Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The changes of transcription profiles of tumor cells with the deletion of components of PRC1 complex, and of the infiltrated NK cells.

ABSTRACT: We report the changes in the transcription profiles of the 4T1 breast cancer cells (control, RNF2 knockout (KO), and RSF1 KO), isolated and enriched from the tumor implanted in the 4th mammary pads by Fluorescence activated cell sorting, and the changes in the infiltrated NK cells. The transcription profiles were measured by RNA sequencing. We found that upon RNF2 KO or RSF1 KO, 4T1 tumor cells express multiple immune related genes, including chemokines, MHCII, and CD74 etc, which are otherwise repressed in cancer cells. We also found that the infiltrated NK cells in RNF2 KO tumors and RSF1 KO tumors express significantly higher levels of granzymes, compared to the NK cells infiltrated into control tumors, suggesting the activated status of these infiltrated NK cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE143352 | GEO | 2021/06/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

RNA-sequencing of tumor-infiltrated T cells in colorectal tumors

Project description:RNA-sequencing of tumor-infiltrated T cells in colorectal tumors

| PRJNA746001 | ENA

Role of remodeling and spacing factor 1 in histone H2A ubiquitination mediated gene silencing

Project description:Posttranslational modification of histones plays important roles in regulating chromatin-based nuclear processes. Histone H2A ubiquitination (H2Aub) is a prevalent modification and has been primarily linked to gene silencing; however, the mechanism by which H2Aub represses gene expression remains largely unclear. Here we report the identification of RSF1 (remodeling and spacing factor 1), a subunit of the RSF (remodeling and spacing factor) complex, as a novel H2Aub binding protein which mediates the repressive function of H2Aub on gene expression. RSF1 preferentially associates with H2Aub nucleosomes through a previously uncharacterized region designated as the ubiquitinated H2A binding (UAB) motif. RSF1 interacts with H2Aub nucleosomes specifically and the UAB motif is required for RSF1 to interact with H2Aub nucleosomes in vitro and in vivo. Genes regulated by RSF1 overlap significantly with genes regulated by RNF2 or Ring1B, the catalytic subunit of Polycomb repressive complex 1, in both human and mouse cells. RSF1 binds to gene promoter regions, and over 92% of H2Aub enriched genes, including the classic PRC1 target Hox genes, are co-bound by RSF1. Reduction of H2Aub levels by Ring1B knockout results in a significant reduction of RSF1 binding. RSF1 knockout does not affect RNF2/Ring1B or H2Aub levels but results in re-expression of H2Aub target genes, accompanied by a reduction in the spacing and stability of H2Aub nucleosomes. The direct role of RSF1 in repressing H2Aub target gene expression is further demonstrated by chromatin based in vitro transcription assay. Finally, RSF1 regulates Xenopus early embryonic development and gene expression in a fashion similar to that of PRC1 subunit Ring1A. Therefore, this study identifies RSF1 as a novel H2Aub binding protein and reveals that RSF1 contributes to H2Aub mediated gene silencing by maintaining a regular spaced, stable nucleosome array at promoter regions.

2018-02-16 | GSE93090 | GEO

Gene expression data of stromal cell subpopulations isolated from human lymph nodes (LNs) infiltrated with melanoma

Project description:Metastasis of human tumours to LNs is a universally negative prognostic factor. LN stromal cells (SCs) play a crucial role in enabling T cell responses, and since tumour metastases modulate their structure and function, this interaction may suppress immune responses to tumour antigens. However the SC subpopulations that respond to infiltration of malignant cells into human LNs have not been defined. Using microarray, we sought to assess gene expression profiles of two distinct SC subpopulations isolated from melanoma-infiltrated LNs. Our data demonstrate distinct profiles of two SC subpopulations isolated from melanoma-infiltrated LNs using fluorescence-activated cell sorting (FACS). FRCs express T cell modulating cytokines, chemokines and adhesion molecules, while CD34+ SCs predominantly express genes associated with ECM organization. Distinguishing between these two SC subpopulations in human LNs will now allow study of their respective impact on T cell responses to tumour antigens and clinical outcomes.

2020-06-26 | GSE150965 | GEO

Transcription profiling of mouse BALB/c strain animals injected with breast cancer 4T1-derived cells to investigate the role of epithelial to mesenchymal transition (EMT) in spontaneous breast cancer metastasis

Project description:Epithelial-mesenchymal transition (EMT) has been linked to cancer progression and metastatic propensity. The 4T1 tumor is a clinically relevant model of spontaneous breast cancer metastasis. Here we characterize 4T1-derived cell lines for EMT, in vitro invasiveness and in vivo metastatic ability. Contrary to expectations, the 67NR cells, which form primary tumors but fail to metastasize, express vimentin and N-cadherin, but not E-cadherin. 4T1 cells, however, express E-cadherin, are highly migratory and invasive, and metastasize to multiple sites. The 66cl4 metastatic cells display mixed epithelial and mesenchymal markers, but are less migratory and invasive than 67NR cells. These findings demonstrate that the metastatic ability of breast cancer cells does not correlate with genotypic and phenotypic properties of EMT per se, and suggest that other processes may govern metastatic capability. Gene expression analysis also has not identified differences in EMT markers, but has identified several candidate genes that may influence metastatic ability. Experiment Overall Design: Female BALB/c mice were injected with 1x10^6 viable cells (3 mice with 4T1/CMVLUC, 3 mice with 66cl4/CMVLUC, and 3 mice with 67NR/CMVLUC) into the right fourth mammary gland. 15 days after injection primary tumors were excised, and total RNA for microarray hybridization was isolated from the tumor part of laser capture microdissected sections.

2009-03-07 | E-GEOD-11259 | biostudies-arrayexpress

The transcriptome alteration in tumoral NK cells in response to dual or monotherapy of STING agonist and IL-35 blocking antibodies

Project description:To investigate the role of STING agonist and IL-35 blocking antibodies in the regulation of NK cell function, tumor-infiltrated NK cells were flow cytometrically separated from control (IgG), cGAMP, anti-IL-35, or combination treated groups We performed gene expression profiling analysis using data obtained from RNA-seq of tumor-infiltrated NK cells sorted from four groups.

2022-08-21 | GSE211386 | GEO

RNA sequencing of NlCSP11-infiltrated Nicotiana benthamiana

Project description:In order to find the differentially expressed RNAs and signaling pathways related to the dwarf phenotype induced by NlCSP11, 35S-NlCSP11, 35S-XopQ and 35S-GFP control were infiltrated into Nicotiana benthamiana. We analyzed the differentially expressed RNAs in the infiltrated leaves (NlCSP11_Z/XopQ_Z) and the upper uninfiltrated leaves (NlCSP11_U/XopQ_U) of N. benthamiana. KEGG annotation revealed a large number of differentially expressed RNAs involved in plant-pathogen interactions, indicating that NlCSP11 resulted in a more strong systemic resistance in N. benthamiana.

2024-05-30 | GSE267686 | GEO

RNA m6A methylation orchestrates cancer growth and metastasis via macrophage reprogramming

Project description:The CD45+ immune-infiltrated cells in B16 tumors from WT or KO mice were enriched. Then, pooled samples of mice per group were analyzed by single cell RNA sequencing （scRNA-seq）

2021-01-19 | GSE159156 | GEO

4T1 breast tumors: SPARC knock down primary tumors vs. Control primary tumors vs. Lung metastasis foci

Project description:Comparative analysis of the transcriptome of primary tumors generated from 4T1 cells transduced with a lentiviral vector expressing a siRNA against murine SPARC (4T1-C18), primary tumors generated from 4T1 cells transduced with a lentiviral vector expressing a scramble sequence (4T1-SCR) or lung metastasis foci from 4T1-SCR tumor-bearing mice (4T1-SCR MTTS). Three experimental conditions, 4T1-C18, 4T1-SCR and 4T1-SCR MTTS. Biological replicates: 4 4T1-C18, 4 4T1-SCR, 4 4T1-SCR MTTS independently grown in different mice. 2 days-old tumors and 30 days old lung foci. One replicate per array. All microarrays were processed the same day

2016-06-29 | E-GEOD-83831 | biostudies-arrayexpress

RNAseq of macrophages and NK cells from MC38 tumors with PtdSer externalization blockade

Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of tumor associated macrophages from WT MC38 tumors and Tmem30a KO tumors; and NK cells from WT and Xkr8 KO MC38 TILs

2022-06-04 | GSE200752 | GEO

RNA sequencing of NlCSP11-infiltrated Nicotiana benthamiana

Project description:RNA sequencing of NlCSP11-infiltrated Nicotiana benthamiana

| PRJNA1112406 | ENA