Comparative RNA‐Seq transcriptome analysis on silica induced pulmonary inflammation and fibrosis in mice silicosis model

Abstract

Silicosis is a long-established public health issue in developing countries due to increasingly serious air pollution and poorly implemented occupational safety regulation. Inhalation of silica triggers cytotoxicity, oxidative stress, pulmonary inflammation and eventually silicosis. Current understanding in the pathogenesis and mechanism of silicosis is limited, and no effective cure is clinically available once silicosis is developed. A number of studies were conducted to investigate silica-induced alternate gene expressions in pulmonary cells. However, transcriptome analysis in a silicosis animal model is needed. This study was performed to evaluate the transcriptional alternations in silicotic mice using comparative RNA-Seq. A silicosis mice model was established by intratracheal instillation of silica suspensions, and validated by histological examinations. High-throughput sequencing and differential gene expression analysis revealed 749 upregulated genes and 70 downregulated genes in the silicosis model. Genes related to immune cell interactions, immune cell responses and inflammation were significantly enriched. Cytokine-cytokine receptor interaction and downstream JAK-STAT signaling pathways were the most significantly enriched KEGG pathways. Reverse transcription-polymerase chain reaction analysis and immunohistochemistry were performed to validate further the differential expression patterns of representative genes. The reported results in this study provide the basis for elucidating the molecular mechanisms for silica-induced pulmonary inflammation and fibrosis, and support the prevention and treatment of silicosis.

Rapid Induction of Pulmonary Inflammation, Autoimmune Gene Expression, and Ectopic Lymphoid Neogenesis Following Acute Silica Exposure in Lupus-Prone Mice

“…Additionally, the heightened cellular inflammatory responses to 2.5 mg cSiO 2 observed here are in agreement with those seen in many other silicosis studies in non-autoimmune prone mice employing the same dose (25)(26)(27)(28)(29)(30). In another relevant study, Chen et al (43) intratracheally instilled C57Bl/6 mice with 2.5 mg cSiO 2 and subjected lungs to RNA sequencing after 60 d. Out of 14,451 total genes, 819 genes were found to be differentially expressed with 749 and 70 being upregulated and downregulated, respectively; many of these transcripts were cytokine, chemokine, and interferon-regulated genes. Together, these findings in a variety of mouse strains support the contention that the 2.5 mg cSiO 2 dose overwhelms normal pulmonary clearance mechanisms and promotes unresolved inflammation, thereby driving an overly robust innate immune response.…”

The pharmacodynamic and differential gene expression analysis of PPAR α/δ agonist GFT505 in CDAHFD-induced NASH model

“…Hematoxylin and eosin (H&E) staining was used to evaluate liver steatosis, inflammation. Hepatocellular steatosis, ballooning and inflammation of the specimens were scored according to the standards as described before [13]. Hepatic fibrosis were evaluated by Sirius red staining and analyzed by Nano Zoomer Digital Pathology S210 and Image-Pro Plus 6.0.…”

“…The extracted RNA quantity and quality were verified by Qubit 1 RNA Assay Kit (Life Technologies, CAT# Q32852) in Qubit 1 2.0 Fluorometer (Life Technologies, CA, USA) and the RNA Nano 6000 Assay Kit (Agilent Technologies, CAT# 5067-1511) of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). The cDNA library construction and RNA sequencing were performed as described before [13].…”

Comparative RNA-sequencing profiled the differential gene expression of liver in response to acetyl-CoA carboxylase inhibitor GS-0976 in a mouse model of NASH

“…The quantity and quality of the extracted RNA were verified by Qubit ® RNA Assay Kit in Qubit ® 2.0 Fluorometer (Life Technologies, CA, USA) and the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). The cDNA library construction and sequencing were performed as described before (Chen et al, 2018).…”

“…The acquired data were processed as previously described (Chen et al, 2018). Briefly, raw data were first processed through Perl scripts to obtain clean data by removing reads containing adapter, ploy-N and with low quality.…”