3. Transcriptomic analysis revealed similarities and differences in the mechanisms underlying the therapeutic effects of PFD and BIBF against silicosis.
To further investigate the mechanisms underlying the therapeutic effects of PFD and BIBF in silicosis, we conducted transcriptomic sequencing on lung tissues from the PBS group, silica group, high-dose PFD group, and high-dose BIBF group (Fig 4A). Firstly, our analysis revealed 5286 DEGs between the PBS and silica groups (Fig 4B, C), including 2784 up-regulated genes and 2502 down-regulated genes. Subsequent KEGG analysis identifies top 40 downregulated pathways such as propanoate metabolism, citrate cycle, valine, leucine, and isoleucine degradation, et al. in the silica group compared to PBS, signifying a close interrelationship between perturbed metabolism of substances such as glucose, lipids, and amino acids and the progression of pulmonary fibrosis (Fig 4D). Additionally, consistent with previous reports, our findings also revealed the presence of upregulated pathways, top 40 signaling pathways including primary immunodeficiency, NF-κB signaling pathway, viral protein interaction with cytokine and cytokine receptor, et al. in the silica group, suggesting potential implications for complex signaling cascades, immune responses, phagocytosis, cell death and more that contribute to the advancement of pulmonary fibrosis (Fig 4E).
Subsequently, a similar analysis was applied to PFD or BIBF group, showing PFD elicits significant modifications in the gene expression profiles, involving of total 1386 altered genes (Fig 4F, G) and signaling pathways (Fig 4H) within the silica group, with notable impacts observed in relation to steroid biosynthesis, and ribosome among others; likewise, the administration of BIBF also elicits 305 dramatically increased DEG and 635 significantly decreased DEGs, resulting in profound alterations in the gene expression patterns (Fig 4I, J) and signaling cascades (Fig 4K) within the silica group, featuring significant ramifications on steroid biosynthesis, and notch signaling pathway alongside other pathways. Ultimately, having delineated the altered pathway profile in silicosis pathogenesis, as well as the pathway alterations associated with PFD or BIBF treatment of silicosis, it is now conceivable to elucidate the most effective and pivotal pathways targeted by PFD or BIBF in silicosis therapy. The Venn diagram depicted that PFD predominantly modulates 15 pathways in the treatment of silicosis, whereas BIBF primarily impacts 10 pathways (Fig 4L). Notably, these two pharmacological agents share 2 common pathways, namely antigen processing and presentation and steroid biosynthesis (Fig 4L, M), exhibiting extensive involvement in the progression of pulmonary fibrosis.