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Gene expression profiles of mouse embryonic stem cells (mESCs) after genetic depletion of Id1 and knock-down of Zrf1

ABSTRACT: Id proteins are dominant negative regulators within the HLH family of proteins. In embryonic stem cells (ESCs), Id1 and Id3 maintain the pluripotent state by preventing neural differentiation. The Id1-interacting protein Zrf1 plays a crucial role as a chromatin-bound factor in specification of the neural fate from ESCs. Here, we show that Id1 blocks Zrf1 recruitment to chromatin, thus preventing the activation of neural genes during ESC differentiation. Moreover, genetic deletion of Id1 in ESCs caused misexpression of more than 6000 genes. Interestingly, the expression of almost half of those genes was restored upon further depletion of Zrf1. We therefore identified Zrf1 as a transcriptional regulator downstream of Id1 in ESCs.

ORGANISM(S): Mus musculus

PROVIDER: GSE58627 | GEO | 2014/11/05

SECONDARY ACCESSION(S): PRJNA253098

REPOSITORIES: GEO

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Project description:The diagnosis of B-Cell acute lymphoblastic leukemia (B-ALL) in adults often carries a poor prognosis. ID1 and ID3 genes have been identified as predictors of poor response in Colombian adult B-ALL patients, playing roles in cancer development. In different cancer models, these genes have been associated with immune regulator populations within the tumor immune microenvironment (TIME). B-ALL development alters the immune cell composition and the bone marrow (BM) tumor microenvironment, affecting disease progression and response to therapy. This study analyzes gene expression levels of ID1 and ID3 in relation to TIME and immune evasion. This exploratory study analyzed BM samples from 10 B-ALL adult patients diagnosed at the National Cancer Institute of Colombia. First, RT-qPCR was used to assess ID1 and ID3 expression in BM tumor cells. Flow cytometry characterized immune populations in the TIME. RNA-seq evaluated immune genes associated with B-ALL immune response, while xCell and cytosig analyzed TIME cell profiles and cytokines. Pathway analysis, gene ontology, and differential gene expression (DEGs) were examined, with functional enrichment analysis performed using KEGG ontology. Patients were divided into two groups based on ID1 and ID3 expression, namely basal and overexpression. A total of 94 differentially expressed genes were identified between these groups, with top overexpressed genes associated with neutrophil pathways. Gene set enrichment analysis revealed increased expression of genes associated with neutrophil degranulation, immune response-related neutrophil activation, and neutrophil-mediated immunity. These findings correlated with xCell data. Overexpression group showed significant differences in neutrophils (p=0.0008), monocytes (<0.0001) and CD4+ naive T cells (p=0.0240) compared to basal group patients. Microenvironment and immune scores were also significantly different (p=0.0016 and p=0.0017, respectively), consistent with the flow cytometry results. Elevated cytokine levels associated with neutrophil activation supported these findings. Validation was performed using the TARGET and MILE B-ALL cohorts. Our results show important differences between the expression level of ID1 and ID3 in cancer cells and the populations of TIME, suggesting a role in evading the immune response of ID1 and ID3 in B-ALL, mainly related to neutrophil pathways.

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Gene expression profiles of mouse embryonic stem cells (mESCs) after genetic depletion of Id1 and knock-down of Zrf1

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