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Profile analysis of circRNAs in human THP-1 derived macrophages infected with intracellular Staphylococcus aureus

ABSTRACT: Background: Intracellular Staphylococcus aureus (S. aureus) infection is generally persistent, recurrent and difficult to treat due to the poor availability of antibiotics within macrophages cells and the lack of ideal diagnostic markers. Circular RNA (circRNA), with covalently closed circular structures, exists in the serum stably and is not easily degraded by nucleases. CircRNAs play important roles in the eukaryotic regulation of genes expression and served as biomarkers in variety disease including infections. However, the function of host circRNAs in intracellular S. aureus infection remains largely unclear. Methods: In this study, an intracellular survival THP-1 derived macrophages model of S. aureus infection was established. Then, the circRNA expression profile was investigated by RNA sequencing technology in both S. aureus -infected THP-1 cells and mock control cells. The differentially expressed (DE) circRNAs with a fold-change ≥2.0 (p<0.05) are analyzed using functional pathway clustering prediction. RT-qPCR was performed to verify the top 9 DE circRNAs. Results: A total of 5,299 circRNAs were detected during the intracellular S. aureus infection. 61 DE circRNAs with a fold-change ≥1.5 (p<0.05) after S. aureus infection were identified. 22 circRNAs were up-regulated while 39 circRNAs were down-regulated. Functional annotation analysis demonstrated that Lysine degradation, RNA degradation and Neurotrophin signaling pathway are most important in intracellular S. aureus infection. Conclusion: Our study provides the first profile analysis of circRNAs involved in intracellular S. aureus infection, which may contribute to the understanding of its host evasion mechanisms.

ORGANISM(S): Homo sapiens

PROVIDER: GSE173495 | GEO | 2022/03/24

REPOSITORIES: GEO

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Project description:In platelets, splicing and translation occur in the absence of a nucleus. However, the integrity and stability of mRNAs derived from megakaryocyte progenitor cells remain poorly quantified on a transcriptome-wide level. As circular RNAs (circRNAs) are resistant to degradation by exonucleases, their abundance relative to linear RNAs can be used as a surrogate marker for mRNA stability in the absence of transcription. Here we show that circRNAs are enriched in human platelets 17-188 fold relative to nucleated tissues, and 14-26 fold relative to samples digested with RNAseR to selectively remove linear RNA. We compare RNAseq read depths inside and outside circRNAs to provide in silico evidence of transcript circularity, show that exons within circRNAs are enriched ~13X in platelets relative to nucleated tissues, and identify 3162 genes significantly enriched for circRNAs including some where all RNAs appear to be derived from circular molecules. We also confirm that this is a feature of other anucleate cells through transcriptome sequencing of mature erythrocytes, demonstrate that circRNAs are not enriched in megakaryocytes, and that linear RNAs decay more rapidly than circRNAs in platelet preparations. Collectively, these results suggest that circulating platelets have lost on aveage over 90% of their progenitor mRNAs, and that translation in platelets occurrs against the backdrop of a highly degraded transcriptome. Finally, we find that transcripts classified as products of reverse transcriptase template switching are both enriched in platelets and resistant to decay, countering the recent suggestion that up to 50% of rearranged RNAs are artefacts. A single rRNA depleted total RNA sample was sequenced. This together with 25 publicly available rRNA depleted total RNA samples (including 3 from platelets) were analysed using PTESFinder v 1 (http://sourceforge.net/projects/ptesfinder-v1/) to identify back-splice junctions, characteristic of circRNA transcripts. The contribution of circRNA producing exons was analysed on a gene by gene basis as follows: All circRNA transcripts identified in any sample were first pooled to define exons which can contribute to circRNA generation using custom scripts (available on request). For each sample, expression estimates (RPKMI) across all circRNA producing exons were computed for each locus using the total size of exons (in bp) and the read counts mapping to them. Similarly, total size and exonic read counts for exons for which no circRNA were detected in any sample were used to compute expression estimates (RPKME) for non-circRNA producing exons for each locus. Abundance ratios (RPKMI/RPKME and RPKMI/RPKMI+RPKME) were calculated and compared between Platelets and human tissues using Wilcoxon signed-rank test. Please note that the '25sample_info_accn_no.txt' contains the accession numbers and tissue/cell type information for 25 samples analyzed together.

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Profile analysis of circRNAs in human THP-1 derived macrophages infected with intracellular Staphylococcus aureus

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