Dataset Information

Early life exposure of pigs to topsoil alters miRNA and mRNA expression in peripheral blood mononuclear cells

ABSTRACT: Exposure to less hygienic conditions during early childhood has been associated with stimulation and development of the immune system. A recent study indicated exposure of piglets to soil-borne microbes during lactation was related with modulation of gut microbiota and immune function. To identify potential molecular mechanisms and pathways impacted by early life topsoil exposure, we analyzed gene expression (mRNA and miRNA) in peripheral blood mononuclear cells (PBMC) from these piglets. Total RNA was extracted from PBMC of piglets exposed to topsoil only from d 4-d 21 of life (mRNA n=6; miRNA n=5) or unexposed control pigs (mRNA n=6; miRNA n=8) at 11, 20, and 56 days of age. Small RNA and mRNA were sequenced with 50-bp single-end reads using Illumina chemistry. Differential expression (DE) analysis was performed using PROC Glimmix of SAS to evaluate changes in expression due to topsoil exposure over time with genes declared DE at a false discovery rate (FDR) of q<0.10. A total of 138 mRNA and 21 miRNAs were identified as DE for the treatment by age interaction. Ontology enrichment analysis of DE mRNA revealed GO terms directly involved in the connection between T-cell and antigen-presenting cells that are associated with T-cell activation. Key regulatory genes identified include PTPRJ, ITGB3, TRBV30, CD3D, mir-143, mir-29, and mir-148a. While these results require validation, this study provides data supporting the hypothesis that less hygienic environments during early life may contribute to the development of the immune system

ORGANISM(S): Sus scrofa

PROVIDER: GSE205321 | GEO | 2022/07/31

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:Introduction: Intracerebral hemorrhage (ICH) is a severe neurological disorder with no proven treatment. microRNA (miRNA) are short, noncoding nucleic acids that are critical regulators gene expression and promising novel therapeutic targets. Our prior research of mRNA-seq in swine demonstrated that ICH increased inflammatory gene expression within six hours of onset. We now present findings from an integrated analysis of miRNA-seq and mRNA-seq in peripheral blood mononuclear cells (PBMCs) from swine ICH. We tested the hypothesis that ICH would induce miRNA within six hours and that differentially expressed (DE) inflammatory genes would be targets of the DE miRNA. Methods: In 10 pigs, one PBMC sample was collected immediately prior to ICH induction and a second six hours later; miRNA-seq and mRNA-seq were performed. To determine the miRNA that primarily regulated the DE mRNA, an aggregate score was calculated for each miRNA of interest that incorporated the combined summary statistics of its DE target mRNA. Networks of molecular interactions were generated for the target mRNA and the combined miRNA/target mRNA. Results: A total of 227 miRNA were identified with alignment to the Sus scrofa (swine) genome, and 46 were DE (FDR <0.05). When analyzed with the aggregate scoring calculation, the miRNA that were most essential for regulating the DE mRNA included the following, all of which were downregulated post-ICH: miR-29a, miR-29b, miR-31, miR-34c, miR-125a, miR-132, miR-142, miR-150, miR-151a, miR-181a, and miR-186. A highly connected network of interactions was generated from these miRNA and their target mRNA. Conclusion: ICH strongly induced numerous miRNA/mRNA targets in swine PBMCs within six hours of onset. To our knowledge, this is the first integrated analysis of miRNA-seq and mRNA-seq in any study of ICH and the first report of miRNA in swine ICH. Further research is needed to determine whether these miRNA are potential therapeutic targets, including analyzing interventions such as miRNA overexpression or inhibition

Project description:Purpose: RNA-Seq has become a powerful tool for investigating transcriptional profiles in gene expression analysis, which would help to reveal the molecular mechanism of Clostridium perfringens type C infecting the piglets. In this study, we analyzed miRNA profiles of the spleen of piglets caused by Clostridium perfringens type C. Methods: 30 normal 7-day-old piglets (Y x L), without infecting Clostridium perfringens type C, Escherichia coli and Salmonella, were selected as experimental subjects. 25 piglets were randomly selected as the experimental group, which were disposed once a day for 5 days. Each piglet was dosed with 1 ml of bouillon culture-medium inoculated Clostridium perfringens type C at 37℃ for 16h, which approximate to 1 x109 CFU per ml. Then, 5 piglets were randomly selected as the control group (SC), which were taken the equal volume medium for 5 days.Based on total diarrhea scores, 25 piglets were ranked from high to low. The top and last five piglet were considered as sensitive group (SS) and resistant group (SR), respectively. Finally, spleen were collected and sequenced for miRNA. Result: 88 differentially expressed miRNAs were found. KEGG pathway analysis for target genes revealed that these miRNAs were involved in MAPK signaling pathway, mTOR signaling pathway, FoxO signaling pathway, p53 signaling pathway and ECM-receptor interaction. And 4 miRNAs (miR-133b, miR-532-3p, miR-339-5p and miR-331-3p) of closely related to piglets resistance to C. perfringens type C were obtained. The expression correlation analysis between these miRNAs and target genes revealed that the expression of miR-133b and miR-532-3p had negative correlation with their target NFATC4, miR-339-5p had negative correlation with target HTRA3, and miR-339-5p and miR-331-3p had negative correlation with target TNFAIP8L2 in spleen, suggesting that miR-133b and miR-532-3p targeting to NFATC4, miR-339-5p targeting to HTRA3, and miR-339-5p and miR-331-3p targeting to TNFAIP8L2 were probably involved in piglet resisting C. perfringens type C. Conclusions:The results will provide value resources for better understanding of the genetic basis of C. perfringens type C resistance in piglet and lays a new foundation for identifying novel markers of C. perfringens type C resistance.

Dataset Information

Early life exposure of pigs to topsoil alters miRNA and mRNA expression in peripheral blood mononuclear cells

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets