Characterization of the epigenetic regulator LSD1 as a druggable dependency in treatment resistant melanoma

Abstract

Melanoma, a deadly form of skin cancer, arises from the malignant transformation of melanocytes. Advances in targeted and immune therapies for melanoma provide clinical benefit but are ultimately met with resistance and inadequate clinical response. Previous analyses of patient biopsies and cell lines revealed that both acquired and intrinsic resistance to these therapies are associated with an undifferentiated cell state characterized by low levels of microphthalmia-associated transcription factor (MITF), the master regulator of melanocyte development, and high levels of AXL receptor tyrosine kinase (AXL). In this thesis, I characterize the epigenetic regulator lysine-specific demethylase-1 (LSD1) as a targetable vulnerability in treatment resistant MITF-low/AXL-high melanoma. I extensively validate the dependence of MITF-low melanoma cells on LSD1 using multiple independent genetic and pharmacologic approaches. Furthermore, the toxicity of LSD1 loss is shown to be specific to MITF-low, but not MITF-high, melanoma cells. To identify a mechanism by which LSD1 mediates survival of MITF-low melanoma cells, we performed genome-wide transcriptome and chromatin analyses and found that LSD1 represses N-myc Downstream-Regulated Gene-1 (NDRG1) via demethylation of dimethyl histone 3 lysine 4 (H3K4me2). We confirmed LSD1 occupancy of the NDRG1 promoter and show that NDRG1 is essential for LSD1 inhibition-mediated suppression of MITF-low melanoma growth, as loss of NDRG1 abrogates the effects of LSD1 inhibition. Using xenografts bearing MITF-low melanoma tumors, I demonstrate that LSD1 inhibition reduces tumor burden and correlates with NDRG1 RNA induction, which I show serves as a biomarker for on-target LSD1 inhibition. I also assessed the anti- tumor effects of LSD1 inhibitors in rational combinations with targeted and immune therapies both in vitro and in vivo. Finally, we demonstrate that the dependency on LSD1 in melanoma cells expressing low levels of MITF and high levels of AXL extends to pancreatic adenocarcinomas characterized by a transcriptional profile defined by high-AXL expression. These findings reveal mechanistic insights and identify a therapeutically vulnerable epigenetic state in poorly differentiated, therapy-resistant cancers, including subsets of melanoma, pancreatic cancer, and possibly other cancer types. LSD1 inhibitors can potentially be valuable additions to the currently limited treatment options for these patients.