Abstract 111: Characterizing subpopulation response to doxorubicin in a barcode-labeled triple negative breast carcinoma cell line

Abstract

Abstract Despite recent advances in diagnosis and late-stage treatment, progression-free survival is not achieved for many cancer patients. Triple negative breast cancer (TNBC) poses a particular challenge as an aggressive and heterogeneous disease lacking the benefit of hormonal therapies. We have utilized a novel genetic lineage-tracking system, ClonMapper in TNBC cells to elucidate the pre-existent and de novo cell states that arise from chemotherapeutic intervention. ClonMapper genetic tags were stably integrated into MDA-MB-231 cells using lentiviral transduction and positively labeled cells were isolated with fluorescence-activated cell sorting to generate a starting library of ~500 uniquely barcoded cells. Barcode-labeled MDA-MB-231 were selected with doxorubicin at 250, 400 and 550 nM for 48 hours and allowed to recover. To determine the contribution of transcriptomic state to cellular drug response we carried out single cell RNA-sequencing (scRNA-seq) on 4 populations: a pretreatment cell library, an intermediary taken 30 h into drug selection, and two recovered populations from the 250 nM group. Importantly, we are able to capture and deconvolve ClonMapper lineage tags from scRNA-seq results and overlay them with transcriptomic state. Following treatment with doxorubicin we found a dose-dependent reduction in the number of unique lineages, with all replicates showing >6-fold decrease. Post-treatment replicates were each significantly comprised (90%) by fewer than three individual lineages. Lineage-resolved transcriptomics revealed two distinct lineage-specific subpopulations within the pretreatment cell library. These subpopulations demonstrated unique survivorship trajectories, beginning 30 h into selection and remaining well-separated following recovery from treatment. Comparing these subpopulations directly we observe enrichment for several pathways with markers genes remaining highly expressed post-treatment. Crucially, both subpopulations harbor a unique set of lineages which are found to survive treatment. However, in the absence of treatment we find that one subpopulation displays a faster growth rate and is likely to outcompete the other in culture conditions. The more proliferative subpopulation is marked by enrichment of Myc targets, compared with enrichment of glycolysis and KRAS signaling in the less proliferative subpopulation. This data demonstrates that subclonal heterogeneity inherent within this TNBC cell model, drives differential cell responses to chemotherapy. Citation Format: Daylin Morgan, Amy Brock. Characterizing subpopulation response to doxorubicin in a barcode-labeled triple negative breast carcinoma cell line [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 111.