Microarray analysis of long non-coding RNA expression profiles in monocytic myeloid-derived suppressor cells in Echinococcus granulosus-infected mice

Abstract

BackgroundCystic echinococcosis is a worldwide chronic zoonotic disease caused by infection with the larval stage of Echinococcus granulosus. Previously, we found significant accumulation of myeloid-derived suppressor cells (MDSCs) in E. granulosus infection mouse models and that they play a key role in immunosuppressing T lymphocytes. Here, we compared the long non-coding RNA (lncRNA) and mRNA expression patterns between the splenic monocytic MDSCs (M-MDSCs) of E. granulosus protoscoleces-infected mice and normal mice using microarray analysis.MethodsLncRNA functions were predicted using Gene Ontology enrichment and the Kyoto Encyclopedia of Genes and Genomes pathway analysis. Cis- and trans-regulation analyses revealed potential relationships between the lncRNAs and their target genes or related transcription factors.ResultsWe found that 649 lncRNAs were differentially expressed (fold change ≥ 2, P < 0.05): 582 lncRNAs were upregulated and 67 lncRNAs were downregulated; respectively, 28 upregulated mRNAs and 1043 downregulated mRNAs were differentially expressed. The microarray data was validated by quantitative reverse transcription-PCR. The results indicated that mRNAs co-expressed with the lncRNAs are mainly involved in regulating the actin cytoskeleton, Salmonella infection, leishmaniasis, and the vascular endothelial growth factor (VEGF) signaling pathway. The lncRNA NONMMUT021591 was predicted to cis-regulate the retinoblastoma gene (Rb1), whose expression is associated with abnormal M-MDSCs differentiation. We found that 372 lncRNAs were predicted to interact with 60 transcription factors; among these, C/EBPβ (CCAAT/enhancer binding protein beta) was previously demonstrated to be a transcription factor of MDSCs.ConclusionsOur study identified dysregulated lncRNAs in the M-MDSCs of E. granulosus infection mouse models; they might be involved in M-MDSC-derived immunosuppression in related diseases.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-2905-6) contains supplementary material, which is available to authorized users.

Genome-wide analysis of differentially expressed profiles of mRNAs, lncRNAs and circRNAs in chickens during Eimeria necatrix infection

“…HIV, porcine circovirus 2, HSV-1, rabies virus, avian leukosis virus J, bovine viral diarrhea virus) and parasites (e.g. Echinococcus granulosus, Cryptosporidium parvum, Cryptosporidium baileyi) in animals and humans [28,33,[66][67][68][69][70][71][72][73]. The expression profiles of host circRNAs were also elucidated after infections of avian leukosis virus J [74], bovine viral diarrhea virus [75], human cytomegalovirus [76], Orf virus [30], porcine endemic diarrhea virus [29], HIV [77], transmissible gastroenteritis virus [78], Mycobacterium tuberculosis [79], Clostridium perfringens [80] and C. baileyi [33].…”

miRNAs and lncRNAs in Echinococcus and Echinococcosis

“…The conservation of miRNAs that are involved in Echinococcus regulation reflects the complex and sophisticated adaptations, which are necessary for different environments, present within the life cycles of parasitic species. High-throughput sequencing and miRNA microarray analyses identified dysregulated miRNAs present during parasite infection in natural hosts and animal models that were present in relevant cells, tissues, and blood; demonstrating the importance of these miRNAs in host responses to pathogen challenges [19,43,55]. Recent research results have shown that circulating non-coding RNAs, including miRNAs and lncRNAs, can be stably detected in the blood of hosts that were infected with E. granulosus and E. multilocularis [19,43,56] (Table 3).…”

“…Large miRNAs, being identified in E. granulosus, E. multilocularis, and E. canadensis (G7), have been found to feature certain characteristics of genes in expression regulation, such as tissue and developmental stage specificity, in their respective hosts [18,19,43]. To date, the miRNA expression profiles of E. granulosus sensu stricto (76 known miRNAs, including adults, cysts, and protoscoleces) [44,45], E. canadensis (46 known miRNAs, including cysts and protoscoleces) [12,46], and E. multilocularis (46 known miRNAs, including cysts) [1] have been reported (Table 1).…”

“…Previous studies have reported that non-coding RNAs play important roles in physiological and pathological processes in eukaryotes [17]. MiRNAs and lncRNAs are widely expressed in Echinococcus spp., such as E. granulosus, E. multilocularis, and E. canadensis [18,19]. MiRNAs are small, yet powerful, regulatory RNAs that are implicated in the post-transcriptional regulation of almost all the cellular signaling pathways in both the animals and plants [20].…”

“…However, lncRNA patterns have been described in several the intermediate hosts, such as sheep [29], goats [30], cattle [31], swine [32], horses [33], and humans [34], and the definitive host, canines [35]. LncRNAs were identified as an important regulatory factor that is crucial in regulating immunological stress during cystic echinococcosis, in an experimental mouse model of cystic echinococcosis [19]. In addition, lncRNAs have also been identified as important in the biological functions of other parasites (e.g., Trichomonas vaginalis [36] and Toxoplasma [37]) and in host immunity.…”