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Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [RNAseq_G1EER]

ABSTRACT: Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [RNAseq_G1EER]

PROVIDER: PRJNA910113 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR22574958_1.fastq.gz	Fastqsanger.gz
	SRR22574958_2.fastq.gz	Fastqsanger.gz
	SRR22574959_1.fastq.gz	Fastqsanger.gz
	SRR22574959_2.fastq.gz	Fastqsanger.gz
	SRR22574960_1.fastq.gz	Fastqsanger.gz

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Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [RNAseq_CMNhuman]

Project description:Myelodysplastic syndromes (MDS) with mutated SF3B1 gene have many features including a favorable outcome that are distinct from MDS with mutations in other splicing factor genes SRSF2 or U2AF1. Molecular bases of these divergences are poorly understood. Here we show that SF3B1-mutated MDS are characterized by a dramatically reduced R-loop formation predominating in gene bodies, which associates with intron retention reduction specifically found in SF3B1-mutated, but not in U2AF1- or SRSF2-mutated MDS. Compared to erythroblasts from SRSF2- or U2AF1-mutated patients, SF3B1-mutated erythroblasts exhibited augmented DNA synthesis, accelerated replication forks, and single-stranded DNA exposure upon differentiation. Importantly, histone deacetylase inhibition using vorinostat restored Rloop formation,slowed down DNA replication forks and improved SF3B1-mutated erythroblast differentiation. In conclusion, loss of R-loops with associated DNA replication stress is a hallmark of SF3B1-mutated MDS ineffective erythropoiesis, which could be used as a new therapeutic target.

2024-02-22 | GSE220525 | GEO

Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [RNAseq_erythroHuman]

2024-02-22 | GSE220523 | GEO

Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [RNAseq_G1EER]

2024-02-22 | GSE220516 | GEO

Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation

Project description:Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation

| PRJNA910130 | ENA

Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [DRIP-seq]

Project description:Myelodysplastic syndromes (MDS) with mutated SF3B1 gene have many features including a favorable outcome that are distinct from MDS with mutations in other splicing factor genes SRSF2 or U2AF1. Molecular bases of these divergences are poorly understood. Here we show that SF3B1-mutated MDS are characterized by a dramatically reduced R-loop formation predominating in gene bodies, which tightly associates with reduced retention of introns specifically found in SF3B1-mutated, but not in U2AF1- or SRSF2-mutated MDS. Compared to erythroblasts from SRSF2- or U2AF1-mutated patients, SF3B1-mutated erythroblasts exhibited augmented DNA synthesis, accelerated replication forks, and single-stranded DNA exposure upon differentiation, which were recapitulated in murine Sf3b1K700E/+ proerythroblasts. Importantly, R-loop formation was restored by histone deacetylase inhibition using SAHA/vorinostat, which improved Sf3b1K700E/+ erythroblast differentiation. In conclusion, loss of R-loops with associated DNA replication stress is a hallmark of SF3B1- mutated MDS ineffective erythropoiesis, which could be used as a new therapeutic target.

2024-02-22 | GSE220271 | GEO

Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [RNAseq_erythroHuman]

Project description:Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [RNAseq_erythroHuman]

| PRJNA910126 | ENA

Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [RNAseq_CMNhuman]

Project description:Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [RNAseq_CMNhuman]

| PRJNA910137 | ENA

Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [DRIP-seq]

Project description:Accelerated DNA replication fork speed due to Loss of R-Loops in Myelodysplastic Syndromes with SF3B1 Mutation [DRIP-seq]

| PRJNA909343 | ENA

Accelerated DNA replication fork speed due to loss of R-loops in myelodysplastic syndromes with SF3B1 mutation.

Project description:Myelodysplastic syndromes (MDS) with mutated SF3B1 gene present features including a favourable outcome distinct from MDS with mutations in other splicing factor genes SRSF2 or U2AF1. Molecular bases of these divergences are poorly understood. Here we find that SF3B1-mutated MDS show reduced R-loop formation predominating in gene bodies associated with intron retention reduction, not found in U2AF1- or SRSF2-mutated MDS. Compared to erythroblasts from SRSF2- or U2AF1-mutated patients, SF3B1-mutated erythroblasts exhibit augmented DNA synthesis, accelerated replication forks, and single-stranded DNA exposure upon differentiation. Importantly, histone deacetylase inhibition using vorinostat restores R-loop formation, slows down DNA replication forks and improves SF3B1-mutated erythroblast differentiation. In conclusion, loss of R-loops with associated DNA replication stress represents a hallmark of SF3B1-mutated MDS ineffective erythropoiesis, which could be used as a therapeutic target.

| S-EPMC11001894 | biostudies-literature

Distinct routes of clonal progression in SF3B1-mutant myelodysplastic syndromes

Project description:Myelodysplastic syndromes (MDS) are clonal stem cell disorders driven by heterogeneous genetic alterations leading to variable clinical course. MDS with splicing factor SF3B1 mutations is a distinct subtype with a favorable outcome. However, selected co-mutations induce poor prognosis and how these genetic lesions cooperate in human hematopoietic stem and progenitor cells (HSPCs) during disease progression is still unclear. Here, we integrated clinical and molecular profiling of patients with SF3B1 mutations with gene editing of primary and iPSC-derived human HSPCs to show that high-risk co-mutations impart distinct effects on lineage programs of SF3B1-mutant HSPCs. Secondary RUNX1 or STAG2 mutations were clinically associated with advanced disease and reduced survival. However, RUNX1 and STAG2 mutations induced opposing regulation of myeloid transcriptional programs and differentiation in SF3B1-mutant HSPCs. Moreover, high-risk RUNX1 and STAG2, but not low-risk TET2, mutations expanded distinct SF3B1-mutant HSPC subpopulations. These findings provide evidence that progression from low- to high-risk MDS involves distinct molecular and cellular routes depending on co-mutation patterns.

2025-03-21 | GSE290183 | GEO

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