Qiulei Zhang , Chang Lu , Weixuan Fan , Yongjie Yin
{"title":"通过综合分析多个数据集探索败血症相关脑病的分子机制","authors":"Qiulei Zhang , Chang Lu , Weixuan Fan , Yongjie Yin","doi":"10.1016/j.cyto.2024.156609","DOIUrl":null,"url":null,"abstract":"<div><h3>Background</h3><p>We aim to deal with the Hub-genes and signalling pathways connected with Sepsis-associated encephalopathy (SAE).</p></div><div><h3>Methods</h3><p>The raw datasets were acquired from the Gene Expression Omnibus (GEO) database (GSE198861 and GSE167610). R software filtered the differentially expressed genes (DEGs) for hub genes exploited for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Hub genes were identified from the intersection of DEGs via protein–protein interaction (PPI) network. And the single-cell dataset (GSE101901) was used to authenticate where the hub genes express in hippocampus cells. Cell–cell interaction analysis and Gene Set Variation Analysis (GSVA) analysis of the whole transcriptome validated the interactions between hippocampal cells.</p></div><div><h3>Results</h3><p>A total of 161 DEGs were revealed in GSE198861 and GSE167610 datasets. Biological function analysis showed that the DEGs were primarily involved in the phagosome pathway and significantly enriched. The PPI network extracted 10 Hub genes. The M2 Macrophage cell decreased significantly during the acute period, and the hub gene may play a role in this biological process. The hippocampal variation pathway was associated with the MAPK signaling pathway.</p></div><div><h3>Conclusion</h3><p>Hub genes (<em>Pecam1</em>, <em>Cdh5</em>, <em>Fcgr</em>, <em>C1qa</em>, <em>Vwf</em>, <em>Vegfa</em>, <em>C1qb</em>, <em>C1qc</em>, Fcgr4 and Fcgr2b) may paticipate in the biological process of SAE.</p></div>","PeriodicalId":297,"journal":{"name":"Cytokine","volume":null,"pages":null},"PeriodicalIF":3.7000,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1043466624001121/pdfft?md5=1e039aee031ab74d47e2ad77d5983341&pid=1-s2.0-S1043466624001121-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Exploring the molecular mechanism of sepsis-associated encephalopathy by integrated analysis of multiple datasets\",\"authors\":\"Qiulei Zhang , Chang Lu , Weixuan Fan , Yongjie Yin\",\"doi\":\"10.1016/j.cyto.2024.156609\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Background</h3><p>We aim to deal with the Hub-genes and signalling pathways connected with Sepsis-associated encephalopathy (SAE).</p></div><div><h3>Methods</h3><p>The raw datasets were acquired from the Gene Expression Omnibus (GEO) database (GSE198861 and GSE167610). R software filtered the differentially expressed genes (DEGs) for hub genes exploited for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Hub genes were identified from the intersection of DEGs via protein–protein interaction (PPI) network. And the single-cell dataset (GSE101901) was used to authenticate where the hub genes express in hippocampus cells. Cell–cell interaction analysis and Gene Set Variation Analysis (GSVA) analysis of the whole transcriptome validated the interactions between hippocampal cells.</p></div><div><h3>Results</h3><p>A total of 161 DEGs were revealed in GSE198861 and GSE167610 datasets. Biological function analysis showed that the DEGs were primarily involved in the phagosome pathway and significantly enriched. The PPI network extracted 10 Hub genes. The M2 Macrophage cell decreased significantly during the acute period, and the hub gene may play a role in this biological process. The hippocampal variation pathway was associated with the MAPK signaling pathway.</p></div><div><h3>Conclusion</h3><p>Hub genes (<em>Pecam1</em>, <em>Cdh5</em>, <em>Fcgr</em>, <em>C1qa</em>, <em>Vwf</em>, <em>Vegfa</em>, <em>C1qb</em>, <em>C1qc</em>, Fcgr4 and Fcgr2b) may paticipate in the biological process of SAE.</p></div>\",\"PeriodicalId\":297,\"journal\":{\"name\":\"Cytokine\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.7000,\"publicationDate\":\"2024-05-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S1043466624001121/pdfft?md5=1e039aee031ab74d47e2ad77d5983341&pid=1-s2.0-S1043466624001121-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Cytokine\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1043466624001121\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Cytokine","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1043466624001121","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Exploring the molecular mechanism of sepsis-associated encephalopathy by integrated analysis of multiple datasets
Background
We aim to deal with the Hub-genes and signalling pathways connected with Sepsis-associated encephalopathy (SAE).
Methods
The raw datasets were acquired from the Gene Expression Omnibus (GEO) database (GSE198861 and GSE167610). R software filtered the differentially expressed genes (DEGs) for hub genes exploited for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Hub genes were identified from the intersection of DEGs via protein–protein interaction (PPI) network. And the single-cell dataset (GSE101901) was used to authenticate where the hub genes express in hippocampus cells. Cell–cell interaction analysis and Gene Set Variation Analysis (GSVA) analysis of the whole transcriptome validated the interactions between hippocampal cells.
Results
A total of 161 DEGs were revealed in GSE198861 and GSE167610 datasets. Biological function analysis showed that the DEGs were primarily involved in the phagosome pathway and significantly enriched. The PPI network extracted 10 Hub genes. The M2 Macrophage cell decreased significantly during the acute period, and the hub gene may play a role in this biological process. The hippocampal variation pathway was associated with the MAPK signaling pathway.
Conclusion
Hub genes (Pecam1, Cdh5, Fcgr, C1qa, Vwf, Vegfa, C1qb, C1qc, Fcgr4 and Fcgr2b) may paticipate in the biological process of SAE.
期刊介绍：
The journal Cytokine has an open access mirror journal Cytokine: X, sharing the same aims and scope, editorial team, submission system and rigorous peer review.
* Devoted exclusively to the study of the molecular biology, genetics, biochemistry, immunology, genome-wide association studies, pathobiology, diagnostic and clinical applications of all known interleukins, hematopoietic factors, growth factors, cytotoxins, interferons, new cytokines, and chemokines, Cytokine provides comprehensive coverage of cytokines and their mechanisms of actions, 12 times a year by publishing original high quality refereed scientific papers from prominent investigators in both the academic and industrial sectors.
We will publish 3 major types of manuscripts:
1) Original manuscripts describing research results.
2) Basic and clinical reviews describing cytokine actions and regulation.
3) Short commentaries/perspectives on recently published aspects of cytokines, pathogenesis and clinical results.
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