DRMref: comprehensive reference map of drug resistance mechanisms in human cancer
Abstract Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profilin...
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| Veröffentlicht in: | Nucleic acids research 2024-01, Vol.52 (D1), p.D1253-D1264 |
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| container_title | Nucleic acids research |
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| creator | Liu, Xiaona Yi, Jiahao Li, Tina Wen, Jianguo Huang, Kexin Liu, Jiajia Wang, Grant Kim, Pora Song, Qianqian Zhou, Xiaobo |
| description | Abstract
Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistance at cell level. Herein, we have built the DRMref database (https://ccsm.uth.edu/DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, covering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimens and 42 drugs. All datasets in DRMref are browsable and searchable, with detailed annotations provided. Meanwhile, DRMref includes analyses of cellular composition, intratumoral heterogeneity, epithelial–mesenchymal transition, cell–cell interaction and differentially expressed genes in resistant cells. Notably, DRMref investigates the drug resistance mechanisms (e.g. Aberration of Drug’s Therapeutic Target, Drug Inactivation by Structure Modification, etc.) in resistant cells. Additional enrichment analysis of hallmark/KEGG (Kyoto Encyclopedia of Genes and Genomes)/GO (Gene Ontology) pathways, as well as the identification of microRNA, motif and transcription factors involved in resistant cells, is provided in DRMref for user’s exploration. Overall, DRMref serves as a unique single-cell-based resource for studying drug resistance, drug combination therapy and discovering novel drug targets.
Graphical Abstract
Graphical Abstract |
| doi_str_mv | 10.1093/nar/gkad1087 |
| format | Article |
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Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistance at cell level. Herein, we have built the DRMref database (https://ccsm.uth.edu/DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, covering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimens and 42 drugs. All datasets in DRMref are browsable and searchable, with detailed annotations provided. Meanwhile, DRMref includes analyses of cellular composition, intratumoral heterogeneity, epithelial–mesenchymal transition, cell–cell interaction and differentially expressed genes in resistant cells. Notably, DRMref investigates the drug resistance mechanisms (e.g. Aberration of Drug’s Therapeutic Target, Drug Inactivation by Structure Modification, etc.) in resistant cells. Additional enrichment analysis of hallmark/KEGG (Kyoto Encyclopedia of Genes and Genomes)/GO (Gene Ontology) pathways, as well as the identification of microRNA, motif and transcription factors involved in resistant cells, is provided in DRMref for user’s exploration. Overall, DRMref serves as a unique single-cell-based resource for studying drug resistance, drug combination therapy and discovering novel drug targets.
Graphical Abstract
Graphical Abstract</description><identifier>ISSN: 0305-1048</identifier><identifier>EISSN: 1362-4962</identifier><identifier>DOI: 10.1093/nar/gkad1087</identifier><identifier>PMID: 37986230</identifier><language>eng</language><publisher>England: Oxford University Press</publisher><subject>Databases, Factual ; Drug Resistance - genetics ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Humans ; Internet ; MicroRNAs - genetics ; Neoplasms - drug therapy ; Neoplasms - genetics</subject><ispartof>Nucleic acids research, 2024-01, Vol.52 (D1), p.D1253-D1264</ispartof><rights>The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research. 2024</rights><rights>The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c291t-6e3bc819f70c065d4803eb3905f97318393e82aac6322d57631430be0400ee9b3</citedby><cites>FETCH-LOGICAL-c291t-6e3bc819f70c065d4803eb3905f97318393e82aac6322d57631430be0400ee9b3</cites><orcidid>0000-0002-4455-5302 ; 0000-0002-8321-6864 ; 0000-0001-7191-6495</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,776,780,860,1598,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37986230$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Liu, Xiaona</creatorcontrib><creatorcontrib>Yi, Jiahao</creatorcontrib><creatorcontrib>Li, Tina</creatorcontrib><creatorcontrib>Wen, Jianguo</creatorcontrib><creatorcontrib>Huang, Kexin</creatorcontrib><creatorcontrib>Liu, Jiajia</creatorcontrib><creatorcontrib>Wang, Grant</creatorcontrib><creatorcontrib>Kim, Pora</creatorcontrib><creatorcontrib>Song, Qianqian</creatorcontrib><creatorcontrib>Zhou, Xiaobo</creatorcontrib><title>DRMref: comprehensive reference map of drug resistance mechanisms in human cancer</title><title>Nucleic acids research</title><addtitle>Nucleic Acids Res</addtitle><description>Abstract
Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistance at cell level. Herein, we have built the DRMref database (https://ccsm.uth.edu/DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, covering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimens and 42 drugs. All datasets in DRMref are browsable and searchable, with detailed annotations provided. Meanwhile, DRMref includes analyses of cellular composition, intratumoral heterogeneity, epithelial–mesenchymal transition, cell–cell interaction and differentially expressed genes in resistant cells. Notably, DRMref investigates the drug resistance mechanisms (e.g. Aberration of Drug’s Therapeutic Target, Drug Inactivation by Structure Modification, etc.) in resistant cells. Additional enrichment analysis of hallmark/KEGG (Kyoto Encyclopedia of Genes and Genomes)/GO (Gene Ontology) pathways, as well as the identification of microRNA, motif and transcription factors involved in resistant cells, is provided in DRMref for user’s exploration. Overall, DRMref serves as a unique single-cell-based resource for studying drug resistance, drug combination therapy and discovering novel drug targets.
Graphical Abstract
Graphical Abstract</description><subject>Databases, Factual</subject><subject>Drug Resistance - genetics</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Neoplastic</subject><subject>Humans</subject><subject>Internet</subject><subject>MicroRNAs - genetics</subject><subject>Neoplasms - drug therapy</subject><subject>Neoplasms - genetics</subject><issn>0305-1048</issn><issn>1362-4962</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>TOX</sourceid><sourceid>EIF</sourceid><recordid>eNp9kMtOwzAQRS0EoqWwY42ygwWhY0_i2OxQeUpFCATryHEmbaB5YDdI_D0pbVmyGunO0ZXuYeyYwwUHjePauPHsw-QcVLLDhhylCCMtxS4bAkIccojUgB14_w7AIx5H-2yAiVZSIAzZ8_XLo6PiMrBN1TqaU-3LLwr6iBzVloLKtEFTBLnrZn3qS780vzHZualLX_mgrIN5V5k6sKuPO2R7hVl4OtrcEXu7vXmd3IfTp7uHydU0tELzZSgJM6u4LhKwIOM8UoCUoYa40AlyhRpJCWOsRCHyOJHII4SMIAIg0hmO2Nm6t3XNZ0d-mValt7RYmJqazqdCaSFkkiD26Pkata7xvt-Wtq6sjPtOOaQriWkvMd1K7PGTTXOXVZT_wVtrPXC6Bpqu_b_qB1sqeqA</recordid><startdate>20240105</startdate><enddate>20240105</enddate><creator>Liu, Xiaona</creator><creator>Yi, Jiahao</creator><creator>Li, Tina</creator><creator>Wen, Jianguo</creator><creator>Huang, Kexin</creator><creator>Liu, Jiajia</creator><creator>Wang, Grant</creator><creator>Kim, Pora</creator><creator>Song, Qianqian</creator><creator>Zhou, Xiaobo</creator><general>Oxford University Press</general><scope>TOX</scope><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/0000-0002-4455-5302</orcidid><orcidid>https://orcid.org/0000-0002-8321-6864</orcidid><orcidid>https://orcid.org/0000-0001-7191-6495</orcidid></search><sort><creationdate>20240105</creationdate><title>DRMref: comprehensive reference map of drug resistance mechanisms in human cancer</title><author>Liu, Xiaona ; Yi, Jiahao ; Li, Tina ; Wen, Jianguo ; Huang, Kexin ; Liu, Jiajia ; Wang, Grant ; Kim, Pora ; Song, Qianqian ; Zhou, Xiaobo</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c291t-6e3bc819f70c065d4803eb3905f97318393e82aac6322d57631430be0400ee9b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Databases, Factual</topic><topic>Drug Resistance - genetics</topic><topic>Gene Expression Profiling</topic><topic>Gene Expression Regulation, Neoplastic</topic><topic>Humans</topic><topic>Internet</topic><topic>MicroRNAs - genetics</topic><topic>Neoplasms - drug therapy</topic><topic>Neoplasms - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Liu, Xiaona</creatorcontrib><creatorcontrib>Yi, Jiahao</creatorcontrib><creatorcontrib>Li, Tina</creatorcontrib><creatorcontrib>Wen, Jianguo</creatorcontrib><creatorcontrib>Huang, Kexin</creatorcontrib><creatorcontrib>Liu, Jiajia</creatorcontrib><creatorcontrib>Wang, Grant</creatorcontrib><creatorcontrib>Kim, Pora</creatorcontrib><creatorcontrib>Song, Qianqian</creatorcontrib><creatorcontrib>Zhou, Xiaobo</creatorcontrib><collection>Oxford University Press Open Access</collection><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>Nucleic acids research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Liu, Xiaona</au><au>Yi, Jiahao</au><au>Li, Tina</au><au>Wen, Jianguo</au><au>Huang, Kexin</au><au>Liu, Jiajia</au><au>Wang, Grant</au><au>Kim, Pora</au><au>Song, Qianqian</au><au>Zhou, Xiaobo</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>DRMref: comprehensive reference map of drug resistance mechanisms in human cancer</atitle><jtitle>Nucleic acids research</jtitle><addtitle>Nucleic Acids Res</addtitle><date>2024-01-05</date><risdate>2024</risdate><volume>52</volume><issue>D1</issue><spage>D1253</spage><epage>D1264</epage><pages>D1253-D1264</pages><issn>0305-1048</issn><eissn>1362-4962</eissn><abstract>Abstract
Drug resistance poses a significant challenge in cancer treatment. Despite the initial effectiveness of therapies such as chemotherapy, targeted therapy and immunotherapy, many patients eventually develop resistance. To gain deep insights into the underlying mechanisms, single-cell profiling has been performed to interrogate drug resistance at cell level. Herein, we have built the DRMref database (https://ccsm.uth.edu/DRMref/) to provide comprehensive characterization of drug resistance using single-cell data from drug treatment settings. The current version of DRMref includes 42 single-cell datasets from 30 studies, covering 382 samples, 13 major cancer types, 26 cancer subtypes, 35 treatment regimens and 42 drugs. All datasets in DRMref are browsable and searchable, with detailed annotations provided. Meanwhile, DRMref includes analyses of cellular composition, intratumoral heterogeneity, epithelial–mesenchymal transition, cell–cell interaction and differentially expressed genes in resistant cells. Notably, DRMref investigates the drug resistance mechanisms (e.g. Aberration of Drug’s Therapeutic Target, Drug Inactivation by Structure Modification, etc.) in resistant cells. Additional enrichment analysis of hallmark/KEGG (Kyoto Encyclopedia of Genes and Genomes)/GO (Gene Ontology) pathways, as well as the identification of microRNA, motif and transcription factors involved in resistant cells, is provided in DRMref for user’s exploration. Overall, DRMref serves as a unique single-cell-based resource for studying drug resistance, drug combination therapy and discovering novel drug targets.
Graphical Abstract
Graphical Abstract</abstract><cop>England</cop><pub>Oxford University Press</pub><pmid>37986230</pmid><doi>10.1093/nar/gkad1087</doi><orcidid>https://orcid.org/0000-0002-4455-5302</orcidid><orcidid>https://orcid.org/0000-0002-8321-6864</orcidid><orcidid>https://orcid.org/0000-0001-7191-6495</orcidid><oa>free_for_read</oa></addata></record> |
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| source | Open Access: PubMed Central; MEDLINE; DOAJ Directory of Open Access Journals; Oxford University Press Open Access; Free Full-Text Journals in Chemistry |
| subjects | Databases, Factual Drug Resistance - genetics Gene Expression Profiling Gene Expression Regulation, Neoplastic Humans Internet MicroRNAs - genetics Neoplasms - drug therapy Neoplasms - genetics |
| title | DRMref: comprehensive reference map of drug resistance mechanisms in human cancer |
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