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Misek SA, Newbury PA, Chekalin E, Paithankar S, Doseff AI, Chen B, Gallo KA, Neubig RR. Ibrutinib Blocks YAP1 Activation and Reverses BRAF Inhibitor Resistance in Melanoma Cells. Mol Pharmacol 2022; 101:1-12. [PMID: 34732527 PMCID: PMC11037454 DOI: 10.1124/molpharm.121.000331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 10/01/2021] [Indexed: 11/22/2022] Open
Abstract
Most B-Raf proto-oncogene (BRAF)-mutant melanoma tumors respond initially to BRAF inhibitor (BRAFi)/mitogen-activated protein kinase kinase 1 inhibitor (MEKi) therapy, although few patients have durable long-term responses to these agents. The goal of this study was to use an unbiased computational approach to identify inhibitors that reverse an experimentally derived BRAFi resistance gene expression signature. Using this approach, we found that ibrutinib effectively reverses this signature, and we demonstrate experimentally that ibrutinib resensitizes a subset of BRAFi-resistant melanoma cells to vemurafenib. Ibrutinib is used clinically as an inhibitor of the Src family kinase Bruton tyrosine kinase (BTK); however, neither BTK deletion nor treatment with acalabrutinib, another BTK inhibitor with reduced off-target activity, resensitized cells to vemurafenib. These data suggest that ibrutinib acts through a BTK-independent mechanism in vemurafenib resensitization. To better understand this mechanism, we analyzed the transcriptional profile of ibrutinib-treated BRAFi-resistant melanoma cells and found that the transcriptional profile of ibrutinib was highly similar to that of multiple Src proto-oncogene kinase inhibitors. Since ibrutinib, but not acalabrutinib, has appreciable off-target activity against multiple Src family kinases, it suggests that ibrutinib may be acting through this mechanism. Furthermore, genes that are differentially expressed in ibrutinib-treated cells are enriched in Yes1-associated transcriptional regulator (YAP1) target genes, and we showed that ibrutinib, but not acalabrutinib, reduces YAP1 activity in BRAFi-resistant melanoma cells. Taken together, these data suggest that ibrutinib, or other Src family kinase inhibitors, may be useful for treating some BRAFi/MEKi-refractory melanoma tumors. SIGNIFICANCE STATEMENT: MAPK-targeted therapies provide dramatic initial responses, but resistance develops rapidly; a subset of these tumors may be rendered sensitive again by treatment with an approved Src family kinase inhibitor-ibrutinub-potentially providing improved clinical outcomes.
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Affiliation(s)
- Sean A Misek
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Patrick A Newbury
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Evgenii Chekalin
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Shreya Paithankar
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Andrea I Doseff
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Bin Chen
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Kathleen A Gallo
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
| | - Richard R Neubig
- Departments of Physiology (S.A.M., A.I.D., K.A.G.), Pediatrics and Human Development (P.A.N., E.C., S.P., B.C.), and Pharmacology (A.I.D., B.C., R.R.N.), Michigan State University, East Lansing, Michigan
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Xing J, Shankar R, Drelich A, Paithankar S, Chekalin E, Dexheimer T, Chua MS, Rajasekaran S, Tseng CTK, Chen B. Analysis of Infected Host Gene Expression Reveals Repurposed Drug Candidates and Time-Dependent Host Response Dynamics for COVID-19. bioRxiv 2020:2020.04.07.030734. [PMID: 32511305 PMCID: PMC7217282 DOI: 10.1101/2020.04.07.030734] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The repurposing of existing drugs offers the potential to expedite therapeutic discovery against the current COVID-19 pandemic caused by the SARS-CoV-2 virus. We have developed an integrative approach to predict repurposed drug candidates that can reverse SARS-CoV-2-induced gene expression in host cells, and evaluate their efficacy against SARS-CoV-2 infection in vitro. We found that 13 virus-induced gene expression signatures computed from various viral preclinical models could be reversed by compounds previously identified to be effective against SARS- or MERS-CoV, as well as drug candidates recently reported to be efficacious against SARS-CoV-2. Based on the ability of candidate drugs to reverse these 13 infection signatures, as well as other clinical criteria, we identified 10 novel candidates. The four drugs bortezomib, dactolisib, alvocidib, and methotrexate inhibited SARS-CoV-2 infection-induced cytopathic effect in Vero E6 cells at < 1 µM, but only methotrexate did not exhibit unfavorable cytotoxicity. Although further improvement of cytotoxicity prediction and bench testing is required, our computational approach has the potential to rapidly and rationally identify repurposed drug candidates against SARS-CoV-2. The analysis of signature genes induced by SARS-CoV-2 also revealed interesting time-dependent host response dynamics and critical pathways for therapeutic interventions (e.g. Rho GTPase activation and cytokine signaling suppression).
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Affiliation(s)
- Jing Xing
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan, USA
| | - Rama Shankar
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan, USA
| | - Aleksandra Drelich
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Shreya Paithankar
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan, USA
| | - Evgenii Chekalin
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan, USA
| | - Thomas Dexheimer
- Department of Pharmacology and Toxicology, Michigan State University, Grand Rapids, Michigan, USA
| | - Mei-Sze Chua
- Department of Surgery, Stanford University School of Medicine, Palo Alto, California, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan, USA
- Helen Devos Children Hospital, Grand Rapids, Michigan, USA
| | - Chien-Te Kent Tseng
- Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Center of Biodefense and Emerging Disease, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bin Chen
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan, USA
- Department of Pharmacology and Toxicology, Michigan State University, Grand Rapids, Michigan, USA
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