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U2 IP-seq from K562 cells expressing SF3B1-3xFlag WT or SF3B1-3xFlag K700E

ABSTRACT: U2 IP-seq from K562 cells expressing SF3B1-3xFlag WT or SF3B1-3xFlag K700E

PROVIDER: PRJNA1179921 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR31169814_1.fastq.gz	Fastqsanger.gz
	SRR31169814_2.fastq.gz	Fastqsanger.gz
	SRR31169815_1.fastq.gz	Fastqsanger.gz
	SRR31169815_2.fastq.gz	Fastqsanger.gz
	SRR31169816_1.fastq.gz	Fastqsanger.gz

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U2 IP-seq from K562 cells expressing SF3B1-3xFlag WT or SF3B1-3xFlag K700E

Project description:The branch site / 3' splice site recognition machinery is a hotspot for disease-associated mutations. A single amino acid substitution K700E in the U2 snRNP-specific protein SF3B1 is frequently associated with cancer and is particularly common among myelodysplastic syndromes. The goal of this study is to employ the U2 IP-seq strategy in examining the differences in branch site selection in cells expressing wild type SF3B1 vs those carrying the K700E mutation.

2025-01-28 | GSE280659 | GEO

RNA-seq of sorted KPC Sf3b1-K700E murine PDAC cells

Project description:We established a mouse model of KrasG12D, Trp53-/- and Sf3b1-K700E murine pancreatic cancer to elucidate the impact of the SF3B1 mutation found in human PDAC on the KPC mouse model.

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Chronic Lymphocytic Leukemia MEC1 SF3B1 K700E and Wild Type Cell Lines' RNA-seq after Treatment with H3B-8800 Splicing Modulator.

Project description:To study the impact of SF3B1 mutations on alternative splicing and the effect of H3B-8800 splicing modulator in wild type and SF3B1-mutant chronic lymphocytic leukemia cells, we established SF3B1 K700E MEC1 CLL isogenic cell line and carried out RNA deep sequencing in SF3B1 wild type and K700E MEC1 cell lines upon H3B-8800 treatment.

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RNA Sequencing of Nalm-6 SF3B1 K700E MT and Nalm-6 SF3B1 WT cells

Project description:SF3B1, a core component of the spliceosome involved in branch point recognition and 3’ splice site selection is frequently mutated in hematopoietic malignancies. Though its associations with clinical outcomes are unclear, mice and zebra fish with conditional SF3B1 knock-in mutations develop macrocytic anemia. A hallmark of SF3B1 mutation is an increase to cryptic 3’ splice site (C3SS) usage, a finding that is recapitulated across multiple isogenic and patient cell types. Mechanisms contributing to cryptic splice site choice and the influence of mis-splicing on posttranscriptional isoform regulation in SF3B1 mutants remains unclear. Our data indicate that SF3B1 K700E mutant Nalm-6 cells carry a significantly different set of cryptic 3’ splice sites than ones utilized in wild type cells.

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Transcriptome analysis of SF3B1-mutation induced changes in K562 cells

Project description:Using RNA-Seq, we determined changes to gene expression and splicing on inducible expression of SF3B1-WT and SF3B1-MUT (K700E) in K562 cells. Using RNA-Seq, we determined changes to gene expression and splicing on inducible expression of SF3B1-WT and SF3B1-MUT (K700E) in K562 cells.

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Cancer-associated SF3B1-K700E mutation controls immune responses by regulating Treg function via aberrant Anapc13 splicing

Project description:Recurrent somatic mutations in spliceosome factor 3b subunit 1 (SF3B1) are identified in hematopoietic cell-derived malignancies, with SF3B1-K700E being the most common one. Here we show that Treg specific expression of SF3B1-K700E (Sf3b1K700Efl/+/Foxp3YFP-Cre) results in spontaneous autoimmune phenotypes including enlarged spleen and tissue infiltration with IFN-γ-producing CD4+ T cells. CD4+ T cells from Sf3b1K700Efl/+/Foxp3YFP-Cre mice display defective Treg differentiation and inhibitory function, which is demonstrated by failed prevention of adoptive transfer colitis by Sf3b1K700Efl/+/Foxp3YFP-Cre Tregs. Mechanically, SF3B1-K700E induces an aberrant splicing event that results in reduced expression of a cell proliferation regulator Anapc13 due to insertion a 231 bp DNA fragment to the 5’ untranslated region (UTR). Forced expression of Anapc13 gene restores the differentiation and ability of Sf3b1K700Efl/+/Foxp3YFP-Cre Tregs to prevent adoptive transfer colitis. Our results thus highlight the impact of a hematological malignancy-associated SF3B1 mutation on immune responses and indicate a potential relationship between splicing factor mutation-dysregulated immune responses and cancer development.

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RNA Sequencing of Nalm-6 SF3B1 K700E MT and Nalm-6 SF3B1 WT cells

Project description:RNA Sequencing of Nalm-6 SF3B1 K700E MT and Nalm-6 SF3B1 WT cells

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Patient-specific MDS-RS iPSCs define the mis-spliced transcript repertoire and chromatin landscape of SF3B1-mutant HSPCs

Project description:SF3B1 K700E is the most frequent mutation in myelodysplastic syndrome (MDS), but the mechanisms by which it drives MDS pathogenesis remain unclear. We derived a panel of 18 genetically matched SF3B1 K700E- and SF3B1 WT-induced pluripotent stem cell (iPSC) lines from patients with MDS with ring sideroblasts (MDS-RS) harboring isolated SF3B1 K700E mutations and performed RNA and ATAC sequencing in purified CD34+/CD45+ hematopoietic stem/progenitor cells (HSPCs) derived from them. We developed a novel computational framework integrating splicing with transcript usage and gene expression analyses and derived a SF3B1 K700E splicing signature consisting of 59 splicing events linked to 34 genes, which associates with the SF3B1 mutational status of primary MDS patient cells. The chromatin landscape of SF3B1 K700E HSPCs showed increased priming toward the megakaryocyte- erythroid lineage. Transcription factor motifs enriched in chromatin regions more accessible in SF3B1 K700E cells included, unexpectedly, motifs of the TEAD family. TEAD expression and transcriptional activity were upregulated in SF3B1-mutant iPSC-HSPCs, in support of a Hippo pathway-independent role of TEAD as a potential novel transcriptional regulator of SF3B1 K700E cells. This study provides a comprehensive characterization of the transcriptional and chromatin landscape of SF3B1 K700E HSPCs and nominates novel mis-spliced genes and transcriptional programs with putative roles in MDS-RS disease biology.

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Project description:RNA-seq of sorted KPC Sf3b1-K700E murine PDAC cells

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