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Overexpression of DDX42 suppresses the altered RNA splicing associated with the K700E mutated SF3B1 in 293T cells

ABSTRACT: We report the bulk RNA-seq in HEK293T cells transfected with DExD/H ATPase and SF3B1

ORGANISM(S): Homo sapiens

PROVIDER: GSE186486 | GEO | 2022/05/20

REPOSITORIES: GEO

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Functional and conformational impact of cancer-associated SF3B1 mutations depends on the position and the charge of amino acid substitution

Project description:RNA-sequencing data from HEK293T cell models: Hek293T transfected with expression vectors of SF3B1-WT, SF3B1-R625H, SF3B1-K666T, SF3B1-K700E.

2021-02-18 | GSE167001 | GEO

Genetic alterations of SUGP1 mimic mutant-SF3B1 splice pattern in lung adenocarcinoma and other cancers

Project description:RNA-sequencing data from HEK293T and HAP1 cell models: Hek293T (SF3B1-K700E, SF3B1-WT, SUGP1-KD and siContol), HAP1 CRISPR-isogenic cell lines WT and SUGP1-P636L

2020-10-10 | GSE159304 | GEO

Overexpression of DDX42 suppresses the altered RNA splicing associated with the K700E mutated SF3B1 in 293T cells

Project description:Overexpression of DDX42 suppresses the altered RNA splicing associated with the K700E mutated SF3B1 in 293T cells

| PRJNA774056 | ENA

SF3B1 Degron knockdown RNA-seq

Project description:Knockdown of mutant and/or wild-type SF3B1 in MEL202 cell line by Degron knock-in, followed by RNA-seq, to identify splicing events governed by mutant SF3B1. Control: parental MEL202 cell line. Experiments: mutant-SF3B1 knockdown; wildtype-SF3B1 knockdown; mutant SF3B1 knockout. Treatments: each of these four conditions plus and minus shld.

2015-03-11 | E-GEOD-66719 | biostudies-arrayexpress

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Project description:To characterize early human hematopoiesis in SF3B1 mutated myelodysplastic syndroms, we performed Single-cell RNA-seq on CD34+ HSPC bone marrow cells.

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Expression profiling of the TC32 Ewing sarcoma cell line following silencing of SUPT6H, SF3B1 or HNRNPH1

Project description:The investigation of the function of SUPT6H, SF3B1 and HNRNPH1 in Ewing sarcoma The expression profiles of TC32 Ewing sarcoma cells were determine 48 hours post siRNA-transfected. Groups consisted of untreated cells (three samples), and negative control (siNeg) transfected-TC32 cells (six samples), and TC32 cells in which either SUPT6H, SF3B1 or HNRNPH1 were silenced; three different siRNAs corresponding to each gene were assessed separately.

2016-01-15 | E-GEOD-67736 | biostudies-arrayexpress

SF3B1

Project description:SF3B1

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Altered DNA Methylation Profiles in SF3B1 Mutated CLL Patients.

Project description:Mutations in splicing factor genes have a severe impact on the survival of cancer patients. Splicing factor 3b subunit 1 (SF3B1) is one of the most frequently mutated genes in chronic lymphocytic leukemia (CLL); patients carrying these mutations have a poor prognosis. Since the splicing machinery and the epigenome are closely interconnected, we investigated whether these alterations may affect the epigenomes of CLL patients. While an overall hypomethylation during CLL carcinogenesis has been observed, the interplay between the epigenetic stage of the originating B cells and SF3B1 mutations, and the subsequent effect of the mutations on methylation alterations in CLL, have not been investigated. We profiled the genome-wide DNA methylation patterns of 27 CLL patients with and without SF3B1 mutations and identified local decreases in methylation levels in SF3B1mut CLL patients at 67 genomic regions, mostly in proximity to telomeric regions. These differentially methylated regions (DMRs) were enriched in gene bodies of cancer-related signaling genes, e.g., NOTCH1, HTRA3, and BCL9L. In our study, SF3B1 mutations exclusively emerged in two out of three epigenetic stages of the originating B cells. However, not all the DMRs could be associated with the methylation programming of B cells during development, suggesting that mutations in SF3B1 cause additional epigenetic aberrations during carcinogenesis.

| S-EPMC8431484 | biostudies-literature

A variant erythroferrone disrupts iron homeostasis in SF3B1-mutated myelodysplastic syndrome (RNA-Seq)

Project description:Myelodysplastic syndromes (MDS) with ring sideroblasts are hematopoietic stem celldisorders with erythroid dysplasia and mutations in the SF3B1 splicing factor gene. MDS patientswith SF3B1 mutations often accumulate excessive tissue iron, even in the absence oftransfusions, but the mechanisms that are responsible for their parenchymal iron overload areunknown. Body iron content, tissue distribution, and the supply of iron for erythropoiesis arecontrolled by the hormone hepcidin, which is regulated by erythroblasts through secretion of theerythroid hormone erythroferrone (ERFE). Here, we identified an alternative ERFE transcript inMDS patients with the SF3B1 mutation. Induction of this ERFE transcript in primary SF3B1-mutated bone marrow erythroblasts generated a variant protein that maintained the capacity tosuppress hepcidin transcription. Plasma concentrations of ERFE were higher in MDS patientswith a SF3B1 gene mutation than in patients with SF3B1 wild-type MDS. Thus, hepcidinsuppression by a variant erythroferrone is likely responsible for the increased iron loading inpatients with SF3B1-mutated MDS, suggesting that ERFE could be targeted to prevent ironmediated toxicity. The expression of the variant ERFE transcript that was restricted to SF3B1-mutated erythroblasts decreased in lenalidomide-responsive anemic patients, identifying variantERFE as a specific biomarker of clonal erythropoiesis.

2019-06-18 | GSE132836 | GEO

Gene expression study in SF3B1-mutated, NOTCH1-mutated and WT CLL cells

Project description:Mutations of SF3B1 in CLL induce alternative splicing in multiple transcripts, including DVL2. DVL2 in turn can act as a negative regulator of NOTCH1 signaling. Gene Expression Profile (GEP) was used to investigate the activation of the NOTCH1 pathway in presence of alternatively spliced DVL2.

2019-09-07 | GSE137024 | GEO

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