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Single cell RNA trajectory analysis reveals a CD9 positive cell state to contribute to exit from stem cell-like and embryonic diapause states and transit to drug resistant states

ABSTRACT: Single cell RNA trajectory analysis reveals a CD9 positive cell state to contribute to exit from stem cell-like and embryonic diapause states and transit to drug resistant states

PROVIDER: PRJNA913570 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22801567.fastq.gz	Fastqsanger.gz
	SRR22801568.fastq.gz	Fastqsanger.gz
	SRR22801569.fastq.gz	Fastqsanger.gz
	SRR22801570.fastq.gz	Fastqsanger.gz

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Similar Datasets

CD9 contributes to exit from a stem cell-like and embryonic diapause states and transit to drug resistant states

Project description:In order to identify state changes that mediate the transition from sensitive to a resistant cell states, we applied RNA velocity analysis to an existing single-cell RNAseq (scRNAseq) dataset of BRD4 inhibitor sensitive and resistant SUM149 and SUM159 triple negative breast cancer cell lines. Both SUM149 and SUM159 cell lines treated with or without JQ1 had similar cell communities and trajectories including a stem cell-like and embryonic diapause (SCLED) cell state, a transiting cell state and a number of drug resistant states. Interestingly a transcriptional signature derived from the transiting state but not the SCLED state was associated with worsened outcomes in basal-like breast cancer patients as well as with a micrometastasis signature suggesting that the ability to transit from the SCLED state to drug resistant states could contribute to patient outcomes. The shift from the SCLED state to a transiting cell state was characterized by elevated expression of the CD9 tetraspanin. CD9 knockdown sensitized SUM149 tumor cells to JQ1 in vitro and in vivo trapping cells in the SCLED state and limiting transit to resistant cell states. CD9 knockdown sensitized SUM149 to multiple additional cytotoxic drugs suggesting a generalized role in drug resistance. Thus, CD9 appears to be critical for the ability of triple negative breast cancer cells to escape from a stem cell-like/embryonic diapause state and transition into a treatment resistant state.

2022-08-25 | GSE196952 | GEO

Single cell RNA trajectory analysis reveals a CD9 positive cell state to contribute to exit from stem cell-like and embryonic diapause states and transit to drug resistant states

Project description:Bromo- and extra-terminal domain (BET) inhibitors (BETi) have been shown to decrease tumor growth in preclinical models and clinical trials. However, toxicity and rapid emergence of resistance have limited their clinical implementation. To identify state changes underlying acquisition of resistance to the JQ1 BETi, we reanalyzed single-cell RNAseq data from JQ1 sensitive and resistant SUM149 and SUM159 triple negative breast cancer cell lines. Parental and JQ1-resistant SUM149 and SUM159 exhibited a stem cell-like and embryonic diapause (SCLED) cell state as well as a transitional cell state between the SCLED state existing both treatment naïve and treated cells, and a number of JQ1 resistant cell states. A transitional cell state transcriptional signature but not a SCLED state transcriptional signature predicted worsened outcomes in basal-like breast cancer patients suggesting that transit from the SCLED state to drug resistant states contributes to patient outcomes. Entry of SUM149 and SUM159 into the transitional cell state was characterized by elevated expression of the CD9 tetraspanin. Knockdown or inhibition of CD9 sensitized cells to multiple targeted and cytotoxic drugs in vitro. Importantly, CD9 knockdown or blockade sensitized SUM149 to JQ1 in vivo by trapping cells in the SCLED state and limiting transit to resistant cell states. Thus, CD9 appears to be critical for transition from a SCLED state into treatment resistant cell states and warrants exploration as a therapeutic target in basal-like breast cancer.

2023-06-01 | GSE221183 | GEO

CD9 contributes to exit from a stem cell-like and embryonic diapause states and transit to drug resistant states

Project description:CD9 contributes to exit from a stem cell-like and embryonic diapause states and transit to drug resistant states

| PRJNA808072 | ENA

Next generation sequencing of Coccinella septempunctata L. with non-diapause, diapause, and diapause-terminated states

Project description:The most commonÂ ladybird beetle, Coccinella septempunctata L., is an excellent predator of crop pests such as aphids and white flies, and it shows a wide range of adaptability, a large appetite and a high reproductive ability. In this study, we collected female adults in three different states, i.e., non-diapause, diapause and diapause termination, for transcriptome sequencing. The experimental insects consisted of three different states as follows: Non-diapause female insects were reared at 24Â±1Â°C, with a RH of 70Â±10% and a 16:8 h light: dark (L: D) photoperiod and collected after their first oviposition. Female adults in diapause were reared at 18Â±1Â°C at an RH of 70Â±10% and a 10:14-h (L:D) photoperiod. The experimental diapause insects were collected after 30 days. Diapause-terminated adults were transferred to another climatic cabinet with the 30-day diapause insects and reared under the same conditions as the non-diapause insects. After their first oviposition, the female insects were collected and stored at -80Â°C. Three biological replicates per treatment (non-diapause, diapause, diapause-terminated) were sequenced using Illumina HiSeq 2500.

2016-06-01 | E-GEOD-75645 | biostudies-arrayexpress

Next generation sequencing of Coccinella septempunctata L. with non-diapause, diapause, and diapause-terminated states

Project description:The most common ladybird beetle, Coccinella septempunctata L., is an excellent predator of crop pests such as aphids and white flies, and it shows a wide range of adaptability, a large appetite and a high reproductive ability. In this study, we collected female adults in three different states, i.e., non-diapause, diapause and diapause termination, for transcriptome sequencing.

2016-06-01 | GSE75645 | GEO

Single-cell trajectory analysis reveals a CD9 positive state to contribute to exit from stem cell-like and embryonic diapause states and transit to drug-resistant states.

Project description:Bromo- and extra-terminal domain (BET) inhibitors (BETi) have been shown to decrease tumor growth in preclinical models and clinical trials. However, toxicity and rapid emergence of resistance have limited their clinical implementation. To identify state changes underlying acquisition of resistance to the JQ1 BETi, we reanalyzed single-cell RNAseq data from JQ1 sensitive and resistant SUM149 and SUM159 triple-negative breast cancer cell lines. Parental and JQ1-resistant SUM149 and SUM159 exhibited a stem cell-like and embryonic diapause (SCLED) cell state as well as a transitional cell state between the SCLED state that is present in both treatment naïve and JQ1 treated cells, and a number of JQ1 resistant cell states. A transitional cell state transcriptional signature but not a SCLED state transcriptional signature predicted worsened outcomes in basal-like breast cancer patients suggesting that transit from the SCLED state to drug-resistant states contributes to patient outcomes. Entry of SUM149 and SUM159 into the transitional cell state was characterized by elevated expression of the CD9 tetraspanin. Knockdown or inhibition of CD9-sensitized cells to multiple targeted and cytotoxic drugs in vitro. Importantly, CD9 knockdown or blockade sensitized SUM149 to JQ1 in vivo by trapping cells in the SCLED state and limiting transit to resistant cell states. Thus, CD9 appears to be critical for the transition from a SCLED state into treatment-resistant cell states and warrants exploration as a therapeutic target in basal-like breast cancer.

| S-EPMC10403509 | biostudies-literature

TRANSIT

Project description:TRANSIT

| PRJEB39096 | ENA

Multiomic Analysis of Adult Diapause in Drosophila melanogaster Identifies Hallmarks of Cellular Quiescence [RNA-Seq]

Project description:Diapause and diapause-like states constitute natural, inducible, and evolutionarily conserved examples of lifespan plasticity that are well-suited to represent physiologically accurate models for longevity. We integrated ATAC-seq and RNA-seq technologies to probe the transcriptional regulatory pathways controlling lifespan plasticity in diapause.

2022-09-10 | GSE212863 | GEO

Multiomic Analysis of Adult Diapause in Drosophila melanogaster Identifies Hallmarks of Cellular Quiescence [ATAC-seq]

2022-09-10 | GSE212862 | GEO

A genome wide CRISPR/Cas9 screening to identifiy potential embryonic diapause and diapause-like cancer cell survival genes

Project description:Diapause-like cancer cells represent a fuel for tumor relapse and strategies that leads to their elimination could be helpful in the context of minimal residual disease and tumor relapse. Here, through a genome-wide CRISPR/Cas9 screen performed in mouse embryonic stem cells undergoing diapause, we identify different genes potentially involved in the survival of diapause-like cancer cells. Further validation experiments in cancer cell lines led to the identification of the pathway NRF2-KEAP1, the 1C metabolism and the DNA methyltransferase DNMT1 as pathways involved in the survival of diapause-like cancer cells.

2024-02-01 | GSE251714 | GEO

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