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Tubío-Pérez RA, Torres-Durán M, Pérez-Ríos M, Fernández-Villar A, Ruano-Raviña A. Lung emphysema and lung cancer: what do we know about it? ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1471. [PMID: 33313216 PMCID: PMC7723574 DOI: 10.21037/atm-20-1180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Emphysema and lung cancer (LC) are two diseases which share common risk factors, e.g., smoking. In recent years, many studies have sought to analyse this association. By way of illustration, we conducted a review of the scientific literature of the studies published to date, whose main designated aim was to demonstrate the relationship between emphysema and LC, and this association's influence on the histology, prognosis and molecular mechanisms responsible. We included over 40 studies (ranging from case-control and cohort studies to systematic reviews and meta-analyses), which highlight the association between emphysema and LC, independently of smoking habit. These studies also report a possible influence on histology, with adenocarcinoma being the most frequent lineage, and an association with poor prognosis, which affects both survival and post-operative complications. Oxidative stress, which generates chronic inflammatory status as well as the presence of certain polymorphisms in various genes (CYP1A1, TERT, CLPTM1L, ERK), gives rise-in the case of patients with emphysema-to alteration of cellular repair mechanisms, which in turn favours the proliferation of neoplastic epithelial cells responsible for the origin of LC.
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Affiliation(s)
- Ramón A Tubío-Pérez
- Pulmonary Department, Hospital Álvaro Cunqueiro, EOXI, Vigo, Spain.,NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), Galicia, Spain
| | - María Torres-Durán
- Pulmonary Department, Hospital Álvaro Cunqueiro, EOXI, Vigo, Spain.,NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), Galicia, Spain
| | - Mónica Pérez-Ríos
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Santiago de Compostela, Spain.,CIBER de Epidemiología y Salud Pública, CIBERESP, Madrid, Spain
| | - Alberto Fernández-Villar
- Pulmonary Department, Hospital Álvaro Cunqueiro, EOXI, Vigo, Spain.,NeumoVigoI+i Research Group, Vigo Biomedical Research Institute (IBIV), Galicia, Spain
| | - Alberto Ruano-Raviña
- Department of Preventive Medicine and Public Health, University of Santiago de Compostela, Santiago de Compostela, Spain.,CIBER de Epidemiología y Salud Pública, CIBERESP, Madrid, Spain
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Rotunno M, Barajas R, Clyne M, Hoover E, Simonds NI, Lam TK, Mechanic LE, Goldstein AM, Gillanders EM. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:1519-1534. [PMID: 32467344 DOI: 10.1158/1055-9965.epi-19-1551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/17/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing (NGS) technologies in cancer research has accelerated the discovery of somatic mutations; however, progress in the identification of germline variation associated with cancer risk is less clear. We conducted a systematic literature review of cancer genetic susceptibility studies that used NGS technologies at an exome/genome-wide scale to obtain a fuller understanding of the research landscape to date and to inform future studies. The variability across studies on methodologies and reporting was considerable. Most studies sequenced few high-risk (mainly European) families, used a candidate analysis approach, and identified potential cancer-related germline variants or genes in a small fraction of the sequenced cancer cases. This review highlights the importance of establishing consensus on standards for the application and reporting of variants filtering strategies. It also describes the progress in the identification of cancer-related germline variation to date. These findings point to the untapped potential in conducting studies with appropriately sized and racially diverse families and populations, combining results across studies and expanding beyond a candidate analysis approach to advance the discovery of genetic variation that accounts for the unexplained cancer heritability.
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Affiliation(s)
- Melissa Rotunno
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland.
| | - Rolando Barajas
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Mindy Clyne
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elise Hoover
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | | | - Tram Kim Lam
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Leah E Mechanic
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Alisa M Goldstein
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elizabeth M Gillanders
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
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Vishweswaraiah S, George L, Purushothaman N, Ganguly K. A candidate gene identification strategy utilizing mouse to human big-data mining: "3R-tenet" in COPD genetic research. Respir Res 2018; 19:92. [PMID: 29871630 PMCID: PMC5989378 DOI: 10.1186/s12931-018-0795-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 04/27/2018] [Indexed: 12/13/2022] Open
Abstract
Background Early life impairments leading to lower lung function by adulthood are considered as risk factors for chronic obstructive pulmonary disease (COPD). Recently, we compared the lung transcriptomic profile between two mouse strains with extreme total lung capacities to identify plausible pulmonary function determining genes using microarray analysis (GSE80078). Advancement of high-throughput techniques like deep sequencing (eg. RNA-seq) and microarray have resulted in an explosion of genomic data in the online public repositories which however remains under-exploited. Strategic curation of publicly available genomic data with a mouse-human translational approach can effectively implement “3R- Tenet” by reducing screening experiments with animals and performing mechanistic studies using physiologically relevant in vitro model systems. Therefore, we sought to analyze the association of functional variations within human orthologs of mouse lung function candidate genes in a publicly available COPD lung RNA-seq data-set. Methods Association of missense single nucleotide polymorphisms, insertions, deletions, and splice junction variants were analyzed for susceptibility to COPD using RNA-seq data of a Korean population (GSE57148). Expression of the associated genes were studied using the Gene Paint (mouse embryo) and Human Protein Atlas (normal adult human lung) databases. The genes were also assessed for replication of the associations and expression in COPD−/mouse cigarette smoke exposed lung tissues using other datasets. Results Significant association (p < 0.05) of variations in 20 genes to higher COPD susceptibility have been detected within the investigated cohort. Association of HJURP, MCRS1 and TLR8 are novel in relation to COPD. The associated ADAM19 and KIT loci have been reported earlier. The remaining 15 genes have also been previously associated to COPD. Differential transcript expression levels of the associated genes in COPD- and/ or mouse emphysematous lung tissues have been detected. Conclusion Our findings suggest strategic mouse-human datamining approaches can identify novel COPD candidate genes using existing datasets in the online repositories. The candidates can be further evaluated for mechanistic role through in vitro studies using appropriate primary cells/cell lines. Functional studies can be limited to transgenic animal models of only well supported candidate genes. This approach will lead to a significant reduction of animal experimentation in respiratory research. Electronic supplementary material The online version of this article (10.1186/s12931-018-0795-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Leema George
- SRM Research Institute, SRM University, Chennai, 603203, India
| | - Natarajan Purushothaman
- Department of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM University, Chennai, 603203, India
| | - Koustav Ganguly
- SRM Research Institute, SRM University, Chennai, 603203, India. .,Work Environment Toxicology, Institute of Environmental Medicine, Karolinska Institutet, Box 287, SE-171 77, Stockholm, Sweden.
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Radder JE, Zhang Y, Gregory AD, Yu S, Kelly NJ, Leader JK, Kaminski N, Sciurba FC, Shapiro SD. Extreme Trait Whole-Genome Sequencing Identifies PTPRO as a Novel Candidate Gene in Emphysema with Severe Airflow Obstruction. Am J Respir Crit Care Med 2017; 196:159-171. [PMID: 28199135 DOI: 10.1164/rccm.201606-1147oc] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Genetic association studies in chronic obstructive pulmonary disease have primarily tested for association with common variants, the results of which explain only a portion of disease heritability. Because rare variation is also likely to contribute to susceptibility, we used whole-genome sequencing of subjects with clinically extreme phenotypes to identify genomic regions enriched for rare variation contributing to chronic obstructive pulmonary disease susceptibility. OBJECTIVES To identify regions of rare genetic variation contributing to emphysema with severe airflow obstruction. METHODS We identified heavy smokers that were resistant (n = 65) or susceptible (n = 64) to emphysema with severe airflow obstruction in the Pittsburgh Specialized Center of Clinically Oriented Research cohort. We filtered whole-genome sequencing results to include only rare variants and conducted single variant tests, region-based tests across the genome, gene-based tests, and exome-wide tests. MEASUREMENTS AND MAIN RESULTS We identified several suggestive associations with emphysema with severe airflow obstruction, including a suggestive association of all rare variation in a region within the gene ZNF816 (19q13.41; P = 4.5 × 10-6), and a suggestive association of nonsynonymous coding rare variation in the gene PTPRO (P = 4.0 × 10-5). Association of rs61754411, a rare nonsynonymous variant in PTPRO, with emphysema and obstruction was demonstrated in all non-Hispanic white individuals in the Pittsburgh Specialized Center of Clinically Oriented Research cohort. We found that cells containing this variant have decreased signaling in cellular pathways necessary for survival and proliferation. CONCLUSIONS PTPRO is a novel candidate gene in emphysema with severe airflow obstruction, and rs61754411 is a previously unreported rare variant contributing to emphysema susceptibility. Other suggestive candidate genes, such as ZNF816, are of interest for future studies.
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Affiliation(s)
- Josiah E Radder
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Yingze Zhang
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Alyssa D Gregory
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Shibing Yu
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Neil J Kelly
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Joseph K Leader
- 2 Department of Radiology, University of Pittsburgh, Pittsburgh, Pennsylvania; and
| | - Naftali Kaminski
- 3 Section of Pulmonary, Critical Care, and Sleep Medicine, Department of Internal Medicine, Yale University, New Haven, Connecticut
| | - Frank C Sciurba
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
| | - Steven D Shapiro
- 1 Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, and
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