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Identify the role of host ATF4 on CAFs in the tumor microenvironment of small size B16F10 tumors

ABSTRACT: Identify the role of host ATF4 on CAFs in the tumor microenvironment of small size B16F10 tumors

PROVIDER: PRJNA671507 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12885978.fastq.gz	Fastqsanger.gz
	SRR12885979.fastq.gz	Fastqsanger.gz

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Identify the role of host ATF4 on CAFs in the tumor microenvironment of large size B16F10 tumors

Project description:To delineate the role of host ATF4 in the sequence of events leading to tumor growth, we performed transcriptional profiling at the single-cell level (scRNA-seq) in larger (300 mm3) size B16F10 tumors grown in Atf4wt/wt and Atf4D/D mice. We surprisingly detected impaired CAFs activation in Atf4D/D mice, based on the expression levels of Acta2 and Pdgfrb, as one of the most commonly used CAF markers. Among our key findings, we identified the vascular CAFs (vCAFs), a spatially distinct CAF subcluster featured by the highest levels of aSMA and PDGFRb, that were reduced in Atf4D/D mice.

2022-05-10 | GSE159994 | GEO

Identify the role of host ATF4 on CAFs in the tumor microenvironment of small size B16F10 tumors

Project description:To delineate the role of host ATF4 in the sequence of events leading to tumor growth, we performed transcriptional profiling at the single-cell level (scRNA-seq) in smaller (150 mm3) size B16F10 tumors grown in Atf4wt/wt and Atf4D/D mice. Among others, we observed striking differences in gene expression in a cluster that corresponds to CAFs. In this cluster, we identified 148 DE genes, including a significant downregulation of Col1a1 and Col1a2 in the Atf4D/D mice-grown tumors. Notably, the expression levels of aSMA and Pdgfrb were nearly absent in the tumors grown in Atf4D/D mice. Finally, after CAFs subclustering, we identified the vCAFs (vascular CAFs) that are considered essential for vascular development and angiogenesis to be significantly reduced in the Atf4D/D mice.

2022-05-10 | GSE159995 | GEO

Identify the role of host ATF4 on CAFs in the tumor microenvironment of large size and small size B16F10 tumors

Project description:Identify the role of host ATF4 on CAFs in the tumor microenvironment of large size and small size B16F10 tumors

| PRJNA671500 | ENA

Identify the role of host ATF4 on CAFs in the tumor microenvironment of large size B16F10 tumors

Project description:Identify the role of host ATF4 on CAFs in the tumor microenvironment of large size B16F10 tumors

| PRJNA671506 | ENA

Identify the role of host ATF4 on CAFs in the tumor microenvironment of large size and small size B16F10 tumors

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

2022-05-10 | GSE159996 | GEO

RNA-Seq experiment to identify genes regulated by ATF4

Project description:Activating Transcription Factor 4 (ATF4) is a transcription factor induced by the integrated stress response (ISR). This experiment is a genome-wide profiling of ATF4-dependent RNA expression in human HAP-1 cells. HAP-1 is a near-haploid human cell line that was derived from KBM-7 cells isolated from a patient with Chronic Myelogenous Leukemia. We analyzed WT and ATF4 KO cells. We induced ATF4 expression by mimicking amino acid starvation with the drug histidinol. RNA expression profiles were generated for WT and ATF4 KO HAP1 cells. ATF4 genes were mutated using Cas9 genome editing technology. Amino acid starvation was mimicked by treating WT and ATF4 KO cells with 2 mM histidinol for 24 hours, which increases ATF4 expression.

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RNA-Seq experiment to identify genes regulated by ATF4

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Project description:In this study, we demonstrated that deletion of the activating transcription factor 4 (ATF4) resulted in severely impaired HSC expansion in the fetal liver at E12.5 and E15.5. In contrast, generation of the first HSC population in the aorta-gonad-mesonephros region at E11.5 was not significantly affected. Furthermore, the HSC-supporting ability of both endothelial and stromal cells in fetal liver was significantly compromised in the absence of ATF4. Gene profiling using RNA-seq revealed down-regulated expression of a panel of cytokines in ATF4-/- stromal cells, including angiopoietin-like protein 3 (Angptl3) and vascular endothelial growth factor-A (VEGFA). To investigate the molecular pathways of ATF4 in the stromal cells and LSK cells in the fetal liver.

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Expression data from gemcitabine treated pancreatic CAFs

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