Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance

Abstract

Resistance to cancer therapy is driven by both cell-intrinsic and microenvironmental factors. Previous work has revealed that multiple resistant cell fates emerge in melanoma following treatment with targeted therapy and that, in vitro, these resistant fates are determined by the transcriptional state of individual cells prior to exposure to treatment. What remains unclear is whether these resistant fates are shared across different genetic backgrounds and how, if at all, these resistant fates interact with the tumor microenvironment. Through spatial transcriptomics and single-cell RNA sequencing, we uncovered distinct resistance programs in melanoma cells shaped by both intrinsic cellular states and the tumor microenvironment. Consensus non-negative matrix factorization revealed shared intrinsic resistance programs across different cell lines, highlighting the presence of universal and unique resistance pathways. In patient samples, we demonstrated that these resistance programs coexist within individual tumors and associate with diverse immune signatures, suggesting that the tumor microenvironment and distribution of resistant fates are closely connected. Single-cell resolution spatial transcriptomics in xenograft models revealed both intrinsically determined and extrinsically influenced resistant fates. Overall, this work demonstrates that each therapy resistant fate coexists with a distinct immune microenvironment in tumors and that, in vivo, tissue features, such as regions of necrosis, can influence which resistant fate is adopted.

AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance

“…Previous results from our lab have shown that resistant colonies can come in multiple resistant types 20,34 , raising the possibility that the frequency of these different resistant types was different in the low-to-high-dose switch condition as compared to high or low dose alone. To assess this possibility, we used FateMap (see Goyal et al 2023 for more details) to quantify transcriptional heterogeneity across resistant colonies in all three conditions (Supp.…”

“…2C-D). At the same time, it is important to note that the fact that resistant cells can adopt different fates at low and high doses means that at least some degree of extrinsic conditions affect the ultimate state of the cell 34 , suggesting some degree of a programmed response as well as an encoding based on the initial state of the cell (see Discussion).…”