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Pan W, An S, Dai L, Xu S, Liu D, Wang L, Zhang R, Wang F, Wang Z. Identification of Potential Differentially-Methylated/Expressed Genes in Chronic Obstructive Pulmonary Disease. COPD 2023; 20:44-54. [PMID: 36655999 DOI: 10.1080/15412555.2022.2158324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease that causes obstructed airflow from the lungs. DNA methylation can regulate gene expression. Understanding the potential molecular mechanism of COPD is of great importance. The aim of this study was to find differentially methylated/expressed genes in COPD. DNA methylation and gene expression profiles in COPD were downloaded from the dataset, followed by functional analysis of differentially-methylated/expressed genes. The potential diagnostic value of these differentially-methylated/expressed genes was determined by receiver operating characteristic (ROC) analysis. Expression validation of differentially-methylated/expressed genes was performed by in vitro experiment and extra online datasets. Totally, 81 hypermethylated-low expression genes and 121 hypomethylated-high expression genes were found in COPD. Among which, 9 core hypermethylated-low expression genes (CD247, CCR7, CD5, IKZF1, SLAMF1, IL2RB, CD3E, CD7 and IL7R) and 8 core hypomethylated-high expression genes (TREM1, AQP9, CD300LF, CLEC12A, NOD2, IRAK3, NLRP3 and LYZ) were identified in the protein-protein interaction (PPI) network. Moreover, these genes had a potential diagnostic utility for COPD. Some signaling pathways were identified in COPD, including T cell receptor signaling pathway, cytokine-cytokine receptor interaction, hematopoietic cell lineage, HTLV-I infection, endocytosis and Jak-STAT signaling pathway. In conclusion, differentially-methylated/expressed genes and involved signaling pathways are likely to be associated with the process of COPD.
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Affiliation(s)
- Wen Pan
- Department of Cardiology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, China
| | - Shuyuan An
- Department of Cardiology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, China
| | - Lina Dai
- Department of Cardiology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, China
| | - Shuo Xu
- Department of Cardiology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, China
| | - Dan Liu
- Clinical Laboratory, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, China
| | - Lizhi Wang
- Department of Cardiology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, China
| | - Ruixue Zhang
- Department of Cardiology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, China
| | - Fengliang Wang
- Department of Cardiology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, China
| | - Zongling Wang
- Department of Cardiology, Qingdao Fuwai Cardiovascular Hospital, Qingdao, Shandong, China
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Zhu J, Wang F, Feng X, Li B, Ma L, Zhang J. Family with sequence similarity 13 member A mediates TGF-β1-induced EMT in small airway epithelium of patients with chronic obstructive pulmonary disease. Respir Res 2021; 22:192. [PMID: 34210319 PMCID: PMC8247231 DOI: 10.1186/s12931-021-01783-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 06/24/2021] [Indexed: 12/28/2022] Open
Abstract
Background To explore the role of family with sequence similarity 13 member A (FAM13A) in TGF-β1-induced EMT in the small airway epithelium of patients with chronic obstructive pulmonary disease (COPD). Methods Small airway wall thickness and protein levels of airway remodeling markers, EMT markers, TGF-β1, and FAM13A were measured in lung tissue samples from COPD and non-COPD patients. The correlations of FAM13A expression with COPD severity and EMT marker expression were evaluated. Gain- and loss-of-function assays were performed to explore the functions of FAM13A in cell proliferation, motility, and TGF-β1-induced EMT marker alterations in human bronchial epithelial cell line BEAS-2B. Results Independent of smoking status, lung tissue samples from COPD patients exhibited significantly increased small airway thickness and collagen fiber deposition, along with enhanced protein levels of remodeling markers (collagen I, fibronectin, and MMP-9), mesenchymal markers (α-SMA, vimentin, and N-cadherin), TGF-β1, and FAM13A, compared with those from non-COPD patients. FAM13A expression negatively correlated with FEV1% and PO2 in COPD patients. In small airway epithelium, FAM13A expression negatively correlated with E-cadherin protein levels and positively correlated with vimentin protein levels. In BEAS-2B cells, TGF-β1 dose-dependently upregulated FAM13A protein levels. FAM13A overexpression significantly promoted cell proliferation and motility in BEAS-2B cells, whereas FAM13A silencing showed contrasting results. Furthermore, FAM13A knockdown partially reversed TGF-β1-induced EMT marker protein alterations in BEAS-2B cells. Conclusions FAM13A upregulation is associated with TGF-β1-induced EMT in the small airway epithelium of COPD patients independent of smoking status, serving as a potential therapeutic target for anti-EMT therapy in COPD. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-021-01783-z.
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Affiliation(s)
- Jinyuan Zhu
- Department of Critical Care Medicine, General Hospital of Ningxia Medical University, Yinchuan, 750004, People's Republic of China
| | - Faxuan Wang
- School of Public Health and Management, Ningxia Medical University, Yinchuan, 750004, People's Republic of China
| | - Xueyan Feng
- Ningxia Medical University, Yinchuan, 750004, People's Republic of China
| | - Beibei Li
- Ningxia Medical University, Yinchuan, 750004, People's Republic of China
| | - Liqiong Ma
- Department of Pathology, General Hospital of Ningxia Medical University, Yinchuan, 750004, People's Republic of China
| | - Jin Zhang
- Department of Respiratory and Critical Care Medicine, General Hospital of Ningxia Medical University, 804 Shengli South Street, Xingqing District, Yinchuan, 750004, People's Republic of China.
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Abstract
Lung cancer in multiple first degree relatives had previously been attributed to smoking and to inherited enzymes associated with increased activation of carcinogens in smoke. There was not clear agreement on the significance of the testing methods for lung cancer susceptibility. More recent studies have identified germline mutations associated with lung cancer even in the absence of smoking and other mutations with plausible explanations for their association with lung cancer caused by smoking. At this time, the clinical significance of the various germline mutations for screening and the implications for therapy are not certain. This review summarizes the currently identified germline mutations associated with lung cancer, but this growing area of research will very likely identify further significant mutations as well.
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Crawford EL, Levin A, Safi F, Lu M, Baugh A, Zhang X, Yeo J, Khuder SA, Boulos AM, Nana-Sinkam P, Massion PP, Arenberg DA, Midthun D, Mazzone PJ, Nathan SD, Wainz R, Silvestri G, Tita J, Willey JC. Lung cancer risk test trial: study design, participant baseline characteristics, bronchoscopy safety, and establishment of a biospecimen repository. BMC Pulm Med 2016; 16:16. [PMID: 26801409 PMCID: PMC4722707 DOI: 10.1186/s12890-016-0178-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Lung Cancer Risk Test (LCRT) trial is a prospective cohort study comparing lung cancer incidence among persons with a positive or negative value for the LCRT, a 15 gene test measured in normal bronchial epithelial cells (NBEC). The purpose of this article is to describe the study design, primary endpoint, and safety; baseline characteristics of enrolled individuals; and establishment of a bio-specimen repository. METHODS/DESIGN Eligible participants were aged 50-90 years, current or former smokers with 20 pack-years or more cigarette smoking history, free of lung cancer, and willing to undergo bronchoscopic brush biopsy for NBEC sample collection. NBEC, peripheral blood samples, baseline CT, and medical and demographic data were collected from each subject. DISCUSSION Over a two-year span (2010-2012), 403 subjects were enrolled at 12 sites. At baseline 384 subjects remained in study and mean age and smoking history were 62.9 years and 50.4 pack-years respectively, with 34% current smokers. Obstructive lung disease (FEV1/FVC <0.7) was present in 157 (54%). No severe adverse events were associated with bronchoscopic brushing. An NBEC and matched peripheral blood bio-specimen repository was established. The demographic composition of the enrolled group is representative of the population for which the LCRT is intended. Specifically, based on baseline population characteristics we expect lung cancer incidence in this cohort to be representative of the population eligible for low-dose Computed Tomography (LDCT) lung cancer screening. Collection of NBEC by bronchial brush biopsy/bronchoscopy was safe and well-tolerated in this population. These findings support the feasibility of testing LCRT clinical utility in this prospective study. If validated, the LCRT has the potential to significantly narrow the population of individuals requiring annual low-dose helical CT screening for early detection of lung cancer and delay the onset of screening for individuals with results indicating low lung cancer risk. For these individuals, the small risk incurred by undergoing once in a lifetime bronchoscopic sample collection for LCRT may be offset by a reduction in their CT-related risks. The LCRT biospecimen repository will enable additional studies of genetic basis for COPD and/or lung cancer risk. TRIAL REGISTRATION The LCRT Study, NCT 01130285, was registered with Clinicaltrials.gov on May 24, 2010.
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Affiliation(s)
- E L Crawford
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - A Levin
- Department of Biostatistics, Henry Ford Hospital System, Detroit, MI, USA
| | - F Safi
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - M Lu
- Department of Biostatistics, Henry Ford Hospital System, Detroit, MI, USA
| | - A Baugh
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - X Zhang
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - J Yeo
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - S A Khuder
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - A M Boulos
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA
| | - P Nana-Sinkam
- Ohio State University James Comprehensive Cancer Center and Solove Research Institute, Columbus, OH, USA
| | - P P Massion
- Thoracic Program, Vanderbilt Ingram Cancer Center, Nashville, TN, USA
| | | | | | | | - S D Nathan
- Inova Fairfax Hospital, Falls Church, VA, USA
| | - R Wainz
- The Toledo Hospital, Toledo, OH, USA
| | - G Silvestri
- Medical University of South Carolina, Charleston, SC, USA
| | - J Tita
- Mercy/St. Vincent's Hospital, Toledo, OH, USA
| | - J C Willey
- Department of Pulmonary and Critical Care, The University of Toledo Medical Center, Toledo, OH, USA.
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Lusk CM, Wenzlaff AS, Dyson G, Purrington KS, Watza D, Land S, Soubani AO, Gadgeel SM, Schwartz AG. Whole-exome sequencing reveals genetic variability among lung cancer cases subphenotyped for emphysema. Carcinogenesis 2015; 37:139-144. [PMID: 26717996 DOI: 10.1093/carcin/bgv248] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/13/2015] [Indexed: 11/13/2022] Open
Abstract
Lung cancer continues to be a major public health challenge in the United States despite efforts to decrease the prevalence of smoking; outcomes are especially poor for African-American patients compared to other races/ethnicities. Chronic obstructive pulmonary disease (COPD) co-occurs with lung cancer frequently, but not always, suggesting both shared and distinct risk factors for these two diseases. To identify germline genetic variation that distinguishes between lung cancer in the presence and absence of emphysema, we performed whole-exome sequencing on 46 African-American lung cancer cases (23 with and 23 without emphysema frequency matched on age, sex, histology and pack years). Using conditional logistic regression, we found 6305 variants (of 168 150 varying sites) significantly associated with lung cancer subphenotype (P ≤ 0.05). Next, we validated 10 of these variants in an independent set of 612 lung cancer cases (267 with emphysema and 345 without emphysema) from the same population of inference as the sequenced cases. We found one variant that was significantly associated with lung cancer subphenotype in the validation sample. These findings contribute to teasing apart shared genetic factors from independent genetic factors for lung cancer and COPD.
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Affiliation(s)
- Christine M Lusk
- Karmanos Cancer Institute, Detroit, MI 48201, USA.,Department of Oncology, School of Medicine and
| | - Angela S Wenzlaff
- Karmanos Cancer Institute, Detroit, MI 48201, USA.,Department of Oncology, School of Medicine and
| | - Greg Dyson
- Karmanos Cancer Institute, Detroit, MI 48201, USA.,Department of Oncology, School of Medicine and
| | - Kristen S Purrington
- Karmanos Cancer Institute, Detroit, MI 48201, USA.,Department of Oncology, School of Medicine and
| | - Donovan Watza
- Karmanos Cancer Institute, Detroit, MI 48201, USA.,Department of Oncology, School of Medicine and
| | - Susan Land
- Karmanos Cancer Institute, Detroit, MI 48201, USA.,Department of Oncology, School of Medicine and
| | - Ayman O Soubani
- Karmanos Cancer Institute, Detroit, MI 48201, USA.,Department of Oncology, School of Medicine and.,Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, Wayne State University, Detroit, MI 48201, USA
| | - Shirish M Gadgeel
- Karmanos Cancer Institute, Detroit, MI 48201, USA.,Department of Oncology, School of Medicine and
| | - Ann G Schwartz
- Karmanos Cancer Institute, Detroit, MI 48201, USA.,Department of Oncology, School of Medicine and
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Patterns and functional implications of rare germline variants across 12 cancer types. Nat Commun 2015; 6:10086. [PMID: 26689913 PMCID: PMC4703835 DOI: 10.1038/ncomms10086] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 11/02/2015] [Indexed: 12/14/2022] Open
Abstract
Large-scale cancer sequencing data enable discovery of rare germline cancer susceptibility variants. Here we systematically analyse 4,034 cases from The Cancer Genome Atlas cancer cases representing 12 cancer types. We find that the frequency of rare germline truncations in 114 cancer-susceptibility-associated genes varies widely, from 4% (acute myeloid leukaemia (AML)) to 19% (ovarian cancer), with a notably high frequency of 11% in stomach cancer. Burden testing identifies 13 cancer genes with significant enrichment of rare truncations, some associated with specific cancers (for example, RAD51C, PALB2 and MSH6 in AML, stomach and endometrial cancers, respectively). Significant, tumour-specific loss of heterozygosity occurs in nine genes (ATM, BAP1, BRCA1/2, BRIP1, FANCM, PALB2 and RAD51C/D). Moreover, our homology-directed repair assay of 68 BRCA1 rare missense variants supports the utility of allelic enrichment analysis for characterizing variants of unknown significance. The scale of this analysis and the somatic-germline integration enable the detection of rare variants that may affect individual susceptibility to tumour development, a critical step toward precision medicine.
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Abstract
INTRODUCTION Computed tomography (CT) plays a central role in lung cancer diagnosis. However, CT has relatively low specificity, presenting a challenge in clinical settings. We previously identified 12 microRNAs (miRNAs) whose expressions in tumor tissues were associated with lung cancer. METHODS Using quantitative reverse transcriptase polymerase chain reaction, we aimed to identify miRNA biomarkers in sputum that could complement CT for diagnosis of lung cancer. RESULTS In a training set consisting of 66 lung cancer patients and 68 cancer-free smokers, 10 of the 12 miRNAs were differentially expressed between the cases and controls (p ≤ 0.01). From the miRNAs, a logistic regression model was built on the basis of miR-31 and miR-210, both of which had the best prediction for lung cancer, producing an area under receiver operating characteristic curve of 0.83. Combined use of the two miRNAs yielded 65.2% sensitivity and 89.7% specificity, CT had 93.9% sensitivity and 83.8% specificity for lung cancer diagnosis. Notably, combined analysis of the miRNA biomarkers and CT produced a higher specificity than does CT used alone (91.2% versus 83.8%; p < 0.05). The diagnostic performance of the biomarkers was confirmed in a testing set comprising 64 lung cancer patients and 73 cancer-free smokers. CONCLUSION The sputum miRNA biomarkers might be useful in improving CT for diagnosis of lung cancer, but further independent validation on an external and prospective cohort of patients is required.
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Changes in water sorption and solubility of dental adhesive systems after cigarette smoke. ISRN DENTISTRY 2013; 2013:605847. [PMID: 23984078 PMCID: PMC3747503 DOI: 10.1155/2013/605847] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 07/10/2013] [Indexed: 11/25/2022]
Abstract
Aim. To evaluate the effect of cigarette smoke on water sorption and solubility of four adhesive systems. Materials and Methods. Sixteen disks of each adhesive system were prepared (Adper Scotchbond Multipurpose Adhesive (SA); Adper Scotchbond Multipurpose Adhesive System (Adhesive + Primer) (SAP); Adper Single Bond Plus (SB); Adper Easy One (EO)). Specimens were desiccated until a constant mass was obtained and divided into two groups (n = 8). One-half of the specimens were immersed in deionized water, while the other half were also immersed, but with daily exposure to tobacco smoke. After 21 days, disks were measured again and stored in desiccators until constant mass was achieved. Data were calculated according to ISO specifications and statistically analyzed. Results. The tobacco smoke only significantly affected the water sorption and solubility of EO. There were significant differences in both analyses among materials tested. The SB exhibited the highest water sorption, followed by EO, which demonstrated significantly higher solubility values than SB. The SA and SAP showed low water sorption and solubility, and there were no significant differences between the two. Conclusion. Regardless of smoke exposure, both simplified adhesive systems presented an inferior performance that could be related to the complex mixture of components in such versions.
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Hickey GA, Keith RL, Miller YE. Common pathobiologic origins of chronic obstructive pulmonary disease and lung cancer: more than just a smoking gun. Lung Cancer Manag 2012. [DOI: 10.2217/lmt.12.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Gregory A Hickey
- Pulmonary Sciences & Critical Care Medicine, University of Colorado, Denver, CO, USA
| | - Robert L Keith
- Pulmonary Sciences & Critical Care Medicine, University of Colorado, Denver, CO, USA
- Denver Veteran’s Affairs Medical Center, Denver, CO, USA
| | - York E Miller
- Pulmonary Sciences & Critical Care Medicine, University of Colorado, Denver, CO, USA
- Denver Veteran’s Affairs Medical Center, Denver, CO, USA
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