| Literature DB >> 32537452 |
Yan Dong1, Hongbao Cao2,3, Rongyuan Cao1, Ancha Baranova2,4,5.
Abstract
Pathogenesis of chronic obstructive pulmonary disease (COPD) is dependent on chronic inflammation and is hypothesized to represent organ-specific senescence phenotype. Identification of senescence-associated gene drivers for the development of COPD is warranted. By employing automated pipeline, we have compiled lists of the genes implicated in COPD (N = 918) and of the genes changing their activity along with cell senescence (N = 262), with a significant (p < 7.06e-60) overlap between these datasets (N = 89). A mega-analysis and a partial mega-analysis were conducted for gene sets linked to senescence but not yet to COPD, in nine independent mRNA expression datasets comprised of tissue samples of COPD cases (N = 171) and controls (N = 256). Mega-analysis of expression has identified CD38 and TNFRSF12A (p < 2.12e-8) as genes not yet explored in a context of senescence-COPD connection. Functional pathway enrichment analysis allowed to generate a model, which explains accelerated aging phenotypes previously observed in COPD patients. Presented results call for investigation of the role of TNFRSF12A/CD38 balance in establishing a vicious cycle of unresolvable tissue remodeling in COPD lungs.Entities:
Keywords: aging; chronic inflammation; lung; network analysis; senescence; tissue remodeling
Year: 2020 PMID: 32537452 PMCID: PMC7268922 DOI: 10.3389/fcell.2020.00330
Source DB: PubMed Journal: Front Cell Dev Biol ISSN: 2296-634X
Datasets utilized for chronic obstructive pulmonary disease (COPD)-senescence expression mega-analysis.
| Study name | Dataset GEO ID | Country | Tissue | ||
| Bastos et al., 2016 | GSE37768 | 20 | 18 | Spain | Peripheral lung |
| Kalko et al., 2014 | GSE27543 | 6 | 10 | United Kingdom | Musculus vastus lateralis |
| Kalko et al., 2013 | GSE27536 | 24 | 30 | United Kingdom | Musculus vastus lateralis |
| Ezzie et al., 2012 | GSE38974 | 9 | 23 | United States | Lung |
| Tilley et al., 2011 | GSE11784 | 135 | 22 | United States | Airway epithelial cells |
| Poliska et al., 2011 | GSE16972 | 6 | 6 | Hungary | Alveolar macrophage; peripheral blood monocytes |
| Bosco et al., 2010 | GSE19903 | 10 | 10 | Australia | Induced sputum cells |
| Boelens et al., 2009 | GSE12472 | 27 | 36 | Netherlands | Large bronchial |
| Bhattacharya et al., 2008 | GSE8581 | 19 | 16 | United States | Lung |
Novel aging/senescence-related genes as highlighted by mega-analysis (MA) and partial MA expression.
| Gene/type of analysis | Significance | Random-effect model | # Study | LFC | ISq (%) | ||
| TNFRSF12A/partial MA | Yes | NO | 4 | 0.54 | 5.80e–10 | 0 | 1.00 |
| TNFRSF12A/MA | Yes | NO | 9 | 0.51 | 1.53e–9 | 0 | 0.96 |
| CD38/partial MA | Yes | NO | 4 | -0.89 | 2.12e–8 | 0 | 0.82 |
| CD38/MA | No | Yes | 8 | -0.49 | 2.19e–2 | 17.34 | 0.29 |
FIGURE 1Effect sizes, 95% confidence intervals, and weights for each of two genes. (A) Mega-analysis results for CD38. (B) Partial mega-analysis results for CD38. (C) Mega-analysis results for TNFRSF12A. (D) Partial mega-analysis results for TNFRSF12A. The bar plot on the right of each figure represents the normalized weights for each dataset/study, ranged within (0, 1); the brighter (green) the color, the larger the relative weight of the study as labeled right next to the bar. For each dataset, the star (in red) and lines (in blue) on the left are the mean of effect size (log fold change), and 95% confidence interval (CI), respectively. References for datasets could be traced by their Gene Expression Omnibus (GEO) numbers.
FIGURE 2QQ plot of the z-scores of chronic obstructive pulmonary disease (COPD) patients versus standard normal distribution. (A) QQ plot built for dataset GSE16972. (B) QQ plot built for dataset GSE27543.
Top 10 GO terms enriched by 91 genes linked to both senescence/aging and COPD phenotypes.
| GO ID | GO name | # of entities | Overlap | Novel gene included | |
| 0070482 | Response to oxygen levels | 544 | 33 | 4.4E–27 | |
| 0010942 | Positive regulation of cell death | 870 | 37 | 1.14E–25 | |
| 0001666 | Response to hypoxia | 424 | 29 | 4.49E–25 | |
| 0036293 | Response to decreased oxygen levels | 461 | 29 | 3.94E–24 | |
| 0048545 | Response to steroid hormone | 418 | 27 | 1.21E–22 | |
| 0031960 | Response to corticosteroid | 325 | 25 | 1.22E–22 | No |
| 0043068 | Positive regulation of programmed cell death | 800 | 33 | 3.06E–22 | |
| 0051384 | Response to glucocorticoid | 299 | 24 | 4.27E–22 | No |
| 0019221 | Cytokine-mediated signaling pathway | 676 | 31 | 4.81E–22 | |
| 0009636 | Response to toxic substance | 634 | 30 | 1.19E–21 | No |
FIGURE 3Function pathway analysis between COPD and the two genes: CD38 and TNFRSF12A. This network was generated in Pathway Studio environment (www.pathwaystudio.com). Each relation (edge) in the figure has one or more supporting references. (A) Pathways connecting COPD and gene TNFRSF12A; (B) Pathways connecting COPD and gene CD38.
FIGURE 4Mechanistic model highlights the roles of TNFRSF12A and CD38 in COPD-related accelerated aging phenotypes, with their balance defining if the lung injury is resolved.