BRAFV600E‐PROTAC versus inhibitors in melanoma cells: Deep transcriptomic characterization
Abstract Aims This study compares the suppression of Mitogen‐activated protein kinase (MAPK) signalling and early resistance potential between a proteolysis‐targeting chimera (PROTAC) and inhibitors targeting BRAFV600E. Methods We performed a detailed in silico analysis of the transcriptomic landsca...
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Wiley
2025-03-01
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| Series: | Clinical and Translational Medicine |
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| Online Access: | https://doi.org/10.1002/ctm2.70251 |
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| author | Solomon O. Alhassan Zakaria Y. Abd Elmageed Youssef Errami Guangdi Wang Joe A. Abi‐Rached Emad Kandil Mourad Zerfaoui |
| author_facet | Solomon O. Alhassan Zakaria Y. Abd Elmageed Youssef Errami Guangdi Wang Joe A. Abi‐Rached Emad Kandil Mourad Zerfaoui |
| author_sort | Solomon O. Alhassan |
| collection | DOAJ |
| description | Abstract Aims This study compares the suppression of Mitogen‐activated protein kinase (MAPK) signalling and early resistance potential between a proteolysis‐targeting chimera (PROTAC) and inhibitors targeting BRAFV600E. Methods We performed a detailed in silico analysis of the transcriptomic landscape of the A375 melanoma cell line treated with a PROTAC and BRAFV600E inhibitors from RNA sequencing data. The study assessed gene dysregulation, MAPK and Phosphoinositide‐3‐kinase (PI3K/AKT) pathway inhibition, and cell survival. Key genes uniquely dysregulated by PROTAC treatment were validated by qPCR. Furthermore, analysis was performed to evaluate dedifferentiation and early resistance signatures to understand melanoma drug‐induced plasticity. Results PROTAC‐treated cells showed significantly lower MAPK pathway activity, strong cell cycle arrest and elevated apoptotic gene expression compared to inhibitor‐treated cells, with no effect on the PI3K/AKT pathway. A high microphtalmia‐associated transcription factor (MITF)/Tyrosine‐Protein Kinase Receptor (AXL) ratio in PROTAC‐treated cells indicated reduced early drug resistance. BRAF degradation induced a melanocytic‐transitory phenotype. Although PROTAC and inhibitor treatments caused overlapping transcriptomic changes, key differences were observed. PROTAC treatment enriched processes such as epithelial‒mesenchymal transition, inflammatory responses, and Tumor necrosis factor‐Alpha (TNF‐α) and IL2/STAT5 signalling. Conclusion PROTAC‐targeting BRAFV600E demonstrates enhanced MAPK suppression, reduced early resistance and distinct transcriptional effects compared to traditional inhibitors. It represents a promising strategy for overcoming resistance in melanoma treatment. |
| format | Article |
| id | doaj-art-29d2b5ef7f4e47ebbc17f2dc67b07b17 |
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| language | English |
| publishDate | 2025-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | Clinical and Translational Medicine |
| spelling | doaj-art-29d2b5ef7f4e47ebbc17f2dc67b07b172025-08-20T02:32:12ZengWileyClinical and Translational Medicine2001-13262025-03-01153n/an/a10.1002/ctm2.70251BRAFV600E‐PROTAC versus inhibitors in melanoma cells: Deep transcriptomic characterizationSolomon O. Alhassan0Zakaria Y. Abd Elmageed1Youssef Errami2Guangdi Wang3Joe A. Abi‐Rached4Emad Kandil5Mourad Zerfaoui6Department of Gastrointestinal Oncology Moffitt Cancer Center Magnolia Campus Tampa Florida USADepartment of Pharmacology, Edward Via College of Osteopathic Medicine University of Louisiana Monroe Louisiana USADepartment of Microbiology Immunology and Molecular Genetics La Jolla California USARCMI Cancer Research Center and Department of Chemistry Xavier University of Louisiana New Orleans Louisiana USATulane University School of Medicine New Orleans Louisiana USATulane University School of Medicine New Orleans Louisiana USACenter for ViroScience and Cure, Department of Pediatrics, Laboratory of Biochemical Pharmacology Emory University School of Medicine Atlanta Georgia USAAbstract Aims This study compares the suppression of Mitogen‐activated protein kinase (MAPK) signalling and early resistance potential between a proteolysis‐targeting chimera (PROTAC) and inhibitors targeting BRAFV600E. Methods We performed a detailed in silico analysis of the transcriptomic landscape of the A375 melanoma cell line treated with a PROTAC and BRAFV600E inhibitors from RNA sequencing data. The study assessed gene dysregulation, MAPK and Phosphoinositide‐3‐kinase (PI3K/AKT) pathway inhibition, and cell survival. Key genes uniquely dysregulated by PROTAC treatment were validated by qPCR. Furthermore, analysis was performed to evaluate dedifferentiation and early resistance signatures to understand melanoma drug‐induced plasticity. Results PROTAC‐treated cells showed significantly lower MAPK pathway activity, strong cell cycle arrest and elevated apoptotic gene expression compared to inhibitor‐treated cells, with no effect on the PI3K/AKT pathway. A high microphtalmia‐associated transcription factor (MITF)/Tyrosine‐Protein Kinase Receptor (AXL) ratio in PROTAC‐treated cells indicated reduced early drug resistance. BRAF degradation induced a melanocytic‐transitory phenotype. Although PROTAC and inhibitor treatments caused overlapping transcriptomic changes, key differences were observed. PROTAC treatment enriched processes such as epithelial‒mesenchymal transition, inflammatory responses, and Tumor necrosis factor‐Alpha (TNF‐α) and IL2/STAT5 signalling. Conclusion PROTAC‐targeting BRAFV600E demonstrates enhanced MAPK suppression, reduced early resistance and distinct transcriptional effects compared to traditional inhibitors. It represents a promising strategy for overcoming resistance in melanoma treatment.https://doi.org/10.1002/ctm2.70251BRAFV600Edifferentiation stateMAPK pathwaymelanomaMITFPROTAC |
| spellingShingle | Solomon O. Alhassan Zakaria Y. Abd Elmageed Youssef Errami Guangdi Wang Joe A. Abi‐Rached Emad Kandil Mourad Zerfaoui BRAFV600E‐PROTAC versus inhibitors in melanoma cells: Deep transcriptomic characterization Clinical and Translational Medicine BRAFV600E differentiation state MAPK pathway melanoma MITF PROTAC |
| title | BRAFV600E‐PROTAC versus inhibitors in melanoma cells: Deep transcriptomic characterization |
| title_full | BRAFV600E‐PROTAC versus inhibitors in melanoma cells: Deep transcriptomic characterization |
| title_fullStr | BRAFV600E‐PROTAC versus inhibitors in melanoma cells: Deep transcriptomic characterization |
| title_full_unstemmed | BRAFV600E‐PROTAC versus inhibitors in melanoma cells: Deep transcriptomic characterization |
| title_short | BRAFV600E‐PROTAC versus inhibitors in melanoma cells: Deep transcriptomic characterization |
| title_sort | brafv600e protac versus inhibitors in melanoma cells deep transcriptomic characterization |
| topic | BRAFV600E differentiation state MAPK pathway melanoma MITF PROTAC |
| url | https://doi.org/10.1002/ctm2.70251 |
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