Ontology highlight
ABSTRACT:
PROVIDER: PRJNA459485 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7119494.fastq.gz | Fastqsanger.gz | |||
| SRR7119495.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:CD47 is a key innate immune checkpoint that enables tumor cells to evade macrophage-mediated clearance. To systematically identify genetic regulators of CD47 surface expression, we performed FACS-based genome-wide CRISPR screens in three murine cancer cell lines, B16 (melanoma), MC38 (colon adenocarcinoma), and EMT6 (breast carcinoma). Comparative analysis of cells with high or low CD47 surface expression using DrugZ revealed CD47 itself as the top hit, validating the screens. Notably, DNAJC13 emerged as a consistent and robust regulator of CD47 expression across all three cell lines. Functional validation using DNAJC13-knockout cells confirmed a significant reduction in CD47 surface levels. Furthermore, in co-culture assays with macrophages, DNAJC13-deficient tumor cells exhibited increased susceptibility to phagocytosis, supporting a functional role for DNAJC13 in innate immune evasion. Finally, we verify that DNAJC13-knockout decrease tumor burden when treated with CD47 blockade. Overall, this study highlights a previously unrecognized regulator of CD47 and demonstrates the utility of high-throughput FACS-based CRISPR screening to uncover modulators of key immune checkpoint pathways.
2026-01-05 | GSE315389 | GEO
Project description:At least 70% of the human protein-coding genes possess more than one poly(A) site (PAS) and undergo a phenomenon known as alternative polyadenylation (APA), leading to distinct transcripts from a single gene. Previously, it has been demonstrated that shortening or lengthening of mRNA, resulting from the APA, could be observed in physiological and pathological conditions. Nevertheless, factors and cellular mechanisms responsible for the APA are largely unknown. CD47 protein localization was previously demonstrated to be regulated by APA. Here, we showed that core 3′ end processing factors regulate the different CD47 mRNA transcripts. This finding led us to develop an immunofluorescence staining method that simultaneously detects cell surface and intracellular CD47 protein and visualizes altered APA. Using this method, we detected the alterations of CD47 protein localization upon the depletion of the long 3′ untranslated region (UTR) mRNA isoform of CD47 or CFIm25. To systematically elucidate potential novel regulators of APA, we integrated an approach using immunofluorescence staining of cell surface and intracellular CD47 with genome-wide CRISPR screen coupled with pooled single guide RNA (sgRNA) libraries targeting human protein-coding genes. The functional genetic screens and systematic analysis of RNA-seq data revealed POLDIP2 as the potential novel regulator of APA that has global impact on APA regulation. These findings suggest that the study of novel identified APA regulators could lead to a deeper understanding of detailed molecular mechanisms governing APA under physiological and pathological conditions.
2025-08-11 | GSE288919 | GEO
Project description:HAP1 haploid genetic screen for LUJV
| PRJNA395972 | ENA
Project description:Haploid genetic screen for components of MLKL-mediated cell death
| PRJEB26694 | ENA
Project description:CD47 is a ubiquitous cell surface receptor that limits cell clearance by phagocytes that express its counter-receptor signal-regulatory protein-α and directly regulates T cell immunity by interacting with its inhibitory ligand thrombospondin-1. Murine natural killer (NK) cells express higher levels of CD47 than other lymphocytes, but the role of CD47 in regulating NK cell homeostasis and immune function remains unclear. Cd47-/- mice exhibited depletion of NK precursors in bone marrow, but antisense Cd47 knockdown or gene disruption resulted in a dose dependent accumulation of immature and mature NK cells in spleen. Cd47-/- mice were impaired in controlling chronic Clone-13 lymphocytic choriomeningitis virus (LCMV) infection, which was associated with depletion of splenic NK cells and loss of effector cytokine and interferon response gene expression in Cd47-/- NK cells. These data identify CD47 as a cell-intrinsic and systemic regulator of NK cell homeostasis and NK cell responses to viral infection.
2019-03-11 | GSE113980 | GEO
Project description:Signaling through the thrombospondin-1 receptor CD47 broadly limits cell and tissue survival of stress, but the molecular mechanisms are incompletely understood. We now show that loss of CD47 permits sustained proliferation of primary murine endothelial cells and enables these cells to spontaneously reprogram to form multipotent embryoid bodies. c-Myc, Klf4, Oct4, and Sox2 expression is elevated in CD47-null endothelial cells, in several tissues of CD47- or thrombospondin-1-null mice, and in a human T cell line lacking CD47. CD47 knockdown acutely increases mRNA levels of c-Myc and other stem cell transcription factors in cells and in vivo, whereas CD47 ligation by thrombospondin-1 suppresses c-Myc expression. The inhibitory effects of increasing CD47 levels can be overcome by maintaining c-Myc expression and are absent in cells with dysregulated c-Myc. Thus, CD47 antagonists enable cell self-renewal and reprogramming by overcoming negative regulation of c-Myc and other stem cell transcription factors. To identify gene expression changes associated with CD47 null cells, we compared the gene expression profile of these cells with WT endothelial cell, CD47 null Embryoid bodies cells and an established Embryonic Stem cell line.
2013-07-10 | E-GEOD-43133 | biostudies-arrayexpress
Project description:CD47 is a marker of self and a signaling receptor for thrombospondin-1 that is also a membrane
component of extracellular vesicles (EVs) released by various cell types. Previous studies identified CD47-dependent functional effects of EVs on target cells, mediated by delivery of their RNA contents, and enrichment of specific subsets of coding and noncoding RNAs in CD47+ EVs. Here, transcriptomic analyses of EVs released by human and murine cells revealed CD47-dependent enrichment of capped microRNAs and mRNAs. Knockdown or loss of CD47 in wild type Jurkat T cells or treatment with thrombospondin-1 enhanced levels of specific capped-RNAs released in EVs, and reexpressing CD47 in null cells decreased their levels. Mass spectrometry and co-immunoprecipitation identified specific interactions of CD47 with components of the exportin-1/Ran nuclear export complex and its known cargo proteins and between the CD47 cytoplasmic adapter ubiquilin-1 and the exportin-1/Ran complex. Interaction with CD47 was inhibited following alkylation of exportin-1 at Cys528 by leptomycin B. Leptomycin B treatment increased levels of cap-dependent RNAs and their association with exportin-1 in EVs released from wild type but not CD47-deficient cells. These results indicate that CD47
regulates the trafficking of cap-dependent RNAs to EVs through physical interactions with the exportin-1/Ran transport complex. Within the files, lmj1038 represents the control pulldown from CD47- JinB8 cells whereas lmj1039 is the CD47+ pulldown from wild-type Jurkat cells.
2021-03-01 | MSV000086969 | MassIVE
Project description:We undertook a unbiased genome-wide haploid genetic screen to identify new components in interferon lambda signaling. In addition, we performed a genome-wide screen to identify genes that repress spontaneous activation of interferon stimulated genes in the absence of interferon. Both of these screens were performed using a HAP1 cell line containing GFP reporter under the transcriptional regulation of the Interferon-Stimulated Response Element from IFIT2. We also overexpressed IL28RA (IFNLR1) in this cell line, in order to sensitize the cells to type III interferon
2017-07-25 | E-MTAB-5866 | biostudies-arrayexpress