The splicing factor Prpf31 is required for hematopoietic stem and progenitor cell expansion during zebrafish embryogenesis
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ABSTRACT:
PROVIDER: PRJNA720429 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14168549_1.fastq.gz | Fastqsanger.gz | |||
| SRR14168549_2.fastq.gz | Fastqsanger.gz | |||
| SRR14168550_1.fastq.gz | Fastqsanger.gz | |||
| SRR14168550_2.fastq.gz | Fastqsanger.gz | |||
| SRR14168551_1.fastq.gz | Fastqsanger.gz |
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Project description:Pre-mRNA splicing is a precise regulated process, and is crucial for system development and homeostasis maintenance. Mutations in spliceosomal components have been found in various hematopoietic malignancies (HMs), and have been considered as oncogenic derivers of HMs. However, the role of spliceosomal components in normal and malignant hematopoiesis remain largely unknown. Pre-mRNA processing factor 31 (PRPF31) is a constitutive spliceosomal component, which mutations are associated with autosomal dominant retinitis pigmentosa. PRPF31 was found to be mutated in several HMs, but the function of PRPF31 in normal hematopoiesis has not been explored. In this study, we generated a prpf31 knockout zebrafish line, and discovered that prpf31 mutants exhibited severe defects in hematopoietic stem and progenitor cell (HSPC) expansion and its sequentially differentiated lineages. Immunofluorescence results showed that Prpf31 deficient HSPCs underwent malformed mitosis and M phase arrest during HSPC expansion. Transcriptome analysis and experimental validations revealed that Prpf31 deficiency extensively perturbed the alternative splicing of mitosis-related genes. Collectively, our findings elucidate a previously undescribed role for Prpf31 in HSPC expansion, through regulating the alternative splicing of mitosis-related genes.
2022-04-07 | GSE171661 | GEO
Project description: Not available
| S-EPMC10959673 | biostudies-literature
Project description:Transcriptional profiling performed from total eye RNA extracts of wildtype control fishes versus Prpf31 morpholino injected larvae (at ~72hpf) two-condition experiment: wildtype zebrafish versus MO-Prpf31 injected zebrafish eye RNA; 6 replicates each (extraction from 6 pools (~200 eyes each) of controls and 6 pools MO-Prpf31 (~200 eyes each))
2010-05-06 | E-GEOD-20424 | biostudies-arrayexpress
Project description:Transcriptional profiling performed from total eye RNA extracts of wildtype control fishes versus Prpf31 morpholino injected larvae (at ~72hpf)
2010-03-01 | GSE20424 | GEO
Project description:Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis, especially in neural tissues. Mutations in pre-mRNAs processing factor 31 (PRPF31) cause autosomal dominant retinitis pigmentosa, a progressive retinal degeneration disease. The transcriptome-wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here, we showed that the differentiation and viability of retinal progenitor cells (RPCs) are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level, significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild-type human PRPF31 rather than the disease-associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak 5′ splicing site. Moreover, genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events, which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis.
2021-01-06 | GSE151273 | GEO
Project description:Pathogenic variants in splicing factors are the second most common cause of autosomal dominant retinitis pigmentosa (RP), with mutations in PRPF31 being the most prevalent. Here, we characterize a novel intronic variant in PRPF31 (c.1074-11C>G) that creates a cryptic 3′ splice site, resulting in an aberrantly spliced transcript predicted to encode a protein with an altered C-terminus. However, the pathogenic protein was not detected in patient-derived induced pluripotent stem cells (iPSCs). In addition, expression of PRPF31 protein was reduced in patient iPSC-derived retinal pigment epithelium (RPE). To correct the splicing defect, we designed a panel of antisense oligonucleotides (ASOs) targeting putative RNA-binding sites in exon 10 and intron 10 and identified a candidate that corrects PRPF31 splicing in a minigene reporter system as well as in patient-derived iPSCs and RPE. Finally, we showed that ASO treatment enhances PRPF31 protein expression in patient iPSC-derived RPE, supporting its potential as a therapeutic approach to restore PRPF31 expression in RP patients.
2026-06-12 | PXD071251 | Pride
Project description:Purpose Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterised by progressive degeneration of the mid-peripheral retina, leading to night blindness and eventual loss of visual acuity. RP11, caused by mutations in the pre-mRNA processing factor 31 (PRPF31) gene, involved in pre-mRNA splicing as a key component of the spliceosome, accounts for approximately 10% of autosomal dominant RP (adRP) cases. Previous studies have shown that PRPF31 mutations disrupt pre-mRNA splicing of other splicing-related genes, resulting in global spliceosome dysregulation, reduced spliceosome activity, leading to accumulation of insoluble cytoplasmic aggregates, cell dysfunction and ultimately retinal cell death. The pathogenic mechanism is consistent with haploinsufficiency, as the mutant PRPF31 is excluded from the active spliceosome and resulting levels of the gene are insufficient. Therefore, PRPF31 gene augmentation via adeno-associated virus (AAV) makes a promising therapeutic strategy. This study aims to assess the efficiency of PRPF31.AAV gene therapy in restoring PRPF31 expression and function in RPE and photoreceptors, focusing on restoring spliceosome dysregulation, reduction of cytoplasmic aggregates and rescuing cellular phenotypes. Approach Using induced pluripotent stem cells (iPSC) derived from patients with severe RP11, we generated retinal organoids and RPE cells models. Both photoreceptors and RPE cells were treated with ShH10.CMV.PRPF31.AAV to enhance PRPF31 expression. The therapeutic impact of PRPF31.AAV was assessed through qPCR and immunoblotting for gene and protein expression of PRPF31 and immunofluorescence analysis of splicing markers, cilia and cytoplasmic aggregates. Lastly, the phagocytotic function of AAV-treated RPE cells was assessed using fluorescently labelled photoreceptor outer segments (POS). Results PRPF31.AAV treatment resulted in a nearly two-fold increase of total PRPF31 expression in RPE cells and a ten-fold increase in photoreceptors, compared to GFP.AAV controls, as assessed by qPCR. Quantification of protein levels confirmed a significant elevated PRPF31 levels in PRPF31.AAV treated photoreceptors. Moreover, PRPF31 localisation was corrected, and nuclear splicing speckles were increased, indicative of restored nuclear speckle morphology and splicing functions in RPE cells. A significant reduction in cytoplasmic aggregates of degradation-related protein HSPB1 and retinal-specific protein RLBP1 was observed in AAV treated RP11-RPE cells and photoreceptors, when compared to controls. A significant increase in both cilia length and incidence was observed in RPE cells upon AAV augmentation. Finally, the phagocytic capacity of RPE cells was restored following PRPF31.AAV treatment, indicating restoration of RPE function. Conclusions Our findings demonstrate that PRPF31.AAV gene augmentation therapy effectively restores critical functions in both RPE and photoreceptors. This highlights the therapeutic potential of an AAV-based gene therapy for patients with PRPF31-related adRP.
2026-08-16 | GSE309908 | GEO
Project description:Mutations in the ubiquitously expressed pre-mRNA processing factor (PRPF) 31, one of the most common cause of dominant form of Retinitis Pigmentosa (RP), lead to retina-specific phenotype. It is uncertain which retinal cell types are affected and animal models do not clearly present the RP phenotype observed in PRPF31 patients. Retinal organoids and retinal pigmented epithelial (RPE) cells derived from human induced pluripotent stem cells (iPSCs) provide potential opportunities for studying human PRPF31-related RP. We demonstrated that RPE cells carrying PRPF31 mutations present important morphological and functional changes and that PRPF31-mutated retinal organoids recapitulate the human RP phenotype, with a rod photoreceptor cell death followed by a loss of cones. The low level of PRPF31 expression may explain the defective phenotypes of PRPF31-mutated RPE and photoreceptor cells, which were not observed in cells derived from asymptomatic patients or after correction of the pathogenic mutation by CRISPR/Cas9. Transcriptome profiles revealed differentially expressed and mis-spliced genes belonging to pathways in line with the observed defective phenotypes. The rescue of RPE and photoreceptor defective phenotypes by PRPF31 gene augmentation, provide the proof of concept for future therapeutic strategies.
2022-08-01 | GSE206529 | GEO
Project description:Mutations in pre-mRNA processing factors (PRPFs) cause autosomal dominant retinitis pigmentosa (RP), but it is unclear why mutations in ubiquitously expressed genes cause retinal disease. We have generated transcriptome profiles from RP11 (PRPF31-mutated) patient-derived retinal organoids and retinal pigment epithelium (RPE), as well as Prpf31+/- mouse tissues, which revealed that disrupted alternative splicing occurred for specific splicing programmes. Mis-splicing of genes encoding pre-mRNA splicing proteins was limited to patient-specific retinal cells and Prpf31+/- mouse retinae and RPE. Mis-splicing of genes implicated in ciliogenesis and cellular adhesion was associated with severe RPE defects that include disrupted apical-basal polarity, reduced trans-epithelial resistance and phagocytic capacity, and decreased cilia length and incidence. Disrupted cilia morphology also occurred in patient-derived photoreceptors, associated with progressive degeneration and cellular stress. In situ gene-editing of a pathogenic mutation rescued protein expression and key cellular phenotypes in RPE and photoreceptors, providing proof-of-concept for future therapeutic strategies.
2018-08-20 | PXD010821 | Pride
Project description:Retinitis pigmentosa (RP) encompasses a group of inherited retinal disorders characterized by progressive degeneration of rod and cone photoreceptors, leading to vision loss. Among RP subtypes, RP11 is linked to mutations in PRPF31, a key spliceosome component, resulting in retinal cell dysfunction. Although PRPF31 is ubiquitously expressed, its mutations predominantly impact retinal cells, leading to the progressive loss of photoreceptors. Human induced pluripotent stem cell (hiPSC)-derived retinal organoids (ROs) offer a powerful in vitro model for studying RP pathophysiology and therapeutic development. Despite significant progress, studies focused on photoreceptor and retinal pigment epithelium dysfunction in late disease stages, leaving early molecular events and the involvement of other retinal cell types unresolved. Moreover, comprehensive single-cell analyses capturing dynamic transcriptional changes across all retinal populations at early and late differentiation stages are still lacking. Using patient-derived ROs, this study investigates the developmental trajectory of PRPF31-RP11 mutation through single-cell RNA sequencing, highlighting early Müller glial expansion, retinal ganglion cell stress, and progressive photoreceptor degeneration. Findings identify dysregulated molecular pathways associated with phototransduction, oxidative stress, and inflammation, providing insights into RP11 pathogenesis and potential therapeutic targets.
2026-03-10 | GSE307923 | GEO