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

1. As <i>RIPK2</i> (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 <i>RIPK2</i> (oeRIPK2) combined with/without avian pathogenic <i>E. coli</i> (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 <i>vs</i>. APEC and oeRIPK2 <i>vs</i>. 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 <i>RIPK2</i>. 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 <i>RIPK2</i>.