Small RNA sequencing and bioinformatics analysis of RAW264.7-derived exosomes after Mycobacterium Bovis Bacillus Calmette-Guérin infection

Abstract

Background The mechanisms through which Mycobacterium tuberculosis evades immune surveillance during tuberculosis (TB) infection remain complex. Previous studies have found that Mycobacteria can manipulate the miRNAs of host cells to promote their survival during host-pathogen interactions, and most of these effects occur at the cellular miRNA level. We attempted to investigate the possible related mechanisms at the exosomal miRNA level. Results High-throughput sequencing revealed that Bacillus Calmette-Guérin (BCG) infection could alter the composition of the macrophage exosome content, and the expression levels of miRNAs in exosomes derived from the cell culture media of macrophages showed significant differences between the BCG-infected and non-infected groups. Compared with the non-infected group, 20 exosomal miRNAs were up-regulated and 7 exosomal miRNAs were down-regulated in the infection group (p < 0.05), of which mmu-miR-27b-3p, mmu-miR-93-5p, mmu-miR-25-3p, mmu-miR-1198-5p, mmu-let-7c-5p and let-7a-5p were significantly up-regulated. A bioinformatic analysis indicated that these differentially expressed exosomal miRNAs were involved in multiple biological processes and pathways. The target genes of top six miRNAs in up-regulated groups were positively correlated with the regulation of apoptosis. Conclusions The expression profile of miRNA in exosomes derived from macrophage were altered after Mycobacterium Bovis Bacillus Calmette-Guérin infection, and the differentially expressed miRNAs were involved in multiple biological processes and signalling pathways. The top six up-regulated miRNAs and their targeted genes were predominantly correlated with the regulation of apoptosis.

Mmu-miR-25-3p promotes macrophage autophagy by targeting DUSP10 to reduce mycobacteria survival

“…In a previous study, we extracted and identified the exosomes of the macrophages after BCG infection and analyzed the differentially expressed miRNAs in macrophage exosomes after 72-h infection by high-throughput sequencing ( Zhan et al., 2022 ). The data showed that compared to the uninfected group, the expression of 20 miRNAs was upregulated and that of 7 miRNAs was downregulated in the infected group ( Table 1 ).…”

“…In previous studies, we extracted and identified the exosomes of the macrophages infected by BCG. The miRNAs were analyzed by high-throughput sequencing analysis of the differences expressed in the exosomes of the macrophages after 72-h BCG infection ( Zhan et al., 2022 ). The high-throughput sequencing data were deposited in the Genome Sequence Archive at the National Genomics Data Center, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (GSA: CRA006010).…”

“…In previous studies, we completed the extraction and identification of exosomes of the macrophages infected by Mycobacterium bovis Bacillus Calmette-Guerin (BCG). The miRNA was analyzed by high-throughput sequencing analysis of the differences in the exosomes of the macrophages after a 72-h BCG infection ( Zhan et al., 2022 ). A total of 1853 miRNAs were detected, of which 506 overlapped between the BCG-infected and uninfected groups.…”

Functions of exosomal non-coding RNAs to the infection with Mycobacterium tuberculosis

“…found 20 upregulated and seven downregulated exosomal miRNAs in M. tb -infected macrophages, of which miR-27b-3p, miR-93-5p, miR-25-3p, miR-1198-5p, let-7c-5p and let-7a-5p were considerably upregulated based on high-throughput sequencing ( 73 ). A bioinformatics experiment implied that these DE exosomal miRNAs were engaged in several bioprocesses and pathways, and the target genes of the top six miRNAs in the upregulated group were positively related to apoptosis modulation ( 73 ). The miRNA expression profile in macrophage exosomes differed after BCG infection, and the DE miRNAs participated in multiple bioprocesses and pathways ( 73 ).…”

“…A bioinformatics experiment implied that these DE exosomal miRNAs were engaged in several bioprocesses and pathways, and the target genes of the top six miRNAs in the upregulated group were positively related to apoptosis modulation ( 73 ). The miRNA expression profile in macrophage exosomes differed after BCG infection, and the DE miRNAs participated in multiple bioprocesses and pathways ( 73 ).…”