Integrated analysis of mRNA and microRNA expression pattern reveals differential transcriptome signatures in RIPK2 over-expressing chicken macrophages infected with avian pathogenic E. coli

ABSTRACT

1. As RIPK2 (receptor interacting serine/threonine kinase 2) has been shown to to alleviate excessive inflammatory responses, the following study conducted a systematic and in-depth analysis of the mRNA-seq and miRNA-seq data from chicken macrophages with/without over-expression of RIPK2 (oeRIPK2) combined with/without avian pathogenic E. coli (APEC) infection to identify the miRNA-mRNA interaction network and potential signalling pathways involved.

2. A total of 9,201 differentially expressed (DE) mRNAs and 300 DE miRNA were identified in both oeRIPK2+APEC vs. APEC and oeRIPK2 vs. the wild-type (WT). Moreover, 4,269 instances of co-expression between miRNAs and mRNAs were seen involving 1,652 DE mRNAs and 164 DE miRNAs.

3. Functional analysis of the DE mRNAs in the miRNA-mRNA interaction network showed that 223 biological processes and five KEGG pathways were significantly enriched in the two comparisons. In total, 128 pairs of miRNA-mRNA interactions were involved in the identified MAPK signalling pathway and focal adhesion immune related pathways.

4. Significantly, these screened miRNAs (gga-miR-222b-5p and gga-miR-214) and their target genes were highly correlated with APEC infection and RIPK2. These recognised key genes, miRNA and the overall miRNA-mRNA regulatory network, enables better understanding of the molecular mechanism of host response to APEC infection, especially related to RIPK2.

KEYWORDS:

• APEC
• mRNA
• miRNA
• over-expression of RIPK2
• co-expression
• miRNA-mRNA interaction

Author contributions

The authors HS and HL designed the experiments and wrote the original manuscript. YY and YM provided the methodology and validated the RNA-seq data. CS, NL, JT and HL revised the manuscript. All authors have read and agreed to the published version of the manuscript.

Disclosure statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Data availability statement

All data generated or analysed in this study are included in this paper, and the datasets have been submitted to the NCBI database with the accession number PRJNA869769 (https://www.ncbi.nlm.nih.gov/sra/PRJNA869769).

Supplemental data

Supplemental data for this article can be accessed online at https://doi.org/10.1080/00071668.2022.2163153.

Additional information

Funding

This research was supported by the National Natural Science Foundation of China (31802053), The Natural Science Foundation of Jiangsu Province (BK20180907), the China Postdoctoral Science Foundation (2019M661950), Jiangsu Postdoctoral Science Foundation (137070510), Jiangsu Graduate Research and Practice Innovation Program (SJCX22_1796), Science and technology innovation fund of Yangzhou University (X20220654), Qing Lan Project in Jiangsu Province, and Yangzhou Fourth ‘talent cultivation plan’ excellent education talent funding project.