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Castaldi PJ, Sauler M. Molecular Characterization of the Distal Lung: Novel Insights from Chronic Obstructive Pulmonary Disease Omics. Am J Respir Crit Care Med 2024; 210:147-154. [PMID: 38701385 PMCID: PMC11273319 DOI: 10.1164/rccm.202310-1972pp] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/02/2024] [Indexed: 05/05/2024] Open
Affiliation(s)
- Peter J. Castaldi
- Channing Division of Network Medicine and
- Division of General Internal Medicine and Primary Care, Brigham and Women’s Hospital, Boston, Massachusetts; and
| | - Maor Sauler
- Division of Pulmonary, Critical Care, and Sleep Medicine, School of Medicine, Yale University, New Haven, Connecticut
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2
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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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Chen K, Han Y, Wang Y, Zhou D, Wu F, Cai W, Zheng S, Xiao Q, Zhang H, Li W. scMoresDB: A comprehensive database of single-cell multi-omics data for human respiratory system. iScience 2024; 27:109567. [PMID: 38617561 PMCID: PMC11015448 DOI: 10.1016/j.isci.2024.109567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/26/2023] [Accepted: 03/22/2024] [Indexed: 04/16/2024] Open
Abstract
The human respiratory system is a complex and important system that can suffer a variety of diseases. Single-cell sequencing technologies, applied in many respiratory disease studies, have enhanced our ability in characterizing molecular and phenotypic features at a single-cell resolution. The exponentially increasing data from these studies have consequently led to difficulties in data sharing and analysis. Here, we present scMoresDB, a single-cell multi-omics database platform with extensive omics types tailored for human respiratory diseases. scMoresDB re-analyzes single-cell multi-omics datasets, providing a user-friendly interface with cross-omics search capabilities, interactive visualizations, and analytical tools for comprehensive data sharing and integrative analysis. Our example applications highlight the potential significance of BSG receptor in SARS-CoV-2 infection as well as the involvement of HHIP and TGFB2 in the development and progression of chronic obstructive pulmonary disease. scMoresDB significantly increases accessibility and utility of single-cell data relevant to human respiratory system and associated diseases.
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Affiliation(s)
- Kang Chen
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Yutong Han
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Yanni Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Dingli Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Fanjie Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Wenhao Cai
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Shikang Zheng
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Qinyuan Xiao
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Haiyue Zhang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
| | - Weizhong Li
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
- Key Laboratory of Tropical Disease Control of Ministry of Education, Sun Yat-Sen University, Guangzhou 510080, Guangdong Province, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, Guangdong Province, China
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4
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Deritei D, Inuzuka H, Castaldi PJ, Yun JH, Xu Z, Anamika WJ, Asara JM, Guo F, Zhou X, Glass K, Wei W, Silverman EK. HHIP protein interactions in lung cells provide insight into COPD pathogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.586839. [PMID: 38617310 PMCID: PMC11014494 DOI: 10.1101/2024.04.01.586839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Chronic obstructive pulmonary disease (COPD) is the third leading cause of death worldwide. The primary causes of COPD are environmental, including cigarette smoking; however, genetic susceptibility also contributes to COPD risk. Genome-Wide Association Studies (GWASes) have revealed more than 80 genetic loci associated with COPD, leading to the identification of multiple COPD GWAS genes. However, the biological relationships between the identified COPD susceptibility genes are largely unknown. Genes associated with a complex disease are often in close network proximity, i.e. their protein products often interact directly with each other and/or similar proteins. In this study, we use affinity purification mass spectrometry (AP-MS) to identify protein interactions with HHIP , a well-established COPD GWAS gene which is part of the sonic hedgehog pathway, in two disease-relevant lung cell lines (IMR90 and 16HBE). To better understand the network neighborhood of HHIP , its proximity to the protein products of other COPD GWAS genes, and its functional role in COPD pathogenesis, we create HUBRIS, a protein-protein interaction network compiled from 8 publicly available databases. We identified both common and cell type-specific protein-protein interactors of HHIP. We find that our newly identified interactions shorten the network distance between HHIP and the protein products of several COPD GWAS genes, including DSP, MFAP2, TET2 , and FBLN5 . These new shorter paths include proteins that are encoded by genes involved in extracellular matrix and tissue organization. We found and validated interactions to proteins that provide new insights into COPD pathobiology, including CAVIN1 (IMR90) and TP53 (16HBE). The newly discovered HHIP interactions with CAVIN1 and TP53 implicate HHIP in response to oxidative stress.
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5
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Guo F, Zhang L, Yu Y, Gong L, Tao S, Werder RB, Mishra S, Zhou Y, Anamika WJ, Lao T, Inuzuka H, Zhang Y, Pham B, Liu T, Tufenkjian TS, Richmond BW, Wei W, Mou H, Wilson AA, Hu M, Chen W, Zhou X. Identification of a distal enhancer regulating hedgehog interacting protein gene in human lung epithelial cells. EBioMedicine 2024; 101:105026. [PMID: 38417378 PMCID: PMC10944180 DOI: 10.1016/j.ebiom.2024.105026] [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: 05/22/2023] [Revised: 01/26/2024] [Accepted: 02/06/2024] [Indexed: 03/01/2024] Open
Abstract
BACKGROUND An intergenic region at chromosome 4q31 is one of the most significant regions associated with COPD susceptibility and lung function in GWAS. In this region, the implicated causal gene HHIP has a unique epithelial expression pattern in adult human lungs, in contrast to dominant expression in fibroblasts in murine lungs. However, the mechanism underlying the species-dependent cell type-specific regulation of HHIP remains largely unknown. METHODS We employed snATAC-seq analysis to identify open chromatin regions within the COPD GWAS region in various human lung cell types. ChIP-quantitative PCR, reporter assays, chromatin conformation capture assays and Hi-C assays were conducted to characterize the regulatory element in this region. CRISPR/Cas9-editing was performed in BEAS-2B cells to generate single colonies with stable knockout of the regulatory element. RT-PCR and Western blot assays were used to evaluate expression of HHIP and epithelial-mesenchymal transition (EMT)-related marker genes. FINDINGS We identified a distal enhancer within the COPD 4q31 GWAS locus that regulates HHIP transcription at baseline and after TGFβ treatment in a SMAD3-dependent, but Hedgehog-independent manner in human bronchial epithelial cells. The distal enhancer also maintains chromatin topological domains near 4q31 locus and HHIP gene. Reduced HHIP expression led to increased EMT induced by TGFβ in human bronchial epithelial cells. INTERPRETATION A distal enhancer regulates HHIP expression both under homeostatic condition and upon TGFβ treatment in human bronchial epithelial cells. The interaction between HHIP and TGFβ signalling possibly contributes to COPD pathogenesis. FUNDING Supported by NIH grants R01HL127200, R01HL148667 and R01HL162783 (to X. Z).
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Affiliation(s)
- Feng Guo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China.
| | - Li Zhang
- Channing Division of Network Medicine, Department of 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, Sichuan 610041, China
| | - Yuzhen Yu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Lu Gong
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Shiyue Tao
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - 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
| | - Shreya Mishra
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Yihan Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Wardatul Jannat Anamika
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Taotao Lao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Yihan Zhang
- The Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Betty Pham
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tao Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Tiffany S Tufenkjian
- Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA; Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Bradley W Richmond
- Department of Veterans Affairs Medical Center, Nashville, TN 37232, USA; Division of Allergy, Pulmonary, and Critical Care Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Hongmei Mou
- The Mucosal Immunology and Biology Research Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, 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
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195, USA
| | - Wei Chen
- Department of Biostatistics, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15224, USA; Division of Pediatric Pulmonary Medicine, UPMC Children's Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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Rojas-Quintero J, Ochsner SA, New F, Divakar P, Yang CX, Wu TD, Robinson J, Chandrashekar DS, Banovich NE, Rosas IO, Sauler M, Kheradmand F, Gaggar A, Margaroli C, San Jose Estepar R, McKenna NJ, Polverino F. Spatial Transcriptomics Resolve an Emphysema-Specific Lymphoid Follicle B Cell Signature in Chronic Obstructive Pulmonary Disease. Am J Respir Crit Care Med 2024; 209:48-58. [PMID: 37934672 PMCID: PMC10870877 DOI: 10.1164/rccm.202303-0507le] [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: 03/15/2023] [Accepted: 10/15/2023] [Indexed: 11/09/2023] Open
Abstract
Rationale: Within chronic obstructive pulmonary disease (COPD), emphysema is characterized by a significant yet partially understood B cell immune component. Objectives: To characterize the transcriptomic signatures from lymphoid follicles (LFs) in ever-smokers without COPD and patients with COPD with varying degrees of emphysema. Methods: Lung sections from 40 patients with COPD and ever-smokers were used for LF proteomic and transcriptomic spatial profiling. Formalin- and O.C.T.-fixed lung samples obtained from biopsies or lung explants were assessed for LF presence. Emphysema measurements were obtained from clinical chest computed tomographic scans. High-confidence transcriptional target intersection analyses were conducted to resolve emphysema-induced transcriptional networks. Measurements and Main Results: Overall, 115 LFs from ever-smokers and Global Initiative for Chronic Obstructive Lung Disease (GOLD) 1-2 and GOLD 3-4 patients were analyzed. No LFs were found in never-smokers. Differential gene expression analysis revealed significantly increased expression of LF assembly and B cell marker genes in subjects with severe emphysema. High-confidence transcriptional analysis revealed activation of an abnormal B cell activity signature in LFs (q-value = 2.56E-111). LFs from patients with GOLD 1-2 COPD with emphysema showed significantly increased expression of genes associated with antigen presentation, inflammation, and B cell activation and proliferation. LFs from patients with GOLD 1-2 COPD without emphysema showed an antiinflammatory profile. The extent of centrilobular emphysema was significantly associated with genes involved in B cell maturation and antibody production. Protein-RNA network analysis showed that LFs in emphysema have a unique signature skewed toward chronic B cell activation. Conclusions: An off-targeted B cell activation within LFs is associated with autoimmune-mediated emphysema pathogenesis.
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Affiliation(s)
| | - Scott A. Ochsner
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Felicia New
- Spatial Data Analysis Services, Nanostring Biotechnologies, Seattle, Washington
| | - Prajan Divakar
- Spatial Data Analysis Services, Nanostring Biotechnologies, Seattle, Washington
| | - Chen Xi Yang
- Center for Heart Lung Innovation, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Jerid Robinson
- Field Application Scientists, Nanostring Biotechnologies, Seattle, Washington
| | | | | | | | - Maor Sauler
- Pulmonary and Critical Care Medicine, Yale University, New Haven, Connecticut
| | - Farrah Kheradmand
- Pulmonary Division, Department of Medicine, and
- Michael E. DeBakey Veterans Affairs Medical Center, Houston, Texas
| | - Amit Gaggar
- Pulmonary and Critical Care Medicine, and
- Birmingham Veterans Affairs Medical Center, Birmingham, Alabama; and
| | - Camilla Margaroli
- Pathology – Division of Cellular and Molecular Pathology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Raul San Jose Estepar
- Applied Chest Imaging Laboratory, Department of Radiology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts
| | - Neil J. McKenna
- Spatial Data Analysis Services, Nanostring Biotechnologies, Seattle, Washington
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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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8
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Yuan J, Wang T, Wang L, Li P, Shen H, Mo Y, Zhang Q, Ni C. Transcriptome-wide association study identifies PSMB9 as a susceptibility gene for coal workers' pneumoconiosis. ENVIRONMENTAL TOXICOLOGY 2022; 37:2103-2114. [PMID: 35506645 DOI: 10.1002/tox.23554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 04/13/2022] [Accepted: 04/23/2022] [Indexed: 06/14/2023]
Abstract
Coal workers' pneumoconiosis (CWP) is a type of typical occupational lung disease caused by prolonged inhalation of coal mine dust. The individuals' different genetic background may underlie their different susceptibility to develop pneumoconiosis, even under the same exposure level. This study aimed to identify susceptibility genes associated with CWP. Based on our previous genome-wide association study (GWAS, 202 CWP cases vs. 198 controls) and gene expression data obtained by analyzing human lungs and whole blood from the Genotype-Tissue Expression (GTEx) Portal, a transcriptome-wide association study (TWAS) was applied to identify CWP risk-related genes. Luciferase report gene assay, qRT-PCR, Western blot, immunofluorescence assay, and TUNEL assay were conducted to explore the potential role of the candidate gene in CWP. Proteasome 20S subunit beta 9 (PSMB9) was identified as a strong risk-related gene of CWP in both lungs and whole blood (Lungs: PTWAS = 4.22 × 10-4 ; Whole blood: PTWAS = 2.11 × 10-4 ). Single nucleotide polymorphisms (SNPs) rs2071480 and rs1351383, which locate in the promoter region and the first intron of the PSMB9 gene, were in high linkage disequilibrium (LD, r2 = 0.98) with the best GWAS SNP rs4713600 (G>T, OR = 0.55, 95% CI: 0.42-0.74, P = 6.86 × 10-5 ). Both rs2071480 and rs1351383 significantly enhanced the transcriptional activity of PSMB9. Functional experiments revealed that silica exposure remarkably reduced the PSMB9 expression and caused cell apoptosis, while overexpression of PSMB9 markedly abolished silica-induced cell apoptosis. We here identified PSMB9 as a novel susceptibility gene for CWP and provided important insights into the further exploration of the CWP pathogenesis.
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Affiliation(s)
- Jiali Yuan
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ting Wang
- Department of Pathology, The Affiliated Drum Tower Hospital, Medical School of Nanjing University, Nanjing, China
| | - Lijuan Wang
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Ping Li
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yiqun Mo
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, Louisville, Kentucky, USA
| | - Qunwei Zhang
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, Louisville, Kentucky, USA
| | - Chunhui Ni
- Center for Global Health, Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, China
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9
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Lin CR, Bahmed K, Kosmider B. Impaired Alveolar Re-Epithelialization in Pulmonary Emphysema. Cells 2022; 11:2055. [PMID: 35805139 PMCID: PMC9265977 DOI: 10.3390/cells11132055] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 01/24/2023] Open
Abstract
Alveolar type II (ATII) cells are progenitors in alveoli and can repair the alveolar epithelium after injury. They are intertwined with the microenvironment for alveolar epithelial cell homeostasis and re-epithelialization. A variety of ATII cell niches, transcription factors, mediators, and signaling pathways constitute a specific environment to regulate ATII cell function. Particularly, WNT/β-catenin, YAP/TAZ, NOTCH, TGF-β, and P53 signaling pathways are dynamically involved in ATII cell proliferation and differentiation, although there are still plenty of unknowns regarding the mechanism. However, an imbalance of alveolar cell death and proliferation was observed in patients with pulmonary emphysema, contributing to alveolar wall destruction and impaired gas exchange. Cigarette smoking causes oxidative stress and is the primary cause of this disease development. Aberrant inflammatory and oxidative stress responses result in loss of cell homeostasis and ATII cell dysfunction in emphysema. Here, we discuss the current understanding of alveolar re-epithelialization and altered reparative responses in the pathophysiology of this disease. Current therapeutics and emerging treatments, including cell therapies in clinical trials, are addressed as well.
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Affiliation(s)
- Chih-Ru Lin
- Department of Microbiology, Immunology and Inflammation, Temple University, Philadelphia, PA 19140, USA;
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA 19140, USA;
| | - Karim Bahmed
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA 19140, USA;
- Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA 19140, USA
| | - Beata Kosmider
- Department of Microbiology, Immunology and Inflammation, Temple University, Philadelphia, PA 19140, USA;
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA 19140, USA;
- Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA 19140, USA
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10
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Cho MH, Hobbs BD, Silverman EK. Genetics of chronic obstructive pulmonary disease: understanding the pathobiology and heterogeneity of a complex disorder. THE LANCET. RESPIRATORY MEDICINE 2022; 10:485-496. [PMID: 35427534 PMCID: PMC11197974 DOI: 10.1016/s2213-2600(21)00510-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/20/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) is a deadly and highly morbid disease. Susceptibility to and heterogeneity of COPD are incompletely explained by environmental factors such as cigarette smoking. Family-based and population-based studies have shown that a substantial proportion of COPD risk is related to genetic variation. Genetic association studies have identified hundreds of genetic variants that affect risk for COPD, decreased lung function, and other COPD-related traits. These genetic variants are associated with other pulmonary and non-pulmonary traits, demonstrate a genetic basis for at least part of COPD heterogeneity, have a substantial effect on COPD risk in aggregate, implicate early-life events in COPD pathogenesis, and often involve genes not previously suspected to have a role in COPD. Additional progress will require larger genetic studies with more ancestral diversity, improved profiling of rare variants, and better statistical methods. Through integration of genetic data with other omics data and comprehensive COPD phenotypes, as well as functional description of causal mechanisms for genetic risk variants, COPD genetics will continue to inform novel approaches to understanding the pathobiology of COPD and developing new strategies for management and treatment.
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Affiliation(s)
- Michael H Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Brian D Hobbs
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
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11
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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12
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Pompe E, Mohamed Hoesein FAA. Role of visual assessment of chronic obstructive pulmonary disease on chest CT: beauty is in the eye of the beholder. J Thorac Dis 2022; 13:6936-6939. [PMID: 35070377 PMCID: PMC8743402 DOI: 10.21037/jtd-21-1527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/12/2021] [Indexed: 11/25/2022]
Affiliation(s)
- Esther Pompe
- Department of Radiology, University Medical Center Utrecht, Utrecht, The Netherlands
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13
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Lin CR, Bahmed K, Kosmider B. Dysregulated Cell Signaling in Pulmonary Emphysema. Front Med (Lausanne) 2022; 8:762878. [PMID: 35047522 PMCID: PMC8762198 DOI: 10.3389/fmed.2021.762878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/06/2021] [Indexed: 01/19/2023] Open
Abstract
Pulmonary emphysema is characterized by the destruction of alveolar septa and irreversible airflow limitation. Cigarette smoking is the primary cause of this disease development. It induces oxidative stress and disturbs lung physiology and tissue homeostasis. Alveolar type II (ATII) cells have stem cell potential and can repair the denuded epithelium after injury; however, their dysfunction is evident in emphysema. There is no effective treatment available for this disease. Challenges in this field involve the large complexity of lung pathophysiological processes and gaps in our knowledge on the mechanisms of emphysema progression. It implicates dysregulation of various signaling pathways, including aberrant inflammatory and oxidative responses, defective antioxidant defense system, surfactant dysfunction, altered proteostasis, disrupted circadian rhythms, mitochondrial damage, increased cell senescence, apoptosis, and abnormal proliferation and differentiation. Also, genetic predispositions are involved in this disease development. Here, we comprehensively review studies regarding dysregulated cell signaling, especially in ATII cells, and their contribution to alveolar wall destruction in emphysema. Relevant preclinical and clinical interventions are also described.
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Affiliation(s)
- Chih-Ru Lin
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States
| | - Karim Bahmed
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA, United States
| | - Beata Kosmider
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States
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14
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Miller PG, Qiao D, Rojas-Quintero J, Honigberg MC, Sperling AS, Gibson CJ, Bick AG, Niroula A, McConkey ME, Sandoval B, Miller BC, Shi W, Viswanathan K, Leventhal M, Werner L, Moll M, Cade BE, Barr RG, Correa A, Cupples LA, Gharib SA, Jain D, Gogarten SM, Lange LA, London SJ, Manichaikul A, O'Connor GT, Oelsner EC, Redline S, Rich SS, Rotter JI, Ramachandran V, Yu B, Sholl L, Neuberg D, Jaiswal S, Levy BD, Owen CA, Natarajan P, Silverman EK, van Galen P, Tesfaigzi Y, Cho MH, Ebert BL. Association of clonal hematopoiesis with chronic obstructive pulmonary disease. Blood 2022; 139:357-368. [PMID: 34855941 PMCID: PMC8777202 DOI: 10.1182/blood.2021013531] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 09/02/2021] [Indexed: 02/02/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is associated with age and smoking, but other determinants of the disease are incompletely understood. Clonal hematopoiesis of indeterminate potential (CHIP) is a common, age-related state in which somatic mutations in clonal blood populations induce aberrant inflammatory responses. Patients with CHIP have an elevated risk for cardiovascular disease, but the association of CHIP with COPD remains unclear. We analyzed whole-genome sequencing and whole-exome sequencing data to detect CHIP in 48 835 patients, of whom 8444 had moderate to very severe COPD, from four separate cohorts with COPD phenotyping and smoking history. We measured emphysema in murine models in which Tet2 was deleted in hematopoietic cells. In the COPDGene cohort, individuals with CHIP had risks of moderate-to-severe, severe, or very severe COPD that were 1.6 (adjusted 95% confidence interval [CI], 1.1-2.2) and 2.2 (adjusted 95% CI, 1.5-3.2) times greater than those for noncarriers. These findings were consistently observed in three additional cohorts and meta-analyses of all patients. CHIP was also associated with decreased FEV1% predicted in the COPDGene cohort (mean between-group differences, -5.7%; adjusted 95% CI, -8.8% to -2.6%), a finding replicated in additional cohorts. Smoke exposure was associated with a small but significant increased risk of having CHIP (odds ratio, 1.03 per 10 pack-years; 95% CI, 1.01-1.05 per 10 pack-years) in the meta-analysis of all patients. Inactivation of Tet2 in mouse hematopoietic cells exacerbated the development of emphysema and inflammation in models of cigarette smoke exposure. Somatic mutations in blood cells are associated with the development and severity of COPD, independent of age and cumulative smoke exposure.
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Affiliation(s)
- Peter G Miller
- Department of Medical Oncology, Dana-Farber Cancer Institute, and
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, and
| | | | - Michael C Honigberg
- Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of Harvard, Cambridge, MA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Adam S Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, and
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Christopher J Gibson
- Department of Medical Oncology, Dana-Farber Cancer Institute, and
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN
| | - Abhishek Niroula
- Department of Medical Oncology, Dana-Farber Cancer Institute, and
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Marie E McConkey
- Department of Medical Oncology, Dana-Farber Cancer Institute, and
| | | | - Brian C Miller
- Department of Medical Oncology, Dana-Farber Cancer Institute, and
| | - Weiwei Shi
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | | | - Matthew Leventhal
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - Lillian Werner
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA
| | - Matthew Moll
- Channing Division of Network Medicine, Department of Medicine, and
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA
| | - R Graham Barr
- Department of Medicine and Department of Epidemiology, Columbia University Medical Center, New York, NY
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
- Framingham Heart Study, Framingham, MA
| | - Sina A Gharib
- Computational Medicine Core, Center for Lung Biology, and
- Division of Pulmonary, Critical Care, and Sleep Medicine, Department of Medicine, and
| | - Deepti Jain
- Department of Biostatistics, University of Washington, Seattle, WA
| | | | - Leslie A Lange
- University of Colorado Anschutz Medical Campus, Denver, CO
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC
| | - Ani Manichaikul
- Center for Public Health Genomics and
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - George T O'Connor
- Division of Pulmonary, Allergy, Sleep, and Critical Care Medicine, Department of Medicine, Boston University School of Medicine, Boston, MA
| | | | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA
| | - Stephen S Rich
- Center for Public Health Genomics and
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-University of California-Los Angeles Medical Center, Torrance, CA
| | - Vasan Ramachandran
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
- Framingham Heart Study, Framingham, MA
- Preventive Medicine Section, Epidemiology Section, and Cardiovascular Medicine Section, Department of Medicine, Boston University School of Medicine, Boston, MA
- Department of Epidemiology, Boston University Center for Computing and Data Science, Boston University School of Public Health, Boston, MA
| | - Bing Yu
- University of Texas Health Science Center, School of Public Health, Houston, TX
| | - Lynette Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA
| | - Donna Neuberg
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA
| | | | - Bruce D Levy
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and
| | - Caroline A Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and
| | - Pradeep Natarajan
- Cardiology Division, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- Program in Medical and Population Genetics, Broad Institute of Harvard, Cambridge, MA
- Cardiovascular Research Center and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, and
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and
| | - Peter van Galen
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Yohannes Tesfaigzi
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and
| | - Michael H Cho
- Channing Division of Network Medicine, Department of Medicine, and
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, and
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, and
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Bethesda, MD
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15
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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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16
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Hikino K, Koido M, Tomizuka K, Liu X, Momozawa Y, Morisaki T, Murakami Y, The Biobank Japan Project, Mushiroda T, Terao C. Susceptibility loci and polygenic architecture highlight population specific and common genetic features in inguinal hernias: genetics in inguinal hernias. EBioMedicine 2021; 70:103532. [PMID: 34392144 PMCID: PMC8374389 DOI: 10.1016/j.ebiom.2021.103532] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The underlying pathology of inguinal hernia is still not fully known; thus, further investigations of genetic backgrounds is needed. Here, we aimed to identify genetic factors attributing to inguinal hernias and explore the polygenic architecture of which some components are population-specific, while others are more common among populations. METHODS We performed a genome-wide association study (GWAS) on subjects with inguinal hernias using BioBank Japan (BBJ) data with 1,983 cases and 172,507 controls, followed by a trans-ethnic meta-analysis with UK Biobank (UKBB) data. We performed downstream analyses in order to identify the mechanisms underlying inguinal hernias supported by genetic findings. FINDINGS We identified a locus closest to ELN, which encodes elastin, at the GWAS significant level. The trans-ethnic meta-analysis revealed 23 additional significant loci, including five loci newly identified not significant in BBJ or UKBB GWAS: TGFB2, RNA5SP214/VGLL2, LOC646588, HMCN2, and ATP5F1CP1/CDKN3. Downstream analyses revealed the overlap of GWAS significant signals in extracellular components, including elastin fiber formation. We also found a highly shared polygenic architecture across different populations (trans-ethnic genetic-effect correlation = 0•77, standard error = 0•26) and population-specific lead variants in ELN, indicating the critical role of elastin in inguinal hernias. INTERPRETATION We identified a significant locus of the ELN gene in the Japanese population and five additional loci across different populations. Downstream analyses revealed highly shared genetic architectures across populations and highlighted the important roles of extracellular components in the development of inguinal hernias. These findings deepen our understanding of the mechanisms underlying inguinal hernia. FUNDING The Japan Agency for Medical Research and Development (AMED) (Grant Number: JP19km0605001).
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Affiliation(s)
- Keiko Hikino
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan; Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
| | - Kohei Tomizuka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Takayuki Morisaki
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
| | - The Biobank Japan Project
- Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokane-dai, Minato-ku, Tokyo, 108-8639, Japan
| | - Taisei Mushiroda
- Laboratory for Pharmacogenomics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan; Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan; The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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17
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Nayor M, Shen L, Hunninghake GM, Kochunov P, Barr RG, Bluemke DA, Broeckel U, Caravan P, Cheng S, de Vries PS, Hoffmann U, Kolossváry M, Li H, Luo J, McNally EM, Thanassoulis G, Arnett DK, Vasan RS. Progress and Research Priorities in Imaging Genomics for Heart and Lung Disease: Summary of an NHLBI Workshop. Circ Cardiovasc Imaging 2021; 14:e012943. [PMID: 34387095 PMCID: PMC8486340 DOI: 10.1161/circimaging.121.012943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Imaging genomics is a rapidly evolving field that combines state-of-the-art bioimaging with genomic information to resolve phenotypic heterogeneity associated with genomic variation, improve risk prediction, discover prevention approaches, and enable precision diagnosis and treatment. Contemporary bioimaging methods provide exceptional resolution generating discrete and quantitative high-dimensional phenotypes for genomics investigation. Despite substantial progress in combining high-dimensional bioimaging and genomic data, methods for imaging genomics are evolving. Recognizing the potential impact of imaging genomics on the study of heart and lung disease, the National Heart, Lung, and Blood Institute convened a workshop to review cutting-edge approaches and methodologies in imaging genomics studies, and to establish research priorities for future investigation. This report summarizes the presentations and discussions at the workshop. In particular, we highlight the need for increased availability of imaging genomics data in diverse populations, dedicated focus on less common conditions, and centralization of efforts around specific disease areas.
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Affiliation(s)
- Matthew Nayor
- Cardiology Division, Department of Medicine, Massachusetts
General Hospital, Harvard Medical School, Boston, MA
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics,
Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Gary M. Hunninghake
- Division of Pulmonary and Critical Care Medicine, Harvard
Medical School, Brigham and Women’s Hospital, Boston, MA
| | - Peter Kochunov
- Maryland Psychiatric Research Center, Department of
Psychiatry, University of Maryland School of Medicine, Baltimore, MD
| | - R. Graham Barr
- Department of Medicine and Department of Epidemiology,
Mailman School of Public Health, Columbia University Irving Medical Center, New
York, NY
| | - David A. Bluemke
- Department of Radiology, University of Wisconsin-Madison
School of Medicine and Public Health, Madison, WI
| | - Ulrich Broeckel
- Section of Genomic Pediatrics, Department of Pediatrics,
Medicine and Physiology, Children’s Research Institute and Genomic Sciences
and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI
| | - Peter Caravan
- Institute for Innovation in Imaging, Athinoula A. Martinos
Center for Biomedical Imaging, Massachusetts General Hospital, Harvard Medical
School, Charlestown, MA
| | - Susan Cheng
- Department of Cardiology, Smidt Heart Institute,
Cedars-Sinai Medical Center, Los Angeles, CA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human
Genetics, and Environmental Sciences, School of Public Health, The University of
Texas Health Science Center at Houston, Houston, TX
| | - Udo Hoffmann
- Department of Radiology, Harvard Medical School,
Massachusetts General Hospital, Boston, Massachusetts
| | - Márton Kolossváry
- Department of Radiology, Harvard Medical School,
Massachusetts General Hospital, Boston, Massachusetts
| | - Huiqing Li
- Division of Cardiovascular Sciences, National Heart,
Lung, and Blood Institute, Bethesda, MD
| | - James Luo
- Division of Cardiovascular Sciences, National Heart,
Lung, and Blood Institute, Bethesda, MD
| | - Elizabeth M. McNally
- Center for Genetic Medicine, Northwestern University
Feinberg School of Medicine, Chicago, IL
| | - George Thanassoulis
- Preventive and Genomic Cardiology, McGill University
Health Center and Research Institute, Montreal, Quebec, Canada
| | - Donna K. Arnett
- College of Public Health, University of Kentucky,
Lexington KY
| | - Ramachandran S. Vasan
- Sections of Preventive Medicine and Epidemiology, and
Cardiology, Department of Medicine, Department of Epidemiology, Boston University
Schools of Medicine and Public Health, and Center for Computing and Data Sciences,
Boston University, Boston, MA
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18
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Gong L, Bates S, Li J, Qiao D, Glass K, Wei W, Hsu VW, Zhou X, Silverman EK. Connecting COPD GWAS genes: FAM13A controls TGFβ2 secretion by modulating AP-3 transport. Am J Respir Cell Mol Biol 2021; 65:532-543. [PMID: 34166600 DOI: 10.1165/rcmb.2021-0016oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Chronic Obstructive Pulmonary Disease (COPD) is a common, complex disease and a major cause of morbidity and mortality. Although multiple genetic determinants of COPD have been implicated by genome-wide association studies (GWAS), the pathophysiologic significance of these associations remains largely unknown. From a COPD protein-protein interaction network module, we selected a network path between two COPD GWAS genes for validation studies: FAM13A-AP3D1-CTGF-TGFB2. We find that TGFβ2, FAM13A, and AP3D1 (but not CTGF) form a cellular protein complex. Functional characterization suggests that this complex mediates the secretion of TGFβ2 through an AP-3-dependent pathway, with FAM13A acting as a negative regulator by targeting a late stage of this transport that involves the dissociation of coat-cargo interaction. Moreover, we find that TGFβ2 is a transmembrane protein that engages the AP-3 complex for delivery to the late endosomal compartments for subsequent secretion through exosomes. These results identify a pathophysiologic context that unifies the biological network role of two COPD GWAS proteins and reveal novel mechanisms of cargo transport through an intracellular pathway.
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Affiliation(s)
- Lu Gong
- Brigham and Women's Hospital, 1861, Channing Division, Boston, Massachusetts, United States
| | - Samuel Bates
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Jian Li
- Brigham And Women's Hospital, Boston, United States
| | - Dandi Qiao
- Brigham and Women's Hospital and Harvard Medical School, Medicine, Boston, Massachusetts, United States.,Harvard School of Public Health, Biostatistics, Boston, Massachusetts, United States
| | - Kimberly Glass
- Brigham and Women\'s Hospital Channing Division of Network Medicine, 1869, Boston, Massachusetts, United States
| | - Wenyi Wei
- Beth Israel Deaconess Medical Center, 1859, Department of Pathology, Boston, Massachusetts, United States.,Harvard Medical School , Boston , Massachusetts, United States
| | - Victor W Hsu
- Brigham and Women's Hospital, 1861, Division of Rheumatology, Inflammation, and Immunity, Boston, Massachusetts, United States
| | - Xiaobo Zhou
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, United States
| | - Edwin K Silverman
- Brigham and Women's Hospital, 1861, Channing Division of Network Medicine, Boston, Massachusetts, United States;
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19
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Tejwani V, Fawzy A, Putcha N, Castaldi P, Cho MH, Pratte KA, Bhatt SP, Lynch DA, Humphries SM, Kinney GL, D'Alessio FR, Hansel NN. Emphysema Progression and Lung Function Decline Among Angiotensin Converting Enzyme Inhibitors and Angiotensin-Receptor Blockade Users in the COPDGene Cohort. Chest 2021; 160:1245-1254. [PMID: 34029566 DOI: 10.1016/j.chest.2021.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 10/21/2022] Open
Abstract
BACKGROUND Attenuation of transforming growth factor β by blocking angiotensin II has been shown to reduce emphysema in a murine model. General population studies have demonstrated that the use of angiotensin converting enzyme inhibitors (ACEis) and angiotensin-receptor blockers (ARBs) is associated with reduction of emphysema progression in former smokers and that the use of ACEis is associated with reduction of FEV1 progression in current smokers. RESEARCH QUESTION Is use of ACEi and ARB associated with less progression of emphysema and FEV1 decline among individuals with COPD or baseline emphysema? METHODS Former and current smokers from the Genetic Epidemiology of COPD Study who attended baseline and 5-year follow-up visits, did not change smoking status, and underwent chest CT imaging were included. Adjusted linear mixed models were used to evaluate progression of adjusted lung density (ALD), percent emphysema (%total lung volume <-950 Hounsfield units [HU]), 15th percentile of the attenuation histogram (attenuation [in HU] below which 15% of voxels are situated plus 1,000 HU), and lung function decline over 5 years between ACEi and ARB users and nonusers in those with spirometry-confirmed COPD, as well as all participants and those with baseline emphysema. Effect modification by smoking status also was investigated. RESULTS Over 5 years of follow-up, compared with nonusers, ACEi and ARB users with COPD showed slower ALD progression (adjusted mean difference [aMD], 1.6; 95% CI, 0.34-2.9). Slowed lung function decline was not observed based on phase 1 medication (aMD of FEV1 % predicted, 0.83; 95% CI, -0.62 to 2.3), but was when analysis was limited to consistent ACEi and ARB users (aMD of FEV1 % predicted, 1.9; 95% CI, 0.14-3.6). No effect modification by smoking status was found for radiographic outcomes, and the lung function effect was more pronounced in former smokers. Results were similar among participants with baseline emphysema. INTERPRETATION Among participants with spirometry-confirmed COPD or baseline emphysema, ACEi and ARB use was associated with slower progression of emphysema and lung function decline. TRIAL REGISTRY ClinicalTrials.gov; No.: NCT00608764; URL: www.clinicaltrials.gov.
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Affiliation(s)
- Vickram Tejwani
- Division of Pulmonary and Critical Care, Johns Hopkins University, Baltimore, MD.
| | - Ashraf Fawzy
- Division of Pulmonary and Critical Care, Johns Hopkins University, Baltimore, MD
| | - Nirupama Putcha
- Division of Pulmonary and Critical Care, Johns Hopkins University, Baltimore, MD
| | | | - Michael H Cho
- Division of Pulmonary and Critical Care Medicine, Boston, MA; Harvard Medical School, Boston, MA
| | | | - Surya P Bhatt
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - David A Lynch
- Department of Radiology, National Jewish Health, Denver, CO
| | | | - Gregory L Kinney
- Department of Epidemiology, Colorado School of Public Health, Aurora, CO
| | - Franco R D'Alessio
- Division of Pulmonary and Critical Care, Johns Hopkins University, Baltimore, MD
| | - Nadia N Hansel
- Division of Pulmonary and Critical Care, Johns Hopkins University, Baltimore, MD
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20
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Portas L, Pereira M, Shaheen SO, Wyss AB, London SJ, Burney PGJ, Hind M, Dean CH, Minelli C. Lung Development Genes and Adult Lung Function. Am J Respir Crit Care Med 2020; 202:853-865. [PMID: 32392078 PMCID: PMC7491406 DOI: 10.1164/rccm.201912-2338oc] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rationale: Poor lung health in adult life may occur partly through
suboptimal growth and development, as suggested by epidemiological evidence
pointing to early life risk factors. Objectives: To systematically investigate the effects of lung
development genes on adult lung function. Methods: Using UK Biobank data, we tested the association of 391
genes known to influence lung development with FVC and FEV1/FVC. We
split the dataset into two random subsets of 207,616 and 138,411 individuals,
using the larger subset to select the most promising signals and the smaller
subset for replication. Measurements and Main Results: We identified 55 genes, of which 36
(16 for FVC, 19 for FEV1/FVC, and one for both) had not been
identified in the largest, most recent genome-wide study of lung function. Most
of these 36 signals were intronic variants; expression data from blood and lung
tissue showed that the majority affect the expression of the genes they lie
within. Further testing of 34 of these 36 signals in the CHARGE and SpiroMeta
consortia showed that 16 replicated after Bonferroni correction and another 12
replicated at nominal significance level. Of the 55 genes, 53 fell into four
biological categories whose function is to regulate organ size and cell
integrity (growth factors; transcriptional regulators; cell-to-cell adhesion;
extracellular matrix), suggesting that these specific processes are important
for adult lung health. Conclusions: Our study demonstrates the importance of lung
development genes in regulating adult lung function and influencing both
restrictive and obstructive patterns. Further investigation of these
developmental pathways could lead to druggable targets.
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Affiliation(s)
- Laura Portas
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Miguel Pereira
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Congenica Ltd., Wellcome Genome Campus, Cambridge, United Kingdom
| | - Seif O Shaheen
- Institute of Population Health Sciences, Queen Mary University of London, London, United Kingdom
| | - Annah B Wyss
- Department of Health and Human Services, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina
| | - Peter G J Burney
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Matthew Hind
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,Department of Respiratory Medicine, Royal Brompton & Harefield NHS Foundation Trust, London, United Kingdom; and
| | - Charlotte H Dean
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.,MRC Harwell Institute, Oxfordshire, United Kingdom
| | - Cosetta Minelli
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
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21
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Beesley J, Sivakumaran H, Moradi Marjaneh M, Shi W, Hillman KM, Kaufmann S, Hussein N, Kar S, Lima LG, Ham S, Möller A, Chenevix-Trench G, Edwards SL, French JD. eQTL Colocalization Analyses Identify NTN4 as a Candidate Breast Cancer Risk Gene. Am J Hum Genet 2020; 107:778-787. [PMID: 32871102 PMCID: PMC7536644 DOI: 10.1016/j.ajhg.2020.08.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
Breast cancer genome-wide association studies (GWASs) have identified 150 genomic risk regions containing more than 13,000 credible causal variants (CCVs). The CCVs are predominantly noncoding and enriched in regulatory elements. However, the genes underlying breast cancer risk associations are largely unknown. Here, we used genetic colocalization analysis to identify loci at which gene expression could potentially explain breast cancer risk phenotypes. Using data from the Breast Cancer Association Consortium (BCAC) and quantitative trait loci (QTL) from the Genotype-Tissue Expression (GTEx) project and The Cancer Genome Project (TCGA), we identify shared genetic relationships and reveal novel associations between cancer phenotypes and effector genes. Seventeen genes, including NTN4, were identified as potential mediators of breast cancer risk. For NTN4, we showed the rs61938093 CCV at this region was located within an enhancer element that physically interacts with the NTN4 promoter, and the risk allele reduced NTN4 promoter activity. Furthermore, knockdown of NTN4 in breast cells increased cell proliferation in vitro and tumor growth in vivo. These data provide evidence linking risk-associated variation to genes that may contribute to breast cancer predisposition.
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Affiliation(s)
- Jonathan Beesley
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia.
| | - Haran Sivakumaran
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Mahdi Moradi Marjaneh
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Wei Shi
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Kristine M Hillman
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Susanne Kaufmann
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Nehal Hussein
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Siddhartha Kar
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK; Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Luize G Lima
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Sunyoung Ham
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
| | - Andreas Möller
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia; Faculty of Medicine, The University of Queensland, Brisbane, QLD 4006, Australia
| | | | - Stacey L Edwards
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia.
| | - Juliet D French
- Cancer Division, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4029, Australia
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22
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Gheorghiu E, Dering BR. Shape facilitates number: brain potentials and microstates reveal the interplay between shape and numerosity in human vision. Sci Rep 2020; 10:12413. [PMID: 32709892 PMCID: PMC7381628 DOI: 10.1038/s41598-020-68788-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/19/2020] [Indexed: 12/04/2022] Open
Abstract
Recognition of simple shapes and numerosity estimation for small quantities are often studied independently of each other, but we know that these processes are both rapid and accurate, suggesting that they may be mediated by common neural mechanisms. Here we address this issue by examining how spatial configuration, shape complexity, and luminance polarity of elements affect numerosity estimation. We directly compared the Event Related Potential (ERP) time-course for numerosity estimation under shape and random configurations and found a larger N2 component for shape over lateral-occipital electrodes (250–400 ms), which also increased with higher numbers. We identified a Left Mid Frontal (LMF; 400–650 ms) component over left-lateralised medial frontal sites that specifically separated low and high numbers of elements, irrespective of their spatial configuration. Different luminance-polarities increased N2 amplitude only, suggesting that shape but not numerosity is selective to polarity. Functional microstates confined numerosity to a strict topographic distribution occurring within the LMF time-window, while a microstate responding only to shape-configuration was evidenced earlier, in the N2 time-window. We conclude that shape-coding precedes numerosity estimation, which can be improved when the number of elements and shape vertices are matched. Thus, numerosity estimation around the subitizing range is facilitated by a shape-template matching process.
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Affiliation(s)
- Elena Gheorghiu
- Department of Psychology, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
| | - Benjamin R Dering
- Department of Psychology, University of Stirling, Stirling, FK9 4LA, Scotland, UK
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23
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Estépar RSJ. Artificial Intelligence in COPD: New Venues to Study a Complex Disease. BARCELONA RESPIRATORY NETWORK REVIEWS 2020; 6:144-160. [PMID: 33521399 PMCID: PMC7842269 DOI: 10.23866/brnrev:2019-0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/02/2020] [Indexed: 06/12/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous disease that can benefit from novel approaches to understanding its evolution and divergent trajectories. Artificial intelligence (AI) has revolutionized how we can use clinical, imaging, and molecular data to understand and model complex systems. AI has shown impressive results in areas related to automated clinical decision making, radiological interpretation and prognostication. The unique nature of COPD and the accessibility to well-phenotyped populations result in an ideal scenario for AI development. This review provides an introduction to AI and deep learning and presents some recent successes in applying AI in COPD. Finally, we will discuss some of the opportunities, challenges, and limitations for AI applications in the context of COPD.
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Affiliation(s)
- Raúl San José Estépar
- Applied Chest Imaging Laboratory, Department of Radiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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24
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Castaldi PJ, Boueiz A, Yun J, Estepar RSJ, Ross JC, Washko G, Cho MH, Hersh CP, Kinney GL, Young KA, Regan EA, Lynch DA, Criner GJ, Dy JG, Rennard SI, Casaburi R, Make BJ, Crapo J, Silverman EK, Hokanson JE. Machine Learning Characterization of COPD Subtypes: Insights From the COPDGene Study. Chest 2019; 157:1147-1157. [PMID: 31887283 DOI: 10.1016/j.chest.2019.11.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/18/2019] [Accepted: 11/29/2019] [Indexed: 12/17/2022] Open
Abstract
COPD is a heterogeneous syndrome. Many COPD subtypes have been proposed, but there is not yet consensus on how many COPD subtypes there are and how they should be defined. The COPD Genetic Epidemiology Study (COPDGene), which has generated 10-year longitudinal chest imaging, spirometry, and molecular data, is a rich resource for relating COPD phenotypes to underlying genetic and molecular mechanisms. In this article, we place COPDGene clustering studies in context with other highly cited COPD clustering studies, and summarize the main COPD subtype findings from COPDGene. First, most manifestations of COPD occur along a continuum, which explains why continuous aspects of COPD or disease axes may be more accurate and reproducible than subtypes identified through clustering methods. Second, continuous COPD-related measures can be used to create subgroups through the use of predictive models to define cut-points, and we review COPDGene research on blood eosinophil count thresholds as a specific example. Third, COPD phenotypes identified or prioritized through machine learning methods have led to novel biological discoveries, including novel emphysema genetic risk variants and systemic inflammatory subtypes of COPD. Fourth, trajectory-based COPD subtyping captures differences in the longitudinal evolution of COPD, addressing a major limitation of clustering analyses that are confounded by disease severity. Ongoing longitudinal characterization of subjects in COPDGene will provide useful insights about the relationship between lung imaging parameters, molecular markers, and COPD progression that will enable the identification of subtypes based on underlying disease processes and distinct patterns of disease progression, with the potential to improve the clinical relevance and reproducibility of COPD subtypes.
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Affiliation(s)
- Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; General Medicine and Primary Care, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
| | - Adel Boueiz
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Jeong Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Raul San Jose Estepar
- Applied Chest Imaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - James C Ross
- Applied Chest Imaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - George Washko
- Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Applied Chest Imaging Laboratory, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - Gregory L Kinney
- Department of Epidemiology, University of Colorado, Denver, Aurora, CO
| | - Kendra A Young
- Department of Epidemiology, University of Colorado, Denver, Aurora, CO
| | | | - David A Lynch
- Department of Radiology, National Jewish Health, Denver, CO
| | - Gerald J Criner
- Department of Thoracic Medicine and Surgery, Lewis Katz School of Medicine at Temple University, Philadelphia, PA
| | - Jennifer G Dy
- Department of Electrical and Computer Engineering, Northeastern University, Boston, MA
| | - Stephen I Rennard
- Pulmonary and Critical Care Medicine, University of Nebraska Medical Center, Omaha, NE
| | - Richard Casaburi
- Rehabilitation Clinical Trials Center, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA
| | | | | | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA; Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA
| | - John E Hokanson
- Department of Epidemiology, University of Colorado, Denver, Aurora, CO
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