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Leukemia dynamics and heterogeneity traced by barcoding in a pre-clinical Cbx7 mouse model

ABSTRACT: Gene expression analysis of different leukemia types after overexpression of Cbx7 in mice hematopoietic stem and progenitor cells followed by transplantation. Mice developed three different types of leukemia, 1) erythroid, 2) T-cell, 3) undifferentiated, as shown in K.Klauke et al. Nat Cell Biol 2013 Total RNA obtained from spleen cells (unsorted) was extracted

ORGANISM(S): Mus musculus

SUBMITTER: Leonid Bystrykh

PROVIDER: E-GEOD-56820 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Leukemia dynamics and heterogeneity traced by barcoding in a pre-clinical Cbx7 mouse model

Project description:Gene expression analysis of different leukemia types after overexpression of Cbx7 in mice hematopoietic stem and progenitor cells followed by transplantation. Mice developed three different types of leukemia, 1) erythroid, 2) T-cell, 3) undifferentiated, as shown in K.Klauke et al. Nat Cell Biol 2013

2014-10-01 | GSE56820 | GEO

Polycomb CBX7 represses expression of tumor suppressor genes

2009-09-23 | GSE10541 | GEO

Polycomb CBX7 represses expression of tumor suppressor genes

Project description:Polycomb CBX7 was stably expressed in embryonal carcinoma cells in order to identify target genes. The study was specifically geared toward unveiling gene targets that are susceptible to DNA hypermethylation in adult cancer. A number of CBX7 target tumor suppressor genes were thereby identified and used in further studies to characterize the mechanism surrounding CBX7 mediated gene suppression. Keywords: CBX7 target gene identification A cDNA encoding the ORF of polycomb CBX7 under the control of EF1alpha promoter was transfected into the Tera-2 embryonal carcinoma cell line. Empty vector was used to transfect control cells. The cells were subject to stable selection using puromycin and a pooled population of CBX7 overexpressing cells was established. Gene expression analysis was performed by comparing the gene expression profile of CBX7 cells to empty vector control cells.

2009-09-23 | E-GEOD-10541 | biostudies-arrayexpress

Genes regulated by CBX7

Project description:We analyzed the expression profile of a thyroid carinoma cell line after the restoration of CBX7 expression.

2014-06-01 | E-MTAB-2420 | biostudies-arrayexpress

Consequence of knock down of CBX7 in multiple cell lines

Project description:We conduct an experiment where CBX7 is knocked down in 4 different cell lines: A549, H1299, K562 and THP-1. After culturing these cell lines for three days with or without knockdown of CBX7, we then perform RNA sequencing (RNA-seq) to assess the impact.

2024-03-01 | GSE254063 | GEO

CBX7 is a tumour suppressor that inhibits bladder cancer

Project description:The Polycomb Group Proteins (PcG) are epigenetic regulatory complexes, dysregulation of which has been associated with multiple biological processes, including maintenance of cell identity, differentiation, proliferation, and cancer progression.PcGs form two multiprotein complexes, Polycomb repressive complex 1 (PRC1) and PRC2(1).The PRC2 protein complex mainly consists of Early embryonic deficient (EED), Suppressor of Zeste (SUZ12) and Enhancer of Zeste (EZH), which can catalyzes the trimethylation of histone H3 lysine 27 (H3K27me3), thereby leaving a transcriptionally repressive mark on the chromatin . Such alterations are recognized and read by canonical PRC1 which is composed of CBX (polycomb), PCGF (polycomb group factor), HPH (human polyhomeotic homolog), and the E3-ligase protein (RING) that catalyzes the monoubiquitination of histone H2A on lysine 119 (H2AK119ub1). The H3K27me3 mark is identified by and binds to the chromodomain within the CBX protein in PRC1, thereby ubiquitinating H2AK119 via the RING proteins. The interaction of PRC2 and PRC1 in chromatin contributes to chromatin compaction and transcriptional silencing of target genes.There are five chromobox proteins in humans, CBX2, 4, 6, 7 and 8. Increasing evidence supports essential roles of CBX proteins in tumorigenesis. Remarkably, CBX proteins have shown an opposite function in distinct cancer types in tumor development. For example, CBX7 is overexpressed in ovarian and prostate cancer , implying its oncogenic role in these tumor types. In contrast, CBX7 functions as a tumor suppressor and loss of CBX7 has been associated with increasing the malignancy grade in bladder, breast, pancreatic, glioma, and colon carcinomas (3 4 5 6 7), but its tumor suppression mechanism is unclear.

2021-06-15 | GSE158244 | GEO

Transcriptome profiling after CBX7 knockdown in LNCaP cells

Project description:An analysis of transcriptomal changes upon knockdown of CBX7 in prostate cancer LNCaP cells.

2017-07-05 | E-MTAB-3730 | biostudies-arrayexpress

Transcriptome Analysis of Cbx7 Knockdown Effects in Ovarian Clear Cell Adenocarcinoma Cell Lines

Project description:Cbx7 knockdown resulted in increase of genes related with apoptosis and inflammation. Expression microarray was performed using RNA extracted from 2 ovarian clear cell adenocarcinoma cell lines, namely, KOC-7C and TOV21G, either trancduced by Cbx7 siRNA or control.

2013-11-01 | E-GEOD-47146 | biostudies-arrayexpress

Transcriptome Analysis of Cbx7 Knockdown Effects in Ovarian Clear Cell Adenocarcinoma Cell Lines

Project description:Cbx7 knockdown resulted in increase of genes related with apoptosis and inflammation.

2013-11-01 | GSE47146 | GEO

Denaturing CLIP (dCLIP) pipeline identifies discrete RNA footprints on chromatin-associated proteins and reveals that CBX7 targets 3’UTRs to regulate mRNA expression

Project description:Interaction networks between chromatin complexes and long noncoding RNAs have become a recurrent theme in epigenetic regulation. However, technical limitations have precluded identification of RNA binding motifs for chromatin-associated proteins. Here we add a denaturation step to UV-crosslink RNA immunoprecipitation (dCLIP), and apply dCLIP to mouse and human chromobox homolog 7 (CBX7), an RNA-binding subunit of Polycomb repressive complex 1 (PRC1). In both species, CBX7 predominantly binds 3’ untranslated regions (UTRs) of messenger RNAs. CBX7 binds with a median RNA “footprint” of 171-183 nucleotides, the small size of which facilitates motif identification by bioinformatics. We find four families of consensus RNA motifs in mouse, and independent analysis of human CBX7 dCLIP data identifies similar motifs. Their mutation abolishes CBX7 binding in vitro. Pharmacological intervention with antisense oligonucleotides paradoxically increases CBX7 binding and enhances gene expression. These data support the utility of dCLIP and reveal an unexpected functional interaction between CBX7 and the 3’UTRs of mRNA.interacts with a range of transcripts, it predominantly binds 3’ untranslated regions (UTRs) of messenger RNAs. CBX7 has a median RNA “footprint” of 171 nucleotides, enabling identification of four families of motifs that tend to co-cluster in the 3’UTR. Manipulating the CBX7-3’UTR interactions and motifs with antisense oligonucleotides results in upregulation of mRNA and protein expression, thereby validating the dCLIP method and revealing functional interactions between CBX7 and mRNA.

2017-10-25 | GSE88823 | GEO

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