Long Noncoding RNA THAP9-AS1 and TSPOAP1-AS1 Provide Potential Diagnostic Signatures for Pediatric Septic Shock

Background. Sepsis is a systemic inflammatory syndrome caused by infection with a high incidence and mortality. Although long noncoding RNAs have been identified to be closely involved in many inflammatory diseases, little is known about the role of lncRNAs in pediatric septic shock. Methods. We dow...

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Veröffentlicht in:BioMed research international 2020, Vol.2020 (2020), p.1-9
Hauptverfasser: Luan, Hengfei, Zhu, Pin, Zhang, Xiaobao, Yin, Qigai, Wu, Yong, Chen, Ying
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Zhu, Pin
Zhang, Xiaobao
Yin, Qigai
Wu, Yong
Chen, Ying
description Background. Sepsis is a systemic inflammatory syndrome caused by infection with a high incidence and mortality. Although long noncoding RNAs have been identified to be closely involved in many inflammatory diseases, little is known about the role of lncRNAs in pediatric septic shock. Methods. We downloaded the mRNA profiles GSE13904 and GSE4607, of which GSE13904 includes 106 blood samples of pediatric patients with septic shock and 18 health control samples; GSE4607 includes 69 blood samples of pediatric patients with septic shock and 15 health control samples. The differentially expressed lncRNAs were identified through the limma R package; meanwhile, GO terms and KEGG pathway enrichment analysis was performed via the clusterProfiler R package. The protein-protein interaction (PPI) network was constructed based on the STRING database using the targets of differently expressed lncRNAs. The MCODE plug-in of Cytoscape was used to screen significant clustering modules composed of key genes. Finally, stepwise regression analysis was performed to screen the optimal lncRNAs and construct the logistic regression model, and the ROC curve was applied to evaluate the accuracy of the model. Results. A total of 13 lncRNAs which simultaneously exhibited significant differences in the septic shock group compared with the control group from two sets were identified. According to the 18 targets of differentially expressed lncRNAs, we identified some inflammatory and immune response-related pathways. In addition, several target mRNAs were predicted to be potentially involved in the occurrence of septic shock. The logistic regression model constructed based on two optimal lncRNAs THAP9-AS1 and TSPOAP1-AS1 could efficiently separate samples with septic shock from normal controls. Conclusion. In summary, a predictive model based on the lncRNAs THAP9-AS1 and TSPOAP1-AS1 provided novel lightings on diagnostic research of septic shock.
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Sepsis is a systemic inflammatory syndrome caused by infection with a high incidence and mortality. Although long noncoding RNAs have been identified to be closely involved in many inflammatory diseases, little is known about the role of lncRNAs in pediatric septic shock. Methods. We downloaded the mRNA profiles GSE13904 and GSE4607, of which GSE13904 includes 106 blood samples of pediatric patients with septic shock and 18 health control samples; GSE4607 includes 69 blood samples of pediatric patients with septic shock and 15 health control samples. The differentially expressed lncRNAs were identified through the limma R package; meanwhile, GO terms and KEGG pathway enrichment analysis was performed via the clusterProfiler R package. The protein-protein interaction (PPI) network was constructed based on the STRING database using the targets of differently expressed lncRNAs. The MCODE plug-in of Cytoscape was used to screen significant clustering modules composed of key genes. Finally, stepwise regression analysis was performed to screen the optimal lncRNAs and construct the logistic regression model, and the ROC curve was applied to evaluate the accuracy of the model. Results. A total of 13 lncRNAs which simultaneously exhibited significant differences in the septic shock group compared with the control group from two sets were identified. According to the 18 targets of differentially expressed lncRNAs, we identified some inflammatory and immune response-related pathways. In addition, several target mRNAs were predicted to be potentially involved in the occurrence of septic shock. The logistic regression model constructed based on two optimal lncRNAs THAP9-AS1 and TSPOAP1-AS1 could efficiently separate samples with septic shock from normal controls. Conclusion. In summary, a predictive model based on the lncRNAs THAP9-AS1 and TSPOAP1-AS1 provided novel lightings on diagnostic research of septic shock.</description><identifier>ISSN: 2314-6133</identifier><identifier>EISSN: 2314-6141</identifier><identifier>DOI: 10.1155/2020/7170464</identifier><identifier>PMID: 33344646</identifier><language>eng</language><publisher>Cairo, Egypt: Hindawi Publishing Corporation</publisher><subject>Adaptor Proteins, Signal Transducing - genetics ; Biomarkers ; Blood ; Cell Line, Tumor ; Cell Movement ; Cell Proliferation ; Child ; Clustering ; Computational Biology ; Databases, Factual ; Diagnosis ; Diagnostic systems ; Disease Progression ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Gene Silencing ; Genetic aspects ; Health aspects ; HT29 Cells ; Humans ; Immune response ; Infections ; Inflammatory diseases ; MicroRNAs ; Minor Histocompatibility Antigens - genetics ; Model accuracy ; Mortality ; mRNA ; Neoplasm Invasiveness ; Pediatric research ; Pediatrics ; Prediction models ; Principal components analysis ; Protein interaction ; Protein Interaction Maps ; Proteins ; Regression analysis ; Regression models ; Repressor Proteins - genetics ; Risk factors ; RNA ; RNA polymerase ; RNA, Long Noncoding - genetics ; RNA, Messenger - genetics ; Sepsis ; Septic shock ; Shock, Septic - genetics ; Software ; Statistical models ; T cell receptors ; Tripartite Motif Proteins - genetics</subject><ispartof>BioMed research international, 2020, Vol.2020 (2020), p.1-9</ispartof><rights>Copyright © 2020 Yong Wu et al.</rights><rights>COPYRIGHT 2020 John Wiley &amp; Sons, Inc.</rights><rights>Copyright © 2020 Yong Wu et al. This is an open access article distributed under the Creative Commons Attribution License (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. https://creativecommons.org/licenses/by/4.0</rights><rights>Copyright © 2020 Yong Wu et al. 2020</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c499t-c69f864ddc703849b94afaba63efa9c83aa651e7b3b7aadcdaff5c8f98d4843a3</citedby><cites>FETCH-LOGICAL-c499t-c69f864ddc703849b94afaba63efa9c83aa651e7b3b7aadcdaff5c8f98d4843a3</cites><orcidid>0000-0001-5217-0966</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7725549/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7725549/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,4010,27900,27901,27902,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33344646$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Bottillo, Irene</contributor><contributor>Irene Bottillo</contributor><creatorcontrib>Luan, Hengfei</creatorcontrib><creatorcontrib>Zhu, Pin</creatorcontrib><creatorcontrib>Zhang, Xiaobao</creatorcontrib><creatorcontrib>Yin, Qigai</creatorcontrib><creatorcontrib>Wu, Yong</creatorcontrib><creatorcontrib>Chen, Ying</creatorcontrib><title>Long Noncoding RNA THAP9-AS1 and TSPOAP1-AS1 Provide Potential Diagnostic Signatures for Pediatric Septic Shock</title><title>BioMed research international</title><addtitle>Biomed Res Int</addtitle><description>Background. Sepsis is a systemic inflammatory syndrome caused by infection with a high incidence and mortality. Although long noncoding RNAs have been identified to be closely involved in many inflammatory diseases, little is known about the role of lncRNAs in pediatric septic shock. Methods. We downloaded the mRNA profiles GSE13904 and GSE4607, of which GSE13904 includes 106 blood samples of pediatric patients with septic shock and 18 health control samples; GSE4607 includes 69 blood samples of pediatric patients with septic shock and 15 health control samples. The differentially expressed lncRNAs were identified through the limma R package; meanwhile, GO terms and KEGG pathway enrichment analysis was performed via the clusterProfiler R package. The protein-protein interaction (PPI) network was constructed based on the STRING database using the targets of differently expressed lncRNAs. The MCODE plug-in of Cytoscape was used to screen significant clustering modules composed of key genes. 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Sepsis is a systemic inflammatory syndrome caused by infection with a high incidence and mortality. Although long noncoding RNAs have been identified to be closely involved in many inflammatory diseases, little is known about the role of lncRNAs in pediatric septic shock. Methods. We downloaded the mRNA profiles GSE13904 and GSE4607, of which GSE13904 includes 106 blood samples of pediatric patients with septic shock and 18 health control samples; GSE4607 includes 69 blood samples of pediatric patients with septic shock and 15 health control samples. The differentially expressed lncRNAs were identified through the limma R package; meanwhile, GO terms and KEGG pathway enrichment analysis was performed via the clusterProfiler R package. The protein-protein interaction (PPI) network was constructed based on the STRING database using the targets of differently expressed lncRNAs. The MCODE plug-in of Cytoscape was used to screen significant clustering modules composed of key genes. Finally, stepwise regression analysis was performed to screen the optimal lncRNAs and construct the logistic regression model, and the ROC curve was applied to evaluate the accuracy of the model. Results. A total of 13 lncRNAs which simultaneously exhibited significant differences in the septic shock group compared with the control group from two sets were identified. According to the 18 targets of differentially expressed lncRNAs, we identified some inflammatory and immune response-related pathways. In addition, several target mRNAs were predicted to be potentially involved in the occurrence of septic shock. The logistic regression model constructed based on two optimal lncRNAs THAP9-AS1 and TSPOAP1-AS1 could efficiently separate samples with septic shock from normal controls. Conclusion. In summary, a predictive model based on the lncRNAs THAP9-AS1 and TSPOAP1-AS1 provided novel lightings on diagnostic research of septic shock.</abstract><cop>Cairo, Egypt</cop><pub>Hindawi Publishing Corporation</pub><pmid>33344646</pmid><doi>10.1155/2020/7170464</doi><tpages>9</tpages><orcidid>https://orcid.org/0000-0001-5217-0966</orcidid><oa>free_for_read</oa></addata></record>
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subjects Adaptor Proteins, Signal Transducing - genetics
Biomarkers
Blood
Cell Line, Tumor
Cell Movement
Cell Proliferation
Child
Clustering
Computational Biology
Databases, Factual
Diagnosis
Diagnostic systems
Disease Progression
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Gene Regulatory Networks
Gene Silencing
Genetic aspects
Health aspects
HT29 Cells
Humans
Immune response
Infections
Inflammatory diseases
MicroRNAs
Minor Histocompatibility Antigens - genetics
Model accuracy
Mortality
mRNA
Neoplasm Invasiveness
Pediatric research
Pediatrics
Prediction models
Principal components analysis
Protein interaction
Protein Interaction Maps
Proteins
Regression analysis
Regression models
Repressor Proteins - genetics
Risk factors
RNA
RNA polymerase
RNA, Long Noncoding - genetics
RNA, Messenger - genetics
Sepsis
Septic shock
Shock, Septic - genetics
Software
Statistical models
T cell receptors
Tripartite Motif Proteins - genetics
title Long Noncoding RNA THAP9-AS1 and TSPOAP1-AS1 Provide Potential Diagnostic Signatures for Pediatric Septic Shock
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