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Li X, Xiong Q, Yang Q, Shi J, Han Y, Dong Y, Qian J, Qian Z, Wang H, Wang T, Wu F. PTPRO inhibits LPS-induced apoptosis in alveolar epithelial cells. Biochem Biophys Res Commun 2024; 718:150083. [PMID: 38735138 DOI: 10.1016/j.bbrc.2024.150083] [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: 03/21/2024] [Revised: 05/03/2024] [Accepted: 05/07/2024] [Indexed: 05/14/2024]
Abstract
Acute lung injury (ALI) and its severe manifestation, acute respiratory distress syndrome (ARDS), represent critical clinical syndromes with multifactorial origins, notably stemming from sepsis within intensive care units (ICUs). Despite their high mortality rates, no selective cure is available beside ventilation support. Apoptosis plays a complex and pivotal role in the pathophysiology of acute lung injury. Excessive apoptosis of alveolar epithelial and microvascular endothelial cells can lead to disruption of lung epithelial barrier integrity, impairing the body's ability to exchange blood and gas. At the same time, apoptosis of damaged or dysfunctional cells, including endothelial and epithelial cells, can help maintain tissue integrity and accelerate recovery from organ pro-inflammatory stress. The balance between pro-survival and pro-apoptotic signals in lung injury determines patient outcomes, making the modulation of apoptosis an area of intense research in the quest for more effective therapies. Here we found that protein tyrosine phosphatase receptor type O (PTPRO), a poorly understood receptor-like protein tyrosine phosphatase, is consistently upregulated in multiple tissue types of mice under septic conditions and in the lung alveolar epithelial cells. PTPRO reduction by its selective short-interfering RNA (siRNA) leads to excessive apoptosis in lung alveolar epithelial cells without affecting cell proliferation. Consistently PTPRO overexpression by a DNA construct attenuates apoptotic signaling induced by LPS. These effects of PTPTO on cellular apoptosis are dependent on an ErbB2/PI3K/Akt/NFκB signaling pathway. Here we revealed a novel regulatory pathway of cellular apoptosis by PTPRO in lung alveolar epithelial cells during sepsis.
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Affiliation(s)
- Xuemeng Li
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Anhui Provincial Key Laboratory of Infection and Immunology, and Department of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui Province, China
| | - Qianqian Xiong
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Anhui Provincial Key Laboratory of Infection and Immunology, and Department of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui Province, China
| | - Qingqing Yang
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Anhui Provincial Key Laboratory of Infection and Immunology, and Department of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui Province, China
| | - Jing Shi
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Anhui Provincial Key Laboratory of Infection and Immunology, and Department of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui Province, China
| | - Yuhong Han
- Department of Clinical Laboratory, The Second People's Hospital of Fuyang City, Fuyang, Anhui Province, China
| | - Yishu Dong
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Anhui Provincial Key Laboratory of Infection and Immunology, and Department of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui Province, China
| | - Jun Qian
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Anhui Provincial Key Laboratory of Infection and Immunology, and Department of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui Province, China
| | - Zhongqing Qian
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Anhui Provincial Key Laboratory of Infection and Immunology, and Department of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui Province, China
| | - Hongtao Wang
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Anhui Provincial Key Laboratory of Infection and Immunology, and Department of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui Province, China
| | - Ting Wang
- Department of Internal Medicine, University of Arizona, Phoenix, AZ, USA
| | - Fengjiao Wu
- Anhui Provincial Key Laboratory of Immunology in Chronic Diseases, Anhui Provincial Key Laboratory of Infection and Immunology, and Department of Laboratory Medicine, Bengbu Medical University, Bengbu, Anhui Province, China.
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2
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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3
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Kim W, Hecker J, Barr RG, Boerwinkle E, Cade B, Correa A, Dupuis J, Gharib SA, Lange L, London SJ, Morrison AC, O'Connor GT, Oelsner EC, Psaty BM, Vasan RS, Redline S, Rich SS, Rotter JI, Yu B, Lange C, Manichaikul A, Zhou JJ, Sofer T, Silverman EK, Qiao D, Cho MH. Assessing the contribution of rare genetic variants to phenotypes of chronic obstructive pulmonary disease using whole-genome sequence data. Hum Mol Genet 2022; 31:3873-3885. [PMID: 35766891 PMCID: PMC9652112 DOI: 10.1093/hmg/ddac117] [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: 01/21/2022] [Revised: 04/13/2022] [Accepted: 05/16/2021] [Indexed: 01/04/2023] Open
Abstract
RATIONALE Genetic variation has a substantial contribution to chronic obstructive pulmonary disease (COPD) and lung function measurements. Heritability estimates using genome-wide genotyping data can be biased if analyses do not appropriately account for the nonuniform distribution of genetic effects across the allele frequency and linkage disequilibrium (LD) spectrum. In addition, the contribution of rare variants has been unclear. OBJECTIVES We sought to assess the heritability of COPD and lung function using whole-genome sequence data from the Trans-Omics for Precision Medicine program. METHODS Using the genome-based restricted maximum likelihood method, we partitioned the genome into bins based on minor allele frequency and LD scores and estimated heritability of COPD, FEV1% predicted and FEV1/FVC ratio in 11 051 European ancestry and 5853 African-American participants. MEASUREMENTS AND MAIN RESULTS In European ancestry participants, the estimated heritability of COPD, FEV1% predicted and FEV1/FVC ratio were 35.5%, 55.6% and 32.5%, of which 18.8%, 19.7%, 17.8% were from common variants, and 16.6%, 35.8%, and 14.6% were from rare variants. These estimates had wide confidence intervals, with common variants and some sets of rare variants showing a statistically significant contribution (P-value < 0.05). In African-Americans, common variant heritability was similar to European ancestry participants, but lower sample size precluded calculation of rare variant heritability. CONCLUSIONS Our study provides updated and unbiased estimates of heritability for COPD and lung function, and suggests an important contribution of rare variants. Larger studies of more diverse ancestry will improve accuracy of these estimates.
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Affiliation(s)
- Wonji Kim
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Julian Hecker
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Eric Boerwinkle
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Brian Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Josée Dupuis
- Department of Biostatistics, Boston University of Public Health, Boston, MA 02118, USA
| | - Sina A Gharib
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Leslie Lange
- Department of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Stephanie J London
- Epidemiology Branch, National Institute of Environmental Health Sciences, Department of Health and Human Services, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Alanna C Morrison
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - George T O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA 02118, USA
| | - Elizabeth C Oelsner
- Departments of Medicine and Epidemiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Departments of Epidemiology and Health Services, University of Washington, Seattle, WA 98101, USA
| | - Ramachandran S Vasan
- Lung and Blood Institute Framingham Heart Study, Boston University and National Heart, Framingham, MA 01702, USA
- Department of Preventive Medicine and Epidemiology, School of Medicine and Public Health, Boston University, Boston, MA 02118, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Bing Yu
- Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Christoph Lange
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Jin J Zhou
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ 85721, USA
| | - Tamar Sofer
- Division of Sleep and Circadian Disorder, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Michael H Cho
- 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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Germain A, Perotin JM, Delepine G, Polette M, Deslée G, Dormoy V. Whole-Exome Sequencing of Bronchial Epithelial Cells Reveals a Genetic Print of Airway Remodelling in COPD. Biomedicines 2022; 10:biomedicines10071714. [PMID: 35885019 PMCID: PMC9313052 DOI: 10.3390/biomedicines10071714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/12/2022] [Accepted: 07/13/2022] [Indexed: 11/16/2022] Open
Abstract
The remodelling of the airways is a hallmark of chronic obstructive pulmonary disease, but it is highly heterogeneous and erratically distributed in the airways. To assess the genetic print of remodelling in chronic obstructive pulmonary disease (COPD), we performed a comparative whole-exome sequencing analysis on microdissected bronchial epithelia. Lung resections from four non-COPD and three COPD subjects (ex-smokers and current smokers) were formalin-fixed paraffin-embedded (FFPE). Non-remodelled and remodelled bronchial epithelia were isolated by laser microdissection. Genomic DNA was captured and sequenced. The comparative quantitative analysis identified a list of 109 genes as having variants in remodelled epithelia and 160 genes as having copy number alterations in remodelled epithelia, mainly in COPD patients. The functional analysis highlighted cilia-associated processes. Therefore, bronchial-remodelled epithelia appeared genetically more altered than non-remodelled epithelia. Characterizing the unique molecular print of airway remodelling in respiratory diseases may help uncover additional factors contributing to epithelial dysfunctions, ultimately providing additional targetable proteins to correct epithelial remodelling and improve lung function.
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Affiliation(s)
- Adeline Germain
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
| | - Jeanne-Marie Perotin
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
- Service de Pneumologie, CHU Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Gonzague Delepine
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
- Service de Chirurgie Thoracique, CHU Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Myriam Polette
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
- Laboratoire de Biopathologie, CHU Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Gaëtan Deslée
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
- Service de Pneumologie, CHU Reims, Hôpital Maison Blanche, 51092 Reims, France
| | - Valérian Dormoy
- Inserm, P3Cell UMR-S1250, Université de Reims Champagne-Ardenne, SFR CAP-SANTE, 51092 Reims, France; (A.G.); (J.-M.P.); (G.D.); (M.P.); (G.D.)
- Correspondence: ; Tel.: +33-(0)3-10-73-62-28
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5
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Abstract
The lungs are continually subjected to noxious and inert substances, are immunologically active, and are in a constant state of damage and repair. This makes the pulmonary system particularly vulnerable to diseases of aging. Aging can be understood as random molecular damage that is unrepaired and accumulates over time, resulting in cellular defects and tissue dysfunction. The breakdown of cellular mechanisms, including stem cell exhaustion, genomic instability, telomere attrition, epigenetic alteration, loss of proteostasis, deregulated nutrient sensing, mitochondrial dysfunction, cellular senescence, altered intercellular communication, and changes in the extracellular matrix is thought to advance the aging process itself. Chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), and cancers illustrate a pathologic breakdown in these mechanisms beyond normal aging. The immune system becomes less effective with advancing age. There is a low-level state of chronic inflammation termed inflammaging which is thought to be driven by immunosenescence, the changes in the innate and adaptive immune systems with advancing age that lead to dysregulation and decreased effectiveness of the immune system. These processes of aging lead to expected changes in the form and function of the respiratory system, most notably a loss of lung elasticity, decrease in respiratory muscle strength, increase in ventilation-perfusion mismatching, and stiffening of the vasculature. The astute clinician is aware of these expected findings and does not often attribute dyspnea to aging alone. Maintaining a low threshold to investigate for comorbid disease and understanding how pulmonary disease presents differently in the elderly than in younger adults can improve clinical outcomes. © 2022 American Physiological Society. Compr Physiol 12:3509-3522, 2022.
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Affiliation(s)
- Julia Budde
- New York City Health and Hospitals/Metropolitan Hospital, New York, New York, USA
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6
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Chen D, Gregory AD, Li X, Wei J, Burton CL, Gibson G, Scott SJ, St Croix CM, Zhang Y, Shapiro SD. RIP3-dependent necroptosis contributes to the pathogenesis of chronic obstructive pulmonary disease. JCI Insight 2021; 6:e144689. [PMID: 34156033 PMCID: PMC8262480 DOI: 10.1172/jci.insight.144689] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 05/12/2021] [Indexed: 12/27/2022] Open
Abstract
Necroptosis has emerged as a potential mechanism in the pathogenesis of chronic obstructive pulmonary disease (COPD). Here, we found that markers of necroptosis, including high mobility group box 1 release and phosphorylation of mixed lineage kinase domain-like protein (p-MLKL), were markedly induced in the late stage of cigarette smoking-induced (CS-induced) emphysema in mouse lung tissue as well as in lung epithelial cells and organoids with higher dosage of or more prolonged exposure to cigarette smoking extract (CSE). Apoptotic signals were also detected and maximally induced in the early stage of CS-exposed mice and CSE-treated epithelial cells. Inhibition of apoptosis by Z-VAD, a pan-caspase inhibitor, switched the cellular stress to enhanced necroptosis in lung epithelial cells and organoids treated with CSE. Depletion or inhibition of receptor-interacting protein kinase 3 (RIP3) or MLKL attenuated the CSE-induced cell death, suggesting that necroptosis contributes to CSE-induced cell death. Silencing or inhibition of RIP1 had no protective effect, indicating a RIP1-independent RIP3 activation pathway. CSE-induced necroptosis released more damage-associated molecular patterns and evoked greater engulfment but slower clearance by bone marrow-derived macrophages, leading to enhanced expression of proinflammatory cytokines Tnfα and Il6. Finally, our in vivo data verified that inhibition of necroptosis by RIP3 inhibitor GSK'872 protected mice from CS-induced emphysema and suppressed the lung inflammation. In conclusion, we provide evidence that necroptosis contributes to the pathogenesis of COPD. Targeting RIP3 and its downstream pathway may be an effective therapy for COPD.
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Affiliation(s)
- Dongshi Chen
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, and
| | - Alyssa D Gregory
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, and
| | - Xiaoyun Li
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, and
| | - Jianxin Wei
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, and
| | - Christine L Burton
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, and
| | - Gregory Gibson
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Stephen J Scott
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, and
| | - Claudette M St Croix
- Department of Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, and
| | - Steven D Shapiro
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, and
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7
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Prognostic signature of lung adenocarcinoma based on stem cell-related genes. Sci Rep 2021; 11:1687. [PMID: 33462260 PMCID: PMC7814011 DOI: 10.1038/s41598-020-80453-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/16/2020] [Indexed: 01/05/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is characterized by high infiltration and rapid growth. The function of the stem cell population is to control and maintain cell regeneration. Therefore, it is necessary to study the prognostic value of stem cell-related genes in LUAD. Signature genes were screened out from 166 stem cell-related genes according to the least absolute shrinkage operator (LASSO) and subsequently multivariate Cox regression analysis, and then established risk model. Immune infiltration and nomogram model were used to evaluate the clinical efficacy of signature. A signature consisting of 10 genes was used to dichotomize the LUAD patients into two groups (cutoff, 1.314), and then validated in GSE20319 and GSE42127. There was a significant correlation between signature and clinical characteristics. Patients with high-risk had a shorter overall survival. Furthermore, significant differences were found in multiple immune cells between the high-risk group and low-risk group. A high correlation was also reflected between signature and immune infiltration. What’s more, the signature could effectively predict the efficacy of chemotherapy in patients with LUAD, and a nomogram based on signature might accurately predict the prognosis of patients with LUAD. The signature-based of stem cell-related genes might be contributed to predicting prognosis of patients with LUAD.
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Abstract
Advances in next-generation sequencing technology have enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into how genetic polymorphisms affect disease phenotypes. The development of different bioinformatics pipelines has continuously improved the variant analysis of WGS data. However, there is a necessity for a systematic performance comparison of these pipelines to provide guidance on the application of WGS-based scientific and clinical genomics. In this study, we evaluated the performance of three variant calling pipelines (GATK, DRAGEN and DeepVariant) using the Genome in a Bottle Consortium, "synthetic-diploid" and simulated WGS datasets. DRAGEN and DeepVariant show better accuracy in SNP and indel calling, with no significant differences in their F1-score. DRAGEN platform offers accuracy, flexibility and a highly-efficient execution speed, and therefore superior performance in the analysis of WGS data on a large scale. The combination of DRAGEN and DeepVariant also suggests a good balance of accuracy and efficiency as an alternative solution for germline variant detection in further applications. Our results facilitate the standardization of benchmarking analysis of bioinformatics pipelines for reliable variant detection, which is critical in genetics-based medical research and clinical applications.
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9
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Zhao S, Agafonov O, Azab A, Stokowy T, Hovig E. Accuracy and efficiency of germline variant calling pipelines for human genome data. Sci Rep 2020; 10:20222. [PMID: 33214604 PMCID: PMC7678823 DOI: 10.1038/s41598-020-77218-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 11/02/2020] [Indexed: 12/30/2022] Open
Abstract
Advances in next-generation sequencing technology have enabled whole genome sequencing (WGS) to be widely used for identification of causal variants in a spectrum of genetic-related disorders, and provided new insight into how genetic polymorphisms affect disease phenotypes. The development of different bioinformatics pipelines has continuously improved the variant analysis of WGS data. However, there is a necessity for a systematic performance comparison of these pipelines to provide guidance on the application of WGS-based scientific and clinical genomics. In this study, we evaluated the performance of three variant calling pipelines (GATK, DRAGEN and DeepVariant) using the Genome in a Bottle Consortium, "synthetic-diploid" and simulated WGS datasets. DRAGEN and DeepVariant show better accuracy in SNP and indel calling, with no significant differences in their F1-score. DRAGEN platform offers accuracy, flexibility and a highly-efficient execution speed, and therefore superior performance in the analysis of WGS data on a large scale. The combination of DRAGEN and DeepVariant also suggests a good balance of accuracy and efficiency as an alternative solution for germline variant detection in further applications. Our results facilitate the standardization of benchmarking analysis of bioinformatics pipelines for reliable variant detection, which is critical in genetics-based medical research and clinical applications.
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Affiliation(s)
- Sen Zhao
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310, Oslo, Norway
| | | | - Abdulrahman Azab
- Center for Bioinformatics, Department of Informatics, University of Oslo, 0316, Oslo, Norway
- Division of Research Computing, University Center for Information Technology (USIT), University of Oslo, 0316, Oslo, Norway
| | - Tomasz Stokowy
- Computational Biology Unit, Institute of Informatics, University of Bergen, 5008, Bergen, Norway
- Department of Clinical Science, University of Bergen, 5021, Bergen, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, 0310, Oslo, Norway.
- Center for Bioinformatics, Department of Informatics, University of Oslo, 0316, Oslo, Norway.
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10
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Genetic profiling for disease stratification in chronic obstructive pulmonary disease and asthma. Curr Opin Pulm Med 2020; 25:317-322. [PMID: 30762612 DOI: 10.1097/mcp.0000000000000568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW In asthma and chronic obstructive pulmonary disease (COPD), the movement towards genetic profiling with a push towards 'personalized medicine' has been hindered by complex environment--gene interactions and lack of tools to identify clear causal genetic traits. In this review, we will discuss the need for genetic profiling in asthma and COPD, what methods are currently used in the clinics and the recent finding using new sequencing methods. RECENT FINDINGS Over the past 10-15 years, genome-wide association studies analysis of common variants has provide little in the way of new genetic profiling markers for asthma and COPD. Whole exome/genome sequencing has provided a new method to identify lowly abundant alleles, which might have a much higher impact. Although, low population numbers due to high costs has hindered early studies, recent studies have reached genome wide significance. SUMMARY The use of genetic profiling of COPD in the clinic is current limited to the identification of Alpha-1 antitrypsin deficiency, while being absent in asthma. Advances in sequencing technology provide new avenues to identify disease causes or therapy response altering variants that in the short-term will allow for the development of screening procedures for disease to identify patients at risk of developing asthma or COPD.
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11
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Exome sequencing of extreme phenotypes in bronchopulmonary dysplasia. Eur J Pediatr 2020; 179:579-586. [PMID: 31848748 DOI: 10.1007/s00431-019-03535-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/19/2019] [Accepted: 11/24/2019] [Indexed: 01/08/2023]
Abstract
Bronchopulmonary dysplasia is the most common chronic respiratory disease in premature infants with growing evidence that genetic factors contribute largely to moderate and severe cases. We assessed by exome sequencing if rare genetic variants could account for extremely severe phenotypes. We selected 6 infants born very preterm with severe bronchopulmonary dysplasia and 8 very preterm born controls for exome sequencing. We filtered whole exome sequencing results to include only rare variants and selected variants and/or genes with variants that were present in at least 2 cases and absent in controls. We selected variants, all heterozygous, in 9 candidate genes, 7 with a putative role in lung development and 2 that displayed 3 variations in 3 different cases, independently of their potential role in lung development. Sequencing of 5 other severe cases for these variants did not replicate our results.Conclusion: In selected preterm born infants with severe bronchopulmonary dysplasia and controls, we failed to find any rare variant shared by several infants with an extremely severe phenotype. Our results are not consistent with the role of rare causative variants in bronchopulmonary dysplasia's development and argue for the highly polygenic nature of susceptibility of this disorder.What is Known:• Bronchopulmonary dysplasia is a multifactorial disease resulting from complex environmental and genetic interactions occurring in an immature lung.• It is not known whether rare genetic variants in coding regions could account for extreme phenotypes of the disease.What is New:• In a group of infants with an extreme phenotype of bronchopulmonary dysplasia and in comparison to controls, no common genetic variants were found, nor did variants that were select in other exome studies in this setting.• These results argue for the highly polygenic nature of susceptibility of bronchopulmonary dysplasia.
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12
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Mallampalli RK, Li X, Jang JH, Kaminski T, Hoji A, Coon T, Chandra D, Welty S, Teng Y, Sembrat J, Rojas M, Zhao Y, Lafyatis R, Zou C, Sciurba F, Sundd P, Lan L, Nyunoya T. Cigarette smoke exposure enhances transforming acidic coiled-coil-containing protein 2 turnover and thereby promotes emphysema. JCI Insight 2020; 5:125895. [PMID: 31996486 PMCID: PMC7098723 DOI: 10.1172/jci.insight.125895] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 12/18/2019] [Indexed: 01/09/2023] Open
Abstract
Our integrative genomic and functional analysis identified transforming acidic coiled-coil-containing protein 2 (TACC2) as a chronic obstructive pulmonary disease (COPD) candidate gene. Here, we found that smokers with COPD exhibit a marked decrease in lung TACC2 protein levels relative to smokers without COPD. Single cell RNA sequencing reveals that TACC2 is expressed primarily in lung epithelial cells in normal human lungs. Furthermore, suppression of TACC2 expression impairs the efficiency of homologous recombination repair and augments spontaneous and cigarette smoke extract-induced (CSE-induced) DNA damage and cytotoxicity in immortalized human bronchial epithelial cells. By contrast, enforced expression of TACC2 attenuates the CSE effects. We also found that CSE enhances TACC2 degradation via the ubiquitin-proteasome system mediated by the ubiquitin E3 ligase subunit, F box L7. Furthermore, cellularly expressed TACC2 proteins harboring naturally occurring mutations exhibited altered protein lifespan coupled with modified DNA damage repair and cytotoxic responses. CS triggers emphysematous changes accompanied by accumulated DNA damage, apoptosis of alveolar epithelia, and lung inflammation in Tacc2-/- compared with Tacc2+/+ mice. Our results suggest that CS destabilizes TACC2 protein in lung epithelia by the ubiquitin proteasome system, leading to subsequent DNA damage, cytotoxicity, and emphysema.
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Affiliation(s)
- Rama K. Mallampalli
- Department of Medicine, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Xiuying Li
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, Pittsburg, Pennsylvania, USA
| | - Jun-Ho Jang
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tomasz Kaminski
- Vascular Medical Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Aki Hoji
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Tiffany Coon
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Divay Chandra
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Starr Welty
- Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- UMPC Hillman Cancer Center, Pittsburgh, Pennsylvania, USA
| | - Yaqun Teng
- School of Medicine, Tsinghua University, No. 1 Tsinghua Yuan, Beijing, China
| | - John Sembrat
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mauricio Rojas
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yutong Zhao
- Department of Physiology and Cell Biology, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Robert Lafyatis
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Chunbin Zou
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, Pittsburg, Pennsylvania, USA
| | - Frank Sciurba
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Prithu Sundd
- Vascular Medical Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Li Lan
- Department of Radiation Oncology, Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Toru Nyunoya
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Medical Specialty Service Line, Veterans Affairs Pittsburgh Healthcare System, Pittsburg, Pennsylvania, USA
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13
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Abstract
Although chronic obstructive pulmonary disease (COPD) risk is strongly influenced by cigarette smoking, genetic factors are also important determinants of COPD. In addition to Mendelian syndromes such as alpha-1 antitrypsin deficiency, many genomic regions that influence COPD susceptibility have been identified in genome-wide association studies. Similarly, multiple genomic regions associated with COPD-related phenotypes, such as quantitative emphysema measures, have been found. Identifying the functional variants and key genes within these association regions remains a major challenge. However, newly identified COPD susceptibility genes are already providing novel insights into COPD pathogenesis. Network-based approaches that leverage these genetic discoveries have the potential to assist in decoding the complex genetic architecture of COPD.
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Affiliation(s)
- Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA;
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14
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Radder JE, Shapiro SD. Identifying Chronic Obstructive Pulmonary Disease Genes: Shining the Light on Dark DNA. Am J Respir Cell Mol Biol 2019; 60:373-374. [PMID: 30376354 PMCID: PMC6444632 DOI: 10.1165/rcmb.2018-0349ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Josiah E Radder
- 1 Department of Medicine University of Pittsburgh Medical Center and University of Pittsburgh Pittsburgh, Pennsylvania
| | - Steven D Shapiro
- 1 Department of Medicine University of Pittsburgh Medical Center and University of Pittsburgh Pittsburgh, Pennsylvania
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15
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Hersh CP. Pharmacogenomics of chronic obstructive pulmonary disease. Expert Rev Respir Med 2019; 13:459-470. [PMID: 30925849 PMCID: PMC6482089 DOI: 10.1080/17476348.2019.1601559] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/27/2019] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Chronic obstructive pulmonary disease (COPD) is a heterogeneous condition, which presents the opportunity for precision therapy based on genetics or other biomarkers. Areas covered: Alpha-1 antitrypsin deficiency, a genetic form of emphysema, provides an example of this precision approach to diagnosis and therapy. To date, research in COPD pharmacogenomics has been limited by small sample sizes, lack of accessible target tissue, failure to consider COPD subtypes, and different outcomes relevant for various medications. There have been several published genome-wide association studies and other omics studies in COPD pharmacogenomics; however, clinical implementation remains far away. There is a growing evidence base for precision prescription of inhaled corticosteroids in COPD, based on clinical phenotypes and blood biomarkers, but not yet based on pharmacogenomics. Expert opinion: At this time, there is insufficient evidence for clinical implementation of COPD pharmacogenomics. Additional genome-wide studies will be required to discover predictors of drug response and to identify genomic biomarkers of COPD subtypes, which could be targeted with subtype-directed therapies.
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Affiliation(s)
- Craig P Hersh
- a Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine , Brigham and Women's Hospital, Harvard Medical School , Boston , MA , USA
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16
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High-Throughput Sequencing in Respiratory, Critical Care, and Sleep Medicine Research. An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc 2019; 16:1-16. [PMID: 30592451 PMCID: PMC6812157 DOI: 10.1513/annalsats.201810-716ws] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
High-throughput, "next-generation" sequencing methods are now being broadly applied across all fields of biomedical research, including respiratory disease, critical care, and sleep medicine. Although there are numerous review articles and best practice guidelines related to sequencing methods and data analysis, there are fewer resources summarizing issues related to study design and interpretation, especially as applied to common, complex, nonmalignant diseases. To address these gaps, a single-day workshop was held at the American Thoracic Society meeting in May 2017, led by the American Thoracic Society Section on Genetics and Genomics. The aim of this workshop was to review the design, analysis, interpretation, and functional follow-up of high-throughput sequencing studies in respiratory, critical care, and sleep medicine research. This workshop brought together experts in multiple fields, including genetic epidemiology, biobanking, bioinformatics, and research ethics, along with physician-scientists with expertise in a range of relevant diseases. The workshop focused on application of DNA and RNA sequencing research in common chronic diseases and did not cover sequencing studies in lung cancer, monogenic diseases (e.g., cystic fibrosis), or microbiome sequencing. Participants reviewed and discussed study design, data analysis and presentation, interpretation, functional follow-up, and reporting of results. This report summarizes the main conclusions of the workshop, specifically addressing the application of these methods in respiratory, critical care, and sleep medicine research. This workshop report may serve as a resource for our research community as well as for journal editors and reviewers of sequencing-based manuscript submissions in our research field.
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17
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Hernandez-Pacheco N, Pino-Yanes M, Flores C. Genomic Predictors of Asthma Phenotypes and Treatment Response. Front Pediatr 2019; 7:6. [PMID: 30805318 PMCID: PMC6370703 DOI: 10.3389/fped.2019.00006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
Asthma is a complex respiratory disease considered as the most common chronic condition in children. A large genetic contribution to asthma susceptibility is predicted by the clustering of asthma and allergy symptoms among relatives and the large disease heritability estimated from twin studies, ranging from 55 to 90%. Genetic basis of asthma has been extensively investigated in the past 40 years using linkage analysis and candidate-gene association studies. However, the development of dense arrays for polymorphism genotyping has enabled the transition toward genome-wide association studies (GWAS), which have led the discovery of several unanticipated asthma genes in the last 11 years. Despite this, currently known risk variants identified using many thousand samples from distinct ethnicities only explain a small proportion of asthma heritability. This review examines the main findings of the last 2 years in genomic studies of asthma using GWAS and admixture mapping studies, as well as the direction of studies fostering integrative perspectives involving omics data. Additionally, we discuss the need for assessing the whole spectrum of genetic variation in association studies of asthma susceptibility, severity, and treatment response in order to further improve our knowledge of asthma genes and predictive biomarkers. Leveraging the individual's genetic information will allow a better understanding of asthma pathogenesis and will facilitate the transition toward a more precise diagnosis and treatment.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
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18
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Supernat A, Vidarsson OV, Steen VM, Stokowy T. Comparison of three variant callers for human whole genome sequencing. Sci Rep 2018; 8:17851. [PMID: 30552369 PMCID: PMC6294778 DOI: 10.1038/s41598-018-36177-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/13/2018] [Indexed: 12/30/2022] Open
Abstract
Testing of patients with genetics-related disorders is in progress of shifting from single gene assays to gene panel sequencing, whole-exome sequencing (WES) and whole-genome sequencing (WGS). Since WGS is unquestionably becoming a new foundation for molecular analyses, we decided to compare three currently used tools for variant calling of human whole genome sequencing data. We tested DeepVariant, a new TensorFlow machine learning-based variant caller, and compared this tool to GATK 4.0 and SpeedSeq, using 30×, 15× and 10× WGS data of the well-known NA12878 DNA reference sample. According to our comparison, the performance on SNV calling was almost similar in 30× data, with all three variant callers reaching F-Scores (i.e. harmonic mean of recall and precision) equal to 0.98. In contrast, DeepVariant was more precise in indel calling than GATK and SpeedSeq, as demonstrated by F-Scores of 0.94, 0.90 and 0.84, respectively. We conclude that the DeepVariant tool has great potential and usefulness for analysis of WGS data in medical genetics.
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Affiliation(s)
- Anna Supernat
- Laboratory of Cell Biology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Gdańsk, Poland
| | | | - Vidar M Steen
- NORMENT & K.J. Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway
- Dr. E. Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Tomasz Stokowy
- Computational Biology Unit, Institute of Informatics, University of Bergen, Bergen, Norway.
- NORMENT & K.J. Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen, Norway.
- Dr. E. Martens Research Group for Biological Psychiatry, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
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19
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Prokopenko D, Sakornsakolpat P, Fier HL, Qiao D, Parker MM, McDonald MLN, Manichaikul A, Rich SS, Barr RG, Williams CJ, Brantly ML, Lange C, Beaty TH, Crapo JD, Silverman EK. Whole-Genome Sequencing in Severe Chronic Obstructive Pulmonary Disease. Am J Respir Cell Mol Biol 2018; 59:614-622. [PMID: 29949718 PMCID: PMC6236690 DOI: 10.1165/rcmb.2018-0088oc] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/27/2018] [Indexed: 01/21/2023] Open
Abstract
Genome-wide association studies have identified common variants associated with chronic obstructive pulmonary disease (COPD). Whole-genome sequencing (WGS) offers comprehensive coverage of the entire genome, as compared with genotyping arrays or exome sequencing. We hypothesized that WGS in subjects with severe COPD and smoking control subjects with normal pulmonary function would allow us to identify novel genetic determinants of COPD. We sequenced 821 patients with severe COPD and 973 control subjects from the COPDGene and Boston Early-Onset COPD studies, including both non-Hispanic white and African American individuals. We performed single-variant and grouped-variant analyses, and in addition, we assessed the overlap of variants between sequencing- and array-based imputation. Our most significantly associated variant was in a known region near HHIP (combined P = 1.6 × 10-9); additional variants approaching genome-wide significance included previously described regions in CHRNA5, TNS1, and SERPINA6/SERPINA1 (the latter in African American individuals). None of our associations were clearly driven by rare variants, and we found minimal evidence of replication of genes identified by previously reported smaller sequencing studies. With WGS, we identified more than 20 million new variants, not seen with imputation, including more than 10,000 of potential importance in previously identified COPD genome-wide association study regions. WGS in severe COPD identifies a large number of potentially important functional variants, with the strongest associations being in known COPD risk loci, including HHIP and SERPINA1. Larger sample sizes will be needed to identify associated variants in novel regions of the genome.
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Affiliation(s)
- Dmitry Prokopenko
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Phuwanat Sakornsakolpat
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Heide Loehlein Fier
- Working Group of Genomic Mathematics, University of Bonn, Bonn, Germany
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Margaret M. Parker
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Merry-Lynn N. McDonald
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - R. Graham Barr
- Department of Medicine, College of Physicians and Surgeons and
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Christopher J. Williams
- Division of Pulmonary Critical Care and Sleep Medicine, College of Medicine, University of Florida, Gainesville, Florida
| | - Mark L. Brantly
- Division of Pulmonary Critical Care and Sleep Medicine, College of Medicine, University of Florida, Gainesville, Florida
| | - Christoph Lange
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
| | - Terri H. Beaty
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland; and
| | | | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - on behalf of COPDGene Study Investigators* and NHLBI TOPMed Investigators‡
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts
- Working Group of Genomic Mathematics, University of Bonn, Bonn, Germany
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, Alabama
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
- Department of Medicine, College of Physicians and Surgeons and
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
- Division of Pulmonary Critical Care and Sleep Medicine, College of Medicine, University of Florida, Gainesville, Florida
- Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland; and
- National Jewish Health, Denver, Colorado
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20
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Hersh CP, Vachani A. Whole-Genome Sequencing in Common Respiratory Diseases. Ready, Set, Go! Am J Respir Crit Care Med 2017; 196:121-122. [PMID: 28707973 DOI: 10.1164/rccm.201703-0479ed] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Affiliation(s)
- Craig P Hersh
- 1 Channing Division of Network Medicine.,2 Division of Pulmonary and Critical Care Medicine Brigham and Women's Hospital and Harvard Medical School Boston, Massachusetts and
| | - Anil Vachani
- 3 Pulmonary, Allergy, and Critical Care Medicine Division University of Pennsylvania Perelman School of Medicine Philadelphia, Pennsylvania
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21
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Ascher K, Elliot SJ, Rubio GA, Glassberg MK. Lung Diseases of the Elderly: Cellular Mechanisms. Clin Geriatr Med 2017; 33:473-490. [PMID: 28991645 DOI: 10.1016/j.cger.2017.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Natural lung aging is characterized by molecular and cellular changes in multiple lung cell populations. These changes include shorter telomeres, increased expression of cellular senescence markers, increased DNA damage, oxidative stress, apoptosis, and stem cell exhaustion. Aging, combined with the loss of protective repair processes, correlates with the development and incidence of chronic respiratory diseases, including idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease. Ultimately, it is the interplay of age-related changes in biology and the subsequent responses to environmental exposures that largely define the physiology and clinical course of the aging lung.
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Affiliation(s)
- Kori Ascher
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Miami Leonard M. Miller School of Medicine, 1600 Northwest 10th Avenue RMSB 7056 (D-60), Miami, FL 33136, USA
| | - Sharon J Elliot
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Gustavo A Rubio
- DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA
| | - Marilyn K Glassberg
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Miami Leonard M. Miller School of Medicine, 1600 Northwest 10th Avenue RMSB 7056 (D-60), Miami, FL 33136, USA; DeWitt Daughtry Family Department of Surgery, University of Miami Leonard M. Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA; Division of Pediatric Pulmonology, Department of Pediatrics, University of Miami Leonard M. Miller School of Medicine, 1600 NW 10th Avenue, Miami, FL 33136, USA.
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