Integrative Analysis Reveals Common and Unique Roles of Tetraspanins in Fibrosis and Emphysema

Abstract

While both chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are multifactorial disorders characterized by distinct clinical and pathological features, their commonalities and differences have not been fully elucidated. We sought to investigate the preventive roles of tetraspanins Cd151 and Cd9 -that are involved in diverse cellular processes in lung pathophysiology- in pulmonary fibrosis and emphysema, respectively, and to obtain a deeper understanding of their underlying molecular mechanisms toward facilitating improved therapeutic outcomes. Using an integrative approach, we examined the transcriptomic changes in the lungs of Cd151- and Cd9-deficient mice using functional-enrichment-analysis, pathway-perturbation-analysis and protein-protein-interaction (PPI) network analysis. Circadian-rhythm, extracellular-matrix (ECM), cell-adhesion and inflammatory responses and associated factors were prominently influenced by Cd151-deletion. Conversely, cellular-junctions, focal-adhesion, vascular-remodeling, and TNF-signaling were deeply impacted by Cd9-deletion. We also highlighted a "common core" of factors and signaling cascades that underlie the functions of both Cd151 and Cd9 in lung pathology. Circadian dysregulation following Cd151-deletion seemingly facilitated progressive fibrotic lung phenotype. Conversely, TGF-β signaling attenuation and TNF-signaling activation emerged as potentially novel functionaries of Cd9-deletion-induced emphysema. Our findings offer promising avenues for developing novel therapeutic treatments for pulmonary fibrosis and emphysema.

Keywords: COPD; IPF; biomarker discovery; cellular networks; disease biology; integrative gene expression analysis; signaling pathways; systems biology; tetraspanins.

FIGURE 1

(A) A multi-omics framework to investigate the transcriptomic changes underlying the deletion of Cd151 and Cd9. (B) Volcano plots for Cd151KO and Cd9KO sDEGs (1.5FC). Upregulated probes (genes) are highlighted in red, whereas the downregulated probes (genes) are highlighted in blue. (C) A heatmap of the significantly fluctuated gene expression levels in Cd151KO (green) and Cd9KO (deep blue). Red indicates relative higher expression, blue indicates relative lower expression; values in each row are normalized gene expression. Both rows and columns were hierarchically clustered and the results were illustrated as dendrograms. (D) Cd151KO (green) and Cd9KO (deep blue) sDEGs show very little overlap in either upregulated genes (red upward arrow) or downregulated genes (blue downward arrow). (E) The similarly affected genes in Cd151KO and Cd9KO indicating convergent underlying mechanisms.

FIGURE 2

(A) Enriched Reactome pathways (p ≤ 0.05) identified in Cd151KO 1.5FC sDEGs. For clarity, only select Reactome pathways are displayed. (B) Cd151KO sDEGs were distinctly enriched in Reactome pathways associated with circadian rhythm (red box) and extracellular matrix (azure box). (C) Enriched GO Slim biological process (BP) terms (p ≤ 0.05) identified in Cd9KO 1.5FC sDEGs. (D) Cd9KO sDEGs were significantly associated with enriched GO Slim BP terms “circulatory system process” (red box) and “extracellular matrix” (blue box); for clarity, only a subset of the heatmap is highlighted here. In (B,D), the upregulated genes are indicated by orange spheres and downregulated genes are indicated by blue spheres.

FIGURE 3

SPIA identified pathway perturbations in Cd151KO. (A) SPIA two-way evidence plots for Cd151 1.2FC sDEGs. Significantly perturbed pathways are highlighted in red. “Activated” pathways are tagged with a red upward arrow. (B) KEGG pathway hsa04710: “Circadian rhythm” was markedly activated in Cd151KO 1.2FC sDEGs. Upregulated genes are highlighted in red and the downregulated genes are highlighted in dark blue (Cry) and light blue (Per), rectangles, respectively, with gene labels within highlighted in yellow. (C) KEGG pathway hsa04512: “ECM-receptor interaction” was activated in Cd151KO Upregulated genes are highlighted in Orange rectangles; their corresponding gene labels within the rectangles are highlighted in yellow.

FIGURE 4

SPIA identified pathway perturbations in Cd9KO. (A) SPIA two-way evidence plots for Cd9KO 1.2FC sDEGs. Significantly perturbed pathways are highlighted in red. “Activated” pathways are tagged with a red upward arrow and “Inhibited” pathways are tagged with a blue downward arrow. (B) KEGG pathway hsa04530: “Tight junction” was identified to be inhibited in Cd9KO. Upregulated genes are highlighted in orange and the downregulated genes are highlighted in dark blue (Claudins) and light blue (others), rectangles, respectively; their corresponding gene labels within the rectangles are highlighted in yellow.

FIGURE 5

(A) Cd151KO 1.5FC sDEGs orthologs and their interacting partners associated with Enriched KEGG pathway hsa04710: “Circadian rhythm.” (B) Cd151KO 1.5FC sDEGs orthologs and their interacting partners associated with Enriched KEGG pathways hsa04110: “Cell cycle,” hsa04710: “Circadian rhythm,” hsa04068: “FoxO signaling pathway,” and hsa04151: “PI3K-Akt signaling pathway.” (C) Cd9KO 1.5FC sDEGs orthologs and their interacting partners associated with enriched KEGG pathway hsa04668: “TNF signaling pathway.”