Melanoma subpopulations that rapidly escape MAPK pathway inhibition incur DNA damage and rely on stress signalling

Abstract

Despite the increasing number of effective anti-cancer therapies, successful treatment is limited by the development of drug resistance. While the contribution of genetic factors to drug resistance is undeniable, little is known about how drug-sensitive cells first evade drug action to proliferate in drug. Here we track the responses of thousands of single melanoma cells to BRAF inhibitors and show that a subset of cells escapes drug via non-genetic mechanisms within the first three days of treatment. Cells that escape drug rely on ATF4 stress signalling to cycle periodically in drug, experience DNA replication defects leading to DNA damage, and yet out-proliferate other cells over extended treatment. Together, our work reveals just how rapidly melanoma cells can adapt to drug treatment, generating a mutagenesis-prone subpopulation that expands over time.

How Neural Crest Transcription Factors Contribute to Melanoma Heterogeneity, Cellular Plasticity, and Treatment Resistance

“…Initially, melanoma cells expressed higher levels of MITF when exposed to BRAFi and MEKi, which was in line with a previous report of Smith et al [72], followed by dedifferentiation and a slow-cycling phenotype marked by a decrease of MITF and an increase in nerve growth factor receptor (NGFR) expression [118]. However, single-cell RNA sequencing revealed that a MITF low AXL high subpopulation was already present during this first phase of acquiring drug resistance [118]. Knockdown experiments showed that the cells were dependent on ATF4 expression to escape MAPK pathway inhibition [118].…”

“…Furthermore, ATF4 that suppresses MITF expression as described above plays also a role in acquired resistance to BRAFi and MEKi. Recently, Yang et al discovered that ATF4 stress signaling mediates to a rapid escape already within the first days after initiating MAPK pathway inhibition [118]. Initially, melanoma cells expressed higher levels of MITF when exposed to BRAFi and MEKi, which was in line with a previous report of Smith et al [72], followed by dedifferentiation and a slow-cycling phenotype marked by a decrease of MITF and an increase in nerve growth factor receptor (NGFR) expression [118].…”

“…Recently, Yang et al discovered that ATF4 stress signaling mediates to a rapid escape already within the first days after initiating MAPK pathway inhibition [118]. Initially, melanoma cells expressed higher levels of MITF when exposed to BRAFi and MEKi, which was in line with a previous report of Smith et al [72], followed by dedifferentiation and a slow-cycling phenotype marked by a decrease of MITF and an increase in nerve growth factor receptor (NGFR) expression [118]. However, single-cell RNA sequencing revealed that a MITF low AXL high subpopulation was already present during this first phase of acquiring drug resistance [118].…”

“…However, single-cell RNA sequencing revealed that a MITF low AXL high subpopulation was already present during this first phase of acquiring drug resistance [118]. Knockdown experiments showed that the cells were dependent on ATF4 expression to escape MAPK pathway inhibition [118].…”

Adaptation through the lens of single-cell multi-omics data

“…We can briefly mention two recent ones from cancer biology. Early (in the first three days) adaptation of melanoma cell population was investigated after application of a potent targeted anticancer drug dabrafenib, belonging to the family of so-called BRAF inhibitors [2]. Most of the cells adapt to such treatment by entering quiescence but some "escapees" manage to maintain their cell cycle and eventually outproliferate other cells.…”