USP31 serves as a potential biomarker for predicting prognosis and immune responses for clear cell renal cell carcinoma via single‐cell and bulk RNA‐sequencing
Background Currently, there is no research available on the prognosis, potential effect and therapeutic value of USP31 in clear cell renal cell carcinoma (ccRCC). To address this gap, the present study aimed to shed light on its potential roles and possible mechanisms in ccRCC. Methods R software wa...
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| Veröffentlicht in: | The journal of gene medicine 2024-01, Vol.26 (1), p.e3594-n/a |
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| creator | Yu, Yaoyu Chen, Guihua Jiang, Chao Guo, Tuanjie Tang, Heting Yuan, Zhihao Wang, Yi Tan, Xiangyin Chen, Jinyuan Zhang, Encheng Wang, Xiang |
| description | Background
Currently, there is no research available on the prognosis, potential effect and therapeutic value of USP31 in clear cell renal cell carcinoma (ccRCC). To address this gap, the present study aimed to shed light on its potential roles and possible mechanisms in ccRCC.
Methods
R software was utilized to conduct bioinformatics analyses with the data derived from The Cancer Genome Atlas (i.e. KIRC) and Gene Expression Omnibus datasets. The expression of USP31 in ccRCC was validated by a PCR. The independent prognostic ability of USP31 was evaluated by Cox regression analysis. We conducted gene set enrichment analysis (GSEA) to explore the potential USP31‐related pathways. We also discussed the relationships between USP31 and immunity, by predicting its possible upstream transcription factors (TFs) by ChEA3.
Results
In ccRCC, USP31 demonstrated a high level of expression and this increased expression was correlated with a poor prognosis (p |
| doi_str_mv | 10.1002/jgm.3594 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2864619616</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2864619616</sourcerecordid><originalsourceid>FETCH-LOGICAL-c3214-a36168c5acb02bb3c00387f39c01a5492c28ff250d90c8651e66f7fbbcd9ec933</originalsourceid><addsrcrecordid>eNp1kctO3DAUhq2qqFCo1CeovOwmU18Sj71EqAwgCoiLxC5ynJORIXGm9mTQ7HiEvgNvxpNwMtCyqmTZR_an79j-CfnK2YQzJn7czbuJLEz-gezwQvBMiCL_iDUzJsuNvt0mn1O6Y4xPtTafyLacKmNUrnfI083VheQ0QVxBohYHXfRLCEtvW1r5vrPxHiJt-kgXEWrvlj7MseznoU8e8VBT33VDABohLfqQUDPSrgWLM7QtHgSUbUpno_MBrXTlLU3oauH58c_mbFRVQ3tPL8_2cS_B7wEC0vM9stXYNsGXt3WX3Bz-vD44yk7PZ8cH-6eZk4LnmZWKK-0K6yomqko6xqSeNtI4xm2RG-GEbhpRsNowp1XBQalm2lSVqw04I-Uu-f7qxedh77QsO5_Gq9kA_ZBKoVWuuMEu76iLfUoRmnIRPf7VuuSsHCMpMZJyjATRb2_Woeqg_gf-zQCB7BV48C2s_ysqT2a_NsIXMVmZ6Q</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2864619616</pqid></control><display><type>article</type><title>USP31 serves as a potential biomarker for predicting prognosis and immune responses for clear cell renal cell carcinoma via single‐cell and bulk RNA‐sequencing</title><source>Wiley Online Library Journals Frontfile Complete</source><creator>Yu, Yaoyu ; Chen, Guihua ; Jiang, Chao ; Guo, Tuanjie ; Tang, Heting ; Yuan, Zhihao ; Wang, Yi ; Tan, Xiangyin ; Chen, Jinyuan ; Zhang, Encheng ; Wang, Xiang</creator><creatorcontrib>Yu, Yaoyu ; Chen, Guihua ; Jiang, Chao ; Guo, Tuanjie ; Tang, Heting ; Yuan, Zhihao ; Wang, Yi ; Tan, Xiangyin ; Chen, Jinyuan ; Zhang, Encheng ; Wang, Xiang</creatorcontrib><description>Background
Currently, there is no research available on the prognosis, potential effect and therapeutic value of USP31 in clear cell renal cell carcinoma (ccRCC). To address this gap, the present study aimed to shed light on its potential roles and possible mechanisms in ccRCC.
Methods
R software was utilized to conduct bioinformatics analyses with the data derived from The Cancer Genome Atlas (i.e. KIRC) and Gene Expression Omnibus datasets. The expression of USP31 in ccRCC was validated by a PCR. The independent prognostic ability of USP31 was evaluated by Cox regression analysis. We conducted gene set enrichment analysis (GSEA) to explore the potential USP31‐related pathways. We also discussed the relationships between USP31 and immunity, by predicting its possible upstream transcription factors (TFs) by ChEA3.
Results
In ccRCC, USP31 demonstrated a high level of expression and this increased expression was correlated with a poor prognosis (p < 0.05). Through univariate and multivariate Cox regression analysis, USP31 was identified as an independent prognostic factor for ccRCC (p < 0.05). Furthermore, eight USP31‐related pathways were identified by GSEA (p < 0.05). Moreover, USP31 was found to be associated with microsatellite instability, tumor microenvironment, a variety of immune cells and immune checkpoints and immune infiltration (p < 0.05). Additionally, Patients with high USP31 expression in ccRCC were shown to have better curative effects after immunotherapy (p < 0.05). Finally, we found that AR, USF1, MXI1 and CLOCK could be the potential upstream TFs of USP31.
Conclusions
USP31 could serve as a potential biomarker for predicting both prognosis and immune responses, revealing its potential mechanisms of TF‐USP31 mRNA networks in ccRCC.
USP31 is highly expressed in clear cell renal cell carcinoma (ccRCC) and is associated with patient prognosis, and its expression levels have been experimentally verified. Further analysis reveals a strong correlation between USP31 and immunity in ccRCC, which has been confirmed at the single‐cell expression level. Moreover, we predict the potential upstream transcription factors of USP31 in ccRCC.</description><identifier>ISSN: 1099-498X</identifier><identifier>EISSN: 1521-2254</identifier><identifier>DOI: 10.1002/jgm.3594</identifier><identifier>PMID: 37699648</identifier><language>eng</language><publisher>England</publisher><subject>ccRCC ; immunity ; prognosis ; transcription factor ; USP31</subject><ispartof>The journal of gene medicine, 2024-01, Vol.26 (1), p.e3594-n/a</ispartof><rights>2023 John Wiley & Sons Ltd.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c3214-a36168c5acb02bb3c00387f39c01a5492c28ff250d90c8651e66f7fbbcd9ec933</citedby><cites>FETCH-LOGICAL-c3214-a36168c5acb02bb3c00387f39c01a5492c28ff250d90c8651e66f7fbbcd9ec933</cites><orcidid>0000-0001-5640-5259 ; 0000-0002-2067-5465</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://onlinelibrary.wiley.com/doi/pdf/10.1002%2Fjgm.3594$$EPDF$$P50$$Gwiley$$H</linktopdf><linktohtml>$$Uhttps://onlinelibrary.wiley.com/doi/full/10.1002%2Fjgm.3594$$EHTML$$P50$$Gwiley$$H</linktohtml><link.rule.ids>314,780,784,1417,27924,27925,45574,45575</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37699648$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yu, Yaoyu</creatorcontrib><creatorcontrib>Chen, Guihua</creatorcontrib><creatorcontrib>Jiang, Chao</creatorcontrib><creatorcontrib>Guo, Tuanjie</creatorcontrib><creatorcontrib>Tang, Heting</creatorcontrib><creatorcontrib>Yuan, Zhihao</creatorcontrib><creatorcontrib>Wang, Yi</creatorcontrib><creatorcontrib>Tan, Xiangyin</creatorcontrib><creatorcontrib>Chen, Jinyuan</creatorcontrib><creatorcontrib>Zhang, Encheng</creatorcontrib><creatorcontrib>Wang, Xiang</creatorcontrib><title>USP31 serves as a potential biomarker for predicting prognosis and immune responses for clear cell renal cell carcinoma via single‐cell and bulk RNA‐sequencing</title><title>The journal of gene medicine</title><addtitle>J Gene Med</addtitle><description>Background
Currently, there is no research available on the prognosis, potential effect and therapeutic value of USP31 in clear cell renal cell carcinoma (ccRCC). To address this gap, the present study aimed to shed light on its potential roles and possible mechanisms in ccRCC.
Methods
R software was utilized to conduct bioinformatics analyses with the data derived from The Cancer Genome Atlas (i.e. KIRC) and Gene Expression Omnibus datasets. The expression of USP31 in ccRCC was validated by a PCR. The independent prognostic ability of USP31 was evaluated by Cox regression analysis. We conducted gene set enrichment analysis (GSEA) to explore the potential USP31‐related pathways. We also discussed the relationships between USP31 and immunity, by predicting its possible upstream transcription factors (TFs) by ChEA3.
Results
In ccRCC, USP31 demonstrated a high level of expression and this increased expression was correlated with a poor prognosis (p < 0.05). Through univariate and multivariate Cox regression analysis, USP31 was identified as an independent prognostic factor for ccRCC (p < 0.05). Furthermore, eight USP31‐related pathways were identified by GSEA (p < 0.05). Moreover, USP31 was found to be associated with microsatellite instability, tumor microenvironment, a variety of immune cells and immune checkpoints and immune infiltration (p < 0.05). Additionally, Patients with high USP31 expression in ccRCC were shown to have better curative effects after immunotherapy (p < 0.05). Finally, we found that AR, USF1, MXI1 and CLOCK could be the potential upstream TFs of USP31.
Conclusions
USP31 could serve as a potential biomarker for predicting both prognosis and immune responses, revealing its potential mechanisms of TF‐USP31 mRNA networks in ccRCC.
USP31 is highly expressed in clear cell renal cell carcinoma (ccRCC) and is associated with patient prognosis, and its expression levels have been experimentally verified. Further analysis reveals a strong correlation between USP31 and immunity in ccRCC, which has been confirmed at the single‐cell expression level. Moreover, we predict the potential upstream transcription factors of USP31 in ccRCC.</description><subject>ccRCC</subject><subject>immunity</subject><subject>prognosis</subject><subject>transcription factor</subject><subject>USP31</subject><issn>1099-498X</issn><issn>1521-2254</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNp1kctO3DAUhq2qqFCo1CeovOwmU18Sj71EqAwgCoiLxC5ynJORIXGm9mTQ7HiEvgNvxpNwMtCyqmTZR_an79j-CfnK2YQzJn7czbuJLEz-gezwQvBMiCL_iDUzJsuNvt0mn1O6Y4xPtTafyLacKmNUrnfI083VheQ0QVxBohYHXfRLCEtvW1r5vrPxHiJt-kgXEWrvlj7MseznoU8e8VBT33VDABohLfqQUDPSrgWLM7QtHgSUbUpno_MBrXTlLU3oauH58c_mbFRVQ3tPL8_2cS_B7wEC0vM9stXYNsGXt3WX3Bz-vD44yk7PZ8cH-6eZk4LnmZWKK-0K6yomqko6xqSeNtI4xm2RG-GEbhpRsNowp1XBQalm2lSVqw04I-Uu-f7qxedh77QsO5_Gq9kA_ZBKoVWuuMEu76iLfUoRmnIRPf7VuuSsHCMpMZJyjATRb2_Woeqg_gf-zQCB7BV48C2s_ysqT2a_NsIXMVmZ6Q</recordid><startdate>202401</startdate><enddate>202401</enddate><creator>Yu, Yaoyu</creator><creator>Chen, Guihua</creator><creator>Jiang, Chao</creator><creator>Guo, Tuanjie</creator><creator>Tang, Heting</creator><creator>Yuan, Zhihao</creator><creator>Wang, Yi</creator><creator>Tan, Xiangyin</creator><creator>Chen, Jinyuan</creator><creator>Zhang, Encheng</creator><creator>Wang, Xiang</creator><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0001-5640-5259</orcidid><orcidid>https://orcid.org/0000-0002-2067-5465</orcidid></search><sort><creationdate>202401</creationdate><title>USP31 serves as a potential biomarker for predicting prognosis and immune responses for clear cell renal cell carcinoma via single‐cell and bulk RNA‐sequencing</title><author>Yu, Yaoyu ; Chen, Guihua ; Jiang, Chao ; Guo, Tuanjie ; Tang, Heting ; Yuan, Zhihao ; Wang, Yi ; Tan, Xiangyin ; Chen, Jinyuan ; Zhang, Encheng ; Wang, Xiang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c3214-a36168c5acb02bb3c00387f39c01a5492c28ff250d90c8651e66f7fbbcd9ec933</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>ccRCC</topic><topic>immunity</topic><topic>prognosis</topic><topic>transcription factor</topic><topic>USP31</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yu, Yaoyu</creatorcontrib><creatorcontrib>Chen, Guihua</creatorcontrib><creatorcontrib>Jiang, Chao</creatorcontrib><creatorcontrib>Guo, Tuanjie</creatorcontrib><creatorcontrib>Tang, Heting</creatorcontrib><creatorcontrib>Yuan, Zhihao</creatorcontrib><creatorcontrib>Wang, Yi</creatorcontrib><creatorcontrib>Tan, Xiangyin</creatorcontrib><creatorcontrib>Chen, Jinyuan</creatorcontrib><creatorcontrib>Zhang, Encheng</creatorcontrib><creatorcontrib>Wang, Xiang</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>The journal of gene medicine</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yu, Yaoyu</au><au>Chen, Guihua</au><au>Jiang, Chao</au><au>Guo, Tuanjie</au><au>Tang, Heting</au><au>Yuan, Zhihao</au><au>Wang, Yi</au><au>Tan, Xiangyin</au><au>Chen, Jinyuan</au><au>Zhang, Encheng</au><au>Wang, Xiang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>USP31 serves as a potential biomarker for predicting prognosis and immune responses for clear cell renal cell carcinoma via single‐cell and bulk RNA‐sequencing</atitle><jtitle>The journal of gene medicine</jtitle><addtitle>J Gene Med</addtitle><date>2024-01</date><risdate>2024</risdate><volume>26</volume><issue>1</issue><spage>e3594</spage><epage>n/a</epage><pages>e3594-n/a</pages><issn>1099-498X</issn><eissn>1521-2254</eissn><abstract>Background
Currently, there is no research available on the prognosis, potential effect and therapeutic value of USP31 in clear cell renal cell carcinoma (ccRCC). To address this gap, the present study aimed to shed light on its potential roles and possible mechanisms in ccRCC.
Methods
R software was utilized to conduct bioinformatics analyses with the data derived from The Cancer Genome Atlas (i.e. KIRC) and Gene Expression Omnibus datasets. The expression of USP31 in ccRCC was validated by a PCR. The independent prognostic ability of USP31 was evaluated by Cox regression analysis. We conducted gene set enrichment analysis (GSEA) to explore the potential USP31‐related pathways. We also discussed the relationships between USP31 and immunity, by predicting its possible upstream transcription factors (TFs) by ChEA3.
Results
In ccRCC, USP31 demonstrated a high level of expression and this increased expression was correlated with a poor prognosis (p < 0.05). Through univariate and multivariate Cox regression analysis, USP31 was identified as an independent prognostic factor for ccRCC (p < 0.05). Furthermore, eight USP31‐related pathways were identified by GSEA (p < 0.05). Moreover, USP31 was found to be associated with microsatellite instability, tumor microenvironment, a variety of immune cells and immune checkpoints and immune infiltration (p < 0.05). Additionally, Patients with high USP31 expression in ccRCC were shown to have better curative effects after immunotherapy (p < 0.05). Finally, we found that AR, USF1, MXI1 and CLOCK could be the potential upstream TFs of USP31.
Conclusions
USP31 could serve as a potential biomarker for predicting both prognosis and immune responses, revealing its potential mechanisms of TF‐USP31 mRNA networks in ccRCC.
USP31 is highly expressed in clear cell renal cell carcinoma (ccRCC) and is associated with patient prognosis, and its expression levels have been experimentally verified. Further analysis reveals a strong correlation between USP31 and immunity in ccRCC, which has been confirmed at the single‐cell expression level. Moreover, we predict the potential upstream transcription factors of USP31 in ccRCC.</abstract><cop>England</cop><pmid>37699648</pmid><doi>10.1002/jgm.3594</doi><tpages>13</tpages><orcidid>https://orcid.org/0000-0001-5640-5259</orcidid><orcidid>https://orcid.org/0000-0002-2067-5465</orcidid></addata></record> |
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| source | Wiley Online Library Journals Frontfile Complete |
| subjects | ccRCC immunity prognosis transcription factor USP31 |
| title | USP31 serves as a potential biomarker for predicting prognosis and immune responses for clear cell renal cell carcinoma via single‐cell and bulk RNA‐sequencing |
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