CARD11 is a prognostic biomarker and correlated with immune infiltrates in uveal melanoma
Uveal melanoma (UVM), the most common primary intraocular malignancy, has a high mortality because of a high propensity to metastasize. Our study analyzed prognostic value and immune-related characteristics of CARD11 in UVM, hoping to provide a potential management and research direction. The RNA-se...
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| Veröffentlicht in: | PloS one 2021-08, Vol.16 (8), p.e0255293 |
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| description | Uveal melanoma (UVM), the most common primary intraocular malignancy, has a high mortality because of a high propensity to metastasize. Our study analyzed prognostic value and immune-related characteristics of CARD11 in UVM, hoping to provide a potential management and research direction. The RNA-sequence data of 80 UVM patients were downloaded from The Cancer Genome Atlas database and divided them into high- and low-expression groups. We analyzed the differentially expressed genes, enrichment analyses and the infiltration of immune cells using the R package and Gene-Set Enrichment Analysis. A clinical prediction nomogram and protein-protein interaction network were constructed and the first 8 genes were considered as the hub-genes. Finally, we constructed a competing endogenous RNA (ceRNA) network by Cytoscape and analyzed the statistical data via the R software. Here we found that CARD11 expression had notable correlation with UVM clinicopathological features, which was also an independent predictor for overall survival (OS). Intriguingly, CARD11 had a positively correlation to autophagy, cellular senescence and apoptosis. Infiltration of monocytes was significantly higher in low CARD11 expression group, and infiltration of T cells regulatory was lower in the same group. Functional enrichment analyses revealed that CARD11 was positively related to T cell activation pathways and cell adhesion molecules. The expressions of hub-genes were all increased in the high CARD11 expression group and the ceRNA network showed the interaction among mRNA, miRNA and lncRNA. These findings show that high CARD11 expression in UVM is associated with poor OS, indicating that CARD11 may serve as a potential biomarker for the diagnosis and prognosis of the UVM. |
| doi_str_mv | 10.1371/journal.pone.0255293 |
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Our study analyzed prognostic value and immune-related characteristics of CARD11 in UVM, hoping to provide a potential management and research direction. The RNA-sequence data of 80 UVM patients were downloaded from The Cancer Genome Atlas database and divided them into high- and low-expression groups. We analyzed the differentially expressed genes, enrichment analyses and the infiltration of immune cells using the R package and Gene-Set Enrichment Analysis. A clinical prediction nomogram and protein-protein interaction network were constructed and the first 8 genes were considered as the hub-genes. Finally, we constructed a competing endogenous RNA (ceRNA) network by Cytoscape and analyzed the statistical data via the R software. Here we found that CARD11 expression had notable correlation with UVM clinicopathological features, which was also an independent predictor for overall survival (OS). Intriguingly, CARD11 had a positively correlation to autophagy, cellular senescence and apoptosis. Infiltration of monocytes was significantly higher in low CARD11 expression group, and infiltration of T cells regulatory was lower in the same group. Functional enrichment analyses revealed that CARD11 was positively related to T cell activation pathways and cell adhesion molecules. The expressions of hub-genes were all increased in the high CARD11 expression group and the ceRNA network showed the interaction among mRNA, miRNA and lncRNA. These findings show that high CARD11 expression in UVM is associated with poor OS, indicating that CARD11 may serve as a potential biomarker for the diagnosis and prognosis of the UVM.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0255293</identifier><identifier>PMID: 34370778</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Analysis ; Apoptosis ; Autophagy ; Biological markers ; Biology and Life Sciences ; Biomarkers ; Biomarkers, Tumor - genetics ; Biomarkers, Tumor - metabolism ; Cancer ; CARD Signaling Adaptor Proteins - genetics ; CARD Signaling Adaptor Proteins - metabolism ; Cell activation ; Cell adhesion ; Cell adhesion molecules ; Correlation ; Dermatology ; Enrichment ; Eye diseases ; Female ; Gene expression ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Gene set enrichment analysis ; Genes ; Genomes ; Hospitals ; Humans ; Immune system ; Infiltration ; Integrative medicine ; Kinases ; Lymphocytes ; Lymphocytes T ; Lymphoma ; Male ; Malignancy ; Medical laboratories ; Medical prognosis ; Medicine ; Medicine and Health Sciences ; Melanoma ; Melanoma - genetics ; Melanoma - immunology ; Melanoma - mortality ; Melanoma - pathology ; Middle Aged ; miRNA ; Monocytes ; Mortality ; mRNA ; Nomograms ; Nomographs ; Nucleotide sequence ; Phagocytosis ; Prognosis ; Prostate cancer ; Protein interaction ; Protein Interaction Maps ; Proteins ; Ribonucleic acid ; RNA ; Senescence ; Uveal Neoplasms - genetics ; Uveal Neoplasms - immunology ; Uveal Neoplasms - mortality ; Uveal Neoplasms - pathology</subject><ispartof>PloS one, 2021-08, Vol.16 (8), p.e0255293</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Shi 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>2021 Shi et al 2021 Shi et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-cc12de394ee7a075a8f7f91bc18e3ea65d51cead040b569b5169de122969b8583</citedby><cites>FETCH-LOGICAL-c692t-cc12de394ee7a075a8f7f91bc18e3ea65d51cead040b569b5169de122969b8583</cites><orcidid>0000-0002-4737-0856</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/PMC8351993/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8351993/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79600,79601</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34370778$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Haass, Nikolas K.</contributor><creatorcontrib>Shi, Xueying</creatorcontrib><creatorcontrib>Xia, Shilin</creatorcontrib><creatorcontrib>Chu, Yingming</creatorcontrib><creatorcontrib>Yang, Nan</creatorcontrib><creatorcontrib>Zheng, Jingyuan</creatorcontrib><creatorcontrib>Chen, Qianyi</creatorcontrib><creatorcontrib>Fen, Zeng</creatorcontrib><creatorcontrib>Jiang, Yuankuan</creatorcontrib><creatorcontrib>Fang, Shifeng</creatorcontrib><creatorcontrib>Lin, Jingrong</creatorcontrib><title>CARD11 is a prognostic biomarker and correlated with immune infiltrates in uveal melanoma</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>Uveal melanoma (UVM), the most common primary intraocular malignancy, has a high mortality because of a high propensity to metastasize. Our study analyzed prognostic value and immune-related characteristics of CARD11 in UVM, hoping to provide a potential management and research direction. The RNA-sequence data of 80 UVM patients were downloaded from The Cancer Genome Atlas database and divided them into high- and low-expression groups. We analyzed the differentially expressed genes, enrichment analyses and the infiltration of immune cells using the R package and Gene-Set Enrichment Analysis. A clinical prediction nomogram and protein-protein interaction network were constructed and the first 8 genes were considered as the hub-genes. Finally, we constructed a competing endogenous RNA (ceRNA) network by Cytoscape and analyzed the statistical data via the R software. Here we found that CARD11 expression had notable correlation with UVM clinicopathological features, which was also an independent predictor for overall survival (OS). Intriguingly, CARD11 had a positively correlation to autophagy, cellular senescence and apoptosis. Infiltration of monocytes was significantly higher in low CARD11 expression group, and infiltration of T cells regulatory was lower in the same group. Functional enrichment analyses revealed that CARD11 was positively related to T cell activation pathways and cell adhesion molecules. The expressions of hub-genes were all increased in the high CARD11 expression group and the ceRNA network showed the interaction among mRNA, miRNA and lncRNA. These findings show that high CARD11 expression in UVM is associated with poor OS, indicating that CARD11 may serve as a potential biomarker for the diagnosis and prognosis of the UVM.</description><subject>Analysis</subject><subject>Apoptosis</subject><subject>Autophagy</subject><subject>Biological markers</subject><subject>Biology and Life Sciences</subject><subject>Biomarkers</subject><subject>Biomarkers, Tumor - genetics</subject><subject>Biomarkers, Tumor - metabolism</subject><subject>Cancer</subject><subject>CARD Signaling Adaptor Proteins - genetics</subject><subject>CARD Signaling Adaptor Proteins - metabolism</subject><subject>Cell activation</subject><subject>Cell adhesion</subject><subject>Cell adhesion molecules</subject><subject>Correlation</subject><subject>Dermatology</subject><subject>Enrichment</subject><subject>Eye diseases</subject><subject>Female</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Gene Regulatory Networks</subject><subject>Gene set enrichment analysis</subject><subject>Genes</subject><subject>Genomes</subject><subject>Hospitals</subject><subject>Humans</subject><subject>Immune system</subject><subject>Infiltration</subject><subject>Integrative medicine</subject><subject>Kinases</subject><subject>Lymphocytes</subject><subject>Lymphocytes T</subject><subject>Lymphoma</subject><subject>Male</subject><subject>Malignancy</subject><subject>Medical laboratories</subject><subject>Medical prognosis</subject><subject>Medicine</subject><subject>Medicine and Health Sciences</subject><subject>Melanoma</subject><subject>Melanoma - genetics</subject><subject>Melanoma - immunology</subject><subject>Melanoma - mortality</subject><subject>Melanoma - pathology</subject><subject>Middle Aged</subject><subject>miRNA</subject><subject>Monocytes</subject><subject>Mortality</subject><subject>mRNA</subject><subject>Nomograms</subject><subject>Nomographs</subject><subject>Nucleotide sequence</subject><subject>Phagocytosis</subject><subject>Prognosis</subject><subject>Prostate cancer</subject><subject>Protein interaction</subject><subject>Protein Interaction Maps</subject><subject>Proteins</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Senescence</subject><subject>Uveal Neoplasms - genetics</subject><subject>Uveal Neoplasms - immunology</subject><subject>Uveal Neoplasms - mortality</subject><subject>Uveal Neoplasms - pathology</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</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>eNqNk9uO0zAQhiMEYpeFN0AQCQnBRYsPcRLfIFXlVGmllZaDxJXl2JPWJYm7drLA2zOl2VWD9gLlwo7zze_MPzNJ8pSSOeUFfbP1Q-h0M9_5DuaECcEkv5ecUsnZLGeE3z_anySPYtwSIniZ5w-TE57xghRFeZp8Xy4u31GaupjqdBf8uvOxdyatnG91-AEh1Z1NjQ8BGt2DTX-6fpO6th06SF1Xu6YPeB5xnw7XoJu0RbDD4MfJg1o3EZ6M61ny9cP7L8tPs_OLj6vl4nxmcsn6mTGUWeAyAyg0KYQu66KWtDK0BA46F1ZQA9qSjFQil5WgubRAGZP4UoqSnyXPD7q7xkc1uhIVGiLzjGCWSKwOhPV6q3bBYWa_lddO_T3wYa10wKQbUIzKrK7rDGxNMyJ1lZnSEGtwqYhgFWq9HW8bqhasgQ7zbyai0y-d26i1v1YlF1RKjgKvRoHgrwaIvWpdNNCgaeCH_X_nWCfJeI7oi3_Qu7MbqbXGBLAkHu81e1G1yAvK0CK2d2l-B4WPhdYZbCGsJEwDXk8CkOnhV7_WQ4xq9fny_9mLb1P25RG7wY7pN9E3Q-98F6dgdgBN8DEGqG9NpkTtJ-DGDbWfADVOAIY9Oy7QbdBNy_M_05QAsA</recordid><startdate>20210809</startdate><enddate>20210809</enddate><creator>Shi, Xueying</creator><creator>Xia, Shilin</creator><creator>Chu, Yingming</creator><creator>Yang, Nan</creator><creator>Zheng, Jingyuan</creator><creator>Chen, Qianyi</creator><creator>Fen, Zeng</creator><creator>Jiang, Yuankuan</creator><creator>Fang, Shifeng</creator><creator>Lin, Jingrong</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>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>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-4737-0856</orcidid></search><sort><creationdate>20210809</creationdate><title>CARD11 is a prognostic biomarker and correlated with immune infiltrates in uveal melanoma</title><author>Shi, Xueying ; Xia, Shilin ; Chu, Yingming ; Yang, Nan ; Zheng, Jingyuan ; Chen, Qianyi ; Fen, Zeng ; Jiang, Yuankuan ; Fang, Shifeng ; Lin, Jingrong</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-cc12de394ee7a075a8f7f91bc18e3ea65d51cead040b569b5169de122969b8583</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Analysis</topic><topic>Apoptosis</topic><topic>Autophagy</topic><topic>Biological markers</topic><topic>Biology and Life Sciences</topic><topic>Biomarkers</topic><topic>Biomarkers, Tumor - genetics</topic><topic>Biomarkers, Tumor - metabolism</topic><topic>Cancer</topic><topic>CARD Signaling Adaptor Proteins - genetics</topic><topic>CARD Signaling Adaptor Proteins - metabolism</topic><topic>Cell activation</topic><topic>Cell adhesion</topic><topic>Cell adhesion molecules</topic><topic>Correlation</topic><topic>Dermatology</topic><topic>Enrichment</topic><topic>Eye diseases</topic><topic>Female</topic><topic>Gene expression</topic><topic>Gene Expression Regulation, Neoplastic</topic><topic>Gene Regulatory Networks</topic><topic>Gene set enrichment analysis</topic><topic>Genes</topic><topic>Genomes</topic><topic>Hospitals</topic><topic>Humans</topic><topic>Immune system</topic><topic>Infiltration</topic><topic>Integrative medicine</topic><topic>Kinases</topic><topic>Lymphocytes</topic><topic>Lymphocytes T</topic><topic>Lymphoma</topic><topic>Male</topic><topic>Malignancy</topic><topic>Medical laboratories</topic><topic>Medical prognosis</topic><topic>Medicine</topic><topic>Medicine and Health Sciences</topic><topic>Melanoma</topic><topic>Melanoma - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Shi, Xueying</au><au>Xia, Shilin</au><au>Chu, Yingming</au><au>Yang, Nan</au><au>Zheng, Jingyuan</au><au>Chen, Qianyi</au><au>Fen, Zeng</au><au>Jiang, Yuankuan</au><au>Fang, Shifeng</au><au>Lin, Jingrong</au><au>Haass, Nikolas K.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>CARD11 is a prognostic biomarker and correlated with immune infiltrates in uveal melanoma</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2021-08-09</date><risdate>2021</risdate><volume>16</volume><issue>8</issue><spage>e0255293</spage><pages>e0255293-</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Uveal melanoma (UVM), the most common primary intraocular malignancy, has a high mortality because of a high propensity to metastasize. Our study analyzed prognostic value and immune-related characteristics of CARD11 in UVM, hoping to provide a potential management and research direction. The RNA-sequence data of 80 UVM patients were downloaded from The Cancer Genome Atlas database and divided them into high- and low-expression groups. We analyzed the differentially expressed genes, enrichment analyses and the infiltration of immune cells using the R package and Gene-Set Enrichment Analysis. A clinical prediction nomogram and protein-protein interaction network were constructed and the first 8 genes were considered as the hub-genes. Finally, we constructed a competing endogenous RNA (ceRNA) network by Cytoscape and analyzed the statistical data via the R software. Here we found that CARD11 expression had notable correlation with UVM clinicopathological features, which was also an independent predictor for overall survival (OS). Intriguingly, CARD11 had a positively correlation to autophagy, cellular senescence and apoptosis. Infiltration of monocytes was significantly higher in low CARD11 expression group, and infiltration of T cells regulatory was lower in the same group. Functional enrichment analyses revealed that CARD11 was positively related to T cell activation pathways and cell adhesion molecules. The expressions of hub-genes were all increased in the high CARD11 expression group and the ceRNA network showed the interaction among mRNA, miRNA and lncRNA. These findings show that high CARD11 expression in UVM is associated with poor OS, indicating that CARD11 may serve as a potential biomarker for the diagnosis and prognosis of the UVM.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>34370778</pmid><doi>10.1371/journal.pone.0255293</doi><tpages>e0255293</tpages><orcidid>https://orcid.org/0000-0002-4737-0856</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2021-08, Vol.16 (8), p.e0255293 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2559640077 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Public Library of Science (PLoS) Journals Open Access; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Analysis Apoptosis Autophagy Biological markers Biology and Life Sciences Biomarkers Biomarkers, Tumor - genetics Biomarkers, Tumor - metabolism Cancer CARD Signaling Adaptor Proteins - genetics CARD Signaling Adaptor Proteins - metabolism Cell activation Cell adhesion Cell adhesion molecules Correlation Dermatology Enrichment Eye diseases Female Gene expression Gene Expression Regulation, Neoplastic Gene Regulatory Networks Gene set enrichment analysis Genes Genomes Hospitals Humans Immune system Infiltration Integrative medicine Kinases Lymphocytes Lymphocytes T Lymphoma Male Malignancy Medical laboratories Medical prognosis Medicine Medicine and Health Sciences Melanoma Melanoma - genetics Melanoma - immunology Melanoma - mortality Melanoma - pathology Middle Aged miRNA Monocytes Mortality mRNA Nomograms Nomographs Nucleotide sequence Phagocytosis Prognosis Prostate cancer Protein interaction Protein Interaction Maps Proteins Ribonucleic acid RNA Senescence Uveal Neoplasms - genetics Uveal Neoplasms - immunology Uveal Neoplasms - mortality Uveal Neoplasms - pathology |
| title | CARD11 is a prognostic biomarker and correlated with immune infiltrates in uveal melanoma |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-24T12%3A47%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=CARD11%20is%20a%20prognostic%20biomarker%20and%20correlated%20with%20immune%20infiltrates%20in%20uveal%20melanoma&rft.jtitle=PloS%20one&rft.au=Shi,%20Xueying&rft.date=2021-08-09&rft.volume=16&rft.issue=8&rft.spage=e0255293&rft.pages=e0255293-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0255293&rft_dat=%3Cgale_plos_%3EA671258328%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=2559640077&rft_id=info:pmid/34370778&rft_galeid=A671258328&rft_doaj_id=oai_doaj_org_article_2194fff4edf1409ab4c8c0dc4c8b052b&rfr_iscdi=true |