Transcriptome analysis reveals key genes modulated by ALK5 inhibition in a bleomycin model of systemic sclerosis

Abstract

Objective Systemic sclerosis (SSc) is a rheumatic autoimmune disease affecting roughly 20 000 people worldwide and characterized by excessive collagen accumulation in the skin and internal organs. Despite the high morbidity and mortality associated with SSc, there are no approved disease-modifying agents. Our objective in this study was to explore transcriptomic and model-based drug discovery approaches for systemic sclerosis. Methods In this study, we explored the molecular basis for SSc pathogenesis in a well-studied mouse model of scleroderma. We profiled the skin and lung transcriptomes of mice at multiple timepoints, analyzing the differential gene expression that underscores the development and resolution of bleomycin-induced fibrosis. Results We observed shared expression signatures of upregulation and downregulation in fibrotic skin and lung tissue, and observed significant upregulation of key pro-fibrotic genes including GDF15, Saa3, Cxcl10, Spp1, and Timp1. To identify changes in gene expression in responses to anti-fibrotic therapy, we assessed the effect of TGF-β pathway inhibition via oral ALK5 (TGF-β receptor I) inhibitor SB525334 and observed a time-lagged response in the lung relative to skin. We also implemented a machine learning algorithm that showed promise at predicting lung function using transcriptome data from both skin and lung biopsies. Conclusion This study provides the most comprehensive look at the gene expression dynamics of an animal model of systemic sclerosis to date, provides a rich dataset for future comparative fibrotic disease research, and helps refine our understanding of pathways at work during SSc pathogenesis and intervention.

Scleroderma-like Impairment in the Network of Telocytes/CD34+ Stromal Cells in the Experimental Mouse Model of Bleomycin-Induced Dermal Fibrosis

“…For instance, preclinical animal models reproducing tissue alterations of TCs/CD34 + stromal cells, much like those found in human diseases, may clearly represent an invaluable tool for elucidating the effective contribution of these cells to disease pathogenesis and/or pathophysiology, which could often only be supposed [25]. In this context, to our knowledge, this is the first study to investigate TCs/CD34 + stromal cells in the mouse model of bleomycin-induced dermal fibrosis, which is widely used in SSc research [37,38,56]. Indeed, we have previously shown that clinically involved skin of patients with SSc displays a progressive impairment in the dermal network of TCs/CD34 + stromal cells, starting from the early cutaneous disease stage up to almost their complete loss in the advanced stage [31,32].…”

“…Moreover, further in-depth investigations utilizing this mouse model will hopefully help identifying the pathogenetic mechanisms underlying the damage of TCs, which could even prove useful as novel therapeutic targets to slow down or halt the progression of skin fibrosis. Finally, since the subcutaneous bleomycin mouse model is widely used in the development of novel therapies for SSc [37,56], we believe that verifying if the efficacy of the tested therapeutic approaches associates with a regeneration of the dermal networks of TCs/CD34 + stromal cells might provide new valuable insights into this still enigmatic cellular entity of the skin microenvironment.…”

“…Nevertheless, the question as to whether these findings may be primarily related to cellular degenerative processes, immunophenotypical changes such as loss of CD34 and acquisition of the myofibroblast marker α-SMA, or both, has not yet been fully elucidated [23,31,32]. Several animal models of SSc are available; however, some models display dermal inflammation followed by fibrosis resembling early disease stages, while some others mainly mimic autonomous fibroblast activation in more advanced disease [56,57]. Thus, in an attempt to gain further insights into the pathological mechanisms underlying the changes in TCs/CD34 + stromal cells that accompany the development of skin fibrosis, here, we have chosen to utilize the bleomycin-induced model, which mimics early stages of human SSc [37,56].…”

“…Several animal models of SSc are available; however, some models display dermal inflammation followed by fibrosis resembling early disease stages, while some others mainly mimic autonomous fibroblast activation in more advanced disease [56,57]. Thus, in an attempt to gain further insights into the pathological mechanisms underlying the changes in TCs/CD34 + stromal cells that accompany the development of skin fibrosis, here, we have chosen to utilize the bleomycin-induced model, which mimics early stages of human SSc [37,56].…”

Single-Walled vs. Multi-Walled Carbon Nanotubes: Influence of Physico-Chemical Properties on Toxicogenomics Responses in Mouse Lungs

“…WGCNA can be used to find clusters of highly correlated genes, which allows for the identification of key modules [ 24 ]. In this study, WGCNA was conducted to identify gene modules whose expression pattern was found in the in vivo pulmonary toxicity induced by different substances such as polycyclic aromatic hydrocarbons, cigarette smoke, diesel exhaust, ozone, particulate matter, bleomycin, radiation, and nanomaterials, among others ( Table S2 ) [ 10 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 ]. Once modules were identified from those publicly available transcriptomic datasets, the biological functions of each module were determined, and GSEA was conducted to ...…”