ABSTRACT
OBJECTIVE: To analyze the differentially expressed genes(DEGs), and screen the key genes and signaling pathways in human lung epithelial A549 cells exposed to silica dust using bioinformatics and gene chip. METHODS: The GSE30215 gene expression profiles of A549 cells exposed to silica dust were downloaded from Public Gene Expression Omnibus database developed by the National Center for Biotechnology Information. The DEGs were screened by using GEO2 R analysis tools. Then, the DEGs were imported into the biological information annotation database for Gene Ontology(GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway enrichment analysis. The protein-protein interaction(PPI) network was constructed with the Search Tool for the Retrieval of Interacting Genes database and visualized using the software Cytoscape. Real-time quantitative polymerase chain reaction(PCR) was used to verify the expression of key DEGs in A549 cells. RESULTS: Of the 52 DEGs screened, 45 were up-regulated and 7 were down-regulated. The results of GO analysis showed that the DEGs were mainly distributed in extracellular region, associated with regulating biological functions such as chemotaxis, transcription factor activity and so on. KEGG pathway enrichment analysis showed that these DEGs were mainly involved in the tumor necrosis factor(TNF) signaling pathway and nucleotide-binding oligomerization domain like receptor signaling pathway. The top 10 key DEGs screened by PPI network were C-C motif chemokine ligand(CCL)2, prostaglandin-endoperoxide synthase 2, interleukin 6, C-X-C motif chemokine ligand(CXCL) 8, CXCL2, jun proto-oncogene, colony stimulating factor 2(CSF2), CCL20, TNF-α induced protein 3(TNFAIP3), and CXCL5. Real-time quantitative PCR results revealed that the changes of key genes were in consistent with the screening results, except the CCL2. CONCLUSION: We found 10 key DEGs that are related to the toxicity caused by exposure to silica dust in A549 cells by bioinformatics. Among them, CSF2, CCL20 and TNFAIP3 may provide new research direction for the mechanisms of the development of multiple pulmonary fibrotic diseases including pneumoconiosis.
ABSTRACT
OBJECTIVE: To investigate the differentially expressed microRNAs(miRNAs) in human embryonic lung fibroblast MRC-5 cells stimulated by transforming growth factor-β1(TGF-β1) using microarray chip, and screen for key genes and signaling pathways of fibroblast trans-differentiation. METHODS: The miRNA expression gene chip dataset GSE43992 on TGF-β1 stimulated MRC-5 cells were downloaded from high-throughput Gene Expression Omnibus(GEO) database of National Center for Biotechnology Information of the United States. The R language Limma package was used to screen the differentially expressed miRNAs. Corresponding target genes were predicted by miRWalk database performed by Gene Ontology(GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG) signaling pathway enrichment analysis. The protein-protein interaction(PPI) network was constructed by the search tool for the Retrieval of Interacting Genes database. RESULTS: A total of five differentially expressed miRNAs were identified, including four up-regulated miRNAs and one down-regulated miRNA; and 42 corresponding differentially expressed target genes were predicted. GO analysis indicated that the target genes were significantly enriched in collagen catabolic process, extracellular matrix organization, membrane organization, collagen fibril organization, and cellular response to amino acid stimulus. The results of KEGG pathway analysis showed that the signaling pathways corresponding to miRNAs and target genes were mainly concentrated in 18 signaling pathways, that were mainly related to the age-ethnic signaling pathways and protein digestion and absorption miRNAs in tumors and diabetic complications. The core genes transfected into the myofibroblasts by the three fibroblasts screened by the PPI network were threonine kinase 1, estrogen receptor 1 and β-catenin. CONCLUSION: Five differentially expressed miRNAs, 42 target genes, 18 signaling pathways, and 3 core genes related to TGF-β1-induced MRC-5 cell trans-differentiation were screened. It can provide new reference for the treatment and research of many diseases including pneumoconiosis and pulmonary fibrosis.
ABSTRACT
OBJECTIVE: To analyze the hotspots and related situations of pneumoconiosis research in China from 2001 to2017. METHODS: China National Knowledge Infrastructure and Wanfang Data were used to retrieve relevant literature on China's pneumoconiosis research from 2001 to 2017. Bibliometrics was used to analyze the distribution of publication time,regions,hotspots,authors and their institutions,carrier journals,keywords,etc. RESULTS: A total of 10 208 literature articles on pneumoconiosis research were screened. The number of published literature in 2001-2017 showed an upward trend year by year( P < 0. 01). Provinces in the Eastern area have the largest number of publications. The areas that have the largest number of publications were in Shandong Province,Beijing City and Hebei Province,followed by Anhui Province,Guangdong Province,Jiangsu Province,Liaoning Province,Shanxi Province and Henan Province. Beijing City,Hebei Province,Tianjin City,Liaoning Province,Anhui Province,Jiangsu Province,Hubei Province and Shanghai City are the hotspots for research on pneumoconiosis. The publications were seen in 1 173 journals. Five occupational medical professional periodicals such as Occupation and Health,Chinese Journal of Industrial Hygiene and Occupational Diseases,China Occupational Medicine,Chinese Journal of Industrial Medicine and Industrial Health and Occupational Diseases publish' the most literature on pneumoconiosis research,accounting for 26. 99% of the effective literature.Occupational disease prevention institutions and hospitals are the main organizations for publishing literatures. The focuses of pneumoconiosis research are silicosis and coal worker's pneumoconiosis,etc. CONCLUSION: Generally,the literature on the research of pneumoconiosis in China from 2001 to 2017 is increasing and is focus on some specific hotspots.Pneumoconiosis research has been specialized. An important carrier for publishing research results has been formed.
ABSTRACT
OBJECTIVE: To analyze transforming growth factor-β1( TGF-β1)-induced differentially expressed genes( DEGs) in human embryonic lung fibroblast( IMR-90) using microarray,and to screen the key genes and signaling pathways related to trans-differentiation of fibroblast.METHODS: The gene chip GSE17518,attained from TGF-β1 stimulated IMR-90 cells,was downloaded from the Gene Expression Omnibus database.The DEGs were screened by GENE-E software.Then,the DEGs were imported into the DAVID online database for Gene Ontology( GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes( KEGG) pathway enrichment analysis.The proteinprotein interaction( PPI) network was constructed and the hub genes were screened using STRING database and Cytoscape software.RESULTS: A total of 394 DEGs related to TGF-β1 stimulation were identified,including 171 down-regulated genes and 223 up-regulated genes.The results of GO analysis showed that the DEGs were widely distributed in cytoplasm,cell membrane,extracellular matrix( ECM) and exosomes,regulating biological functions such as ECM organization,cell migration and adhesion,cell proliferation and apoptosis.The results of the KEGG pathway analysis indicated that most of DEGs were enriched in cell focal adhesion,ECM-receptor interaction and phosphoinositide 3 kinase-Protein kinase B( PI3K-Akt) signaling pathways.The PPI network screened 10 core genes,included nucleolar protein 2( NOP2),succinate dehydrogenase B,glutamyl-prolyl-tRNA synthetase( EPRS),FtsJ homolog 3( FTSJ3),prefoldin subunit 4,Ras-related C3 botulinum toxin substrate 2,signal recognition particle receptor subunit beta,succinate-Co A ligase GDPforming beta subunit,pumilio RNA binding family member 3( KIAA0020),and general vesicular transport factor p115.NOP2,EPRS,FTSJ3,KIAA0020 were mainly distributed in M1 module.The NOP2 is the core gene with the highest number of nodes in M1 module.CONCLUSION: A total of 10 core differential genes and 7 signaling pathways related to TGF-β1 stimulation were screened.Among them,focal adhesion,ECM-receptor interaction,PI3K-Akt and NOP2,EPRS,FTSJ3,KIAA0020 may provide new direction for research of mechanisms of abnormal activation of fibrotic diseases including silicosis in incidence and development of multiple lung fibrotic diseases.
ABSTRACT
OBJECTIVE: To investigate the epithelial-mesenchymal transition(EMT) induced by direct or indirect exposure to free silicon dioxide(SiO_2) and the expression of surface protein marker in rat typeⅡalveolar epithelial cell RLE-6TN.METHODS: i) The alveolar macrophages(AM) were isolated from specific pathogen-free SD rat by bronchoalveolar lavage.AM and RLE-6TN were treated with 0-140 mg/L(final concentration) of SiO_2 suspension and were cultured conventionally for 24,48 and 72 hours. The cell viability was detected by CCK-8 assay. The result of CCK-8 essay was used to choose the SiO_2 concentration for the following study. ii) To establish models of RLE-6TN co-cultured with AM that were seeded in Transwell. The cells were divided into 4 groups: the direct control group(RLE-6TN,no SiO_2 exposed),the direct exposure group(RLE-6TN,treated with 100 mg/L SiO_2),the indirect control group(RLE-6TN and AM were cocultured,no SiO_2 exposed) and the indirect exposure group(RLE-6TN and AM were co-cultured,AM was treated with 100 mg/L SiO_2 directly). Western blotting was used to detect the expression of E-cadherin(E-cad) and α-smooth muscle protein(α-SMA) after cells were cultured for 0,24,48 and 72 hours. RESULTS: i) According to the CCK-8 assay,the final concentration of 100 mg/L SiO_2 was chosen for the following study. ii) The difference of relative expression of E-cad andα-SMA in RLE-6TN was statistically significant in different treatment combination and time(P < 0. 01). The E-cad expression of RLE-6TN at 48 and 72 hours in the direct exposure group and the indirect exposure group was lower than that in direct control group at the same time point(P < 0. 05). The E-cad expression in RLE-6TN at 72 hours in the direct exposure group was lower than that in the 0 and 24 hours(P < 0. 05). The E-cad expression in RLE-6TN at 48 and 72 hours in the indirect exposure group was lower than that in the 0 hour(P < 0. 05). At 48 and 72 hours,the α-SMA expression in the indirect exposure group and the direct exposure group was higher than that in their control groups at the same time point(P < 0. 05). The expression of α-SMA in the indirect exposure group was higher than that in the direct exposure group(P < 0. 05). The expression of α-SMA in both exposure groups increased in a time-effect relationship(P <0. 05). CONCLUSION: Direct or indirect exposure to free SiO_2 can induce EMT in RLE-6TN,and decrease the expression of E-cad and increase the expression of α-SMA in a time-effect relationship. Indirect exposure group is more susceptible to EMT.
ABSTRACT
OBJECTIVE To analyze trimethylation of genome-wide histone H3 lysine 4(H3K4met3) induced by silicon dioxide(SiO2)through chromatin immunoprecipitation linked to microarrays(ChIP-chip)in lung fibroblast(LF)of rats. METHODS A primary co-culture model of rat alveolar macrophages (AM)and LF in vitro. AM were exposed to 100 mg · L-1 free SiO2 for 24 h,before LF were collected and the phenotype of LF was determined after transdifferentiation by immunohistochemistry. ChIP-chip was used to profile the variations of trimethylation in H3K4 of lung fibroblasts in CpG island regions. ChIP-qPCR was used to validate the microarray results. The mRNA expression of nfib and kpna3 was analyzed by qRT-PCR. RESULTS Totally 1815 (518 increased and 1297 decreased) genes of H3K4met3 displayed significant differences in SiO2 100 mg·L-1 group compared with control group(Cy3/Cy5 value>2.0 or <0.5,NimbleScan V2.5 software). The results of ChIP-qPCR were quite consistent with those of microarray. CONCLUSION There are significant differences in methylation of genome-wide H3K4 between SiO2 100 mg·L-1 group and control group. These novel candidate genes may become potential biomarkers or new interfered targets.