College of Medicine, Korea University, Seoul 136701, Korea; (S.K.); (S.L.)
| | - Ahra Do
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (D.L.); (A.D.)
| | - Wonji Kim
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (W.K.); (E.K.S.); (M.C.)
| | - Sanghun Lee
- Department of Medical Consilience, Graduate School, Dankook University, Yongin 16890, Korea;
| | - Dankyu Yoon
- Division of Allergy and Respiratory Disease Research, Department of Chronic Disease Convergence Research, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju 28159, Korea;
| | - Kwangbae Lee
- Korea Medical Institute, Seoul 03173, Korea; (K.L.); (S.H.)
| | - Seounguk Ha
- Korea Medical Institute, Seoul 03173, Korea; (K.L.); (S.H.)
| | - Edwin K. Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (W.K.); (E.K.S.); (M.C.)
| | - Michael Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA; (W.K.); (E.K.S.); (M.C.)
| | - Chol Shin
- Institute for Human Genomic Study, College of Medicine, Korea University, Seoul 136701, Korea; (S.K.); (S.L.)
- Division of Pulmonary Sleep and Critical Care Medicine, Department of Internal Medicine, Korea University Ansan Hospital, Ansan 15355, Korea
- Correspondence: (C.S.); (S.W.)
| | - Sungho Won
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea; (D.L.); (A.D.)
- Department of Public Health Science, Graduate School of Public Health, Seoul National University, Seoul 08826, Korea;
- Institute of Health and Environment, Seoul National University, Seoul 08826, Korea
- RexSoft Inc., Seoul 08826, Korea
- Correspondence: (C.S.); (S.W.)
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22
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Werder RB, Liu T, Abo KM, Lindstrom-Vautrin J, Villacorta-Martin C, Huang J, Hinds A, Boyer N, Bullitt E, Liesa M, Silverman EK, Kotton DN, Cho MH, Zhou X, Wilson AA. CRISPR interference interrogation of COPD GWAS genes reveals the functional significance of desmoplakin in iPSC-derived alveolar epithelial cells. SCIENCE ADVANCES 2022; 8:eabo6566. [PMID: 35857525 PMCID: PMC9278866 DOI: 10.1126/sciadv.abo6566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Genome-wide association studies (GWAS) have identified dozens of loci associated with chronic obstructive pulmonary disease (COPD) susceptibility; however, the function of associated genes in the cell type(s) affected in disease remains poorly understood, partly due to a lack of cell models that recapitulate human alveolar biology. Here, we apply CRISPR interference to interrogate the function of nine genes implicated in COPD by GWAS in induced pluripotent stem cell-derived type 2 alveolar epithelial cells (iAT2s). We find that multiple genes implicated by GWAS affect iAT2 function, including differentiation potential, maturation, and/or proliferation. Detailed characterization of the GWAS gene DSP demonstrates that it regulates iAT2 cell-cell junctions, proliferation, mitochondrial function, and response to cigarette smoke-induced injury. Our approach thus elucidates the biological function, as well as disease-relevant consequences of dysfunction, of genes implicated in COPD by GWAS in type 2 alveolar epithelial cells.
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Affiliation(s)
- Rhiannon B. Werder
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
- QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
| | - Tao Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kristine M. Abo
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | | | - Carlos Villacorta-Martin
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
| | - Jessie Huang
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anne Hinds
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nathan Boyer
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Esther Bullitt
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marc Liesa
- Department of Medicine, Endocrinology, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA 90095, USA
- Institut de Biologia Molecular De Barcelona (IBMB-CSIC), Barcelona, Catalonia 08028, Spain
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Darrell N. Kotton
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Michael H. Cho
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew A. Wilson
- Center for Regenerative Medicine, Boston University and Boston Medical Center, Boston, MA 02118, USA
- Pulmonary Center and Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
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23
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Senescence: Pathogenic Driver in Chronic Obstructive Pulmonary Disease. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58060817. [PMID: 35744080 PMCID: PMC9228143 DOI: 10.3390/medicina58060817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 01/10/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is recognized as a disease of accelerated lung aging. Over the past two decades, mounting evidence suggests an accumulation of senescent cells within the lungs of patients with COPD that contributes to dysregulated tissue repair and the secretion of multiple inflammatory proteins, termed the senescence-associated secretory phenotype (SASP). Cellular senescence in COPD is linked to telomere dysfunction, DNA damage, and oxidative stress. This review gives an overview of the mechanistic contributions and pathologic consequences of cellular senescence in COPD and discusses potential therapeutic approaches targeting senescence-associated signaling in COPD.
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24
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Zani ALS, Gouveia MH, Aquino MM, Quevedo R, Menezes RL, Rotimi C, Lwande GO, Ouma C, Mekonnen E, Fagundes NJR. Genetic differentiation in East African ethnicities and its relationship with endurance running success. PLoS One 2022; 17:e0265625. [PMID: 35588128 PMCID: PMC9119534 DOI: 10.1371/journal.pone.0265625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 03/04/2022] [Indexed: 12/02/2022] Open
Abstract
Since the 1960s, East African athletes, mainly from Kenya and Ethiopia, have dominated long-distance running events in both the male and female categories. Further demographic studies have shown that two ethnic groups are overrepresented among elite endurance runners in each of these countries: the Kalenjin, from Kenya, and the Oromo, from Ethiopia, raising the possibility that this dominance results from genetic or/and cultural factors. However, looking at the life history of these athletes or at loci previously associated with endurance athletic performance, no compelling explanation has emerged. Here, we used a population approach to identify peaks of genetic differentiation for these two ethnicities and compared the list of genes close to these regions with a list, manually curated by us, of genes that have been associated with traits possibly relevant to endurance running in GWAS studies, and found a significant enrichment in both populations (Kalenjin, P = 0.048, and Oromo, P = 1.6x10-5). Those traits are mainly related to anthropometry, circulatory and respiratory systems, energy metabolism, and calcium homeostasis. Our results reinforce the notion that endurance running is a systemic activity with a complex genetic architecture, and indicate new candidate genes for future studies. Finally, we argue that a deterministic relationship between genetics and sports must be avoided, as it is both scientifically incorrect and prone to reinforcing population (racial) stereotyping.
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Affiliation(s)
- André L. S. Zani
- Postgraduate Program in Genetics and Molecular Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Mateus H. Gouveia
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Marla M. Aquino
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rodrigo Quevedo
- School of Physical Education, Physical Therapy and Dance, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Rodrigo L. Menezes
- School of Physical Education, Physical Therapy and Dance, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Gerald O. Lwande
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Collins Ouma
- Department of Biomedical Sciences and Technology, Maseno University, Maseno, Kenya
| | - Ephrem Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Nelson J. R. Fagundes
- Postgraduate Program in Genetics and Molecular Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- Postgraduate Program in Animal Biology, Institute of Biosciences, Federal University of Rio Grande do Sul, Porto Alegre, RS, Brazil
- * E-mail:
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25
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Garcia-Arcos I, Park SS, Mai M, Alvarez-Buve R, Chow L, Cai H, Baumlin-Schmid N, Agudelo CW, Martinez J, Kim MD, Dabo AJ, Salathe M, Goldberg IJ, Foronjy RF. LRP1 loss in airway epithelium exacerbates smoke-induced oxidative damage and airway remodeling. J Lipid Res 2022; 63:100185. [PMID: 35202607 PMCID: PMC8953659 DOI: 10.1016/j.jlr.2022.100185] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 02/04/2023] Open
Abstract
The LDL receptor-related protein 1 (LRP1) partakes in metabolic and signaling events regulated in a tissue-specific manner. The function of LRP1 in airways has not been studied. We aimed to study the function of LRP1 in smoke-induced disease. We found that bronchial epithelium of patients with chronic obstructive pulmonary disease and airway epithelium of mice exposed to smoke had increased LRP1 expression. We then knocked out LRP1 in human bronchial epithelial cells in vitro and in airway epithelial club cells in mice. In vitro, LRP1 knockdown decreased cell migration and increased transforming growth factor β activation. Tamoxifen-inducible airway-specific LRP1 knockout mice (club Lrp1-/-) induced after complete lung development had increased inflammation in the bronchoalveolar space and lung parenchyma at baseline. After 6 months of smoke exposure, club Lrp1-/- mice showed a combined restrictive and obstructive phenotype, with lower compliance, inspiratory capacity, and forced expiratory volume0.05/forced vital capacity than WT smoke-exposed mice. This was associated with increased values of Ashcroft fibrotic index. Proteomic analysis of room air exposed-club Lrp1-/- mice showed significantly decreased levels of proteins involved in cytoskeleton signaling and xenobiotic detoxification as well as decreased levels of glutathione. The proteome fingerprint created by smoke eclipsed many of the original differences, but club Lrp1-/- mice continued to have decreased lung glutathione levels and increased protein oxidative damage and airway cell proliferation. Therefore, LRP1 deficiency leads to greater lung inflammation and damage and exacerbates smoke-induced lung disease.
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Affiliation(s)
- Itsaso Garcia-Arcos
- Departments of Medicine and Cell Biology, SUNY Downstate Medical Center, New York, NY, USA.
| | - Sangmi S Park
- Departments of Medicine and Cell Biology, SUNY Downstate Medical Center, New York, NY, USA
| | - Michelle Mai
- Departments of Medicine and Cell Biology, SUNY Downstate Medical Center, New York, NY, USA
| | - Roger Alvarez-Buve
- Respiratory Department, Hospital University Arnau de Vilanova and Santa Maria, IRB Lleida, University of Lleida, Lleida, Catalonia, Spain
| | - Lillian Chow
- Departments of Medicine and Cell Biology, SUNY Downstate Medical Center, New York, NY, USA
| | - Huchong Cai
- Departments of Medicine and Cell Biology, SUNY Downstate Medical Center, New York, NY, USA
| | | | - Christina W Agudelo
- Departments of Medicine and Cell Biology, SUNY Downstate Medical Center, New York, NY, USA
| | - Jennifer Martinez
- Departments of Medicine and Cell Biology, SUNY Downstate Medical Center, New York, NY, USA
| | - Michael D Kim
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Abdoulaye J Dabo
- Departments of Medicine and Cell Biology, SUNY Downstate Medical Center, New York, NY, USA
| | - Matthias Salathe
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, KS, USA
| | - Ira J Goldberg
- Department of Medicine, NYU Langone School of Medicine, New York, NY, USA
| | - Robert F Foronjy
- Departments of Medicine and Cell Biology, SUNY Downstate Medical Center, New York, NY, USA
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26
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Günes Günsel G, Conlon TM, Jeridi A, Kim R, Ertüz Z, Lang NJ, Ansari M, Novikova M, Jiang D, Strunz M, Gaianova M, Hollauer C, Gabriel C, Angelidis I, Doll S, Pestoni JC, Edelmann SL, Kohlhepp MS, Guillot A, Bassler K, Van Eeckhoutte HP, Kayalar Ö, Konyalilar N, Kanashova T, Rodius S, Ballester-López C, Genes Robles CM, Smirnova N, Rehberg M, Agarwal C, Krikki I, Piavaux B, Verleden SE, Vanaudenaerde B, Königshoff M, Dittmar G, Bracke KR, Schultze JL, Watz H, Eickelberg O, Stoeger T, Burgstaller G, Tacke F, Heissmeyer V, Rinkevich Y, Bayram H, Schiller HB, Conrad M, Schneider R, Yildirim AÖ. The arginine methyltransferase PRMT7 promotes extravasation of monocytes resulting in tissue injury in COPD. Nat Commun 2022; 13:1303. [PMID: 35288557 PMCID: PMC8921220 DOI: 10.1038/s41467-022-28809-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/01/2022] [Indexed: 12/13/2022] Open
Abstract
Extravasation of monocytes into tissue and to the site of injury is a fundamental immunological process, which requires rapid responses via post translational modifications (PTM) of proteins. Protein arginine methyltransferase 7 (PRMT7) is an epigenetic factor that has the capacity to mono-methylate histones on arginine residues. Here we show that in chronic obstructive pulmonary disease (COPD) patients, PRMT7 expression is elevated in the lung tissue and localized to the macrophages. In mouse models of COPD, lung fibrosis and skin injury, reduced expression of PRMT7 associates with decreased recruitment of monocytes to the site of injury and hence less severe symptoms. Mechanistically, activation of NF-κB/RelA in monocytes induces PRMT7 transcription and consequential mono-methylation of histones at the regulatory elements of RAP1A, which leads to increased transcription of this gene that is responsible for adhesion and migration of monocytes. Persistent monocyte-derived macrophage accumulation leads to ALOX5 over-expression and accumulation of its metabolite LTB4, which triggers expression of ACSL4 a ferroptosis promoting gene in lung epithelial cells. Conclusively, inhibition of arginine mono-methylation might offer targeted intervention in monocyte-driven inflammatory conditions that lead to extensive tissue damage if left untreated.
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Affiliation(s)
- Gizem Günes Günsel
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Thomas M Conlon
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Aicha Jeridi
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Rinho Kim
- Institute of Functional Epigenetics, Helmholtz Munich, 85764, Munich, Germany
| | - Zeynep Ertüz
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Niklas J Lang
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Meshal Ansari
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
- Institute of Computational Biology, Helmholtz Munich, 85764, Munich, Germany
| | - Mariia Novikova
- Institute of Metabolism and Cell Death, Helmholtz Munich, 85764, Munich, Germany
- Pirogov Russian National Research Medical University, Laboratory of Experimental Oncology, Ostrovityanova 1, Moscow, 117997, Russia
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Ostrovityanova1 bldg 10, 117997, Moscow, Russia
| | - Dongsheng Jiang
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Maximilian Strunz
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Mariia Gaianova
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Christine Hollauer
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Christina Gabriel
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Ilias Angelidis
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Sebastian Doll
- Institute of Computational Biology, Helmholtz Munich, 85764, Munich, Germany
| | - Jeanine C Pestoni
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Stephanie L Edelmann
- Research Unit Molecular Immune Regulation, Helmholtz Munich, 81377, Munich, Germany
| | - Marlene Sophia Kohlhepp
- Department of Hepatology & Gastroenterology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), 13353, Berlin, Germany
| | - Adrien Guillot
- Department of Hepatology & Gastroenterology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), 13353, Berlin, Germany
| | - Kevin Bassler
- Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn, 53115, Bonn, Germany
- aimed analytics, 53121, Bonn, Germany
| | - Hannelore P Van Eeckhoutte
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University, University Hospital Ghent, 9000, Ghent, Belgium
| | - Özgecan Kayalar
- Koç University Research Center for Translational Medicine (KUTTAM), 34010, Istanbul, Turkey
| | - Nur Konyalilar
- Koç University Research Center for Translational Medicine (KUTTAM), 34010, Istanbul, Turkey
| | - Tamara Kanashova
- Max-Delbrück Center for Molecular Medicine, 13125, Berlin, Germany
| | - Sophie Rodius
- Proteomics of cellular signalling, Luxembourg Institute of Health, 1272, Strassen, Luxembourg
| | - Carolina Ballester-López
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | | | - Natalia Smirnova
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
- Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado, Denver, CO, 80045, USA
| | - Markus Rehberg
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Charu Agarwal
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Ioanna Krikki
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Benoit Piavaux
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, 25242, Vestec, Czech Republic
| | - Stijn E Verleden
- Division of Pneumology, KU Leuven, 3000, Leuven, Belgium
- Antwerp Surgical Training, Anatomy and Research Centre, University of Antwerp, 2650, Edegem, Belgium
| | | | - Melanie Königshoff
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Gunnar Dittmar
- Proteomics of cellular signalling, Luxembourg Institute of Health, 1272, Strassen, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, L-4365, Esch-sur-Alzette, Luxembourg
| | - Ken R Bracke
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Respiratory Medicine, Ghent University, University Hospital Ghent, 9000, Ghent, Belgium
| | - Joachim L Schultze
- Department for Genomics & Immunoregulation, LIMES-Institute, University of Bonn, 53115, Bonn, Germany
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., PRECISE Platform for Single Cell Genomics and Epigenomics at DZNE and the University of Bonn, 53115, Bonn, Germany
| | - Henrik Watz
- Pulmonary Research Institute at LungenClinic Grosshansdorf, Airway Research Center North (ARCN), German Center for Lung Research (DZL), 22927, Grosshansdorf, Germany
| | - Oliver Eickelberg
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Tobias Stoeger
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Gerald Burgstaller
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Frank Tacke
- Department of Hepatology & Gastroenterology, Charité - Universitätsmedizin Berlin, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), 13353, Berlin, Germany
| | - Vigo Heissmeyer
- Research Unit Molecular Immune Regulation, Helmholtz Munich, 81377, Munich, Germany
- Institute for Immunology, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, 82152, Planegg-Martinsried, Germany
| | - Yuval Rinkevich
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Hasan Bayram
- Koç University Research Center for Translational Medicine (KUTTAM), 34010, Istanbul, Turkey
| | - Herbert B Schiller
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany
| | - Marcus Conrad
- Institute of Metabolism and Cell Death, Helmholtz Munich, 85764, Munich, Germany
- Pirogov Russian National Research Medical University, Laboratory of Experimental Oncology, Ostrovityanova 1, Moscow, 117997, Russia
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Munich, 85764, Munich, Germany
| | - Ali Önder Yildirim
- Institute of Lung Health and Immunity (LHI), Comprehensive Pneumology Center (CPC), Helmholtz Munich, Member of the German Center for Lung Research (DZL), 85764, Munich, Germany.
- Koç University Research Center for Translational Medicine (KUTTAM), 34010, Istanbul, Turkey.
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A year of Covid-19 GWAS results from the GRASP portal reveals potential genetic risk factors. HGG ADVANCES 2022; 3:100095. [PMID: 35224516 PMCID: PMC8863308 DOI: 10.1016/j.xhgg.2022.100095] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
Host genetic variants influence the susceptibility and severity of several infectious diseases, and the discovery of genetic associations with Covid-19 phenotypes could help developing new therapeutic strategies to reduce its burden. Between May 2020 and June 2021, we used Covid-19 data released periodically by UK Biobank and performed 65 Genome-Wide Association Studies (GWAS) in up to 18 releases of Covid-19 susceptibility (N=18,481 cases in June 2021), hospitalization (N=3,260), severe outcomes (N=1,244) and death (N=1,104), stratified by sex and ancestry. In coherence with previous studies, we observed 2 independent signals at the chr3p21.31 locus (rs73062389-A, OR=1.21, P=4.26×10-15 and rs71325088-C, OR=1.62, P=2.25×10-9) modulating susceptibility and severity, respectively, and a signal influencing susceptibility at the ABO locus (rs9411378-A, OR=1.10, P=3.30×10-12), suggesting an increased risk of infection in non-O blood groups carriers. Additional signals at the APOE (associated with severity and death) LRMDA (susceptibility in non-European) and chr2q32.3 (susceptibility in women) loci were also identified but did not replicate in independent datasets. We then devised an approach to extract variants suggestively associated (P<10-5) exhibiting an increase in significance over time. When applied to the susceptibility, hospitalization and severity analyses, this approach revealed the known RPL24, DPP9, and MAPT loci, respectively, amongst hundreds of other signals. These results, freely available on the GRASP portal, provide insights on the genetic mechanisms involved in Covid-19 phenotypes.
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28
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Daghals I, Sargurupremraj M, Danning R, Gormley P, Malik R, Amouyel P, Metso T, Pezzini A, Kurth T, Debette S, Chasman D. Migraine, Stroke, and Cervical Arterial Dissection: Shared Genetics for a Triad of Brain Disorders With Vascular Involvement. Neurol Genet 2022; 8:e653. [PMID: 35128049 PMCID: PMC8808356 DOI: 10.1212/nxg.0000000000000653] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/07/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND AND OBJECTIVES Migraine, stroke, and cervical artery dissection (CeAD) represent a triad of cerebrovascular disorders with pairwise comorbid relationships and vascular involvement. Larger samples and recent advances in methodology invite systematic exploration of their shared genetics. METHODS Genetic analyses leveraged summary statistics from genome-wide association studies of the largest available samples of each disorder, including subtypes of stroke (ischemic stroke, large artery stroke, small vessel stroke, and cardioembolic stroke) and migraine (with aura and without aura). For each pair of disorders, genetic correlation was assessed both on a genome-wide basis and within independent segments across the genome including known specific loci for each disorder. A cross-trait meta-analysis was used to identify novel candidate loci. Finally, potential causality of migraine susceptibility on stroke and CeAD was assessed by Mendelian randomization. RESULTS Among all pairs of disorders, genome-wide genetic correlation was observed only between CeAD and migraine, particularly MO. Local genetic correlations were more extensive between migraine and CeAD than those between migraine and stroke or CeAD and stroke and revealed evidence for novel CeAD associations at rs6693567 (ADAMTSL4/ECM1), rs11187838 (PLCE1), and rs7940646 (MRVI1) while strengthening prior subthreshold evidence at rs9486725 (FHL5) and rs650724 (LRP1). At known migraine loci, novel associations with stroke had concordant risk alleles for small vessel stroke at rs191602009 (CARF) and for cardioembolic stroke at rs55884259 (NKX2-5). Known migraine loci also revealed novel associations but with opposite risk alleles for all stroke, ischemic stroke, and small vessel stroke at rs55928386 (HTRA1), for large artery stroke at rs11172113 (LRP1), and for all stroke and ischemic stroke at rs1535791 and rs4942561 (both LRCH1), respectively. rs182923402 (near PTCH1) was a novel concordant locus for migraine and cardioembolic stroke. Mendelian randomization supported potential causal influences of migraine on CeAD (odds ratio [95% confidence interval] per doubling migraine prevalence = 1.69 [1.24-2.3], p = 0.0009) with concordant risk, but with opposite risk on large artery stroke (0.86 [0.76-0.96], p = 0.0067). DISCUSSION The findings emphasize shared genetic risk between migraine and CeAD while identifying loci with likely vascular function in migraine and shared but opposite genetic risk between migraine and stroke subtypes, and a central role of LRP1 in all 3 cerebrovascular disorders.
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Affiliation(s)
| | | | - Rebecca Danning
- From the Harvard Medical School (I.D., D.C.), Boston, MA; Division of Preventive Medicine (I.D., R.D., D.C.), Brigham and Women's Hospital, Boston, MA; University of Bordeaux (M.S., S.D.), Inserm, Bordeaux Population Health Research Center, Team VINTAGE, UMR 1219, France; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases (M.S.), University of Texas Health, San Antonio; Massachusetts General Hospital (P.G.), Boston; Institute for Stroke and Dementia Research (R.M.), Klinikum der Universität München, Ludwig-Maximilians-University, Germany; LabEx DISTALZ-U1167 (P.A.), RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille; Inserm U1167 (P.A.), Lille; Centre Hospitalier Universitaire Lille (P.A.); Institut Pasteur de Lille (P.A.), France; Department of Neurology (T.M.), Helsinki University Central Hospital, Finland; Department of Clinical and Experimental Sciences (A.P.), Neurology Clinic, Brescia University Hospital, Italy; Institute of Public Health (T.K.), Charité—Universitätsmedizin Berlin, Germany; and Department of Neurology (S.D.), CHU de Bordeaux, France
| | - Padhraig Gormley
- From the Harvard Medical School (I.D., D.C.), Boston, MA; Division of Preventive Medicine (I.D., R.D., D.C.), Brigham and Women's Hospital, Boston, MA; University of Bordeaux (M.S., S.D.), Inserm, Bordeaux Population Health Research Center, Team VINTAGE, UMR 1219, France; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases (M.S.), University of Texas Health, San Antonio; Massachusetts General Hospital (P.G.), Boston; Institute for Stroke and Dementia Research (R.M.), Klinikum der Universität München, Ludwig-Maximilians-University, Germany; LabEx DISTALZ-U1167 (P.A.), RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille; Inserm U1167 (P.A.), Lille; Centre Hospitalier Universitaire Lille (P.A.); Institut Pasteur de Lille (P.A.), France; Department of Neurology (T.M.), Helsinki University Central Hospital, Finland; Department of Clinical and Experimental Sciences (A.P.), Neurology Clinic, Brescia University Hospital, Italy; Institute of Public Health (T.K.), Charité—Universitätsmedizin Berlin, Germany; and Department of Neurology (S.D.), CHU de Bordeaux, France
| | - Rainer Malik
- From the Harvard Medical School (I.D., D.C.), Boston, MA; Division of Preventive Medicine (I.D., R.D., D.C.), Brigham and Women's Hospital, Boston, MA; University of Bordeaux (M.S., S.D.), Inserm, Bordeaux Population Health Research Center, Team VINTAGE, UMR 1219, France; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases (M.S.), University of Texas Health, San Antonio; Massachusetts General Hospital (P.G.), Boston; Institute for Stroke and Dementia Research (R.M.), Klinikum der Universität München, Ludwig-Maximilians-University, Germany; LabEx DISTALZ-U1167 (P.A.), RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille; Inserm U1167 (P.A.), Lille; Centre Hospitalier Universitaire Lille (P.A.); Institut Pasteur de Lille (P.A.), France; Department of Neurology (T.M.), Helsinki University Central Hospital, Finland; Department of Clinical and Experimental Sciences (A.P.), Neurology Clinic, Brescia University Hospital, Italy; Institute of Public Health (T.K.), Charité—Universitätsmedizin Berlin, Germany; and Department of Neurology (S.D.), CHU de Bordeaux, France
| | - Philippe Amouyel
- From the Harvard Medical School (I.D., D.C.), Boston, MA; Division of Preventive Medicine (I.D., R.D., D.C.), Brigham and Women's Hospital, Boston, MA; University of Bordeaux (M.S., S.D.), Inserm, Bordeaux Population Health Research Center, Team VINTAGE, UMR 1219, France; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases (M.S.), University of Texas Health, San Antonio; Massachusetts General Hospital (P.G.), Boston; Institute for Stroke and Dementia Research (R.M.), Klinikum der Universität München, Ludwig-Maximilians-University, Germany; LabEx DISTALZ-U1167 (P.A.), RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille; Inserm U1167 (P.A.), Lille; Centre Hospitalier Universitaire Lille (P.A.); Institut Pasteur de Lille (P.A.), France; Department of Neurology (T.M.), Helsinki University Central Hospital, Finland; Department of Clinical and Experimental Sciences (A.P.), Neurology Clinic, Brescia University Hospital, Italy; Institute of Public Health (T.K.), Charité—Universitätsmedizin Berlin, Germany; and Department of Neurology (S.D.), CHU de Bordeaux, France
| | - Tiina Metso
- From the Harvard Medical School (I.D., D.C.), Boston, MA; Division of Preventive Medicine (I.D., R.D., D.C.), Brigham and Women's Hospital, Boston, MA; University of Bordeaux (M.S., S.D.), Inserm, Bordeaux Population Health Research Center, Team VINTAGE, UMR 1219, France; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases (M.S.), University of Texas Health, San Antonio; Massachusetts General Hospital (P.G.), Boston; Institute for Stroke and Dementia Research (R.M.), Klinikum der Universität München, Ludwig-Maximilians-University, Germany; LabEx DISTALZ-U1167 (P.A.), RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille; Inserm U1167 (P.A.), Lille; Centre Hospitalier Universitaire Lille (P.A.); Institut Pasteur de Lille (P.A.), France; Department of Neurology (T.M.), Helsinki University Central Hospital, Finland; Department of Clinical and Experimental Sciences (A.P.), Neurology Clinic, Brescia University Hospital, Italy; Institute of Public Health (T.K.), Charité—Universitätsmedizin Berlin, Germany; and Department of Neurology (S.D.), CHU de Bordeaux, France
| | - Alessandro Pezzini
- From the Harvard Medical School (I.D., D.C.), Boston, MA; Division of Preventive Medicine (I.D., R.D., D.C.), Brigham and Women's Hospital, Boston, MA; University of Bordeaux (M.S., S.D.), Inserm, Bordeaux Population Health Research Center, Team VINTAGE, UMR 1219, France; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases (M.S.), University of Texas Health, San Antonio; Massachusetts General Hospital (P.G.), Boston; Institute for Stroke and Dementia Research (R.M.), Klinikum der Universität München, Ludwig-Maximilians-University, Germany; LabEx DISTALZ-U1167 (P.A.), RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille; Inserm U1167 (P.A.), Lille; Centre Hospitalier Universitaire Lille (P.A.); Institut Pasteur de Lille (P.A.), France; Department of Neurology (T.M.), Helsinki University Central Hospital, Finland; Department of Clinical and Experimental Sciences (A.P.), Neurology Clinic, Brescia University Hospital, Italy; Institute of Public Health (T.K.), Charité—Universitätsmedizin Berlin, Germany; and Department of Neurology (S.D.), CHU de Bordeaux, France
| | - Tobias Kurth
- From the Harvard Medical School (I.D., D.C.), Boston, MA; Division of Preventive Medicine (I.D., R.D., D.C.), Brigham and Women's Hospital, Boston, MA; University of Bordeaux (M.S., S.D.), Inserm, Bordeaux Population Health Research Center, Team VINTAGE, UMR 1219, France; Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases (M.S.), University of Texas Health, San Antonio; Massachusetts General Hospital (P.G.), Boston; Institute for Stroke and Dementia Research (R.M.), Klinikum der Universität München, Ludwig-Maximilians-University, Germany; LabEx DISTALZ-U1167 (P.A.), RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, University of Lille; Inserm U1167 (P.A.), Lille; Centre Hospitalier Universitaire Lille (P.A.); Institut Pasteur de Lille (P.A.), France; Department of Neurology (T.M.), Helsinki University Central Hospital, Finland; Department of Clinical and Experimental Sciences (A.P.), Neurology Clinic, Brescia University Hospital, Italy; Institute of Public Health (T.K.), Charité—Universitätsmedizin Berlin, Germany; and Department of Neurology (S.D.), CHU de Bordeaux, France
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29
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Pascoe CD, Basu S, Schwartz J, Fonseca M, Kahnamoui S, Jha A, Dolinsky VW, Halayko AJ. Maternal diabetes promotes offspring lung dysfunction and inflammation in a sex-dependent manner. Am J Physiol Lung Cell Mol Physiol 2022; 322:L373-L384. [PMID: 35043678 DOI: 10.1152/ajplung.00425.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Exposure to maternal diabetes is increasingly recognized as a risk factor for chronic respiratory disease in children. It is currently unclear, however, whether maternal diabetes affects the lung health of male and female offspring equally. This study characterizes the sex-specific impact of a murine model of diet-induced gestational diabetes (GDM) on offspring lung function and airway inflammation. Female adult mice are fed a high-fat (45% kcal) diet for 6-weeks prior to mating. Control offspring are from mothers fed a low fat (10% kcal) diet. Offspring were weaned and fed a chow diet until 10-weeks of age, at which point lung function was measured and lung lavage was collected. Male, but not female offspring exposed to GDM had increased lung compliance and reduced lung resistance at baseline. Female offspring exposed to GDM displayed increased methacholine reactivity and elevated levels of pro-inflammatory cytokines (e.g. interleukin (IL)-1β, IL-5, and CXCL1) in lung lavage. Female GDM offspring also displayed elevated abundance of matrix metalloproteinases (MMP) within their airways, namely MMP-3 and MMP-8. These results indicate disparate effects of maternal diabetes on lung health and airway inflammation of male and female offspring exposed to GDM. Female mice may be at greater risk of inflammatory lung conditions, such as asthma, while male offspring display changes that more closely align with models of chronic obstructive pulmonary disease. In conclusion, there are important sex-based differences in the impact of maternal diabetes on offspring lung health that could signal differences in future disease risk.
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Affiliation(s)
- Christopher D Pascoe
- Deptartment of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Group, The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Sujata Basu
- Deptartment of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Group, The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Jacquie Schwartz
- Deptartment of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Group, The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Mario Fonseca
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, Manitoba, Canada.,Diabetes Research Envisioned and Accomplished in Manitoba, The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Shana Kahnamoui
- Deptartment of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Group, The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Aruni Jha
- Deptartment of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Group, The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Vernon W Dolinsky
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, Manitoba, Canada.,Diabetes Research Envisioned and Accomplished in Manitoba, The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
| | - Andrew John Halayko
- Deptartment of Physiology and Pathophysiology, University of Manitoba, Winnipeg, Manitoba, Canada.,Biology of Breathing Group, The Children's Hospital Research Institute of Manitoba, Winnipeg, Manitoba, Canada
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30
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Lechtreck KF, Liu Y, Dai J, Alkhofash RA, Butler J, Alford L, Yang P. Chlamydomonas ARMC2/PF27 is an obligate cargo adapter for intraflagellar transport of radial spokes. eLife 2022; 11:74993. [PMID: 34982025 PMCID: PMC8789290 DOI: 10.7554/elife.74993] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/03/2022] [Indexed: 12/19/2022] Open
Abstract
Intraflagellar transport (IFT) carries proteins into flagella but how IFT trains interact with the large number of diverse proteins required to assemble flagella remains largely unknown. Here, we show that IFT of radial spokes in Chlamydomonas requires ARMC2/PF27, a conserved armadillo repeat protein associated with male infertility and reduced lung function. Chlamydomonas ARMC2 was highly enriched in growing flagella and tagged ARMC2 and the spoke protein RSP3 co-migrated on anterograde trains. In contrast, a cargo and an adapter of inner and outer dynein arms moved independently of ARMC2, indicating that unrelated cargoes distribute stochastically onto the IFT trains. After concomitant unloading at the flagellar tip, RSP3 attached to the axoneme whereas ARMC2 diffused back to the cell body. In armc2/pf27 mutants, IFT of radial spokes was abolished and the presence of radial spokes was limited to the proximal region of flagella. We conclude that ARMC2 is a cargo adapter required for IFT of radial spokes to ensure their assembly along flagella. ARMC2 belongs to a growing class of cargo-specific adapters that enable flagellar transport of preassembled axonemal substructures by IFT.
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Affiliation(s)
- Karl F Lechtreck
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Yi Liu
- Department of Biological Sciences, Marquette University, Milwaukee, United States
| | - Jin Dai
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Rama A Alkhofash
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Jack Butler
- Department of Cellular Biology, University of Georgia, Athens, United States
| | - Lea Alford
- Division of Natural Sciences,, Oglethorpe University, Atlanta, United States
| | - Pinfen Yang
- Department of Biological Sciences, Marquette University, Milwaukee, United States
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31
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Huang Y, Jiang Z, Gao X, Luo P, Jiang X. ARMC Subfamily: Structures, Functions, Evolutions, Interactions, and Diseases. Front Mol Biosci 2021; 8:791597. [PMID: 34912852 PMCID: PMC8666550 DOI: 10.3389/fmolb.2021.791597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/15/2021] [Indexed: 12/29/2022] Open
Abstract
Armadillo repeat-containing proteins (ARMCs) are widely distributed in eukaryotes and have important influences on cell adhesion, signal transduction, mitochondrial function regulation, tumorigenesis, and other processes. These proteins share a similar domain consisting of tandem repeats approximately 42 amino acids in length, and this domain constitutes a substantial platform for the binding between ARMCs and other proteins. An ARMC subfamily, including ARMC1∼10, ARMC12, and ARMCX1∼6, has received increasing attention. These proteins may have many terminal regions and play a critical role in various diseases. On the one hand, based on their similar central domain of tandem repeats, this ARMC subfamily may function similarly to other ARMCs. On the other hand, the unique domains on their terminals may cause these proteins to have different functions. Here, we focus on the ARMC subfamily (ARMC1∼10, ARMC12, and ARMCX1∼6), which is relatively conserved in vertebrates and highly conserved in mammals, particularly primates. We review the structures, biological functions, evolutions, interactions, and related diseases of the ARMC subfamily, which involve more than 30 diseases and 40 bypasses, including interactions and relationships between more than 100 proteins and signaling molecules. We look forward to obtaining a clearer understanding of the ARMC subfamily to facilitate further in-depth research and treatment of related diseases.
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Affiliation(s)
- Yutao Huang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Institue of Neurosurgery of People's Liberation Army of China (PLA), PLA's Key Laboratory of Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Zijian Jiang
- Department of Hepato-biliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiangyu Gao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, China
| | - Peng Luo
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Institue of Neurosurgery of People's Liberation Army of China (PLA), PLA's Key Laboratory of Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xiaofan Jiang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Institue of Neurosurgery of People's Liberation Army of China (PLA), PLA's Key Laboratory of Critical Care Medicine, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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Role of the LRP1-pPyk2-MMP9 pathway in hyperoxia-induced lung injury in neonatal rats. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23:1289-1294. [PMID: 34911615 PMCID: PMC8690715 DOI: 10.7499/j.issn.1008-8830.2108125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVES To study the role of the low-density lipoprotein receptor-related protein 1 (LRP1)-proline-rich tyrosine kinase 2 phosphorylation (pPyk2)-matrix metalloproteinases 9 (MMP9) pathway in hyperoxia-induced lung injury in neonatal rats. METHODS A total of 16 neonatal rats were randomly placed in chambers containing room air (air group) or 95% medical oxygen (hyperoxia group) immediately after birth, with 8 rats in each group. All of the rats were sacrificed on day 8 of life. Hematoxylin and eosin staining was used to observe the pathological changes of lung tissue. ELISA was used to measure the levels of soluble LRP1 (sLRP1) and MMP9 in serum and bronchoalveolar lavage fluid (BALF). Western blot was used to measure the protein expression levels of LRP1, MMP9, Pyk2, and pPyk2 in lung tissue. RT-PCR was used to measure the mRNA expression levels of LRP1 and MMP9 in lung tissue. RESULTS The hyperoxia group had significantly higher levels of sLRP1 and MMP9 in serum and BALF than the air group (P<0.05). Compared with the air group, the hyperoxia group had significant increases in the protein expression levels of LRP1, MMP9, and pPyk2 in lung tissue (P<0.05). The hyperoxia group had significantly higher relative mRNA expression levels of LRP1 and MMP9 in lung tissue than the air group (P<0.05). CONCLUSIONS The activation of the LRP1-pPyk2-MMP9 pathway is enhanced in hyperoxia-induced lung injury in neonatal rats, which may be involved in the pathogenesis of bronchopulmonary dysplasia.
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Nasri A, Foisset F, Ahmed E, Lahmar Z, Vachier I, Jorgensen C, Assou S, Bourdin A, De Vos J. Roles of Mesenchymal Cells in the Lung: From Lung Development to Chronic Obstructive Pulmonary Disease. Cells 2021; 10:3467. [PMID: 34943975 PMCID: PMC8700565 DOI: 10.3390/cells10123467] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022] Open
Abstract
Mesenchymal cells are an essential cell type because of their role in tissue support, their multilineage differentiation capacities and their potential clinical applications. They play a crucial role during lung development by interacting with airway epithelium, and also during lung regeneration and remodeling after injury. However, much less is known about their function in lung disease. In this review, we discuss the origins of mesenchymal cells during lung development, their crosstalk with the epithelium, and their role in lung diseases, particularly in chronic obstructive pulmonary disease.
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Affiliation(s)
- Amel Nasri
- Institute for Regenerative Medicine and Biotherapy, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France; (A.N.); (F.F.); (C.J.); (S.A.)
| | - Florent Foisset
- Institute for Regenerative Medicine and Biotherapy, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France; (A.N.); (F.F.); (C.J.); (S.A.)
| | - Engi Ahmed
- Department of Respiratory Diseases, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France; (E.A.); (Z.L.); (I.V.); (A.B.)
- PhyMedExp, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
| | - Zakaria Lahmar
- Department of Respiratory Diseases, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France; (E.A.); (Z.L.); (I.V.); (A.B.)
- PhyMedExp, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
| | - Isabelle Vachier
- Department of Respiratory Diseases, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France; (E.A.); (Z.L.); (I.V.); (A.B.)
| | - Christian Jorgensen
- Institute for Regenerative Medicine and Biotherapy, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France; (A.N.); (F.F.); (C.J.); (S.A.)
| | - Said Assou
- Institute for Regenerative Medicine and Biotherapy, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France; (A.N.); (F.F.); (C.J.); (S.A.)
| | - Arnaud Bourdin
- Department of Respiratory Diseases, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34090 Montpellier, France; (E.A.); (Z.L.); (I.V.); (A.B.)
- PhyMedExp, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34295 Montpellier, France
| | - John De Vos
- Institute for Regenerative Medicine and Biotherapy, Université de Montpellier, INSERM, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France; (A.N.); (F.F.); (C.J.); (S.A.)
- Department of Cell and Tissue Engineering, Université de Montpellier, Centre Hospitalier Universitaire de Montpellier, 34000 Montpellier, France
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Elastic Correlation Adjusted Regression (ECAR) scores for high dimensional variable importance measuring. Sci Rep 2021; 11:23354. [PMID: 34857823 PMCID: PMC8640025 DOI: 10.1038/s41598-021-02706-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 11/22/2021] [Indexed: 11/08/2022] Open
Abstract
Investigation of the genetic basis of traits or clinical outcomes heavily relies on identifying relevant variables in molecular data. However, characteristics such as high dimensionality and complex correlation structures of these data hinder the development of related methods, resulting in the inclusion of false positives and negatives. We developed a variable importance measure method, termed the ECAR scores, that evaluates the importance of variables in the dataset. Based on this score, ranking and selection of variables can be achieved simultaneously. Unlike most current approaches, the ECAR scores aim to rank the influential variables as high as possible while maintaining the grouping property, instead of selecting the ones that are merely predictive. The ECAR scores' performance is tested and compared to other methods on simulated, semi-synthetic, and real datasets. Results showed that the ECAR scores improve the CAR scores in terms of accuracy of variable selection and high-rank variables' predictive power. It also outperforms other classic methods such as lasso and stability selection when there is a high degree of correlation among influential variables. As an application, we used the ECAR scores to analyze genes associated with forced expiratory volume in the first second in patients with lung cancer and reported six associated genes.
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35
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Scaffa A, Yao H, Oulhen N, Wallace J, Peterson AL, Rizal S, Ragavendran A, Wessel G, De Paepe ME, Dennery PA. Single-cell transcriptomics reveals lasting changes in the lung cellular landscape into adulthood after neonatal hyperoxic exposure. Redox Biol 2021; 48:102091. [PMID: 34417156 PMCID: PMC8710996 DOI: 10.1016/j.redox.2021.102091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 01/11/2023] Open
Abstract
Ventilatory support, such as supplemental oxygen, used to save premature infants impairs the growth of the pulmonary microvasculature and distal alveoli, leading to bronchopulmonary dysplasia (BPD). Although lung cellular composition changes with exposure to hyperoxia in neonatal mice, most human BPD survivors are weaned off oxygen within the first weeks to months of life, yet they may have persistent lung injury and pulmonary dysfunction as adults. We hypothesized that early-life hyperoxia alters the cellular landscape in later life and predicts long-term lung injury. Using single-cell RNA sequencing, we mapped lung cell subpopulations at postnatal day (pnd)7 and pnd60 in mice exposed to hyperoxia (95% O2) for 3 days as neonates. We interrogated over 10,000 cells and identified a total of 45 clusters within 32 cell states. Neonatal hyperoxia caused persistent compositional changes in later life (pnd60) in all five type II cell states with unique signatures and function. Premature infants requiring mechanical ventilation with different durations also showed similar alterations in these unique signatures of type II cell states. Pathologically, neonatal hyperoxic exposure caused alveolar simplification in adult mice. We conclude that neonatal hyperoxia alters the lung cellular landscape in later life, uncovering neonatal programing of adult lung dysfunction.
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Affiliation(s)
- Alejandro Scaffa
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Hongwei Yao
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Nathalie Oulhen
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Joselynn Wallace
- Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, Providence, RI, United States
| | - Abigail L Peterson
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Salu Rizal
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Ashok Ragavendran
- Center for Computational Biology of Human Disease and Center for Computation and Visualization, Brown University, Providence, RI, United States
| | - Gary Wessel
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States
| | - Monique E De Paepe
- Department of Pathology, Women and Infants Hospital, Providence, RI, United States
| | - Phyllis A Dennery
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI, United States; Department of Pediatrics, Warren Alpert Medical School of Brown University, Providence, RI, United States.
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36
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Yamada M, Motoike IN, Kojima K, Fuse N, Hozawa A, Kuriyama S, Katsuoka F, Tadaka S, Shirota M, Sakurai M, Nakamura T, Hamanaka Y, Suzuki K, Sugawara J, Ogishima S, Uruno A, Kodama EN, Fujino N, Numakura T, Ichikawa T, Mitsune A, Ohe T, Kinoshita K, Ichinose M, Sugiura H, Yamamoto M. Genetic loci for lung function in Japanese adults with adjustment for exhaled nitric oxide levels as airway inflammation indicator. Commun Biol 2021; 4:1288. [PMID: 34782693 PMCID: PMC8593164 DOI: 10.1038/s42003-021-02813-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 10/27/2021] [Indexed: 11/08/2022] Open
Abstract
Lung function reflects the ability of the respiratory system and is utilized for the assessment of respiratory diseases. Because type 2 airway inflammation influences lung function, genome wide association studies (GWAS) for lung function would be improved by adjustment with an indicator of the inflammation. Here, we performed a GWAS for lung function with adjustment for exhaled nitric oxide (FeNO) levels in two independent Japanese populations. Our GWAS with genotype imputations revealed that the RNF5/AGER locus including AGER rs2070600 SNP, which introduces a G82S substitution of AGER, was the most significantly associated with FEV1/FVC. Three other rare missense variants of AGER were further identified. We also found genetic loci with three candidate genes (NOS2, SPSB2 and RIPOR2) associated with FeNO levels. Analyses with the BioBank-Japan GWAS resource revealed genetic links of FeNO and asthma-related traits, and existence of common genetic background for allergic diseases and their biomarkers. Our study identified the genetic locus most strongly associated with airway obstruction in the Japanese population and three genetic loci associated with FeNO, an indicator of type 2 airway inflammation in adults.
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Affiliation(s)
- Mitsuhiro Yamada
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ikuko N Motoike
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kaname Kojima
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Atsushi Hozawa
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shinichi Kuriyama
- Department of Preventive Medicine and Epidemiology, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Fumiki Katsuoka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Shu Tadaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Miyuki Sakurai
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Tomohiro Nakamura
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Yohei Hamanaka
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Kichiya Suzuki
- Department of Biobank, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Junichi Sugawara
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Soichi Ogishima
- Department of Health Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
| | - Akira Uruno
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Eiichi N Kodama
- Department of Community Medical Supports, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
| | - Naoya Fujino
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tadahisa Numakura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Tomohiro Ichikawa
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Ayumi Mitsune
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takashi Ohe
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Kengo Kinoshita
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Japan
- Department of System Bioinformatics, Tohoku University Graduate School of Information Sciences, Sendai, Japan
| | | | - Hisatoshi Sugiura
- Department of Respiratory Medicine, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Masayuki Yamamoto
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
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37
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Rare and low-frequency exonic variants and gene-by-smoking interactions in pulmonary function. Sci Rep 2021; 11:19365. [PMID: 34588469 PMCID: PMC8481467 DOI: 10.1038/s41598-021-98120-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 09/02/2021] [Indexed: 02/08/2023] Open
Abstract
Genome-wide association studies have identified numerous common genetic variants associated with spirometric measures of pulmonary function, including forced expiratory volume in one second (FEV1), forced vital capacity, and their ratio. However, variants with lower minor allele frequencies are less explored. We conducted a large-scale gene-smoking interaction meta-analysis on exonic rare and low-frequency variants involving 44,429 individuals of European ancestry in the discovery stage and sought replication in the UK BiLEVE study with 45,133 European ancestry samples and UK Biobank study with 59,478 samples. We leveraged data on cigarette smoking, the major environmental risk factor for reduced lung function, by testing gene-by-smoking interaction effects only and simultaneously testing the genetic main effects and interaction effects. The most statistically significant signal that replicated was a previously reported low-frequency signal in GPR126, distinct from common variant associations in this gene. Although only nominal replication was obtained for a top rare variant signal rs142935352 in one of the two studies, interaction and joint tests for current smoking and PDE3B were significantly associated with FEV1. This study investigates the utility of assessing gene-by-smoking interactions and underscores their effects on potential pulmonary function.
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38
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Okyere DO, Bui DS, Washko GR, Lodge CJ, Lowe AJ, Cassim R, Perret JL, Abramson MJ, Walters EH, Waidyatillake NT, Dharmage SC. Predictors of lung function trajectories in population-based studies: A systematic review. Respirology 2021; 26:938-959. [PMID: 34490723 DOI: 10.1111/resp.14142] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/08/2021] [Accepted: 08/11/2021] [Indexed: 01/11/2023]
Abstract
Despite the growing body of evidence on lung function trajectories over the life course and their risk factors, the literature has not been systematically synthesized. Publications related to lung function trajectories were identified from PubMed, EMBASE and CINAHL databases. Two authors independently identified publications for inclusion according to predefined selection criteria. Studies that modelled lung function trajectories and reported associated exposures were included. Meta-analyses could not be conducted due to heterogeneity in the exposures and methods used to model lung function trajectories. Nine publications were eligible for inclusion of which four used group-based trajectory modelling to model lung function trajectories, while five used latent profile analysis. Studies with repeated lung function measurements over the life course identified more trajectories than others. Only one study spanning from childhood to middle age reported catch-up trajectory. The following childhood risk factors for subnormal lung function trajectories were observed in at least across two studies: low birth weight, early wheezing, asthma, allergic sensitization, eczema, allergic rhinitis, lower respiratory tract infections, family history of asthma and second-hand smoke exposure. Adult active asthma and personal cigarette smoking were observed to be associated with accelerated decline lung trajectories. Our review identified 10 risk factors associated with the growth, catch-up, reduced plateau and decline trajectories of lung function. Intervention directed at childhood asthma and infections, and tobacco smoke exposure at all ages would help promote lung health and prevent subnormal lung function trajectories.
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Affiliation(s)
- Daniel O Okyere
- Allergy and Lung Health Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dinh S Bui
- Allergy and Lung Health Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - George R Washko
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Applied Chest Imaging Laboratory, Brigham and Women's Hospital, Boston, Massachusetts, USA.,Laboratory of Mathematics in Imaging, Harvard Medical School, Boston, Massachusetts, USA
| | - Caroline J Lodge
- Allergy and Lung Health Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Adrian J Lowe
- Allergy and Lung Health Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Raisa Cassim
- Allergy and Lung Health Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Jennifer L Perret
- Allergy and Lung Health Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Michael J Abramson
- School of Public Health & Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - E Haydn Walters
- Allergy and Lung Health Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia.,School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Nilakshi T Waidyatillake
- Allergy and Lung Health Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Shyamali C Dharmage
- Allergy and Lung Health Unit, Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia.,Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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Ekström M, Johannessen A, Abramson MJ, Benediktsdottir B, Franklin K, Gislason T, Gómez Real F, Holm M, Janson C, Jogi R, Lowe A, Malinovschi A, Martínez-Moratalla J, Oudin A, Sánchez-Ramos JL, Schlünssen V, Svanes C. Breathlessness across generations: results from the RHINESSA generation study. Thorax 2021; 77:172-177. [PMID: 34127557 PMCID: PMC8762033 DOI: 10.1136/thoraxjnl-2021-217271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/15/2021] [Indexed: 11/04/2022]
Abstract
Background Breathlessness is a major cause of suffering and disability globally. The symptom relates to multiple factors including asthma and lung function, which are influenced by hereditary factors. No study has evaluated potential inheritance of breathlessness itself across generations. Methods We analysed the association between breathlessness in parents and their offspring in the Respiratory Health in Northern Europe, Spain and Australia generation study. Data on parents and offspring aged ≥18 years across 10 study centres in seven countries included demographics, self-reported breathlessness, asthma, depression, smoking, physical activity level, measured Body Mass Index and spirometry. Data were analysed using multivariable logistic regression accounting for clustering within centres and between siblings. Results A total of 1720 parents (mean age at assessment 36 years, 55% mothers) and 2476 offspring (mean 30 years, 55% daughters) were included. Breathlessness was reported by 809 (32.7%) parents and 363 (14.7%) offspring. Factors independently associated with breathlessness in parents and offspring included obesity, current smoking, asthma, depression, lower lung function and female sex. After adjusting for potential confounders, parents with breathlessness were more likely to have offspring with breathlessness, adjusted OR 1.8 (95% CI 1.1 to 2.9). The association was not modified by sex of the parent or offspring. Conclusion Parents with breathlessness were more likely to have children who developed breathlessness, after adjusting for asthma, lung function, obesity, smoking, depression and female sex in both generations. The hereditary components of breathlessness need to be further explored.
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Affiliation(s)
- Magnus Ekström
- Department of Respiratory Medicine and Allergology, Lund University, Lund, Sweden
| | - Ane Johannessen
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Michael J Abramson
- School of Public Health & Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Bryndis Benediktsdottir
- Department of Sleep, Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Karl Franklin
- Department of Surgery and Perioperative Sciences, Umeå University, Umeå, Sweden
| | - Thorarinn Gislason
- Department of Sleep, Landspitali University Hospital, Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Francisco Gómez Real
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Obstetrics and Gynecology, Haukeland University Hospital, Bergen, Norway
| | - Mathias Holm
- Occupational and Environmental Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Christer Janson
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Rain Jogi
- The Lung Clinic, Tartu University Hospital, Tartu, Estonia
| | - Adrian Lowe
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Jesús Martínez-Moratalla
- Servicio de Pneumologıa del Complejo Hospitalario Universitario de Albacete (CHUA), Servicio de Salud de Castilla-La Mancha (SESCAM), Albacete, Spain
| | - Anna Oudin
- Department of Public Health and Clinical Medicine, Sustainable Health, Umeå University, Umeå, Sweden
| | | | - Vivi Schlünssen
- Department of Public Health, Environment, Work and Health, Danish Ramazzini Center, Aarhus University, Aarhus, Denmark.,Department of Public Health, Department of Public Health, Environment, Work and Health, Danish Ramazzini Center, Copenhagen, Denmark
| | - Cecilie Svanes
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.,Department of Occupational Medicine, Haukeland University Hospital, Bergen, Norway
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40
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Haider S, Simpson A, Custovic A. Genetics of Asthma and Allergic Diseases. Handb Exp Pharmacol 2021; 268:313-329. [PMID: 34085121 DOI: 10.1007/164_2021_484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Asthma genes have been identified through a range of approaches, from candidate gene association studies and family-based genome-wide linkage analyses to genome-wide association studies (GWAS). The first GWAS of asthma, reported in 2007, identified multiple markers on chromosome 17q21 as associates of the childhood-onset asthma. This remains the best replicated asthma locus to date. However, notwithstanding undeniable successes, genetic studies have produced relatively heterogeneous results with limited replication, and despite considerable promise, genetics of asthma and allergy has, so far, had limited impact on patient care, our understanding of disease mechanisms, and development of novel therapeutic targets. The paucity of precise replication in genetic studies of asthma is partly explained by the existence of numerous gene-environment interactions. Another important issue which is often overlooked is that of time of the assessment of the primary outcome(s) and the relevant environmental exposures. Most large GWASs use the broadest possible definition of asthma to increase the sample size, but the unwanted consequence of this is increased phenotypic heterogeneity, which dilutes effect sizes. One way of addressing this is to precisely define disease subtypes (e.g. by applying novel mathematical approaches to rich phenotypic data) and use these latent subtypes in genetic studies.
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Affiliation(s)
- Sadia Haider
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Adnan Custovic
- National Heart and Lung Institute, Imperial College London, London, UK.
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41
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Sikdar S, Wyss AB, Lee MK, Hoang TT, Richards M, Beane Freeman LE, Parks C, Thorne PS, Hankinson JL, Umbach DM, Motsinger-Reif A, London SJ. Interaction between Genetic Risk Scores for reduced pulmonary function and smoking, asthma and endotoxin. Thorax 2021; 76:1219-1226. [PMID: 33963087 PMCID: PMC8572320 DOI: 10.1136/thoraxjnl-2020-215624] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 02/17/2021] [Accepted: 03/22/2021] [Indexed: 01/04/2023]
Abstract
Rationale Genome-wide association studies (GWASs) have identified numerous loci associated with lower pulmonary function. Pulmonary function is strongly related to smoking and has also been associated with asthma and dust endotoxin. At the individual SNP level, genome-wide analyses of pulmonary function have not identified appreciable evidence for gene by environment interactions. Genetic Risk Scores (GRSs) may enhance power to identify gene–environment interactions, but studies are few. Methods We analysed 2844 individuals of European ancestry with 1000 Genomes imputed GWAS data from a case–control study of adult asthma nested within a US agricultural cohort. Pulmonary function traits were FEV1, FVC and FEV1/FVC. Using data from a recent large meta-analysis of GWAS, we constructed a weighted GRS for each trait by combining the top (p value<5×10−9) genetic variants, after clumping based on distance (±250 kb) and linkage disequilibrium (r2=0.5). We used linear regression, adjusting for relevant covariates, to estimate associations of each trait with its GRS and to assess interactions. Results Each trait was highly significantly associated with its GRS (all three p values<8.9×10−8). The inverse association of the GRS with FEV1/FVC was stronger for current smokers (pinteraction=0.017) or former smokers (pinteraction=0.064) when compared with never smokers and among asthmatics compared with non-asthmatics (pinteraction=0.053). No significant interactions were observed between any GRS and house dust endotoxin. Conclusions Evaluation of interactions using GRSs supports a greater impact of increased genetic susceptibility on reduced pulmonary function in the presence of smoking or asthma.
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Affiliation(s)
- Sinjini Sikdar
- Department of Mathematics and Statistics, Old Dominion University, Norfolk, Virginia, USA.,Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Annah B Wyss
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Mi Kyeong Lee
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Thanh T Hoang
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | | | - Laura E Beane Freeman
- Occupational and Environmental Epidemiology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Christine Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Peter S Thorne
- Department of Occupational and Environmental Health, University of Iowa, Iowa City, Iowa, USA
| | | | - David M Umbach
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Alison Motsinger-Reif
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, Durham, North Carolina, USA
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42
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Yamamoto R, Hwang J, Ishikawa T, Kon T, Sale WS. Composition and function of ciliary inner-dynein-arm subunits studied in Chlamydomonas reinhardtii. Cytoskeleton (Hoboken) 2021; 78:77-96. [PMID: 33876572 DOI: 10.1002/cm.21662] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/30/2021] [Accepted: 04/15/2021] [Indexed: 11/09/2022]
Abstract
Motile cilia (also interchangeably called "flagella") are conserved organelles extending from the surface of many animal cells and play essential functions in eukaryotes, including cell motility and environmental sensing. Large motor complexes, the ciliary dyneins, are present on ciliary outer-doublet microtubules and drive movement of cilia. Ciliary dyneins are classified into two general types: the outer dynein arms (ODAs) and the inner dynein arms (IDAs). While ODAs are important for generation of force and regulation of ciliary beat frequency, IDAs are essential for control of the size and shape of the bend, features collectively referred to as waveform. Also, recent studies have revealed unexpected links between IDA components and human diseases. In spite of their importance, studies on IDAs have been difficult since they are very complex and composed for several types of IDA motors, each unique in composition and location in the axoneme. Thanks in part to genetic, biochemical, and structural analysis of Chlamydomonas reinhardtii, we are beginning to understand the organization and function of the ciliary IDAs. In this review, we summarize the composition of Chlamydomonas IDAs particularly focusing on each subunit, and discuss the assembly, conservation, and functional role(s) of these IDA subunits. Furthermore, we raise several additional questions/challenges regarding IDAs, and discuss future perspectives of IDA studies.
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Affiliation(s)
- Ryosuke Yamamoto
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Juyeon Hwang
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Takashi Ishikawa
- Department of Biology and Chemistry, Paul Scherrer Institute, Villigen PSI, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Takahide Kon
- Department of Biological Sciences, Graduate School of Science, Osaka University, Osaka, Japan
| | - Winfield S Sale
- Department of Cell Biology, Emory University School of Medicine, Atlanta, Georgia, USA
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43
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Li Y, Zhang L, Polverino F, Guo F, Hao Y, Lao T, Xu S, Li L, Pham B, Owen CA, Zhou X. Hedgehog interacting protein (HHIP) represses airway remodeling and metabolic reprogramming in COPD-derived airway smooth muscle cells. Sci Rep 2021; 11:9074. [PMID: 33907231 PMCID: PMC8079715 DOI: 10.1038/s41598-021-88434-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 04/07/2021] [Indexed: 02/05/2023] Open
Abstract
Although HHIP locus has been consistently associated with the susceptibility to COPD including airway remodeling and emphysema in genome-wide association studies, the molecular mechanism underlying this genetic association remains incompletely understood. By utilizing Hhip+/- mice and primary human airway smooth muscle cells (ASMCs), here we aim to determine whether HHIP haploinsufficiency increases airway smooth muscle mass by reprogramming glucose metabolism, thus contributing to airway remodeling in COPD pathogenesis. The mRNA levels of HHIP were compared in normal and COPD-derived ASMCs. Mitochondrial oxygen consumption rate and lactate levels in the medium were measured in COPD-derived ASMCs with or without HHIP overexpression as readouts of glucose oxidative phosphorylation and aerobic glycolysis rates. The proliferation rate was measured in healthy and COPD-derived ASMCs treated with or without 2-DG. Smooth muscle mass around airways was measured by immunofluorescence staining for α-smooth muscle actin (α-SMA) in lung sections from Hhip+/- mice and their wild type littermates, Hhip+/+ mice. Airway remodeling was assessed in Hhip+/- and Hhip+/- mice exposed to 6 months of cigarette smoke. Our results show HHIP inhibited aerobic glycolysis and represses cell proliferation in COPD-derived ASMCs. Notably, knockdown of HHIP in normal ASMCs increased PKM2 activity. Importantly, Hhip+/- mice demonstrated increased airway remodeling and increased intensity of α-SMA staining around airways compared to Hhip+/+ mice. In conclusion, our findings suggest that HHIP represses aerobic glycolysis and ASMCs hyperplasia, which may contribute to the increased airway remodeling in Hhip+/- mice.
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Affiliation(s)
- Yan Li
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong Province, China.
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong Province, China.
| | - Li Zhang
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Integrated Traditional Chinese and Western Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Francesca Polverino
- Asthma and Airway Disease Research Center, University of Arizona, Medicine, Tucson, AZ, 85724, USA
| | - Feng Guo
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yuan Hao
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Taotao Lao
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Boston, MA, 02129, USA
| | - Shuang Xu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Lijia Li
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Betty Pham
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Caroline A Owen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
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Fieldes M, Bourguignon C, Assou S, Nasri A, Fort A, Vachier I, De Vos J, Ahmed E, Bourdin A. Targeted therapy in eosinophilic chronic obstructive pulmonary disease. ERJ Open Res 2021; 7:00437-2020. [PMID: 33855061 PMCID: PMC8039900 DOI: 10.1183/23120541.00437-2020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a common and preventable airway disease causing significant worldwide mortality and morbidity. Lifetime exposure to tobacco smoking and environmental particles are the two major risk factors. Over recent decades, COPD has become a growing public health problem with an increase in incidence. COPD is defined by airflow limitation due to airway inflammation and small airway remodelling coupled to parenchymal lung destruction. Most patients exhibit neutrophil-predominant airway inflammation combined with an increase in macrophages and CD8+ T-cells. Asthma is a heterogeneous chronic inflammatory airway disease. The most studied subtype is type 2 (T2) high eosinophilic asthma, for which there are an increasing number of biologic agents developed. However, both asthma and COPD are complex and share common pathophysiological mechanisms. They are known as overlapping syndromes as approximately 40% of patients with COPD present an eosinophilic airway inflammation. Several studies suggest a putative role of eosinophilia in lung function decline and COPD exacerbation. Recently, pharmacological agents targeting eosinophilic traits in uncontrolled eosinophilic asthma, especially monoclonal antibodies directed against interleukins (IL-5, IL-4, IL-13) or their receptors, have shown promising results. This review examines data on the rationale for such biological agents and assesses efficacy in T2-endotype COPD patients. Patients with severe COPD and eosinophilic inflammation experience uncontrolled symptoms despite optimal pharmaceutical treatment. The development of new biomarkers is needed for better phenotyping of patients to propose innovative targeted therapy.https://bit.ly/2KzWuNO
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Affiliation(s)
- Mathieu Fieldes
- IRMB, INSERM, Montpellier University Hospital, Montpellier, France
| | | | - Said Assou
- IRMB, INSERM, Montpellier University Hospital, Montpellier, France
| | - Amel Nasri
- IRMB, INSERM, Montpellier University Hospital, Montpellier, France
| | - Aurélie Fort
- Dept of Respiratory Diseases, Montpellier University Hospital, INSERM, Montpellier, France.,PhyMedExp, University of Montpellier, INSERM U1046, Montpellier, France
| | - Isabelle Vachier
- Dept of Respiratory Diseases, Montpellier University Hospital, INSERM, Montpellier, France
| | - John De Vos
- IRMB, INSERM, Montpellier University Hospital, Montpellier, France.,Dept of Cell and Tissue Engineering, Montpellier University Hospital, Montpellier, France
| | - Engi Ahmed
- Dept of Respiratory Diseases, Montpellier University Hospital, INSERM, Montpellier, France
| | - Arnaud Bourdin
- Dept of Respiratory Diseases, Montpellier University Hospital, INSERM, Montpellier, France.,PhyMedExp, University of Montpellier, INSERM U1046, Montpellier, France
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Nichols CE, House JS, Li H, Ward JM, Wyss A, Williams JG, Deterding LJ, Bradbury JA, Miller L, Zeldin DC, London SJ. Lrp1 Regulation of Pulmonary Function. Follow-Up of Human GWAS in Mice. Am J Respir Cell Mol Biol 2021; 64:368-378. [PMID: 33290178 DOI: 10.1165/rcmb.2019-0444oc] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Human genome-wide association studies (GWASs) have identified more than 270 loci associated with pulmonary function; however, follow-up studies to determine causal genes at these loci are few. SNPs in low-density lipoprotein receptor-related protein 1 (LRP1) are associated with human pulmonary function in GWASs. Using murine models, we investigated the effect of genetic disruption of the Lrp1 gene in smooth muscle cells on pulmonary function in naive animals and after exposure to bacterial LPS or house dust mite extract. Disruption of Lrp1 in smooth muscle cells leads to an increase in tissue resistance, elastance, and tissue elastance at baseline. Furthermore, disruption of Lrp1 in smooth muscle increases airway responsiveness as measured by increased total lung resistance and airway resistance after methacholine. Immune cell counts in BAL fluid were increased in animals with Lrp1 disruption. The difference in airway responsiveness by genotype observed in naive animals was not observed after LPS or house dust mite extract exposure. To further explore the mechanisms contributing to changes in pulmonary function, we identified several ligands dysregulated with Lrp1 disruption in smooth muscle cells. These data suggest that dysregulation of LRP1 in smooth muscle cells affects baseline pulmonary function and airway responsiveness and helps establish LRP1 as the causal gene at this GWAS locus.
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Affiliation(s)
| | | | - Huiling Li
- Immunity, Inflammation, and Disease Laboratory
| | | | | | - Jason G Williams
- Mass Spectrometry Research and Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina
| | - Leesa J Deterding
- Mass Spectrometry Research and Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina
| | | | | | | | - Stephanie J London
- Immunity, Inflammation, and Disease Laboratory.,Epidemiology Branch, and
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46
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Yao X, Levine SJ. The Long and Winding Road from GWAS to Obstructive Lung Disease: Is There a Role for LRP1? Am J Respir Cell Mol Biol 2021; 64:279-280. [PMID: 33352084 PMCID: PMC7909341 DOI: 10.1165/rcmb.2020-0567ed] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Affiliation(s)
- Xianglan Yao
- Laboratory of Asthma and Lung Inflammation National Heart, Lung, and Blood Institute, National Institutes of Health Bethesda, Maryland
| | - Stewart J Levine
- Laboratory of Asthma and Lung Inflammation National Heart, Lung, and Blood Institute, National Institutes of Health Bethesda, Maryland
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Stanojevic S. Socioeconomic disadvantage and lung health: accumulating evidence to support health policy. Eur Respir J 2021; 57:57/3/2004025. [PMID: 33737378 DOI: 10.1183/13993003.04025-2020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 11/05/2022]
Affiliation(s)
- Sanja Stanojevic
- Dept of Community Health and Epidemiology, Dalhousie University, Halifax, NS, Canada
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48
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Lee KS, Kim KH, Oh YM, Han B, Kim WJ. A genome wide association study for lung function in the Korean population using an exome array. Korean J Intern Med 2021; 36:S142-S150. [PMID: 32336055 PMCID: PMC8009153 DOI: 10.3904/kjim.2019.204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND/AIMS Lung function is an objective indicator of diagnosis and prognosis of respiratory diseases. Many common genetic variants have been associated with lung function in multiple ethnic populations. We looked for coding variants associated with forced expiratory volume in 1 second (FEV1) and FEV1/forced vital capacity (FVC) in the Korean general population. METHODS We carried out exome array analysis and lung function measurements of the FEV1 and FEV1/FVC in 7,524 individuals of the Korean population. We evaluated single variants with minor allele frequency greater than 0.5%. We performed look-ups for candidate coding variants associations in the UK Biobank, SpiroMeta, and CHARGE consortia. RESULTS We identified coding variants in the SMIM29 (C6orf1) (p = 1.2 × 10-5) and HMGA1 locus on chromosome 6p21, the GIT2 (p = 6.5 × 10-5) locus on chromosome 12q24, and the ARHGEF40 (p = 9.9 × 10-5) locus on chromosome 14q11 as having a significant association with lung function (FEV1). We also confirmed a previously reported association with lung function and chronic obstructive pulmonary disease in the FAM13A (p = 4.54 × 10-6) locus on chromosome 4q22, in TNXB (p = 1.30 × 10-6) and in AGER (p = 1.09 × 10-8) locus on chromosome 6p21. CONCLUSION Our exome array analysis identified that several protein coding variants were associated with lung function in the Korean population. Common coding variants in SMIM29 (C6orf1), HMGA1, GIT2, FAM13A, TNXB, AGER and low-frequency variant in ARHGEF40 potentially affect lung function, which warrant further study.
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Affiliation(s)
- Kyu-Sun Lee
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
| | - Kun Hee Kim
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Yeon-Mok Oh
- Department of Pulmonary and Critical Care Medicine and Clinical Research Center for Chronic Obstructive Airway Disease, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Buhm Han
- Department of Medical Science, Seoul National University College of Medicine, Seoul, Korea
| | - Woo Jin Kim
- Department of Internal Medicine, Kangwon National University School of Medicine, Chuncheon, Korea
- Correspondence to Woo Jin Kim, M.D. Department of Internal Medicine, Kangwon National University School of Medicine, 156 Baengnyeong-ro, Chuncheon 24289, Korea Tel: +82-33-250-7815 Fax: +82-33-255-6567 E-mail:
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49
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Next Generation Exome Sequencing of Pediatric Asthma Identifies Rare and Novel Variants in Candidate Genes. DISEASE MARKERS 2021; 2021:8884229. [PMID: 33628342 PMCID: PMC7888305 DOI: 10.1155/2021/8884229] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/21/2021] [Accepted: 02/03/2021] [Indexed: 12/16/2022]
Abstract
Multiple genes have been implicated to have a role in asthma predisposition by association studies. Pediatric patients often manifest a more extensive form of this disease and a particularly severe disease course. It is likely that genetic predisposition could play a more substantial role in this group. This study is aimed at identifying the spectrum of rare and novel variation in known pediatric asthma susceptibility genes using whole exome sequencing analysis in nine individual cases of childhood onset allergic asthma. DNA samples from the nine children with a history of bronchial asthma diagnosis underwent whole exome sequencing on Ion Proton. For each patient, the entire complement of rare variation within strongly associated candidate genes was catalogued. The analysis showed 21 variants in the subjects, 13 had been previously identified, and 8 were novel. Also, among of which, nineteen were nonsynonymous and 2 were nonsense. With regard to the novel variants, the 2 nonsynonymous variants in the PRKG1 gene (PRKG1: p.C519W and PRKG1: p.G520W) were presented in 4 cases, and a nonsynonymous variant in the MAVS gene (MAVS: p.A45V) was identified in 3 cases. The variants we found in this study will enrich the variant spectrum and build up the database in the Saudi population. Novel eight variants were identified in the study which provides more evidence in the genetic susceptibility in asthma among Saudi children, providing a genetic screening map for the molecular genetic determinants of allergic disease in Saudi children, with the goal of reducing the impact of chronic diseases on the health and the economy. We believe that the advanced specified statistical filtration/annotation programs used in this study succeeded to release such results in a preliminary study, exploring the genetic map of that disease in Saudi children.
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50
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Papanikolaou M, Crump SM, Abbott GW. The focal adhesion protein Testin modulates KCNE2 potassium channel β subunit activity. Channels (Austin) 2021; 15:229-238. [PMID: 33464998 PMCID: PMC7833772 DOI: 10.1080/19336950.2021.1874119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Coronary Artery Disease (CAD) typically kills more people globally each year than any other single cause of death. A better understanding of genetic predisposition to CAD and the underlying mechanisms will help to identify those most at risk and contribute to improved therapeutic approaches. KCNE2 is a functionally versatile, ubiquitously expressed potassium channel β subunit associated with CAD and cardiac arrhythmia susceptibility in humans and mice. Here, to identify novel KCNE2 interaction partners, we employed yeast two-hybrid screening of adult and fetal human heart libraries using the KCNE2 intracellular C-terminal domain as bait. Testin (encoded by TES), an endothelial cell-expressed, CAD-associated, focal adhesion protein, was identified as a high-confidence interaction partner for KCNE2. We confirmed physical association between KCNE2 and Testin in vitro by co-immunoprecipitation. Whole-cell patch clamp electrophysiology revealed that KCNE2 negative-shifts the voltage dependence and increases the rate of activation of the endothelial cell and cardiomyocyte-expressed Kv channel α subunit, Kv1.5 in CHO cells, whereas Testin did not alter Kv1.5 function. However, Testin nullified KCNE2 effects on Kv1.5 voltage dependence and gating kinetics. In contrast, Testin did not prevent KCNE2 regulation of KCNQ1 gating. The data identify a novel role for Testin as a tertiary ion channel regulatory protein. Future studies will address the potential role for KCNE2-Testin interactions in arterial and myocyte physiology and CAD.
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Affiliation(s)
- Maria Papanikolaou
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California , Irvine, CA, USA
| | - Shawn M Crump
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California , Irvine, CA, USA
| | - Geoffrey W Abbott
- Bioelectricity Laboratory, Department of Physiology and Biophysics, School of Medicine, University of California , Irvine, CA, USA
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