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Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb
SIMPLE SUMMARY: Diarrhea and vomiting caused by Escherichia coli (E. coli) F17 are considered significant threats to animal farming. In the present study, RNA-Seq was performed to investigate the potential circRNA and miRNA biomarkers for E. coli F17-antagonism (AN) and -sensitive (SE) lambs. The re...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8945857/ https://www.ncbi.nlm.nih.gov/pubmed/35336723 http://dx.doi.org/10.3390/biology11030348 |
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author | Chen, Weihao Lv, Xiaoyang Zhang, Weibo Hu, Tingyan Cao, Xiukai Ren, Ziming Getachew, Tesfaye Mwacharo, Joram M. Haile, Aynalem Sun, Wei |
author_facet | Chen, Weihao Lv, Xiaoyang Zhang, Weibo Hu, Tingyan Cao, Xiukai Ren, Ziming Getachew, Tesfaye Mwacharo, Joram M. Haile, Aynalem Sun, Wei |
author_sort | Chen, Weihao |
collection | PubMed |
description | SIMPLE SUMMARY: Diarrhea and vomiting caused by Escherichia coli (E. coli) F17 are considered significant threats to animal farming. In the present study, RNA-Seq was performed to investigate the potential circRNA and miRNA biomarkers for E. coli F17-antagonism (AN) and -sensitive (SE) lambs. The results indicated that circRNA and miRNA expression is closely associated with the susceptibility of E. coli F17 in lambs. Numbers of circRNAs and miRNAs may serve as potential biomarkers for intestinal inflammatory response against E. coli F17 infection. Our study can provide a preliminary understanding of the underlying mechanisms of intestinal immunity. ABSTRACT: It has long been recognized that enterotoxigenic Escherichia coli (ETEC) is the major pathogen responsible for vomiting and diarrhea. E. coli F17, a main subtype of ETEC, is characterized by high morbidity and mortality in young livestock. However, the transcriptomic basis underlying E. coli F17 infection has not been fully understood. In this study, RNA sequencing was performed to explore the expression profiles of circRNAs and miRNAs in the jejunum of E. coli F17-antagonism (AN) and -sensitive (SE) lambs. A total of 16,534 circRNAs and 271 miRNAs (125 novel miRNAs and 146 annotated miRNAs) were screened, and 214 differentially expressed (DE) circRNAs and 53 DE miRNAs were detected between the AN and SE lambs (i.e., novel_circ_0025840, novel_circ_0022779, novel_miR_107, miR-10b). Functional enrichment analyses showed that source genes of DE circRNAs were mainly involved in metabolic-related pathways, while target genes of DE miRNAs were mainly enriched in the immune response pathways. Then, a two-step machine learning approach combining Random Forest (RF) and XGBoost (candidates were first selected by RF and further assessed by XGBoost) was performed, which identified 44 circRNAs and 39 miRNAs as potential biomarkers (i.e., novel_circ_0000180, novel_circ_0000365, novel_miR_192, oar-miR-496-3p) for E. coli infection. Furthermore, circRNA-related and lncRNA-related ceRNA networks were constructed, containing 46 circRNA-miRNA-mRNA competing triplets and 630 lncRNA-miRNA-mRNA competing triplets, respectively. By conducting a serious of bioinformatic analyses, our results revealed important circRNAs and miRNAs that could be potentially developed as candidate biomarkers for intestinal inflammatory response against E. coli F17 infection; our study can provide novel insights into the underlying mechanisms of intestinal immunity. |
format | Online Article Text |
id | pubmed-8945857 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-89458572022-03-25 Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb Chen, Weihao Lv, Xiaoyang Zhang, Weibo Hu, Tingyan Cao, Xiukai Ren, Ziming Getachew, Tesfaye Mwacharo, Joram M. Haile, Aynalem Sun, Wei Biology (Basel) Article SIMPLE SUMMARY: Diarrhea and vomiting caused by Escherichia coli (E. coli) F17 are considered significant threats to animal farming. In the present study, RNA-Seq was performed to investigate the potential circRNA and miRNA biomarkers for E. coli F17-antagonism (AN) and -sensitive (SE) lambs. The results indicated that circRNA and miRNA expression is closely associated with the susceptibility of E. coli F17 in lambs. Numbers of circRNAs and miRNAs may serve as potential biomarkers for intestinal inflammatory response against E. coli F17 infection. Our study can provide a preliminary understanding of the underlying mechanisms of intestinal immunity. ABSTRACT: It has long been recognized that enterotoxigenic Escherichia coli (ETEC) is the major pathogen responsible for vomiting and diarrhea. E. coli F17, a main subtype of ETEC, is characterized by high morbidity and mortality in young livestock. However, the transcriptomic basis underlying E. coli F17 infection has not been fully understood. In this study, RNA sequencing was performed to explore the expression profiles of circRNAs and miRNAs in the jejunum of E. coli F17-antagonism (AN) and -sensitive (SE) lambs. A total of 16,534 circRNAs and 271 miRNAs (125 novel miRNAs and 146 annotated miRNAs) were screened, and 214 differentially expressed (DE) circRNAs and 53 DE miRNAs were detected between the AN and SE lambs (i.e., novel_circ_0025840, novel_circ_0022779, novel_miR_107, miR-10b). Functional enrichment analyses showed that source genes of DE circRNAs were mainly involved in metabolic-related pathways, while target genes of DE miRNAs were mainly enriched in the immune response pathways. Then, a two-step machine learning approach combining Random Forest (RF) and XGBoost (candidates were first selected by RF and further assessed by XGBoost) was performed, which identified 44 circRNAs and 39 miRNAs as potential biomarkers (i.e., novel_circ_0000180, novel_circ_0000365, novel_miR_192, oar-miR-496-3p) for E. coli infection. Furthermore, circRNA-related and lncRNA-related ceRNA networks were constructed, containing 46 circRNA-miRNA-mRNA competing triplets and 630 lncRNA-miRNA-mRNA competing triplets, respectively. By conducting a serious of bioinformatic analyses, our results revealed important circRNAs and miRNAs that could be potentially developed as candidate biomarkers for intestinal inflammatory response against E. coli F17 infection; our study can provide novel insights into the underlying mechanisms of intestinal immunity. MDPI 2022-02-22 /pmc/articles/PMC8945857/ /pubmed/35336723 http://dx.doi.org/10.3390/biology11030348 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Chen, Weihao Lv, Xiaoyang Zhang, Weibo Hu, Tingyan Cao, Xiukai Ren, Ziming Getachew, Tesfaye Mwacharo, Joram M. Haile, Aynalem Sun, Wei Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb |
title | Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb |
title_full | Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb |
title_fullStr | Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb |
title_full_unstemmed | Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb |
title_short | Non-Coding Transcriptome Provides Novel Insights into the Escherichia coli F17 Susceptibility of Sheep Lamb |
title_sort | non-coding transcriptome provides novel insights into the escherichia coli f17 susceptibility of sheep lamb |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8945857/ https://www.ncbi.nlm.nih.gov/pubmed/35336723 http://dx.doi.org/10.3390/biology11030348 |
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