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Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells

ABSTRACT: Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells

PROVIDER: PRJNA980241 | ENA |

REPOSITORIES: ENA

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Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq]

Project description:Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq]

| PRJNA980249 | ENA

Long-term multi-modal recording reveals unpredictable nongenetic adaptation routes in dormant breast cancer cells. [gBarcodes]

Project description:Long-term multi-modal recording reveals unpredictable nongenetic adaptation routes in dormant breast cancer cells. [gBarcodes]

| PRJNA980235 | ENA

Long-term multi-modal recording reveals unpredictable nongenetic adaptation routes in dormant breast cancer cells. [WGS]

Project description:Long-term multi-modal recording reveals unpredictable nongenetic adaptation routes in dormant breast cancer cells. [WGS]

| PRJNA980234 | ENA

Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [RNA-Seq]

Project description:Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [RNA-Seq]

| PRJNA980226 | ENA

Long-term multi-modal recording reveals unpredictable nongenetic adaptation routes in dormant breast cancer cells. [gBarcodes]

Project description:Patients diagnosed with hormone dependent breast cancer (HDBC) receive five or more years of adjuvant endocrine therapies (ET). Adjuvant treatment delays relapse by targeting hidden micro-metastatic deposits, yet up to 50% of treated patients experience recurrent disease, often many years after surgery. The mechanisms driving these subtype-specific clinical dynamics are largely unknown but likely involve dormancy2. We developed two approaches to study the long-term fate of dormant cells in unprecedented details. Firstly, we took advantage of a rare cohort of patients treated upfront with first line ETs until progression to dissect the contribution of genomic events to tumour awakening. Next, we developed a first of its kind in vitro evolutionary study to systematically record adaptive strategies of individual clonal lineages in parallel unperturbed systems during a period of several months. Collectively our data suggest that ETs induce an inherently unstable persister dormant state in a stochastically selected fraction of lineages. Over time, single cells spontaneously escape dormancy and divergently adapt via heritable transcriptional reprogramming, often developing distinct collateral resistance. Overall, this study uncovers previously unsuspected roles for non-genetic plasticity during dormancy with profound clinical implications for breast cancer.

2024-04-16 | GSE234174 | GEO

Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [scRNA-Seq]

Project description:Patients diagnosed with hormone dependent breast cancer (HDBC) receive five or more years of adjuvant endocrine therapies (ETs). Adjuvant ETs delay relapse by targeting clinically undetectable micro-metastatic deposits, yet up to 50% of patients receiving ET relapse at a constant rate over the course of decades after surgery. The mechanisms driving these clinical dynamics are largely unknown but likely involve dormancy. We developed two approaches to study the fate of dormant cells in long-term experiments. Firstly, we profiled samples from late relapse (10-35 yrs.) and patients treated with 16-44 months of neoadjuvant ETs until progression to dissect the contribution of genetic and transcriptional changes to tumour awakening. Next, we developed a first of its kind in vitro evolutionary study to systematically record adaptive strategies of individual lineages in unperturbed parallel experiments through several months. Collectively our data demonstrate that ETs induce a heritable cell state transition into dormancy via epigenetic reprogramming. Single lineages with divergent phenotypes awaken unpredictably via epigenetic erosion. Targeting the dormant epigenome shows promising activity against adapting cancer cells. Overall, this study uncovers the contribution of epigenetic adaptation to the evolution of resistance to ETs with profound implications for breast cancer.

2024-04-16 | GSE234181 | GEO

Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells [RNA-Seq]

2024-04-16 | GSE234171 | GEO

Long-term multi-modal recording reveals unpredictable nongenetic adaptation routes in dormant breast cancer cells. [WGS]

Project description:Patients diagnosed with hormone dependent breast cancer (HDBC) receive five or more years of adjuvant endocrine therapies (ET). Adjuvant treatment delays relapse1,2 by targeting hidden micro-metastatic deposits, yet up to 50% of treated patients experience recurrent disease, often many years after surgery1. The mechanisms driving these subtype-specific clinical dynamics are largely unknown but likely involve dormancy2. We developed two approaches to study the long-term fate of dormant cells in unprecedented details. Firstly, we took advantage of a rare cohort of patients treated upfront with first line ETs until progression to dissect the contribution of genomic events to tumour awakening. Next, we developed a first of its kind in vitro evolutionary study to systematically record adaptive strategies of individual clonal lineages in parallel unperturbed systems during a period of several months. Collectively our data suggest that ETs induce an inherently unstable persister dormant state in a stochastically selected fraction of lineages. Over time, single cells spontaneously escape dormancy, often without developing resistance. Ultimately, single lineages and divergently divergently adapt via heritable transcriptional reprogramming, often developing distinct collateral resistance. Overall, this study uncovers previously unsuspected roles for non-genetic plasticity during dormancy with profound clinical implications for breast cancer.

2024-04-16 | GSE234173 | GEO

Long-term multi-modal recording reveals epigenetic adaptation routes in dormant breast cancer cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-04-16 | GSE234185 | GEO

Transcriptional changes in dormant and non_dormant potato meristems

Project description:RNA was sequenced from meristems excised from dormant and non-dormant potato tubers harvested from four different harvest years. Expression based on mapped RNA-sequences was accomplished from excised meristems from fall harvested (dormant tubers) and the same harvested tubers were stored under standard commercial conditions until sprouting was present (non-dormant). The experiment was replicated for four different harvest years.

2014-09-24 | E-GEOD-61690 | biostudies-arrayexpress

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