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Identification of a shared drug-tolerant persister program in triple-negactive breast cancer across treatments and patients [RNA-Seq]

ABSTRACT: Acquisition of resistance to anti-cancer therapies is a multistep process, which initiates with the survival of drug tolerant persister cells. Understanding the mechanisms driving the emergence of drug tolerant persister cells remains challenging, primarily because of their limited accessibility in patients. Here, using multiple patient-derived models to isolate persister cells, we show these cells are transcriptionally plastic in vivo and return to a common treatment-naïve like state upon relapse, regardless of the treatment they have been exposed to. We reveal hallmarks of the persister state in TNBC across treatment modalities: high expression of basal keratins together with activation of a stress response and inflammation pathways. HER2+ breast and lunger cancer cells also activate these hallmarks of drug tolerance in response to targeted therapies. Leveraging gene regulatory networks, we identify AP-1, NFKB and IRF/STAT as the key drivers of this hallmark persister state. As a proof of concept, we show that FOSL1 - an AP-1 member - is sufficient to drive cells to the persister state by binding enhancers and reprogramming the transcriptome of cancer cells. On the contrary, cancer cells without FOSL1 have a decreased ability to reach the persister state. By defining hallmarks of drug persistence to multiple therapies of the standard of care in TNBC, our study provides a resource to design novel combination therapeutic strategies to limit resistance.

ORGANISM(S): Homo sapiens

PROVIDER: GSE303200 | GEO | 2025/09/22

REPOSITORIES: GEO

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Identification of a shared drug-tolerant persister program in triple-negative breast cancer across treatments and patients [CUT&Tag]

Project description:Acquisition of resistance to anti-cancer therapies is a multistep process, which initiates with the survival of drug tolerant persister cells. Understanding the mechanisms driving the emergence of drug tolerant persister cells remains challenging, primarily because of their limited accessibility in patients. Here, using multiple patient-derived models to isolate persister cells, we show these cells are transcriptionally plastic in vivo and return to a common treatment-naïve like state upon relapse, regardless of the treatment they have been exposed to. We reveal hallmarks of the persister state in TNBC across treatment modalities: high expression of basal keratins together with activation of a stress response and inflammation pathways. HER2+ breast and lunger cancer cells also activate these hallmarks of drug tolerance in response to targeted therapies. Leveraging gene regulatory networks, we identify AP-1, NFKB and IRF/STAT as the key drivers of this hallmark persister state. As a proof of concept, we show that FOSL1 - an AP-1 member - is sufficient to drive cells to the persister state by binding enhancers and reprogramming the transcriptome of cancer cells. On the contrary, cancer cells without FOSL1 have a decreased ability to reach the persister state. By defining hallmarks of drug persistence to multiple therapies of the standard of care in TNBC, our study provides a resource to design novel combination therapeutic strategies to limit resistance.

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Identification of a shared drug-tolerant persister program in triple-negative breast cancer across treatments and patients [CITE-seq]

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Gene expression profiling of drug-tolerant persister BT474 breast cancer cells derived from lapatinib treatment

Project description:Acquired drug resistance prevents targeted cancer therapy from achieving stable and complete responses. Emerging evidence implicates a key role for nonmutational mechanisms including changes in cell state during early stages of acquired drug resistance. Targeting nonmutational resistance may therefore present a therapeutic opportunity to eliminate residual surviving tumor cells and impede relapse. A variety of cancer cell lines harbor quiescent, reversibly drug-tolerant âpersisterâ cells which survive cytotoxic drugs including targeted therapies and chemotherapies. These persister cells survive drug through nonmutational mechanisms which are poorly understood. Specifically targeting persister cells is a promising strategy to prevent tumor relapse. We sought to identify therapeutically exploitable vulnerabilities in persister cells using the HER2-amplified breast cancer line BT474 as an experimental model. Similar to other persister cell models, upon treatment with the HER2 inhibitor lapatinib (2uM concentration) for nine or more days, the majority of BT474 cells die, revealing a small population of quiescent surviving persister cells. Removal of lapatinib allows the persister cells to regrow and to re-acquire sensitivity to lapatinib. Subsequent lapatinib treatment re-derives persister cells. The reversibility of persister cell drug resistance indicates a nonmutational resistance mechanism. Here we provide RNAseq gene expression profiling data generated from parental BT474 cells compared to BT474 persister cells generated from nine days of treatment with 2 uM lapatinib. These data can be used to identify genes and pathways which are upregulated in persister cells, revealing potential therapeutic targets. 3 biological replicates of BT474 persister cells, two biological replicates of BT474 parental cells

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