Abstract 4399: HMGA1 is an epigenetic regulator and plays a critical role in melanoma recurrence

Abstract

Abstract Among various genetic mutation in melanoma, BRAFV600E is one of the key drivers of melanoma initiation and progression and has become the frontline target in clinical trials. Although BRAF/MEK inhibitors show very promising therapeutic outcomes, recurrence or relapse is still a major challenge and its underlying mechanisms are still poorly understood. We hypothesized that survival of recurrent tumors is BRAF independent and relies on epigenetic reprogramming. To test our hypothesis, we used either pharmacological inhibition of BRAF/MEK or CRISPR/Cas9 mediated knockout of BRAF to create cell/tumor models of BRAF-independent survival. Cut&Run sequencing was then used to identify epigenetic alterations regulated by H3K4me3 or H3K27Ac in a genome scale and capture the landscape of epigenetic alterations of BRAF-independent cell survival. Combining regular bulk RNAseq, we narrowed down our top candidates and focused on one of the functionally validated candidates, HMGA1. Interestingly, CRISPR/Cas9 mediated HMGA1 knockout cells show significantly slower growth in both in vitro colony formation assays and in vivo xenografts assay in BRAF/MEK resistant Patient-Derived-Xenograft (PDX) tumor models resembling melanoma recurrence. Furthermore, we selected CRISPR/Cas9 single knockout cells of HMGA1, which is a pure genetic depletion model, and confirmed the phenotype of impaired tumor growth of HMGA1 knockout cells. We then performed RNAseq and ChIPseq, and identified downstream targets of HMGA1 and elucidated mechanisms by which HMGA1 reprograms epigenetics of recurrence. Utilizing the single knockout cell, we re-introduced HMGA1 in the pure knockout cells, and anticipated that restoration of HMGA1 in pure HMGA1 knockout cells rescues impaired tumor growth and confer cells resistance to BRAF/MEK inhibition. Finally, we subcutaneously injected the HMGA1 single knockout cells into humanized mice and tested whether epigenetic alterations perturb the immune microenvironment and sensitize cells to immunotherapy. In conclusion, this study sheds new lights on how melanoma cells reprogram the epigenome to develop mechanisms of recurrence. Identification of HMGA1 and its upstream or downstream targets provides potential druggable targets of overcoming relapse after BRAF/MEK inhibitor therapy. Citation Format: Haiwei Mou, Kristen DeRosa, Veronika Yakovishina, Yeqing Chen, Abdiel Mandella Reynolds, Min Xiao, Monzy Thomas, Meenhard Herlyn. HMGA1 is an epigenetic regulator and plays a critical role in melanoma recurrence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4399.