The pharmacogenomic and immune landscape of snoRNAs in human cancers
Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs primarily known for their role in the chemical modification of other RNAs. Recent studies suggested that snoRNAs may play a broader role in anti-cancer treatments such as targeted therapies and immunotherapies. Despite these insights, the...
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| Veröffentlicht in: | Cancer letters 2024-11, Vol.605, p.217304, Article 217304 |
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| container_title | Cancer letters |
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| creator | Wang, Runhao Chen, Chengxuan Liu, Yuan Luo, Mei Yang, Jingwen Chen, Yamei Ma, Lifei Yang, Liuqing Lin, Chunru Diao, Lixia Han, Leng |
| description | Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs primarily known for their role in the chemical modification of other RNAs. Recent studies suggested that snoRNAs may play a broader role in anti-cancer treatments such as targeted therapies and immunotherapies. Despite these insights, the comprehensive landscape of snoRNA associations with drug response and immunotherapy outcomes remains unexplored. In this study, we identified 79,448 and 75,185 associations between snoRNAs and drug response using data from VAEN and CancerRxTissue, respectively. Additionally, we discovered 29,199 associations between snoRNAs and immune checkpoint genes and 47,194 associations between snoRNAs and immune cell infiltrations. Sixteen snoRNAs were significantly correlated with immunotherapy objective response rate (ORR), and 92 snoRNAs showed significantly differential expression between cancers with high and low ORR. Furthermore, we identified 17 snoRNAs with significantly differential expression between cancer types with high and low immune-related adverse event (irAE) reporting odds ratio (ROR). Several snoRNAs, such as SNORD92, and SNORD83B, may represent promising biomarkers or therapeutic targets that needs further investigation. To facilitate further research, we developed a user-friendly portal, Pharmacogenomic and Immune Landscape of SnoRNA (PISNO, https://hanlaboratory.com/PISNO/), enabling researchers to visualize, browse, and download multi-dimensional data. This study highlights the potential of snoRNAs as biomarkers or therapeutic targets, paving the way for more effective and personalized anti-cancer treatments.
•We characterized the effects of snoRNAs on drug response.•We identified snoRNAs associated with immune check point genes and immune cell infiltration.•We identified snoRNAs associated with efficacy and toxicity of immunotherapy.•We developed a data portal for pharmacogenomic and immune landscape of snoRNAs. |
| doi_str_mv | 10.1016/j.canlet.2024.217304 |
| format | Article |
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•We characterized the effects of snoRNAs on drug response.•We identified snoRNAs associated with immune check point genes and immune cell infiltration.•We identified snoRNAs associated with efficacy and toxicity of immunotherapy.•We developed a data portal for pharmacogenomic and immune landscape of snoRNAs.</description><identifier>ISSN: 0304-3835</identifier><identifier>ISSN: 1872-7980</identifier><identifier>EISSN: 1872-7980</identifier><identifier>DOI: 10.1016/j.canlet.2024.217304</identifier><identifier>PMID: 39426663</identifier><language>eng</language><publisher>Ireland: Elsevier B.V</publisher><subject>Antineoplastic Agents - pharmacology ; Antineoplastic Agents - therapeutic use ; Biomarkers, Tumor - genetics ; Drug response ; Gene Expression Regulation, Neoplastic - drug effects ; Humans ; Immune checkpoint ; Immune infiltration ; Immunotherapy - methods ; Immunotherapy efficacy ; irAE ; Neoplasms - drug therapy ; Neoplasms - genetics ; Neoplasms - immunology ; Pharmacogenetics ; RNA, Small Nucleolar - genetics ; RNA, Small Nucleolar - immunology ; SnoRNA</subject><ispartof>Cancer letters, 2024-11, Vol.605, p.217304, Article 217304</ispartof><rights>2024 Elsevier B.V.</rights><rights>Copyright © 2024 Elsevier B.V. All rights reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c241t-e34d294ff3ab9a732e39551edce664d265bd25f601c8e54e48ce7c5a4a97be563</cites><orcidid>0000-0003-2030-1153 ; 0009-0004-2225-5458 ; 0000-0002-7380-2640 ; 0000-0002-9072-5157</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.canlet.2024.217304$$EHTML$$P50$$Gelsevier$$H</linktohtml><link.rule.ids>314,780,784,3550,27924,27925,45995</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39426663$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Wang, Runhao</creatorcontrib><creatorcontrib>Chen, Chengxuan</creatorcontrib><creatorcontrib>Liu, Yuan</creatorcontrib><creatorcontrib>Luo, Mei</creatorcontrib><creatorcontrib>Yang, Jingwen</creatorcontrib><creatorcontrib>Chen, Yamei</creatorcontrib><creatorcontrib>Ma, Lifei</creatorcontrib><creatorcontrib>Yang, Liuqing</creatorcontrib><creatorcontrib>Lin, Chunru</creatorcontrib><creatorcontrib>Diao, Lixia</creatorcontrib><creatorcontrib>Han, Leng</creatorcontrib><title>The pharmacogenomic and immune landscape of snoRNAs in human cancers</title><title>Cancer letters</title><addtitle>Cancer Lett</addtitle><description>Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs primarily known for their role in the chemical modification of other RNAs. Recent studies suggested that snoRNAs may play a broader role in anti-cancer treatments such as targeted therapies and immunotherapies. Despite these insights, the comprehensive landscape of snoRNA associations with drug response and immunotherapy outcomes remains unexplored. In this study, we identified 79,448 and 75,185 associations between snoRNAs and drug response using data from VAEN and CancerRxTissue, respectively. Additionally, we discovered 29,199 associations between snoRNAs and immune checkpoint genes and 47,194 associations between snoRNAs and immune cell infiltrations. Sixteen snoRNAs were significantly correlated with immunotherapy objective response rate (ORR), and 92 snoRNAs showed significantly differential expression between cancers with high and low ORR. Furthermore, we identified 17 snoRNAs with significantly differential expression between cancer types with high and low immune-related adverse event (irAE) reporting odds ratio (ROR). Several snoRNAs, such as SNORD92, and SNORD83B, may represent promising biomarkers or therapeutic targets that needs further investigation. To facilitate further research, we developed a user-friendly portal, Pharmacogenomic and Immune Landscape of SnoRNA (PISNO, https://hanlaboratory.com/PISNO/), enabling researchers to visualize, browse, and download multi-dimensional data. This study highlights the potential of snoRNAs as biomarkers or therapeutic targets, paving the way for more effective and personalized anti-cancer treatments.
•We characterized the effects of snoRNAs on drug response.•We identified snoRNAs associated with immune check point genes and immune cell infiltration.•We identified snoRNAs associated with efficacy and toxicity of immunotherapy.•We developed a data portal for pharmacogenomic and immune landscape of snoRNAs.</description><subject>Antineoplastic Agents - pharmacology</subject><subject>Antineoplastic Agents - therapeutic use</subject><subject>Biomarkers, Tumor - genetics</subject><subject>Drug response</subject><subject>Gene Expression Regulation, Neoplastic - drug effects</subject><subject>Humans</subject><subject>Immune checkpoint</subject><subject>Immune infiltration</subject><subject>Immunotherapy - methods</subject><subject>Immunotherapy efficacy</subject><subject>irAE</subject><subject>Neoplasms - drug therapy</subject><subject>Neoplasms - genetics</subject><subject>Neoplasms - immunology</subject><subject>Pharmacogenetics</subject><subject>RNA, Small Nucleolar - genetics</subject><subject>RNA, Small Nucleolar - immunology</subject><subject>SnoRNA</subject><issn>0304-3835</issn><issn>1872-7980</issn><issn>1872-7980</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kEtLAzEQgIMotlb_gUiOXnbNe3cvQqlPKApSzyGbnbUp-6hJV_Dfm7LVo6cZJt888iF0SUlKCVU3m9SaroFdyggTKaMZJ-IITWmesSQrcnKMpiSWEp5zOUFnIWwIIVJk8hRNeCGYUopP0d1qDXi7Nr41tv-Arm-dxaarsGvboQPcxDxYswXc1zh0_dvLPGDX4fXQmg7HCyz4cI5OatMEuDjEGXp_uF8tnpLl6-PzYr5MLBN0lwAXFStEXXNTFibjDHghJYXKglLxScmyYrJWhNocpACRW8isNMIUWQlS8Rm6Huduff85QNjp1gULTTwS-iFoTmkusr2PiIoRtb4PwUOtt961xn9rSvTen97o0Z_e83r0F9uuDhuGsoXqr-lXWARuRwDiP78ceB2sg2ihch7sTle9-3_DD79sgl0</recordid><startdate>20241128</startdate><enddate>20241128</enddate><creator>Wang, Runhao</creator><creator>Chen, Chengxuan</creator><creator>Liu, Yuan</creator><creator>Luo, Mei</creator><creator>Yang, Jingwen</creator><creator>Chen, Yamei</creator><creator>Ma, Lifei</creator><creator>Yang, Liuqing</creator><creator>Lin, Chunru</creator><creator>Diao, Lixia</creator><creator>Han, Leng</creator><general>Elsevier B.V</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>7X8</scope><orcidid>https://orcid.org/0000-0003-2030-1153</orcidid><orcidid>https://orcid.org/0009-0004-2225-5458</orcidid><orcidid>https://orcid.org/0000-0002-7380-2640</orcidid><orcidid>https://orcid.org/0000-0002-9072-5157</orcidid></search><sort><creationdate>20241128</creationdate><title>The pharmacogenomic and immune landscape of snoRNAs in human cancers</title><author>Wang, Runhao ; Chen, Chengxuan ; Liu, Yuan ; Luo, Mei ; Yang, Jingwen ; Chen, Yamei ; Ma, Lifei ; Yang, Liuqing ; Lin, Chunru ; Diao, Lixia ; Han, Leng</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c241t-e34d294ff3ab9a732e39551edce664d265bd25f601c8e54e48ce7c5a4a97be563</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Antineoplastic Agents - pharmacology</topic><topic>Antineoplastic Agents - therapeutic use</topic><topic>Biomarkers, Tumor - genetics</topic><topic>Drug response</topic><topic>Gene Expression Regulation, Neoplastic - drug effects</topic><topic>Humans</topic><topic>Immune checkpoint</topic><topic>Immune infiltration</topic><topic>Immunotherapy - methods</topic><topic>Immunotherapy efficacy</topic><topic>irAE</topic><topic>Neoplasms - drug therapy</topic><topic>Neoplasms - genetics</topic><topic>Neoplasms - immunology</topic><topic>Pharmacogenetics</topic><topic>RNA, Small Nucleolar - genetics</topic><topic>RNA, Small Nucleolar - immunology</topic><topic>SnoRNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Wang, Runhao</creatorcontrib><creatorcontrib>Chen, Chengxuan</creatorcontrib><creatorcontrib>Liu, Yuan</creatorcontrib><creatorcontrib>Luo, Mei</creatorcontrib><creatorcontrib>Yang, Jingwen</creatorcontrib><creatorcontrib>Chen, Yamei</creatorcontrib><creatorcontrib>Ma, Lifei</creatorcontrib><creatorcontrib>Yang, Liuqing</creatorcontrib><creatorcontrib>Lin, Chunru</creatorcontrib><creatorcontrib>Diao, Lixia</creatorcontrib><creatorcontrib>Han, Leng</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Cancer letters</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wang, Runhao</au><au>Chen, Chengxuan</au><au>Liu, Yuan</au><au>Luo, Mei</au><au>Yang, Jingwen</au><au>Chen, Yamei</au><au>Ma, Lifei</au><au>Yang, Liuqing</au><au>Lin, Chunru</au><au>Diao, Lixia</au><au>Han, Leng</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The pharmacogenomic and immune landscape of snoRNAs in human cancers</atitle><jtitle>Cancer letters</jtitle><addtitle>Cancer Lett</addtitle><date>2024-11-28</date><risdate>2024</risdate><volume>605</volume><spage>217304</spage><pages>217304-</pages><artnum>217304</artnum><issn>0304-3835</issn><issn>1872-7980</issn><eissn>1872-7980</eissn><abstract>Small nucleolar RNAs (snoRNAs) are a class of non-coding RNAs primarily known for their role in the chemical modification of other RNAs. Recent studies suggested that snoRNAs may play a broader role in anti-cancer treatments such as targeted therapies and immunotherapies. Despite these insights, the comprehensive landscape of snoRNA associations with drug response and immunotherapy outcomes remains unexplored. In this study, we identified 79,448 and 75,185 associations between snoRNAs and drug response using data from VAEN and CancerRxTissue, respectively. Additionally, we discovered 29,199 associations between snoRNAs and immune checkpoint genes and 47,194 associations between snoRNAs and immune cell infiltrations. Sixteen snoRNAs were significantly correlated with immunotherapy objective response rate (ORR), and 92 snoRNAs showed significantly differential expression between cancers with high and low ORR. Furthermore, we identified 17 snoRNAs with significantly differential expression between cancer types with high and low immune-related adverse event (irAE) reporting odds ratio (ROR). Several snoRNAs, such as SNORD92, and SNORD83B, may represent promising biomarkers or therapeutic targets that needs further investigation. To facilitate further research, we developed a user-friendly portal, Pharmacogenomic and Immune Landscape of SnoRNA (PISNO, https://hanlaboratory.com/PISNO/), enabling researchers to visualize, browse, and download multi-dimensional data. This study highlights the potential of snoRNAs as biomarkers or therapeutic targets, paving the way for more effective and personalized anti-cancer treatments.
•We characterized the effects of snoRNAs on drug response.•We identified snoRNAs associated with immune check point genes and immune cell infiltration.•We identified snoRNAs associated with efficacy and toxicity of immunotherapy.•We developed a data portal for pharmacogenomic and immune landscape of snoRNAs.</abstract><cop>Ireland</cop><pub>Elsevier B.V</pub><pmid>39426663</pmid><doi>10.1016/j.canlet.2024.217304</doi><orcidid>https://orcid.org/0000-0003-2030-1153</orcidid><orcidid>https://orcid.org/0009-0004-2225-5458</orcidid><orcidid>https://orcid.org/0000-0002-7380-2640</orcidid><orcidid>https://orcid.org/0000-0002-9072-5157</orcidid></addata></record> |
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| ispartof | Cancer letters, 2024-11, Vol.605, p.217304, Article 217304 |
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| subjects | Antineoplastic Agents - pharmacology Antineoplastic Agents - therapeutic use Biomarkers, Tumor - genetics Drug response Gene Expression Regulation, Neoplastic - drug effects Humans Immune checkpoint Immune infiltration Immunotherapy - methods Immunotherapy efficacy irAE Neoplasms - drug therapy Neoplasms - genetics Neoplasms - immunology Pharmacogenetics RNA, Small Nucleolar - genetics RNA, Small Nucleolar - immunology SnoRNA |
| title | The pharmacogenomic and immune landscape of snoRNAs in human cancers |
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