{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T10:19:39Z","timestamp":1783937979480,"version":"3.55.0"},"reference-count":20,"publisher":"MDPI AG","issue":"7","license":[{"start":{"date-parts":[[2026,7,12]],"date-time":"2026-07-12T00:00:00Z","timestamp":1783814400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"KAKENHI","doi-asserted-by":"publisher","award":["24K12458"],"award-info":[{"award-number":["24K12458"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"KAKENHI","doi-asserted-by":"publisher","award":["24K11347"],"award-info":[{"award-number":["24K11347"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"KAKENHI","doi-asserted-by":"publisher","award":["24K12641"],"award-info":[{"award-number":["24K12641"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Cabozantinib is a tyrosine kinase inhibitor that primarily targets MET. It has become an important drug in the treatment of renal cell carcinoma (RCC); however, many patients do not respond to cabozantinib treatment and there is no effective next-line therapy. In this study, we identified molecular-targeted drugs that exhibit synergistic effects with cabozantinib using CRISPR\/Cas9 screening. Methods: A kinome-wide synthetic lethal CRISPR\/Cas9 screen was used to identify target molecules using 786-o RCC cells. A library was generated, and treatment with vehicle or cabozantinib was carried out, followed by next-generation sequencing to identify candidate genes. A combination index based on the Chou\u2013Talalay method was used to evaluate the synergistic effect of cabozantinib through cell viability assays. Xenograft assays were conducted to determine the effect in vivo. Results: CRISPR\/Cas9-based screening revealed four genes (MEK1, DCLK1, DYRK3, and FGFR1) that were candidates for synthetic lethality by cabozantinib in RCC cells. We focused on MEK1 because the MEK1 inhibitor cobimetinib has been approved for melanoma treatment. In a cell proliferation assay using 786-o and A498 RCC cells, the combination of cobimetinib and cabozantinib exhibited a synergistic effect. A xenograft assay also revealed a significant synergistic effect of cobimetinib and cabozantinib. Conclusions: CRISPR\/Cas9 screening identified MEK1 as a candidate for a synthetic lethal target with cabozantinib in RCC. The combined inhibition of MET\/VEGFR and MEK1 suppressed compensatory MAPK reactivation and downregulated the PI3K-Akt pathway, including the survival-associated genes PPP2R3B and ATF6B, and produced significant tumor growth suppression in vivo. These findings highlight the potential of cabozantinib plus cobimetinib, an already-FDA-approved MEK inhibitor, as a readily translatable combination strategy to overcome cabozantinib resistance in RCC.<\/jats:p>","DOI":"10.3390\/genes17070789","type":"journal-article","created":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T09:51:09Z","timestamp":1783936269000},"page":"789","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["MEK1 as a Synthetic Lethal Target with Cabozantinib in Renal Cell Carcinoma: Insights from CRISPR\/Cas9 Screening"],"prefix":"10.3390","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5470-7445","authenticated-orcid":false,"given":"Hirofumi","family":"Yoshino","sequence":"first","affiliation":[{"name":"Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ikumi","family":"Fukuda","sequence":"additional","affiliation":[{"name":"Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hideki","family":"Enokida","sequence":"additional","affiliation":[{"name":"Department of Urology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4731-7956","authenticated-orcid":false,"given":"Naohiko","family":"Seki","sequence":"additional","affiliation":[{"name":"Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7720-9740","authenticated-orcid":false,"given":"Yusuke","family":"Goto","sequence":"additional","affiliation":[{"name":"Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan"},{"name":"Department of Urology, Teikyo University Chiba Medical Centre, Chiba 299-0111, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1001\/jama.2024.12848","article-title":"Renal Cell Carcinoma: A Review","volume":"332","author":"Rose","year":"2024","journal-title":"JAMA"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1685","DOI":"10.1093\/annonc\/mdw241","article-title":"Sequential pathogenesis of metastatic VHL mutant clear cell renal cell carcinoma: Putting it together with a translational perspective","volume":"27","author":"Shenoy","year":"2016","journal-title":"Ann. Oncol. Off. J. Eur. Soc. Med. Oncol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e162480","DOI":"10.1172\/JCI162480","article-title":"Von Hippel-Lindau disease: Insights into oxygen sensing, protein degradation, and cancer","volume":"132","author":"Kaelin","year":"2022","journal-title":"J. Clin. Investig."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1519","DOI":"10.1038\/s41591-020-1093-z","article-title":"Targeting the HIF2-VEGF axis in renal cell carcinoma","volume":"26","author":"Choueiri","year":"2020","journal-title":"Nat. Med."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1016\/S1470-2045(23)00473-4","article-title":"Immunotherapy in renal cell carcinoma","volume":"24","author":"Navani","year":"2023","journal-title":"Lancet Oncol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"4781","DOI":"10.21873\/anticanres.16675","article-title":"Renal Cell Cancer\u2014Insights in Drug Resistance Mechanisms","volume":"43","author":"Aweys","year":"2023","journal-title":"Anticancer Res."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"1814","DOI":"10.1056\/NEJMoa1510016","article-title":"Cabozantinib versus Everolimus in Advanced Renal-Cell Carcinoma","volume":"373","author":"Choueiri","year":"2015","journal-title":"N. Engl. J. Med."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1158\/1078-0432.CCR-15-0187","article-title":"Cabozantinib (XL184) Inhibits Growth and Invasion of Preclinical TNBC Models","volume":"22","author":"Sameni","year":"2016","journal-title":"Clin. Cancer Res. Off. J. Am. Assoc. Cancer Res."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1126\/science.1247005","article-title":"Genome-scale CRISPR-Cas9 knockout screening in human cells","volume":"343","author":"Shalem","year":"2014","journal-title":"Science"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1850","DOI":"10.1158\/2767-9764.CRC-24-0247","article-title":"A Kinome-Wide Synthetic Lethal CRISPR\/Cas9 Screen Reveals That mTOR Inhibition Prevents Adaptive Resistance to CDK4\/CDK6 Blockade in HNSCC","volume":"4","author":"Goto","year":"2024","journal-title":"Cancer Res. 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Rep."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"440","DOI":"10.1158\/0008-5472.CAN-09-1947","article-title":"Drug combination studies and their synergy quantification using the Chou-Talalay method","volume":"70","author":"Chou","year":"2010","journal-title":"Cancer Res."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"20881","DOI":"10.18632\/oncotarget.14930","article-title":"microRNA-210-3p depletion by CRISPR\/Cas9 promoted tumorigenesis through revival of TWIST1 in renal cell carcinoma","volume":"8","author":"Yoshino","year":"2017","journal-title":"Oncotarget"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1016\/S1470-2045(25)00209-8","article-title":"Cabozantinib plus atezolizumab in metastatic prostate cancer (CONTACT-02): Final analyses from a phase 3, open-label, randomised trial","volume":"26","author":"Agarwal","year":"2025","journal-title":"Lancet Oncol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"5578","DOI":"10.1158\/1078-0432.CCR-15-0824","article-title":"Cabozantinib Inhibits Abiraterone\u2019s Upregulation of IGFIR Phosphorylation and Enhances Its Anti-Prostate Cancer Activity","volume":"21","author":"Wang","year":"2015","journal-title":"Clin. Cancer Res. Off. J. Am. Assoc. Cancer Res."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1867","DOI":"10.1056\/NEJMoa1408868","article-title":"Combined vemurafenib and cobimetinib in BRAF-mutated melanoma","volume":"371","author":"Larkin","year":"2014","journal-title":"N. Engl. J. Med."},{"key":"ref_17","first-page":"1636","article-title":"Inherited duplications of PPP2R3B predispose to nevi and melanoma via a C21orf91-driven proliferative phenotype","volume":"23","author":"Polubothu","year":"2021","journal-title":"Genet. Med. Off. J. Am. Coll. Med. Genet."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1480","DOI":"10.4049\/jimmunol.0900017","article-title":"Activation of the Akt-NF-kappaB pathway by subtilase cytotoxin through the ATF6 branch of the unfolded protein response","volume":"183","author":"Yamazaki","year":"2009","journal-title":"J. Immunol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1007\/s10637-024-01428-0","article-title":"A phase 1 trial of the MEK inhibitor selumetinib in combination with pembrolizumab for advanced or metastatic solid tumors","volume":"42","author":"Hansen","year":"2024","journal-title":"Investig. New Drugs"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1835","DOI":"10.1016\/S0140-6736(20)30934-X","article-title":"Atezolizumab, vemurafenib, and cobimetinib as first-line treatment for unresectable advanced BRAF(V600) mutation-positive melanoma (IMspire150): Primary analysis of the randomised, double-blind, placebo-controlled, phase 3 trial","volume":"395","author":"Gutzmer","year":"2020","journal-title":"Lancet"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/7\/789\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T10:00:29Z","timestamp":1783936829000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/7\/789"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,12]]},"references-count":20,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2026,7]]}},"alternative-id":["genes17070789"],"URL":"https:\/\/doi.org\/10.3390\/genes17070789","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,12]]}}}