Abstract 6942: Single cell resolution of intrapatient drug resistance mechanisms in metastatic melanoma

Abstract

Abstract Intrapatient heterogeneity among different metastatic sites contributes to immunotherapy (ICi) and targeted therapy resistance. Determining the evolution of metastatic melanoma lesions that develop within the same patient could help elucidate adaptive mechanisms that drive tumor progression during therapy. To assess how metastatic melanoma persists through immunotherapy and targeted inhibitor treatments, we utilized samples from a single patient who had received anti-CTLA4, BRAFi/MEKi, and BRAFi/MEKi+CDK4/6i treatments during the LOGIC2 clinical trial. Eight short-term cultures were established from different metastatic site biopsies at chronological time points throughout the patient’s treatment and subsequent post-mortem resection of the bone, ovary, and brain metastatic sites. While the initial treatment naïve metastatic tumor in the breast was BRAFV600E mutant, NRASQ61 mutations were acquired after treatment with CDK4/6i in the bone and ovary tumors. Tumors that persist through treatment and colonize distant organs adapt to and rely on organ-specific microenvironments. To assess treatment- and organ-specific adaptations, single-cell RNA sequencing was performed on seven of the short-term cultures to identify subpopulations that persist through each treatment. We analyzed samples and subpopulations of each culture to determine differences in their transcriptional cell states. The regulon transcriptional network of each sample and subpopulation was evaluated to determine site- and treatment-specific transcriptional regulation differences. In addition, we identified the treatment naïve culture is split into two major subpopulations by therapy resistance features which are further made up of six distinct subpopulations with heterogeneous regulatory networks. We determined the longitudinal evolution of subpopulations in response to treatment and organ site to evaluate how the pressure of therapies and the microenvironment influence metastatic progression. We further evaluated site-specific resistance mechanisms and detected increased HER3 expression in the melanoma brain metastasis (MBM) sample. Treatment with Neuregulin 1, a ligand for the HER3 receptor that is abundant in brain tissue, partially rescued the growth of MBM cells and restored MAPK and AKT-mTOR signaling in the presence of BRAFi/MEKi. Targeting the NRG1-HER3 signaling axis could have therapeutic potential in melanoma patients with active brain metastases. Additionally, we evaluated treatment-specific resistance mechanisms and identified high Brevican (BCAN) expression in an early emerging subpopulation that arises after ICi in this patient and in others. BCAN is implicated in both ICi- and cross-resistance. We will functionally investigate whether targeting BCAN sensitizes cells to ICi. Future studies aim to functionally examine novel site- and treatment-specific cross patient targets. Citation Format: Haley P. Wilson, Glenn L. Mersky, Jelan I. Haj, Jessica Teh, Phil F. Cheng, Signe Caksa, Casey D. Stefanski, Vivian Chua, Claudia Capparelli, Mitch P. Levesque, Reinhard Dummer, Timothy J. Purwin, Andrew E. Aplin. Single cell resolution of intrapatient drug resistance mechanisms in metastatic melanoma [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 6942.