Acquired tumor resistance to vascular endothelial growth factor (VEGF) receptor tyrosine kinase inhibitors (RTKi) constitutes a major obstacle for sustained efficacy of antiangiogenic cancer therapy. We sought to decipher the molecular landscape of tumor resistance to continuous VEGF-RTKi sunitinib (SU11248, SU) treatment via serial transplantation of a syngeneic LLC/C57bl6 model and genome-wide mouse lentiviral shRNA library (150K complexity). The abundance of each single knock down (kd) was longitudinally traced via molecular barcodes. After three in-vivo panning rounds (p3-SU) tumor cells containing the kd of H3K4 histone demethylase (KDM5C) were 212-fold enriched compared to the in-vivo passaged library without the SU selection pressure (p3-ctrl). Interestingly, KDM5C is among the top 5 frequently mutated genes in clear cell renal cell carcinoma (RCC). SU constitutes a cornerstone in the therapy of metastatic RCC. We hypothesized that KDM5C mutation status might be prognostic for therapy refractoriness of RCC. Indeed, whole exome analysis of the cancer genome atlas (TCGA) RCC collective revealed a trend towards poor overall survival (OS) for patients with mutated KDM5C tumors. In LLC and RCC xenograft models, loss of KDM5C (shKDM5C) was attributed to SU resistance with significantly enhanced hypoxia tolerance, increased proliferation (Ki67, 13-fold, p = 0.04) and microvascular density (CD31, 23-fold increase, p<0.02) compared to SU treated shCtrl. We aimed to identify a consensus set of genes differentially expressed in tumors with KDM5C kd/mutation. Applying this KDM5C gene signature to RNAseq data of 533 RCC patients separated the cohort into a poor-prognosis KDM5Cmut-like (median OS 4.5 years) vs. good prognosis KDM5Cwt-like group (median OS not reached, p = 0.0001). Genes regulating cancer cell survival, redox-balance and angiogenesis were enriched in this signature. Together, these data indicate a critical role for the epigenetic modulator KDM5C in development of tumor resistance to VEGF-RTKi. The here-identified KDM5C dependent gene-signature might be instructive to prognosticate patients at risk for therapy refractoriness to RTKi.

Citation Format: Azadeh Fahim Golestaneh, Maoyun Sun, Christian Schwager, Zili Tang, Stephan Macher-Goeppinger, Lila Ma, Philip Hahnfeldt, Mahmoud Moustafa, Wilko Weichert, Sascha Pahernik, Carsten Grüllich, Wilfried Roth, Jürgen Debus, Lynn Hlatky, Amir Abdollahi. Discovery of histone demethylase KDM5C inactivation as a novel mechanism for tumors resistant to VEGF RTKi via genome-wide in-vivo RNAi. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3254.