Novel MicroRNA Involved in Host Response to Avian Pathogenic Escherichia coli Identified by Deep Sequencing and Integration Analysis

Abstract

Avian pathogenic Escherichia coli (APEC) causes one of the most common bacterial diseases of poultry worldwide. Effective control methods are therefore desirable and will be facilitated by a better understanding of the host response to the pathogen. Currently, microRNAs (miRNAs) involved in host resistance to APEC are unknown. Here, we applied RNA sequencing to explore the changed miRNAs and deregulated genes in the spleen of three groups of broilers: nonchallenged (NC), APEC-challenged with mild pathology (CM), and APEC-challenged with severe pathology (CS). Twenty-seven differentially expressed miRNAs (fold change >1.5; P value <0.01) were identified, including 13 miRNAs between the NC and CM, 17 between the NC and CS, and 14 between the CM and CS groups. Through functional analysis of these miRNA targets, 12 immune-related biological processes were found to be significantly enriched. Based on combined analyses of differentially expressed miRNAs and mRNAs within each of the three groups, 43 miRNA-mRNA pairs displayed significantly negative correlations (r < −0.8). Notably, gga-miR-429 was greatly increased in the CS group compared to levels in both the CM and NC groups. In vitro, gga-miR-429 directly repressed luciferase reporter gene activity via binding to 3′ untranslated regions of TMEFF2, NTRK2, and SHISA2. Overexpression of gga-miR-429 in the HD11 macrophage cell line significantly inhibited TMEFF2 and SHISA2 expression, which are involved in the lipopolysaccharide-induced platelet-derived growth factor (PDGF) and Wnt signaling pathways. In summary, we provide the first report characterizing the miRNA changes during APEC infection, which may help to shed light on the roles of these recently identified genetic elements in the mechanisms of host resistance and susceptibility to APEC.

Splenic microRNA Expression Profiles and Integration Analyses Involved in Host Responses to Salmonella enteritidis Infection in Chickens

“…Several miRNAs (gga-miR-125b-5p, gga-miR-34a-5p, gga-miR-1416-5p, and gga-miR-166) associated with SE infection were identified recently in laying chicken cecum by next generation sequencing (Wu et al, 2017 ). A novel splenic miRNA, gga-miR-429, involved in the host response to Avian pathogenic Escherichia coli (APEC) was also detected by deep sequencing (Jia et al, 2017 ). Despite these studies, there is still limited information about the function of miRNAs in the host response and resistance to Salmonella infection in chickens.…”

Translating ‘big data’: better understanding of host-pathogen interactions to control bacterial foodborne pathogens in poultry

“…These miRNAs are responsible for maintaining the homeostasis between metabolism and immunity; thereby, enhancing the resistance of chickens toward Salmonella infection. A similar study was performed in APEC O1-infected chickens using deep sequencing (Jia et al , 2016). The authors identified gga-miR-429 miRNA, which is associated with the enhanced susceptibility of APEC in chickens, upregulated.…”

Distinct miRNA Profile of Cellular and Extracellular Vesicles Released from Chicken Tracheal Cells Following Avian Influenza Virus Infection

“…Our results indicated that gga-miR-12244-5p may target TLR signaling pathways. The miRNA gga-miR-146b-5p was previously suggested to be involved in the general process of inflammation during Avian pathogenic Escherichia coli (APEC) infection in chickens [ 28 ].…”

“…Recent studies in humans have also demonstrated that cellular miRNAs are capable of regulating translation and replication in RNA viruses by directly binding to the virus genome [ 22 , 23 , 24 , 25 , 26 , 27 ]. In addition, studies in chickens have identified several miRNAs that are involved in immune responses against avian pathogens, such as avian pathogenic Escherichia coli (APEC), Newcastle disease virus (NDV), and Marek’s disease virus (MDV) [ 28 , 29 , 30 , 31 ]. Moreover, previous studies demonstrated the expression of miRNAs following AIV infections in chickens [ 32 , 33 ].…”