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Identification and targeting of extremely high-risk gamma delta T-ALL in children [RNA-seq]

ABSTRACT: STAG2/LMO2 subtype in T-ALL was investigated through integrative genomic analysis. H3K27ac HiChIP was used to investigate the impact of LMO2::STAG2 translocations in MOLT-14 and PER-117 cell lines. ChIP-seq was used to explore the effects of STAG2 inactivation by using gene-edited MOLT-14 and PF382 cell lines.

ORGANISM(S): Homo sapiens

PROVIDER: GSE243775 | GEO | 2024/03/01

REPOSITORIES: GEO

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Identification and targeting of extremely high-risk gamma delta T-ALL in children [HiChIP, ChIP and ATAC]

Project description:STAG2/LMO2 subtype in T-ALL was investigated through integrative genomic analysis. H3K27ac HiChIP was used to investigate the impact of LMO2::STAG2 translocations in MOLT-14 and PER-117 cell lines. ChIP-seq was used to explore the effects of STAG2 inactivation by using gene-edited MOLT-14 and PF382 cell lines.

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Expression profiling in cohesin mutant MCF10A epithelial and CMK leukaemia cells

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HiChIP data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out)

Project description:STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma. Using a CRISPR/Cas9 approach, we generated two STAG2 knock-out isogenic clones (A673_SA2m#1 and TC71_SA2m#2) derived from A673 and TC71 STAG2 wild type (WT) Ewing sarcoma cell line. A STAG2 rescue model (A673_SA2r) was generated by correcting the CRISPR mutation in the A673_SA2m#1 model. These STAG1/2 proficient and deficient models were profiled by CTCF HiChIP experiments. STAG2 isogenic models were also profiled by H3K27ac HiChIP experiments. Analyses of HiChIP data allowed to show that STAG2 promotes CTCF-anchored loop extrusion and cis-promoter and -enhancer interactions.

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Expression profiling in STAG2 mutant K562 cells

Project description:K562 (female chronic myelogenous leukemia) cells were CRISPR-Cas9 edited to contain STAG2 R614* mutation. STAG2 is encoded on the X-chromosome and normally mutation on one allele is sufficient for complete loss of STAG2 protein due to the wild type allele being mosaically silenced. However, we obtained both heterozygous and homozygous mutant lines that showed partial and complete loss of STAG2 protein respectively. We here examined the impact of STAG2 R614* mutation on gene expression and chromatin acessibilty.

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Identification and targeting of extremely high-risk gamma delta T-ALL in children

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

2024-03-01 | GSE243776 | GEO

HiChIP data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out)

Project description:HiChIP data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out)

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