Drepmel—A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment
Although substantial progress has been made in treating patients with advanced melanoma with targeted and immuno-therapies, de novo and acquired resistance is commonplace. After treatment failure, therapeutic options are very limited and novel strategies are urgently needed. Combination therapies ar...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-09-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/11/18/2894 |
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| author | Zachary J. Thompson Jamie K. Teer Jiannong Li Zhihua Chen Eric A. Welsh Yonghong Zhang Noura Ayoubi Zeynep Eroglu Aik Choon Tan Keiran S. M. Smalley Yian Ann Chen |
| author_facet | Zachary J. Thompson Jamie K. Teer Jiannong Li Zhihua Chen Eric A. Welsh Yonghong Zhang Noura Ayoubi Zeynep Eroglu Aik Choon Tan Keiran S. M. Smalley Yian Ann Chen |
| author_sort | Zachary J. Thompson |
| collection | DOAJ |
| description | Although substantial progress has been made in treating patients with advanced melanoma with targeted and immuno-therapies, de novo and acquired resistance is commonplace. After treatment failure, therapeutic options are very limited and novel strategies are urgently needed. Combination therapies are often more effective than single agents and are now widely used in clinical practice. Thus, there is a strong need for a comprehensive computational resource to define rational combination therapies. We developed a Shiny app, DRepMel to provide rational combination treatment predictions for melanoma patients from seventy-three thousand combinations based on a multi-omics drug repurposing computational approach using whole exome sequencing and RNA-seq data in bulk samples from two independent patient cohorts. DRepMel provides robust predictions as a resource and also identifies potential treatment effects on the tumor microenvironment (TME) using single-cell RNA-seq data from melanoma patients. Availability: DRepMel is accessible online. |
| first_indexed | 2024-03-10T00:25:56Z |
| format | Article |
| id | doaj.art-ac45d504ae06489ea9a0020319ae808d |
| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-10T00:25:56Z |
| publishDate | 2022-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-ac45d504ae06489ea9a0020319ae808d2023-11-23T15:34:01ZengMDPI AGCells2073-44092022-09-011118289410.3390/cells11182894Drepmel—A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor MicroenvironmentZachary J. Thompson0Jamie K. Teer1Jiannong Li2Zhihua Chen3Eric A. Welsh4Yonghong Zhang5Noura Ayoubi6Zeynep Eroglu7Aik Choon Tan8Keiran S. M. Smalley9Yian Ann Chen10Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USADepartment of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USABiostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USABiostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USABiostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USABiostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USADepartment of Dermatology and Cutaneous Surgery, University of South Florida, Tampa, FL 33612, USADepartment of Cutaneous Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USADepartment of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USADepartment of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USADepartment of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USAAlthough substantial progress has been made in treating patients with advanced melanoma with targeted and immuno-therapies, de novo and acquired resistance is commonplace. After treatment failure, therapeutic options are very limited and novel strategies are urgently needed. Combination therapies are often more effective than single agents and are now widely used in clinical practice. Thus, there is a strong need for a comprehensive computational resource to define rational combination therapies. We developed a Shiny app, DRepMel to provide rational combination treatment predictions for melanoma patients from seventy-three thousand combinations based on a multi-omics drug repurposing computational approach using whole exome sequencing and RNA-seq data in bulk samples from two independent patient cohorts. DRepMel provides robust predictions as a resource and also identifies potential treatment effects on the tumor microenvironment (TME) using single-cell RNA-seq data from melanoma patients. Availability: DRepMel is accessible online.https://www.mdpi.com/2073-4409/11/18/2894multi-omicsmelanomadrug repurposingmicroenvironment |
| spellingShingle | Zachary J. Thompson Jamie K. Teer Jiannong Li Zhihua Chen Eric A. Welsh Yonghong Zhang Noura Ayoubi Zeynep Eroglu Aik Choon Tan Keiran S. M. Smalley Yian Ann Chen Drepmel—A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment Cells multi-omics melanoma drug repurposing microenvironment |
| title | Drepmel—A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment |
| title_full | Drepmel—A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment |
| title_fullStr | Drepmel—A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment |
| title_full_unstemmed | Drepmel—A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment |
| title_short | Drepmel—A Multi-Omics Melanoma Drug Repurposing Resource for Prioritizing Drug Combinations and Understanding Tumor Microenvironment |
| title_sort | drepmel a multi omics melanoma drug repurposing resource for prioritizing drug combinations and understanding tumor microenvironment |
| topic | multi-omics melanoma drug repurposing microenvironment |
| url | https://www.mdpi.com/2073-4409/11/18/2894 |
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