Particulate matter-induced gene expression patterns in human-derived cells based on 11 public gene expression datasets

• Published in: Genes & genomics 2024, 46(7), , pp.743-749
• Main Authors: Roh, Sanghyun, Hwang, Jeongeun, Park, Joo-Hoo, Song, Dae Jin, Gim, Jeong-An
• Format: Article
• Language: English
• Subjects: Animal Genetics and Genomics; Animals; Biomedical and Life Sciences; Cell death; Cell Line; Cell lines; data collection; Datasets; disease prevention; DNA microarrays; dust mites; Gene expression; Gene Expression Profiling - methods; gene expression regulation; Gene Expression Regulation - drug effects; genes; Human Genetics; Humans; Life Sciences; microarray technology; Microbial Genetics and Genomics; Oxidative stress; Particulate matter; Particulate Matter - adverse effects; Particulate Matter - toxicity; particulates; Peripheral blood mononuclear cells; Plant Genetics and Genomics; Pyroglyphidae; Research Article; Respiration; Respiratory diseases; sequence analysis; Transcriptome; 생물학
• ISSN: 1976-9571; 2092-9293; 2092-9293
• DOI: 10.1007/s13258-024-01512-y

Background Exposure to particulate matter (PM) and house dust mite (HDM) can change the expression patterns of inflammation-, oxidative stress-, and cell death-related genes. We investigated the changes in gene expression patterns owing to PM exposure. Objective This study examined the changes in gene expression patterns following PM exposure. Methods We searched for differentially expressed genes (DEGs) following PM exposure using five cell line-based RNA-seq or microarray datasets and six human-derived datasets. The enrichment terms of the DEGs were assessed. Results DEG analysis yielded two gene sets. Thus, enrichment analysis was performed for each gene set, and the enrichment terms related to respiratory diseases were presented. The intersection of six human-derived datasets and two gene sets was obtained, and the expression patterns following PM exposure were observed. Conclusions Two gene sets were obtained for cells treated with PM and their expression patterns were presented following verification in human-derived cells. Our findings suggest that exposure to PM 2.5 and HDM may reveal changes in genes that are associated with diseases, such as allergies, highlighting the importance of mitigating PM 2.5 and HDM exposure for disease prevention. Highlights Two gene sets with differences in expression were obtained after the treatment of cells with PM. Enrichment terms for each gene set were extracted. DEGs in patient-derived cells after PM treatment were compared with those in cell lines. When PBMC-derived cells were treated with PM, a relatively high overlap of DEGs was found.