Integrated analysis of mRNA and microRNA expression pattern reveals differential transcriptome signatures in RIPK2
1School of Biological and Chemical Engineering, Yangzhou Polytechnic College, Yangzhou, China.
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.
Insights
This study reveals how receptor interacting serine/threonine kinase 2 (RIPK2) influences chicken immune responses to avian pathogenic E. coli (APEC). It identifies key microRNAs and gene networks involved in the host
Area of Science:
- Immunology
- Molecular Biology
- Genomics
Background:
- Receptor interacting serine/threonine kinase 2 (RIPK2) plays a role in regulating inflammatory responses.
- Avian pathogenic E. coli (APEC) is a significant pathogen causing economic losses in poultry.
- Understanding host-pathogen interactions is crucial for developing effective disease control strategies.
Purpose of the Study:
- To systematically analyze mRNA and miRNA sequencing data from chicken macrophages.
- To identify the miRNA-mRNA interaction network and signaling pathways involved in RIPK2-mediated immune responses to APEC infection.
- To uncover key molecular mechanisms underlying host defense against APEC.
Main Methods:
- Analysis of mRNA-seq and miRNA-seq data from chicken macrophages with and without RIPK2 overexpression (oeRIPK2) and APEC infection.
- Identification of differentially expressed (DE) mRNAs and miRNAs.
- Construction of miRNA-mRNA co-expression networks and functional enrichment analysis (KEGG pathways).
Main Results:
- 9,201 DE mRNAs and 300 DE miRNAs were identified.
- 4,269 co-expression instances involving 1,652 DE mRNAs and 164 DE miRNAs were found.
- The MAPK signaling pathway and focal adhesion pathways were significantly enriched, with 128 miRNA-mRNA interactions identified.
Conclusions:
- Specific miRNAs (gga-miR-222b-5p, gga-miR-214) and their target genes are strongly correlated with APEC infection and RIPK2 expression.
- The identified miRNA-mRNA regulatory network provides insights into the molecular mechanisms of host response to APEC, particularly concerning RIPK2.
- This study enhances our understanding of the host's innate immune response to bacterial infection.
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