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Craig DJ, Crawford EL, Chen H, Grogan EL, Deppen SA, Morrison T, Antic SL, Massion PP, Willey JC. TP53 mutation prevalence in normal airway epithelium as a biomarker for lung cancer risk. BMC Cancer 2023; 23:783. [PMID: 37612638 PMCID: PMC10464352 DOI: 10.1186/s12885-023-11266-7] [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: 05/19/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND There is a need for biomarkers that improve accuracy compared with current demographic risk indices to detect individuals at the highest lung cancer risk. Improved risk determination will enable more effective lung cancer screening and better stratification of lung nodules into high or low-risk category. We previously reported discovery of a biomarker for lung cancer risk characterized by increased prevalence of TP53 somatic mutations in airway epithelial cells (AEC). Here we present results from a validation study in an independent retrospective case-control cohort. METHODS Targeted next generation sequencing was used to identify mutations within three TP53 exons spanning 193 base pairs in AEC genomic DNA. RESULTS TP53 mutation prevalence was associated with cancer status (P < 0.001). The lung cancer detection receiver operator characteristic (ROC) area under the curve (AUC) for the TP53 biomarker was 0.845 (95% confidence limits 0.749-0.942). In contrast, TP53 mutation prevalence was not significantly associated with age or smoking pack-years. The combination of TP53 mutation prevalence with PLCOM2012 risk score had an ROC AUC of 0.916 (0.846-0.986) and this was significantly higher than that for either factor alone (P < 0.03). CONCLUSIONS These results support the validity of the TP53 mutation prevalence biomarker and justify taking additional steps to assess this biomarker in AEC specimens from a prospective cohort and in matched nasal brushing specimens as a potential non-invasive surrogate specimen.
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Affiliation(s)
- Daniel J Craig
- University of Toledo College of Medicine, 3000 Arlington Ave, OH, 43614, Toledo, USA
| | - Erin L Crawford
- University of Toledo College of Medicine, 3000 Arlington Ave, OH, 43614, Toledo, USA
| | - Heidi Chen
- Vanderbilt University Medical Center, 1301 Medical Center Dr., TN, 37232, Nashville, USA
| | - Eric L Grogan
- Vanderbilt University Medical Center, 1301 Medical Center Dr., TN, 37232, Nashville, USA
- Tennessee Valley VA Healthcare System, 1310 24Th Avenue South, Nashville, TN, 37212, USA
| | - Steven A Deppen
- Vanderbilt University Medical Center, 1301 Medical Center Dr., TN, 37232, Nashville, USA
| | - Thomas Morrison
- Accugenomics Inc, 1410 Commonwealth Dr #105, Wilmington, NC, 28403, USA
| | - Sanja L Antic
- Vanderbilt University Medical Center, 1301 Medical Center Dr., TN, 37232, Nashville, USA
| | - Pierre P Massion
- Vanderbilt University Medical Center, 1301 Medical Center Dr., TN, 37232, Nashville, USA
| | - James C Willey
- University of Toledo College of Medicine, 3000 Arlington Ave, OH, 43614, Toledo, USA.
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Jia Y, Qi X, Ma M, Cheng S, Cheng B, Liang C, Guo X, Zhang F. Integrating genome-wide association study with regulatory SNP annotations identified novel candidate genes for osteoporosis. Bone Joint Res 2023; 12:147-154. [PMID: 37051837 PMCID: PMC10003063 DOI: 10.1302/2046-3758.122.bjr-2022-0206.r1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Osteoporosis (OP) is a metabolic bone disease, characterized by a decrease in bone mineral density (BMD). However, the research of regulatory variants has been limited for BMD. In this study, we aimed to explore novel regulatory genetic variants associated with BMD. We conducted an integrative analysis of BMD genome-wide association study (GWAS) and regulatory single nucleotide polymorphism (rSNP) annotation information. Firstly, the discovery GWAS dataset and replication GWAS dataset were integrated with rSNP annotation database to obtain BMD associated SNP regulatory elements and SNP regulatory element-target gene (E-G) pairs, respectively. Then, the common genes were further subjected to HumanNet v2 to explore the biological effects. Through discovery and replication integrative analysis for BMD GWAS and rSNP annotation database, we identified 36 common BMD-associated genes for BMD irrespective of regulatory elements, such as FAM3C (pdiscovery GWAS = 1.21 × 10-25, preplication GWAS = 1.80 × 10-12), CCDC170 (pdiscovery GWAS = 1.23 × 10-11, preplication GWAS = 3.22 × 10-9), and SOX6 (pdiscovery GWAS = 4.41 × 10-15, preplication GWAS = 6.57 × 10-14). Then, for the 36 common target genes, multiple gene ontology (GO) terms were detected for BMD such as positive regulation of cartilage development (p = 9.27 × 10-3) and positive regulation of chondrocyte differentiation (p = 9.27 × 10-3). We explored the potential roles of rSNP in the genetic mechanisms of BMD and identified multiple candidate genes. Our study results support the implication of regulatory genetic variants in the development of OP.
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Affiliation(s)
- Yumeng Jia
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mei Ma
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Shiqiang Cheng
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Bolun Cheng
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Chujun Liang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Xiong Guo
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
| | - Feng Zhang
- School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, China
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3
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The establishment of COPD organoids to study host-pathogen interaction reveals enhanced viral fitness of SARS-CoV-2 in bronchi. Nat Commun 2022; 13:7635. [PMID: 36496442 PMCID: PMC9735280 DOI: 10.1038/s41467-022-35253-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterised by airflow limitation and infective exacerbations, however, in-vitro model systems for the study of host-pathogen interaction at the individual level are lacking. Here, we describe the establishment of nasopharyngeal and bronchial organoids from healthy individuals and COPD that recapitulate disease at the individual level. In contrast to healthy organoids, goblet cell hyperplasia and reduced ciliary beat frequency were observed in COPD organoids, hallmark features of the disease. Single-cell transcriptomics uncovered evidence for altered cellular differentiation trajectories in COPD organoids. SARS-CoV-2 infection of COPD organoids revealed more productive replication in bronchi, the key site of infection in severe COVID-19. Viral and bacterial exposure of organoids induced greater pro-inflammatory responses in COPD organoids. In summary, we present an organoid model that recapitulates the in vivo physiological lung microenvironment at the individual level and is amenable to the study of host-pathogen interaction and emerging infectious disease.
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Chen Z, Wei D, Chen X, Huang Y, Shen Z, He W. RNA sequencing uncover crucial genes mediating progression of large-artery atherosclerotic and small-artery occlusion ischemic stroke. Brain Res 2022; 1796:148078. [PMID: 36096198 DOI: 10.1016/j.brainres.2022.148078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/04/2022] [Accepted: 09/04/2022] [Indexed: 02/05/2023]
Abstract
PURPOSE The goal of our study is to uncover the pathogenesis of large-artery atherosclerotic ischemic stroke (LAAIS) and small-artery occlusion ischemic stroke (SAOIS) and analyze their difference using RNA sequencing. METHODS RNA sequencing was used to filtrate differentially expressed mRNAs (DEmRNAs) and differentially expressed lncRNAs (DElncRNAs) in LAAIS and SAOIS. Specific DEmRNAs and DElncRNAs in LAAIS and SAOIS were further found. Functional annotation and DElncRNA-DEmRNA co-expression network were built to reveal biological function of DEmRNAs. RESULTS A total of 832 DEmRNAs and 96 DElncRNAs were identified in LAAIS vs normal controls. 587 DEmRNAs and 105 DElncRNAs were identified in SAOIS vs normal controls. In LAAIS vs SAOIS, 636 DEmRNAs and 112 DElncRNAs were identified. Among which, 571 DEmRNAs and 61 DElncRNAs were LAAIS specific DEmRNAs and DElncRNAs, respectively. 325 DEmRNAs and 66 DElncRNAs were respectively SAOIS specific DEmRNAs and DElncRNAs. We also obtained 3086 LAAIS specific DElncRNA-DEmRNA co-expression pairs and 661 SAOIS specific DElncRNA-DEmRNA co-expression pairs. Oxidative phosphorylation and Alzheimer's disease were significantly enriched pathways in both LAAIS specific DEmRNAs and DEmRNAs in LAAIS specific DElncRNA-DEmRNA co-expression network. ECM-receptor interaction, hypertrophic cardiomyopathy and dilated cardiomyopathy were significantly enriched pathways in both SAOIS specific DEmRNAs and DEmRNAs in SAOIS specific DElncRNA-DEmRNA co-expression network. CONCLUSION This finding may help to understand the mechanisms of LAAIS and SAOIS and offer novel clues for finding specific biomarkers for LAAIS and SAOIS.
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Affiliation(s)
- Zhaolin Chen
- Department of Neurology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Duncai Wei
- Department of Pharmacy, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaopu Chen
- Department of Neurology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yinting Huang
- Department of Neurology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zibin Shen
- Department of Neurology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Wenzhen He
- Department of Neurology, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
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Kammer MN, Deppen SA, Antic S, Jamshedur Rahman S, Eisenberg R, Maldonado F, Aldrich MC, Sandler KL, Landman B, Massion PP, Grogan EL. The impact of the lung EDRN-CVC on Phase 1, 2, & 3 biomarker validation studies. Cancer Biomark 2022; 33:449-465. [DOI: 10.3233/cbm-210382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The Early Detection Research Network’s (EDRN) purpose is to discover, develop and validate biomarkers and imaging methods to detect early-stage cancers or at-risk individuals. The EDRN is composed of sites that fall into four categories: Biomarker Developmental Laboratories (BDL), Biomarker Reference Laboratories (BRL), Clinical Validation Centers (CVC) and Data Management and Coordinating Centers. Each component has a crucial role to play within the mission of the EDRN. The primary role of the CVCs is to support biomarker developers through validation trials on promising biomarkers discovered by both EDRN and non-EDRN investigators. The second round of funding for the EDRN Lung CVC at Vanderbilt University Medical Center (VUMC) was funded in October 2016 and we intended to accomplish the three missions of the CVCs: To conduct innovative research on the validation of candidate biomarkers for early cancer detection and risk assessment of lung cancer in an observational study; to compare biomarker performance; and to serve as a resource center for collaborative research within the Network and partner with established EDRN BDLs and BRLs, new laboratories and industry partners. This report outlines the impact of the VUMC EDRN Lung CVC and describes the role in promoting and validating biological and imaging biomarkers.
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Affiliation(s)
- Michael N. Kammer
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Stephen A. Deppen
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Tennessee Valley Healthcare System, Veterans Affairs, Nashville, TN, USA
| | - Sanja Antic
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - S.M. Jamshedur Rahman
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rosana Eisenberg
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Fabien Maldonado
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kim L. Sandler
- Department of Radiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bennett Landman
- Department of Biomedical Engineering, Vanderbilt University, Nashville, TN, USA
| | - Pierre P. Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
- Tennessee Valley Healthcare System, Veterans Affairs, Nashville, TN, USA
- Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Eric L. Grogan
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, TN, USA
- Tennessee Valley Healthcare System, Veterans Affairs, Nashville, TN, USA
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Ke L, Chen L, Yaling Y, Can G, Jun L, Chuan Z. Investigation on the Pathological Mechanism of Frequent Exacerbators With Chronic Obstructive Pulmonary Disease Based on the Characteristics of Respiratory Flora. Front Med (Lausanne) 2022; 8:816802. [PMID: 35127772 PMCID: PMC8811034 DOI: 10.3389/fmed.2021.816802] [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: 11/17/2021] [Accepted: 12/15/2021] [Indexed: 11/17/2022] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is a common obstructive respiratory disease characterized by persistent respiratory symptoms and limited airflow due to airway obstruction. The present study investigates the distribution characteristics of respiratory tract flora in both frequent and infrequent exacerbators of COPD. The 16S sequencing technique was adopted to differentiate the inherent differences of respiratory tract flora between frequent exacerbators and infrequent exacerbators. Additionally, cell counting kit 8 (CCK8), lactate dehydrogenase (LDH) test, flow cytometry, enzyme-linked immunosorbent assay (ELISA), and western blot were carried out in human bronchial epithelial cells cultured in vitro and the regulatory effects of differential flora were verified. The results revealed that the observed species index, Chao1 index, and the ACE estimator of COPD frequent exacerbators were markedly higher than those of COPD infrequent exacerbators. The top five strains of COPD frequent exacerbators included g_Streptococcus (15.565%), g_Prevotella (10.683%), g_Veillonella (6.980%), g_Haemophilus (5.601%), and g_Neisseria (4.631%). Veillonella parvula generated obvious cytotoxicity and substantially reduced the activity of human bronchial epithelial cells (p < 0.01). Furthermore, the results of flow cytometry indicated that the proportion of human bronchial epithelial cells in both the S phase and G2 phase decreased following Veillonella parvula treatment indicated that Veillonella parvula inhibited cell proliferation. Meanwhile, being treated using Veillonella parvula, the expressions of interleukin-1 (IL-1), IL-6, Tumor Necrosis Factor α (TNF-α), and p-nuclear factor kappa B (NF-κB) of the cells were increased markedly (p < 0.01). Taken together, the current research demonstrated that the relative abundance of Veillonella in COPD frequent exacerbators was higher than that of infrequent exacerbators. Veillonella parvula activated the inflammatory pathway, ultimately destroyed the cell viability, and greatly impaired the activity of human bronchial epithelial cells, thereby inhibiting cell proliferation.
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Affiliation(s)
- Li Ke
- Department of Laboratory Medicine, Chongqing the Seventh People's Hospital, Chongqing, China
- *Correspondence: Li Ke
| | - Luo Chen
- Department of Respiratory and Critical Care, Chongqing the Seventh People's Hospital, Chongqing, China
| | - Yuan Yaling
- Department of Laboratory Medicine, Chongqing the Seventh People's Hospital, Chongqing, China
| | - Gao Can
- Department of Laboratory Medicine, Chongqing the Seventh People's Hospital, Chongqing, China
| | - Lin Jun
- Department of Laboratory Medicine, Chongqing the Seventh People's Hospital, Chongqing, China
| | - Zhang Chuan
- Department of Laboratory Medicine, Chongqing the Seventh People's Hospital, Chongqing, China
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Shen W, Wang S, Wang R, Zhang Y, Tian H, Yang X, Wei W. Analysis of the polarization states of the alveolar macrophages in chronic obstructive pulmonary disease samples based on miRNA-mRNA network signatures. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1333. [PMID: 34532470 PMCID: PMC8422127 DOI: 10.21037/atm-21-3815] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/12/2021] [Indexed: 12/12/2022]
Abstract
Background Multiple gene expression studies have been performed to investigate the biomarkers of chronic obstructive pulmonary disease (COPD). However, few studies have related COPD to macrophage cells. Methods The gene expression levels of clinical samples of COPD smokers (COPD; n=6), healthy smokers (Smoke; n=11), and never smokers (Never; n=4) were downloaded from the Gene Expression Omnibus (GEO) repository of GSE124180. The expression levels of messenger RNAs (mRNAs) and microRNAs (miRNAs) in macrophage cells of M0 (n=7), M1 (n=7), and M2 (n=7) were downloaded from the GEO repository of GSE46903 and GSE51307. Differentially expressed (DE) mRNAs (DEmRNAs) were identified by edgeR and GEO2R, with an adjusted P value <0.05 and |log2fold change (FC)| ≥1 chosen as the cut-off threshold. The potential target genes of miRNA were identified using miRanda (v3.3a) and TargetScan (v6.0) with default settings. Gene Ontology (GO) and Reactome pathway analyses were performed. Results The composition of macrophages was quite different between COPD, Never, and Smoke samples. The proportion of M1 cells was lower than that of M0 and M2 cells in Smokers and COPD samples. Most of the genes specifically up-regulated in M1 are related to inflammation/immunity. The expression levels of miR-30a-5p, miR-200c-3p, miR-20b-5p, miR-199b-5p, and miR-301b-3p in M1 macrophages were all lower than that of M0. Their expression levels in M2 macrophages compared with M1 varied, with higher expression in miR-30a-5p, miR-20b-5p, and lower expression in miR-200c-3p, and miR-301b-3p. The mRNAs of the fms related receptor tyrosine kinase 1 (FLT1), cardiotrophin like cytokine factor 1 (CLCF1), phosphodiesterase 4D (PDE4D), coagulation factor III, and tissue factor (F3) were dysregulated in COPD and macrophage cells. Conclusions The present study mined the miRNA-mRNA signature which might play an essential role in COPD and macrophage polarization.
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Affiliation(s)
- Wen Shen
- Respiratory Medicine Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shukun Wang
- Respiratory Medicine Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Ruili Wang
- Respiratory Medicine Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yang Zhang
- Respiratory Medicine Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Hong Tian
- Respiratory Medicine Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaolei Yang
- Respiratory Medicine Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Wei Wei
- Respiratory Medicine Department, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
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Association between genetic polymorphisms of miRNAs (miR-8079 and miR-5007) and susceptibility of chronic obstructive pulmonary disease in Chinese people. Microb Pathog 2021; 160:105160. [PMID: 34455057 DOI: 10.1016/j.micpath.2021.105160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 07/02/2021] [Accepted: 08/20/2021] [Indexed: 11/23/2022]
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) has been recognized as a heterogeneous disease, which is caused by biological heterogeneity. The purpose of our study is to determine the association between the single nucleotide polymorphisms (SNPs) of miRNAs (miR-8079 and miR-5007) and the susceptibility to COPD in Chinese population. METHODS We conducted a 'case-control' study involving 315 COPD patients and 314 healthy individuals. Three SNPs of miR-8079 (rs9533803, rs9525927, rs7981875) and three SNPs of miR-5007 (rs9527345, rs2252932, rs2997119) were selected, then we used logistic regression to analyze the association between candidate SNPs and COPD susceptibility under different genetic models. Multi-factor dimensionality reduction (MDR) was used to analyze the interaction of "SNP-SNP" in COPD risk studies. Finally, we used univariate and ANOVA to analyze the differences in clinical characteristics among different genotypes. RESULTS Our results showed that miR-8079-rs9525927 was significant associated with COPD susceptibility whether in overall and stratified analysis. miR-5007-rs2997119 was associated with the increased risk of COPD in women under multiple genetic models; miR-8079-rs9525927 and miR-5007-rs9527345 had a certain association with clinical indicator Fev_1 of COPD patients; rs9527345 or rs2252932 on miR-5007 was associated with the risk of COPD with wheezing dyspnea or wheezing. CONCLUSION Our results suggested that the genetic polymorphisms of miR-8079 or miR-5007 were potentially associated with COPD risk, of which miR-8079-rs9525927 was more prominent.
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Liu P, Li S, Tang L. Nerve Growth Factor: A Potential Therapeutic Target for Lung Diseases. Int J Mol Sci 2021; 22:ijms22179112. [PMID: 34502019 PMCID: PMC8430922 DOI: 10.3390/ijms22179112] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 12/19/2022] Open
Abstract
The lungs play a very important role in the human respiratory system. However, many factors can destroy the structure of the lung, causing several lung diseases and, often, serious damage to people's health. Nerve growth factor (NGF) is a polypeptide which is widely expressed in lung tissues. Under different microenvironments, NGF participates in the occurrence and development of lung diseases by changing protein expression levels and mediating cell function. In this review, we summarize the functions of NGF as well as some potential underlying mechanisms in pulmonary fibrosis (PF), coronavirus disease 2019 (COVID-19), pulmonary hypertension (PH), asthma, chronic obstructive pulmonary disease (COPD), and lung cancer. Furthermore, we highlight that anti-NGF may be used in future therapeutic strategies.
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Affiliation(s)
- Piaoyang Liu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China;
| | - Shun Li
- Department of Immunology, School of Basic Medical Sciences, Chengdu Medical College, Chengdu 610500, China
- Non-Coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu 610500, China
- Correspondence: (S.L.); (L.T.)
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China;
- Correspondence: (S.L.); (L.T.)
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10
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Adam G, Shiomi T, Monica G, Jarrod S, Vincent A, Becky M, Tina Z, Jeanine D. Suppression of cigarette smoke induced MMP1 expression by selective serotonin re-uptake inhibitors. FASEB J 2021; 35:e21519. [PMID: 34137477 PMCID: PMC9292461 DOI: 10.1096/fj.202001966rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 11/16/2022]
Abstract
Globally, COPD remains a major cause of disability and death. In the United States alone, it is estimated that approximately 14 million people suffer from the disease. Given the high disease burden and requirement for chronic, long‐term medical care associated with COPD, it is essential that new disease modifying agents are developed to complement the symptomatic therapeutics currently available. In the present report, we have identified a potentially novel therapeutic agent through the use of a high throughput screen based on the knowledge that cigarette smoke induces the proteolytic enzyme MMP1 leading to destruction of the lung in COPD. A construct utilizing the cigarette responsive promoter element of MMP‐1 was conjugated to a luciferase reporter and utilized in an in vitro assay to screen the NIH Molecular Libraries Small Molecule Repository to identify putative targets that suppressed luciferase expression in response to cigarette smoke extract (CSE). Selective serotonin reuptake inhibitors potently inhibited luciferase expression and were further validated. SSRI treatment suppressed MMP‐1 production in small airway epithelial cells exposed to (CSE) in vitro as well as in smoke exposed rabbits. In addition, SSRI treatment inhibited inflammatory cytokine production while rescuing cigarette smoke induced downregulation in vivo of the anti‐inflammatory lipid transporter ABCA1, previously shown by our laboratory to be lung protective. Importantly, SSRI treatment prevented lung destruction in smoke exposed rabbits as measured by morphometry. These studies support further investigation into SSRIs as a novel therapeutic for COPD may be warranted.
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Affiliation(s)
- Gerber Adam
- Department of Medicine, Anesthesiology, Physiology and Cell Biology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Takayuki Shiomi
- Center for Basic Medical Sciences, Graduate School, International University of Health and Welfare, Chiba, Japan
| | - Goldklang Monica
- Department of Medicine, Anesthesiology, Physiology and Cell Biology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Sonett Jarrod
- Department of Medicine, Anesthesiology, Physiology and Cell Biology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Anguiano Vincent
- Department of Oncological Sciences, Icahn School of Medicine, Mount Sinai Hospital, New York, NY, USA
| | - Mercer Becky
- Office of Academic Affairs, Palm Beach State College, Florida, USA
| | - Zelonina Tina
- Department of Medicine, Anesthesiology, Physiology and Cell Biology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - D'Armiento Jeanine
- Department of Medicine, Anesthesiology, Physiology and Cell Biology, College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
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11
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Huang Y, Lin L, Shen Z, Li Y, Cao H, Peng L, Qiu Y, Cheng X, Meng M, Lu D, Yin D. CEBPG promotes esophageal squamous cell carcinoma progression by enhancing PI3K-AKT signaling. Am J Cancer Res 2020; 10:3328-3344. [PMID: 33163273 PMCID: PMC7642652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023] Open
Abstract
CCAAT/enhancer binding proteins (CEBPs, including CEBPA, CEBPB, CEBPD, CEBPE, CEBPG, and CEBPZ) play critical roles in a variety of physiological and pathological processes. However, the molecular characteristics and biological significance of CEBPs in esophageal squamous cell carcinoma (ESCC) have rarely been reported. Here, we show that most of the CEBPs are upregulated and accompanied with copy number amplifications in ESCC. Of note, high CEBPG expression is regulated by the ESCC specific transcription factor TP63 and serves as a prognostic factor for poor survival in ESCC patients. Functionally, CEBPG significantly promotes the proliferation and migration of ESCC cells both in vitro and in vivo. Mechanistically, CEBPG activates the PI3K-AKT signaling pathway through directly binding to distal enhancers and/or promoters of genes involved in this pathway, including genes of CCND1, MYC, CDK2, etc. These findings provide new insights into CEBPs dysregulation in ESCC and elucidate a crucial role for CEBPG in the progression of ESCC, highlighting its potential therapeutic value for ESCC treatment.
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Affiliation(s)
- Yongsheng Huang
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Lehang Lin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Zhuojian Shen
- Department of Thoracic Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Yu Li
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Haotian Cao
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Li Peng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Yuntan Qiu
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Xu Cheng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Meng Meng
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Daning Lu
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
| | - Dong Yin
- Guangdong Province Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou 510120, China
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12
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Qi X, Wen Y, Li P, Liang C, Cheng B, Ma M, Cheng S, Zhang L, Liu L, Kafle OP, Zhang F. An integrative analysis of genome-wide association study and regulatory SNP annotation datasets identified candidate genes for bipolar disorder. Int J Bipolar Disord 2020; 8:6. [PMID: 32009227 PMCID: PMC6995798 DOI: 10.1186/s40345-019-0170-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/06/2019] [Indexed: 12/25/2022] Open
Abstract
Background Bipolar disorder (BD) is a complex mood disorder. The genetic mechanism of BD remains largely unknown. Methods We conducted an integrative analysis of genome-wide association study (GWAS) and regulatory SNP (rSNP) annotation datasets, including transcription factor binding regions (TFBRs), chromatin interactive regions (CIRs), mature microRNA regions (miRNAs), long non-coding RNA regions (lncRNAs), topologically associated domains (TADs) and circular RNAs (circRNAs). Firstly, GWAS dataset 1 of BD (including 20,352 cases and 31,358 controls) and GWAS dataset 2 of BD (including 7481 BD patients and 9250 controls) were integrated with rSNP annotation database to obtain BD associated SNP regulatory elements and SNP regulatory element-target gene (E–G) pairs, respectively. Secondly, a comparative analysis of the two datasets results was conducted to identify the common rSNPs and also their target genes. Then, gene sets enrichment analysis (FUMA GWAS) and HumanNet-XC analysis were conducted to explore the functional relevance of identified target genes with BD. Results After the integrative analysis, we identified 52 TFBRs target genes, 44 TADs target genes, 55 CIRs target genes and 21 lncRNAs target genes for BD, such as ITIH4 (Pdataset1 = 6.68 × 10−8, Pdataset2 = 6.64 × 10−7), ITIH3 (Pdataset1 = 1.09 × 10−8, Pdataset2 = 2.00 × 10−7), SYNE1 (Pdataset1 = 1.80 × 10−6, Pdataset2 = 4.33 × 10−9) and OPRM1 (Pdataset1 = 1.80 × 10−6, Pdataset2 = 4.33 × 10−9). Conclusion We conducted a large-scale integrative analysis of GWAS and 6 common rSNP information datasets to explore the potential roles of rSNPs in the genetic mechanism of BD. We identified multiple candidate genes for BD, supporting the importance of rSNP in the development of BD.
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Affiliation(s)
- Xin Qi
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Ping Li
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Chujun Liang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Mei Ma
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Lu Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Om Prakash Kafle
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases of National Health and Family Planning Commission, School of Public Health, Health Science Center, Xi'an Jiaotong University, No. 76 Yan Ta West Road, Xi'an, 710061, People's Republic of China.
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13
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Chu SG, Poli De Frias S, Raby BA, Rosas IO. An RNA-seq primer for pulmonologists. Eur Respir J 2020; 55:13993003.01625-2018. [PMID: 31601712 DOI: 10.1183/13993003.01625-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 09/16/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Sarah G Chu
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sergio Poli De Frias
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Benjamin A Raby
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Channing Division of Network Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Division of Pulmonary and Respiratory Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ivan O Rosas
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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14
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Craig DJ, Morrison T, Khuder SA, Crawford EL, Wu L, Xu J, Blomquist TM, Willey JC. Technical advance in targeted NGS analysis enables identification of lung cancer risk-associated low frequency TP53, PIK3CA, and BRAF mutations in airway epithelial cells. BMC Cancer 2019; 19:1081. [PMID: 31711466 PMCID: PMC6844032 DOI: 10.1186/s12885-019-6313-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/30/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Standardized Nucleic Acid Quantification for SEQuencing (SNAQ-SEQ) is a novel method that utilizes synthetic DNA internal standards spiked into each sample prior to next generation sequencing (NGS) library preparation. This method was applied to analysis of normal appearing airway epithelial cells (AEC) obtained by bronchoscopy in an effort to define a somatic mutation field effect associated with lung cancer risk. There is a need for biomarkers that reliably detect those at highest lung cancer risk, thereby enabling more effective screening by annual low dose CT. The purpose of this study was to test the hypothesis that lung cancer risk is characterized by increased prevalence of low variant allele frequency (VAF) somatic mutations in lung cancer driver genes in AEC. METHODS Synthetic DNA internal standards (IS) were prepared for 11 lung cancer driver genes and mixed with each AEC genomic (g) DNA specimen prior to competitive multiplex PCR amplicon NGS library preparation. A custom Perl script was developed to separate IS reads and respective specimen gDNA reads from each target into separate files for parallel variant frequency analysis. This approach identified nucleotide-specific sequencing error and enabled reliable detection of specimen mutations with VAF as low as 5 × 10- 4 (0.05%). This method was applied in a retrospective case-control study of AEC specimens collected by bronchoscopic brush biopsy from the normal airways of 19 subjects, including eleven lung cancer cases and eight non-cancer controls, and the association of lung cancer risk with AEC driver gene mutations was tested. RESULTS TP53 mutations with 0.05-1.0% VAF were more prevalent (p < 0.05) and also enriched for tobacco smoke and age-associated mutation signatures in normal AEC from lung cancer cases compared to non-cancer controls matched for smoking and age. Further, PIK3CA and BRAF mutations in this VAF range were identified in AEC from cases but not controls. CONCLUSIONS Application of SNAQ-SEQ to measure mutations in the 0.05-1.0% VAF range enabled identification of an AEC somatic mutation field of injury associated with lung cancer risk. A biomarker comprising TP53, PIK3CA, and BRAF somatic mutations may better stratify individuals for optimal lung cancer screening and prevention outcomes.
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Affiliation(s)
- Daniel J. Craig
- Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH 43614 USA
| | - Thomas Morrison
- Accugenomics, Inc, 1410 Commonwealth Dr #105, Wilmington, NC 28403 USA
| | - Sadik A. Khuder
- Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH 43614 USA
| | - Erin L. Crawford
- Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH 43614 USA
| | - Leihong Wu
- National Center for Toxicological Research, U.S. Food & Drug Administration, Jefferson, AR USA
| | - Joshua Xu
- National Center for Toxicological Research, U.S. Food & Drug Administration, Jefferson, AR USA
| | - Thomas M. Blomquist
- Department of Pathology, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH 43614 USA
| | - James C. Willey
- Department of Medicine, The University of Toledo College of Medicine, 3000 Arlington Avenue, Toledo, OH 43614 USA
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15
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Matana A, Ziros PG, Chartoumpekis DV, Renaud CO, Polašek O, Hayward C, Zemunik T, Sykiotis GP. Rare and common genetic variations in the Keap1/Nrf2 antioxidant response pathway impact thyroglobulin gene expression and circulating levels, respectively. Biochem Pharmacol 2019; 173:113605. [PMID: 31421134 DOI: 10.1016/j.bcp.2019.08.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 08/12/2019] [Indexed: 12/15/2022]
Abstract
Nuclear factor, erythroid 2-like 2 (Nrf2) is a transcription factor that has been gaining attention in the field of pharmacology and especially in the chemoprevention of diseases such as cancer, metabolic and neurodegenerative diseases, etc. This is because natural compounds such as sulforaphane, which is found in broccoli sprout extracts, can activate Nrf2. The repertoire of the roles of Nrf2 is ever increasing; besides its traditional antioxidant and cytoprotective effects, Nrf2 can have other functions as a transcription factor. We have recently shown that Nrf2 directly regulates the expression of thyroglobulin (Tg), which is the most abundant thyroidal protein and the precursor of thyroid hormones. Two functional binding sites for Nrf2 (antioxidant response elements, AREs) were identified in the regulatory region of the TG gene. Interestingly, we then observed that one of these AREs harbors a rare single-nucleotide polymorphism (SNP). Also recently, we performed the first genome-wide association study (GWAS) for common SNPs that impact the circulating levels of Tg. Based on these investigations, we were triggered (i) to investigate whether common SNPs in the Nrf2 pathway correlate with circulating Tg levels; and (ii) to examine whether the rare SNP in one of the TG regulatory AREs may affect gene expression. To address the first question, we analyzed GWAS data from a general population and its two subpopulations, one with thyroid disease and/or abnormal thyroid function tests and the other without, in which circulating Tg levels had been measured. Statistically significant associations with Tg levels were observed in the genes encoding Nrf2 and Keap1, including, notably, a known functional SNP in the promoter of the gene encoding Nrf2. Regarding the rare SNP (rs778940395) in the proximal ARE of the TG enhancer, luciferase reporter gene expression studies in PCCL3 rat thyroid follicular cells showed that this SNP abrogated the basal and sulforaphane- or TSH-induced luciferase activity, behaving as a complete loss-of-function mutation. Thus, both rare and common genetic variation in the Keap1/Nrf2 pathway can impact TG expression and Tg circulating levels, respectively.
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Affiliation(s)
- Antonela Matana
- Department of Medical Biology, University of Split, School of Medicine, Split, Šoltanska 2, Split, Croatia
| | - Panos G Ziros
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dionysios V Chartoumpekis
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland; Department of Internal Medicine, Division of Endocrinology, School of Medicine, University of Patras, Patras, Greece
| | - Cedric O Renaud
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Ozren Polašek
- Department of Public Health, University of Split, School of Medicine, Split, Croatia
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh, United Kingdom
| | - Tatijana Zemunik
- Department of Medical Biology, University of Split, School of Medicine, Split, Šoltanska 2, Split, Croatia.
| | - Gerasimos P Sykiotis
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
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16
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Caramori G, Ruggeri P, Mumby S, Ieni A, Lo Bello F, Chimankar V, Donovan C, Andò F, Nucera F, Coppolino I, Tuccari G, Hansbro PM, Adcock IM. Molecular links between COPD and lung cancer: new targets for drug discovery? Expert Opin Ther Targets 2019; 23:539-553. [DOI: 10.1080/14728222.2019.1615884] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Gaetano Caramori
- Unità Operativa Complessa di Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Paolo Ruggeri
- Unità Operativa Complessa di Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Sharon Mumby
- Airway Disease Section, National Heart and Lung Institute, Imperial College, London, UK
| | - Antonio Ieni
- Department of Human Pathology in Adult and Developmental Age “Gaetano Barresi”, Section of Anatomic Pathology, University of Messina, Messina, Italy
| | - Federica Lo Bello
- Unità Operativa Complessa di Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Vrushali Chimankar
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and The University of Newcastle, Newcastle, Australia
| | - Chantal Donovan
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and The University of Newcastle, Newcastle, Australia
| | - Filippo Andò
- Unità Operativa Complessa di Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Francesco Nucera
- Unità Operativa Complessa di Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Irene Coppolino
- Unità Operativa Complessa di Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università di Messina, Messina, Italy
| | - Giovanni Tuccari
- Department of Human Pathology in Adult and Developmental Age “Gaetano Barresi”, Section of Anatomic Pathology, University of Messina, Messina, Italy
| | - Philip M. Hansbro
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and The University of Newcastle, Newcastle, Australia
- Faculty of Science, Ultimo, and Centenary Institute, Centre for Inflammation, University of Technology Sydney, Sydney, Australia
| | - Ian M. Adcock
- Airway Disease Section, National Heart and Lung Institute, Imperial College, London, UK
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17
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Morrow JD, Chase RP, Parker MM, Glass K, Seo M, Divo M, Owen CA, Castaldi P, DeMeo DL, Silverman EK, Hersh CP. RNA-sequencing across three matched tissues reveals shared and tissue-specific gene expression and pathway signatures of COPD. Respir Res 2019; 20:65. [PMID: 30940135 PMCID: PMC6446359 DOI: 10.1186/s12931-019-1032-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Accepted: 03/25/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Multiple gene expression studies have been performed separately in peripheral blood, lung, and airway tissues to study COPD. We performed RNA-sequencing gene expression profiling of large-airway epithelium, alveolar macrophage and peripheral blood samples from the same subset of COPD cases and controls from the COPDGene study who underwent bronchoscopy at a single center. Using statistical and gene set enrichment approaches, we sought to improve the understanding of COPD by studying gene sets and pathways across these tissues, beyond the individual genomic determinants. METHODS We performed differential expression analysis using RNA-seq data obtained from 63 samples from 21 COPD cases and controls (includes four non-smokers) via the R package DESeq2. We tested associations between gene expression and variables related to lung function, smoking history, and CT scan measures of emphysema and airway disease. We examined the correlation of differential gene expression across the tissues and phenotypes, hypothesizing that this would reveal preserved and private gene expression signatures. We performed gene set enrichment analyses using curated databases and findings from prior COPD studies to provide biological and disease relevance. RESULTS The known smoking-related genes CYP1B1 and AHRR were among the top differential expression results for smoking status in the large-airway epithelium data. We observed a significant overlap of genes primarily across large-airway and macrophage results for smoking and airway disease phenotypes. We did not observe specific genes differentially expressed in all three tissues for any of the phenotypes. However, we did observe hemostasis and immune signaling pathways in the overlaps across all three tissues for emphysema, and amyloid and telomere-related pathways for smoking. In peripheral blood, the emphysema results were enriched for B cell related genes previously identified in lung tissue studies. CONCLUSIONS Our integrative analyses across COPD-relevant tissues and prior studies revealed shared and tissue-specific disease biology. These replicated and novel findings in the airway and peripheral blood have highlighted candidate genes and pathways for COPD pathogenesis.
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Affiliation(s)
- Jarrett D Morrow
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Kimberly Glass
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Minseok Seo
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Miguel Divo
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Caroline A Owen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Peter Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA, 02115, USA.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, 02115, USA
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18
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Zeneyedpour L, Dekker LJM, van Sten‐van`t Hoff JJM, Burgers PC, ten Hacken NHT, Luider TM. Neoantigens in Chronic Obstructive Pulmonary Disease and Lung Cancer: A Point of View. Proteomics Clin Appl 2019; 13:e1800093. [PMID: 30706659 PMCID: PMC6593722 DOI: 10.1002/prca.201800093] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 01/21/2019] [Indexed: 12/20/2022]
Abstract
The goal of this manuscript is to explore the role of clinical proteomics for detecting mutations in chronic obstructive pulmonary disease (COPD) and lung cancer by mass spectrometry-based technology. COPD and lung cancer caused by smoke inhalation are most likely linked by challenging the immune system via partly shared pathways. Genome-wide association studies have identified several single nucleotide polymorphisms which predispose an increased susceptibility to COPD and lung cancer. In lung cancer, this leads to coding mutations in the affected tissues, development of neoantigens, and different functionality and abundance of proteins in specific pathways. If a similar reasoning can also be applied in COPD will be discussed. The technology of mass spectrometry has developed into an advanced technology for proteome research detecting mutated peptides or proteins and finding relevant molecular mechanisms that will enable predicting the response to immunotherapy in COPD and lung cancer patients.
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Affiliation(s)
| | | | | | | | - Nick H. T. ten Hacken
- Department of PulmonologyUniversity Medical Center Groningen/University of Groningen9713 GroningenNetherlands
| | - Theo M. Luider
- Department of NeurologyErasmus MCRotterdam3015 GENetherlands
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19
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Zhang X, Guo Y, Yang J, Niu J, Du L, Li H, Li X. A functional variant alters binding of activating protein 1 regulating expression of FGF7 gene associated with chronic obstructive pulmonary disease. BMC MEDICAL GENETICS 2019; 20:33. [PMID: 30777021 PMCID: PMC6380023 DOI: 10.1186/s12881-019-0761-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/29/2019] [Indexed: 02/07/2023]
Abstract
Background Genome-wide association studies (GWASs) of a large cohort of subjects with chronic obstructive pulmonary disease (COPD) have successfully identified multiple risk genes, including fibroblast growth factor 7 (FGF7). However, the underlying molecular mechanism influencing function of FGF7 and risk of COPD remains further study. Methods In this study, we replicated the genetic association of variants near the FGF7 gene in 258 Chinese Han patients with COPD and 311 healthy controls. Additionally, we functionally evaluated a candidate causal variant upstream of the FGF7 gene. Results The most significant association was observed at rs12905203 (P = 5.9 × 10− 3, odd ratio, OR = 1.516) that explains associations of previously reported variants at the FGF7 locus. Electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation-quantitative polymerase chain reaction (ChIP-qPCR) assays showed that the risk allele of the variant was bound to activator protein 1 transcription factors (c-Fos and c-Jun) with a significantly reduced affinity and associated with decreased mRNA expression of FGF7 in fibroblast cells at both resting and PMA/Ionomycin-stimulated conditions. Overexpression of c-Fos and c-Jun proteins or stimulation with PMA/Ionomycin significantly increases mRNA expression of FGF7 in fibroblast cells. Bioinformatic analysis showed that the variant overlaps with multiple genetic regulatory marks, suggesting the regulatory DNA element might function as an enhancer for the FGF7 gene. Luciferase enhancer activity assays demonstrated that the DNA sequences carrying the variant produce enhancer activity while the risk allele of the variant reduces its activity. Conclusions In this study, we demonstrated a consistent association of the FGF7 gene with COPD and mechanistically characterized a candidate functional variant upstream of the FGF7 gene. These data highlighted the important role of the risk variant and the FGF7 gene in influencing risk for COPD. Electronic supplementary material The online version of this article (10.1186/s12881-019-0761-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiaomei Zhang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, NO. 2888, XinCheng Avenue, Changchun, 130118, China.
| | - Yongxin Guo
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, NO. 2888, XinCheng Avenue, Changchun, 130118, China
| | - Jing Yang
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, NO. 2888, XinCheng Avenue, Changchun, 130118, China
| | - Jianlou Niu
- School of Pharmacy, Wenzhou Medical University, Chashan Avenue, Wenzhou, 325035, Zhejiang, China
| | - Lina Du
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, NO. 2888, XinCheng Avenue, Changchun, 130118, China
| | - Haiyan Li
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, NO. 2888, XinCheng Avenue, Changchun, 130118, China.
| | - Xiaokun Li
- College of Life Science, Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical Development, Jilin Agricultural University, NO. 2888, XinCheng Avenue, Changchun, 130118, China. .,School of Pharmacy, Wenzhou Medical University, Chashan Avenue, Wenzhou, 325035, Zhejiang, China.
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20
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Sears CR. DNA repair as an emerging target for COPD-lung cancer overlap. Respir Investig 2019; 57:111-121. [PMID: 30630751 DOI: 10.1016/j.resinv.2018.11.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/14/2018] [Accepted: 11/22/2018] [Indexed: 02/06/2023]
Abstract
Cigarette smoking is the leading cause of lung cancer and chronic obstructive pulmonary disease (COPD). Many of the detrimental effects of cigarette smoke have been attributed to the development of DNA damage, either directly from chemicals contained in cigarette smoke or as a product of cigarette smoke-induced inflammation and oxidative stress. In this review, we discuss the environmental, epidemiological, and physiological links between COPD and lung cancer and the likely role of DNA damage and repair in COPD and lung cancer development. We explore alterations in DNA damage repair by DNA repair proteins and pathways. We discuss emerging data supporting a key role for the DNA repair protein, xeroderma pigmentosum group C (XPC), in cigarette smoke-induced COPD and early lung cancer development. Understanding the interplay between cigarette smoke, DNA damage repair, COPD, and lung cancer may lead to prognostic tools and new, potentially targetable, pathways for lung cancer prevention and treatment.
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Affiliation(s)
- Catherine R Sears
- Division of Pulmonary, Critical Care, Sleep and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, Indiana; The Richard L. Roudebush Veterans Affairs Medical Center; 980W, Walnut Street, Walther Hall, C400, Indianapolis, IN, 46202, USA.
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