Cargando…
RNA-Sequencing Characterization of lncRNA and mRNA Functions in Septic Pig Liver Injury
We assessed differentially expressed (DE) mRNAs and lncRNAs in the liver of septic pigs to explore the key factors regulating lipopolysaccharide (LPS)-induced liver injury. We identified 543 DE lncRNAs and 3642 DE mRNAs responsive to LPS. Functional enrichment analysis revealed the DE mRNAs were inv...
Autores principales: | , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10137529/ https://www.ncbi.nlm.nih.gov/pubmed/37107704 http://dx.doi.org/10.3390/genes14040945 |
_version_ | 1785032487045431296 |
---|---|
author | Zhang, Jing Xue, Zhihui Zhao, Qingbo Zhang, Keke Zhou, Ao Shi, Liangyu Liu, Yulan |
author_facet | Zhang, Jing Xue, Zhihui Zhao, Qingbo Zhang, Keke Zhou, Ao Shi, Liangyu Liu, Yulan |
author_sort | Zhang, Jing |
collection | PubMed |
description | We assessed differentially expressed (DE) mRNAs and lncRNAs in the liver of septic pigs to explore the key factors regulating lipopolysaccharide (LPS)-induced liver injury. We identified 543 DE lncRNAs and 3642 DE mRNAs responsive to LPS. Functional enrichment analysis revealed the DE mRNAs were involved in liver metabolism and other pathways related to inflammation and apoptosis. We also found significantly upregulated endoplasmic reticulum stress (ERS)-associated genes, including the receptor protein kinase receptor-like endoplasmic reticulum kinase (PERK), the eukaryotic translation initiation factor 2α (EIF2S1), the transcription factor C/EBP homologous protein (CHOP), and activating transcription factor 4 (ATF4). In addition, we predicted 247 differentially expressed target genes (DETG) of DE lncRNAs. The analysis of protein-protein interactions (PPI) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway detected key DETGs that are involved in metabolic pathways, such as N-Acetylgalactosaminyltransferase 2 (GALNT2), argininosuccinate synthetase 1 (ASS1), and fructose 1,6-bisphosphatase 1 (FBP1). LNC_003307 was the most abundant DE lncRNA in the pig liver, with a marked upregulation of >10-fold after LPS stimulation. We identified three transcripts for this gene using the rapid amplification of the cDNA ends (RACE) technique and obtained the shortest transcript sequence. This gene likely derives from the nicotinamide N-methyltransferase (NNMT) gene in pigs. According to the identified DETGs of LNC_003307, we hypothesize that this gene regulates inflammation and endoplasmic reticulum stress in LPS-induced liver damage in pigs. This study provides a transcriptomic reference for further understanding of the regulatory mechanisms underlying septic hepatic injury. |
format | Online Article Text |
id | pubmed-10137529 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-101375292023-04-28 RNA-Sequencing Characterization of lncRNA and mRNA Functions in Septic Pig Liver Injury Zhang, Jing Xue, Zhihui Zhao, Qingbo Zhang, Keke Zhou, Ao Shi, Liangyu Liu, Yulan Genes (Basel) Article We assessed differentially expressed (DE) mRNAs and lncRNAs in the liver of septic pigs to explore the key factors regulating lipopolysaccharide (LPS)-induced liver injury. We identified 543 DE lncRNAs and 3642 DE mRNAs responsive to LPS. Functional enrichment analysis revealed the DE mRNAs were involved in liver metabolism and other pathways related to inflammation and apoptosis. We also found significantly upregulated endoplasmic reticulum stress (ERS)-associated genes, including the receptor protein kinase receptor-like endoplasmic reticulum kinase (PERK), the eukaryotic translation initiation factor 2α (EIF2S1), the transcription factor C/EBP homologous protein (CHOP), and activating transcription factor 4 (ATF4). In addition, we predicted 247 differentially expressed target genes (DETG) of DE lncRNAs. The analysis of protein-protein interactions (PPI) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway detected key DETGs that are involved in metabolic pathways, such as N-Acetylgalactosaminyltransferase 2 (GALNT2), argininosuccinate synthetase 1 (ASS1), and fructose 1,6-bisphosphatase 1 (FBP1). LNC_003307 was the most abundant DE lncRNA in the pig liver, with a marked upregulation of >10-fold after LPS stimulation. We identified three transcripts for this gene using the rapid amplification of the cDNA ends (RACE) technique and obtained the shortest transcript sequence. This gene likely derives from the nicotinamide N-methyltransferase (NNMT) gene in pigs. According to the identified DETGs of LNC_003307, we hypothesize that this gene regulates inflammation and endoplasmic reticulum stress in LPS-induced liver damage in pigs. This study provides a transcriptomic reference for further understanding of the regulatory mechanisms underlying septic hepatic injury. MDPI 2023-04-20 /pmc/articles/PMC10137529/ /pubmed/37107704 http://dx.doi.org/10.3390/genes14040945 Text en © 2023 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 Zhang, Jing Xue, Zhihui Zhao, Qingbo Zhang, Keke Zhou, Ao Shi, Liangyu Liu, Yulan RNA-Sequencing Characterization of lncRNA and mRNA Functions in Septic Pig Liver Injury |
title | RNA-Sequencing Characterization of lncRNA and mRNA Functions in Septic Pig Liver Injury |
title_full | RNA-Sequencing Characterization of lncRNA and mRNA Functions in Septic Pig Liver Injury |
title_fullStr | RNA-Sequencing Characterization of lncRNA and mRNA Functions in Septic Pig Liver Injury |
title_full_unstemmed | RNA-Sequencing Characterization of lncRNA and mRNA Functions in Septic Pig Liver Injury |
title_short | RNA-Sequencing Characterization of lncRNA and mRNA Functions in Septic Pig Liver Injury |
title_sort | rna-sequencing characterization of lncrna and mrna functions in septic pig liver injury |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10137529/ https://www.ncbi.nlm.nih.gov/pubmed/37107704 http://dx.doi.org/10.3390/genes14040945 |
work_keys_str_mv | AT zhangjing rnasequencingcharacterizationoflncrnaandmrnafunctionsinsepticpigliverinjury AT xuezhihui rnasequencingcharacterizationoflncrnaandmrnafunctionsinsepticpigliverinjury AT zhaoqingbo rnasequencingcharacterizationoflncrnaandmrnafunctionsinsepticpigliverinjury AT zhangkeke rnasequencingcharacterizationoflncrnaandmrnafunctionsinsepticpigliverinjury AT zhouao rnasequencingcharacterizationoflncrnaandmrnafunctionsinsepticpigliverinjury AT shiliangyu rnasequencingcharacterizationoflncrnaandmrnafunctionsinsepticpigliverinjury AT liuyulan rnasequencingcharacterizationoflncrnaandmrnafunctionsinsepticpigliverinjury |