Molecular characterization of PANoptosis-related genes in chronic kidney disease
Chronic kidney disease (CKD) is characterized by fibrosis and inflammation in renal tissues. Several types of cell death have been implicated in CKD onset and progression. Unlike traditional forms of cell death, PANoptosis is characterized by the crosstalk among programmed cell death pathways. Howev...
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| description | Chronic kidney disease (CKD) is characterized by fibrosis and inflammation in renal tissues. Several types of cell death have been implicated in CKD onset and progression. Unlike traditional forms of cell death, PANoptosis is characterized by the crosstalk among programmed cell death pathways. However, the interaction between PANoptosis and CKD remains unclear. Here, we used bioinformatics methods to identify differentially expressed genes and differentially expressed PANoptosis-related genes (DE-PRGs) using data from the GSE37171 dataset. Following this, we further performed gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and gene set enrichment analysis using the data. We adopted a combined approach to select hub genes, using the STRING database and CytoHubba plug-in, and we used the GSE66494 as a validation dataset. In addition, we constructed ceRNA, transcription factor (TF)-gene, and drug-gene networks using Cytoscape. Lastly, we conducted immunohistochemical analysis and western blotting to validate the hub genes. We identified 57 PANoptosis-associated genes as DE-PRGs. We screened nine hub genes from the 57 DE-PRGs. We identified two hub genes (FOS and PTGS2) using the GSE66494 database, Nephroseq, immunohistochemistry, and western blotting. A common miRNA (Hsa-miR-101-3p) and three TFs (CREB1, E2F1, and RELA) may play a crucial role in the onset and progression of PANoptosis-related CKD. In our analysis of the drug-gene network, we identified eight drugs targeting FOS and 52 drugs targeting PTGS2. |
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Several types of cell death have been implicated in CKD onset and progression. Unlike traditional forms of cell death, PANoptosis is characterized by the crosstalk among programmed cell death pathways. However, the interaction between PANoptosis and CKD remains unclear. Here, we used bioinformatics methods to identify differentially expressed genes and differentially expressed PANoptosis-related genes (DE-PRGs) using data from the GSE37171 dataset. Following this, we further performed gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and gene set enrichment analysis using the data. We adopted a combined approach to select hub genes, using the STRING database and CytoHubba plug-in, and we used the GSE66494 as a validation dataset. In addition, we constructed ceRNA, transcription factor (TF)-gene, and drug-gene networks using Cytoscape. Lastly, we conducted immunohistochemical analysis and western blotting to validate the hub genes. We identified 57 PANoptosis-associated genes as DE-PRGs. We screened nine hub genes from the 57 DE-PRGs. We identified two hub genes (FOS and PTGS2) using the GSE66494 database, Nephroseq, immunohistochemistry, and western blotting. A common miRNA (Hsa-miR-101-3p) and three TFs (CREB1, E2F1, and RELA) may play a crucial role in the onset and progression of PANoptosis-related CKD. In our analysis of the drug-gene network, we identified eight drugs targeting FOS and 52 drugs targeting PTGS2.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0312696</identifier><identifier>PMID: 39466748</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Apoptosis ; Apoptosis - genetics ; Bioinformatics ; Biology and Life Sciences ; Biomarkers ; Care and treatment ; Cell death ; Chronic kidney failure ; Computational Biology - methods ; Computer and Information Sciences ; Cyclooxygenase 2 - genetics ; Databases, Genetic ; Datasets ; Diagnosis ; Drug delivery ; Drug dosages ; Drugs ; Ferroptosis ; Fibrosis ; Gene expression ; Gene Expression Profiling ; Gene Ontology ; Gene Regulatory Networks ; Gene set enrichment analysis ; Genes ; Genetic aspects ; Humans ; Identification methods ; Immunohistochemistry ; Inflammation ; Kidney diseases ; Kidneys ; Medicine and Health Sciences ; MicroRNAs ; miRNA ; Molecular dynamics ; Mortality ; Online data bases ; Pathogenesis ; Protein Interaction Maps - genetics ; Proteins ; Proto-Oncogene Proteins c-fos - genetics ; Proto-Oncogene Proteins c-fos - metabolism ; Quality of life ; Renal Insufficiency, Chronic - genetics ; Renal Insufficiency, Chronic - pathology ; Software ; Western blotting</subject><ispartof>PloS one, 2024-10, Vol.19 (10), p.e0312696</ispartof><rights>Copyright: © 2024 Zhang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</rights><rights>COPYRIGHT 2024 Public Library of Science</rights><rights>2024 Zhang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2024 Zhang et al 2024 Zhang et al</rights><rights>2024 Zhang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c526t-634b215dd601d99f56fe3a6d4fab455813f7b8de836c8ad270eaa02f6455966e3</cites><orcidid>0000-0003-2569-5657</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/PMC11515967/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515967/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39466748$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Dey, Avanti</contributor><creatorcontrib>Zhang, Wen-Tao</creatorcontrib><creatorcontrib>Ge, Hong-Wei</creatorcontrib><creatorcontrib>Wei, Yuan</creatorcontrib><creatorcontrib>Gao, Jing-Lin</creatorcontrib><creatorcontrib>Tian, Fang</creatorcontrib><creatorcontrib>Zhou, En-Chao</creatorcontrib><title>Molecular characterization of PANoptosis-related genes in chronic kidney disease</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Chronic kidney disease (CKD) is characterized by fibrosis and inflammation in renal tissues. Several types of cell death have been implicated in CKD onset and progression. Unlike traditional forms of cell death, PANoptosis is characterized by the crosstalk among programmed cell death pathways. However, the interaction between PANoptosis and CKD remains unclear. Here, we used bioinformatics methods to identify differentially expressed genes and differentially expressed PANoptosis-related genes (DE-PRGs) using data from the GSE37171 dataset. Following this, we further performed gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and gene set enrichment analysis using the data. We adopted a combined approach to select hub genes, using the STRING database and CytoHubba plug-in, and we used the GSE66494 as a validation dataset. In addition, we constructed ceRNA, transcription factor (TF)-gene, and drug-gene networks using Cytoscape. Lastly, we conducted immunohistochemical analysis and western blotting to validate the hub genes. We identified 57 PANoptosis-associated genes as DE-PRGs. We screened nine hub genes from the 57 DE-PRGs. We identified two hub genes (FOS and PTGS2) using the GSE66494 database, Nephroseq, immunohistochemistry, and western blotting. A common miRNA (Hsa-miR-101-3p) and three TFs (CREB1, E2F1, and RELA) may play a crucial role in the onset and progression of PANoptosis-related CKD. In our analysis of the drug-gene network, we identified eight drugs targeting FOS and 52 drugs targeting PTGS2.</description><subject>Analysis</subject><subject>Apoptosis</subject><subject>Apoptosis - genetics</subject><subject>Bioinformatics</subject><subject>Biology and Life Sciences</subject><subject>Biomarkers</subject><subject>Care and treatment</subject><subject>Cell death</subject><subject>Chronic kidney failure</subject><subject>Computational Biology - methods</subject><subject>Computer and Information Sciences</subject><subject>Cyclooxygenase 2 - genetics</subject><subject>Databases, Genetic</subject><subject>Datasets</subject><subject>Diagnosis</subject><subject>Drug delivery</subject><subject>Drug dosages</subject><subject>Drugs</subject><subject>Ferroptosis</subject><subject>Fibrosis</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Ontology</subject><subject>Gene Regulatory Networks</subject><subject>Gene set enrichment analysis</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Humans</subject><subject>Identification methods</subject><subject>Immunohistochemistry</subject><subject>Inflammation</subject><subject>Kidney diseases</subject><subject>Kidneys</subject><subject>Medicine and Health Sciences</subject><subject>MicroRNAs</subject><subject>miRNA</subject><subject>Molecular dynamics</subject><subject>Mortality</subject><subject>Online data bases</subject><subject>Pathogenesis</subject><subject>Protein Interaction Maps - genetics</subject><subject>Proteins</subject><subject>Proto-Oncogene Proteins c-fos - genetics</subject><subject>Proto-Oncogene Proteins c-fos - metabolism</subject><subject>Quality of life</subject><subject>Renal Insufficiency, Chronic - genetics</subject><subject>Renal Insufficiency, Chronic - pathology</subject><subject>Software</subject><subject>Western blotting</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqNkltv1DAQhSMEoqXwDxBEQkLwkMWOEyd5qlYVl5UKrbi9WhN7suvFGy-2gyi_Hm83rTaoDygPiexvzsycnCR5SsmMsoq-WdvB9WBmW9vjjDCa84bfS45pw_KM54TdP_g-Sh55vyakZDXnD5Mj1hScV0V9nFx-tAblYMClcgUOZECn_0DQtk9tl17OP9ltsF77zKGBgCpdYo8-1X3kne21TH9o1eNVqrRH8Pg4edCB8fhkfJ8k3969_Xr2ITu_eL84m59nssx5yDgr2pyWSnFCVdN0Je-QAVdFB21RljVlXdXWCmvGZQ0qrwgCkLzj8bLhHNlJ8nyvuzXWi9EML6IPtIxr5iwSiz2hLKzF1ukNuCthQYvrA-uWAlzQ0qBouWwrAoqRtiwKlreES6w4YyQOlpd51Doduw3tBpXEPjgwE9HpTa9XYml_CUpLGgeuosKrUcHZnwP6IDbaSzQGerTDOHjdVNfNXvyD3r3eSC0hbqD7zsbGcicq5tG-hkc1EqnZHVR8FG60jNHpdDyfFLyeFEQm4O-whMF7sfjy-f_Zi-9T9uUBu0IwYeWtGXZJ81Ow2IPSWe8ddrcuUyJ2yb9xQ-ySL8bkx7Jnh3_otugm6uwvrEj9Tg</recordid><startdate>20241028</startdate><enddate>20241028</enddate><creator>Zhang, Wen-Tao</creator><creator>Ge, Hong-Wei</creator><creator>Wei, Yuan</creator><creator>Gao, Jing-Lin</creator><creator>Tian, Fang</creator><creator>Zhou, En-Chao</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>COVID</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0003-2569-5657</orcidid></search><sort><creationdate>20241028</creationdate><title>Molecular characterization of PANoptosis-related genes in chronic kidney disease</title><author>Zhang, Wen-Tao ; Ge, Hong-Wei ; Wei, Yuan ; Gao, Jing-Lin ; Tian, Fang ; Zhou, En-Chao</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-634b215dd601d99f56fe3a6d4fab455813f7b8de836c8ad270eaa02f6455966e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Analysis</topic><topic>Apoptosis</topic><topic>Apoptosis - genetics</topic><topic>Bioinformatics</topic><topic>Biology and Life Sciences</topic><topic>Biomarkers</topic><topic>Care and treatment</topic><topic>Cell death</topic><topic>Chronic kidney failure</topic><topic>Computational Biology - methods</topic><topic>Computer and Information Sciences</topic><topic>Cyclooxygenase 2 - genetics</topic><topic>Databases, Genetic</topic><topic>Datasets</topic><topic>Diagnosis</topic><topic>Drug delivery</topic><topic>Drug dosages</topic><topic>Drugs</topic><topic>Ferroptosis</topic><topic>Fibrosis</topic><topic>Gene expression</topic><topic>Gene Expression Profiling</topic><topic>Gene Ontology</topic><topic>Gene Regulatory Networks</topic><topic>Gene set enrichment analysis</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Humans</topic><topic>Identification methods</topic><topic>Immunohistochemistry</topic><topic>Inflammation</topic><topic>Kidney diseases</topic><topic>Kidneys</topic><topic>Medicine and Health Sciences</topic><topic>MicroRNAs</topic><topic>miRNA</topic><topic>Molecular dynamics</topic><topic>Mortality</topic><topic>Online data bases</topic><topic>Pathogenesis</topic><topic>Protein Interaction Maps - 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Several types of cell death have been implicated in CKD onset and progression. Unlike traditional forms of cell death, PANoptosis is characterized by the crosstalk among programmed cell death pathways. However, the interaction between PANoptosis and CKD remains unclear. Here, we used bioinformatics methods to identify differentially expressed genes and differentially expressed PANoptosis-related genes (DE-PRGs) using data from the GSE37171 dataset. Following this, we further performed gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, and gene set enrichment analysis using the data. We adopted a combined approach to select hub genes, using the STRING database and CytoHubba plug-in, and we used the GSE66494 as a validation dataset. In addition, we constructed ceRNA, transcription factor (TF)-gene, and drug-gene networks using Cytoscape. Lastly, we conducted immunohistochemical analysis and western blotting to validate the hub genes. We identified 57 PANoptosis-associated genes as DE-PRGs. We screened nine hub genes from the 57 DE-PRGs. We identified two hub genes (FOS and PTGS2) using the GSE66494 database, Nephroseq, immunohistochemistry, and western blotting. A common miRNA (Hsa-miR-101-3p) and three TFs (CREB1, E2F1, and RELA) may play a crucial role in the onset and progression of PANoptosis-related CKD. In our analysis of the drug-gene network, we identified eight drugs targeting FOS and 52 drugs targeting PTGS2.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>39466748</pmid><doi>10.1371/journal.pone.0312696</doi><tpages>e0312696</tpages><orcidid>https://orcid.org/0000-0003-2569-5657</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Apoptosis Apoptosis - genetics Bioinformatics Biology and Life Sciences Biomarkers Care and treatment Cell death Chronic kidney failure Computational Biology - methods Computer and Information Sciences Cyclooxygenase 2 - genetics Databases, Genetic Datasets Diagnosis Drug delivery Drug dosages Drugs Ferroptosis Fibrosis Gene expression Gene Expression Profiling Gene Ontology Gene Regulatory Networks Gene set enrichment analysis Genes Genetic aspects Humans Identification methods Immunohistochemistry Inflammation Kidney diseases Kidneys Medicine and Health Sciences MicroRNAs miRNA Molecular dynamics Mortality Online data bases Pathogenesis Protein Interaction Maps - genetics Proteins Proto-Oncogene Proteins c-fos - genetics Proto-Oncogene Proteins c-fos - metabolism Quality of life Renal Insufficiency, Chronic - genetics Renal Insufficiency, Chronic - pathology Software Western blotting |
| title | Molecular characterization of PANoptosis-related genes in chronic kidney disease |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-23T12%3A36%3A49IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Molecular%20characterization%20of%20PANoptosis-related%20genes%20in%20chronic%20kidney%20disease&rft.jtitle=PloS%20one&rft.au=Zhang,%20Wen-Tao&rft.date=2024-10-28&rft.volume=19&rft.issue=10&rft.spage=e0312696&rft.pages=e0312696-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0312696&rft_dat=%3Cgale_plos_%3EA813965890%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=3121553823&rft_id=info:pmid/39466748&rft_galeid=A813965890&rft_doaj_id=oai_doaj_org_article_b6cb70ad30b54432b06ce76330f56252&rfr_iscdi=true |