Genes related to emphysema are enriched for ubiquitination pathways

Abstract

Background: Increased small airway resistance and decreased lung elasticity contribute to the airflow limitation in chronic obstructive pulmonary disease (COPD). The lesion that corresponds to loss of lung elasticity is emphysema; the small airway obstruction is due to inflammatory narrowing and obliteration. Despite their convergence in altered physiology, different mechanisms contribute to these processes. The relationships between gene expression and these specific phenotypes may be more revealing than comparison with lung function.

Methods: We measured the ratio of alveolar surface area to lung volume (SA/V) in lung tissue from 43 smokers. Two samples from 21 subjects, in which SA/V differed by >49 cm2/mL were profiled to select genes whose expression correlated with SA/V. Significant genes were tested for replication in the 22 remaining subjects.

Results: The level of expression of 181 transcripts was related to SA/V ( p < 0.05). When these genes were tested in the 22 remaining subjects as a replication, thirty of the 181 genes remained significantly associated with SA/V (P < 0.05) and the direction of association was the same in 164/181. Pathway and network analysis revealed enrichment of genes involved in protein ubiquitination, and western blotting showed altered expression of genes involved in protein ubiquitination in obstructed individuals.

Conclusion: This study implicates modified protein ubiquitination and degradation as a potentially important pathway in the pathogenesis of emphysema.

Figure 1

A heat map shows the relationship between the level of expression of the 181 SA/V-correlated genes (columns) for all 42 of the samples in the discovery set. The samples are shown in rows ordered by increasing SA/V. Genes whose expression was negatively related to SA/V are shown by the yellow bar while those whose expression was positively related to SA/V are indicated with the blue bar.

Figure 2

A heat map shows the relationship between the level of expression of the 181 SA/V-correlated genes (columns) for the 22 samples in the replication set. The samples are shown in rows ordered by increasing SA/V. Genes whose expression was negatively related to SA/V are shown by the yellow bar while those whose expression was positively related to SA/V are indicated with the blue bar. The pattern is similar to the discovery set.

Figure 3

Slopes of regression for 181 selected genes are compared between the discovery and replication sets. The comparison shows a good concordance in the findings.

Figure 4

Slopes of regression for the 30 genes that replicated at p < 0.05 in the replication data set. The slopes for the replication data are on the x axis and those from the discovery set are on the y axis.

Figure 5

Protein expression of ubiquitination genes in lung tissues from control and COPD patients. Lung homogenates were prepared and Western blotting was performed to examine protein levels with the antibodies specified. β-actin was probed as a protein loading control. Protein levels were quantified by densitometric analysis wit the NIH ImageJ program and normalized to β-actin expression. A: results for FBXL3, FBXO30, and USP38 showing upregulation in COPD. B: results for UBB and RNF6 showing downregulation in COPD. Data are means ± SE, and significance was determined by Students’ t-tests.

Figure 6

Proposed model of dysregulation of the ubiquitin-proteasome system leading to the pathogenesis and progression of emphysema/COPD. Oxidative stress and inflammation induced by smoke, genetic or environmental insults result in dysregulation of ubiquitination-related genes and impairment of the proteasome function. Accumulation of abnormal proteins in the lung as a result of increased production and decreased degradation causes further damage of the proteasome function and dysregulation of UPS-related genes. Aberrant regulation of the UPS results in apoptosis, inflammation, and matrix remodeling, pathogenic characteristics of emphysema/COPD. Damaged proteasome function can also cause compensatory upregulation of genes associated with the UPS.