RNA-seq data for edited and unedited GAA repeats in FRDA patient iPSC-derived neurons
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ABSTRACT:
PROVIDER: PRJNA1025300 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26318719_1.fastq.gz | Fastqsanger.gz | |||
| SRR26318719_2.fastq.gz | Fastqsanger.gz | |||
| SRR26318720_1.fastq.gz | Fastqsanger.gz | |||
| SRR26318720_2.fastq.gz | Fastqsanger.gz | |||
| SRR26318721_1.fastq.gz | Fastqsanger.gz |
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Project description:Friedreich ataxia (FRDA) is a multisystemic, autosomal recessive disorder caused by a homozygous GAA expansion mutation in the first intron of frataxin (FXN) gene. FXN is a mitochondrial protein critical for iron-sulfur cluster biosynthesis and deficiency impairs mitochondrial electron transport chain functions and iron homeostasis within the organelle. Currently, there is no effective treatment for FRDA. We have previously demonstrated that a single infusion of wild-type hematopoietic stem and progenitor cells (HSPCs) resulted in the prevention of the neurologic and cardiac complications of FRDA in YG8R mice, and the rescue was mediated by FXN transfer from tissue engrafted HSPC-derived microglia/macrophages to diseased neurons/myocytes. For a future clinical translation of this approach, we developed an autologous stem cell transplantation approach using CRISPR/Cas9 for the excision of the GAA repeats in FRDA patients’ CD34+ HSPCs; this strategy leading to increased FXN expression and improved mitochondrial functions in the cells. The aim of the current study is to validate the efficiency and safety of our gene editing approach in a disease-relevant model. To this end, we generated a cohort of FRDA patient-derived iPSCs and isogenic lines that were gene edited with our CRISPR/Cas9 approach. FRDA neurons generated from these iPSCs displayed characteristic apoptotic and mitochondrial phenotype of the disease, such as non-homogenous microtubule staining in neurites, increased caspase-3 expression, mitochondrial superoxide levels, mitochondrial fragmentation, and partial degradation of the cristae compared to healthy controls. These defects were fully prevented in the gene edited neurons. RNASeq analysis of FRDA and gene edited neurons demonstrated striking improvement in gene clusters associated with endoplasmic reticulum (ER) stress in the isogenic lines. These results were validated by molecular and functional studies, and gene edited neurons demonstrated improved ER-calcium release, normalization of ER stress response gene, XBP-1, and significantly increased ER-mitochondrial contacts that are critical for functional homeostasis of both organelles, as compared to FRDA neurons. Ultrastructural analysis for these contact sites displayed severe structural damage to the ER in FRDA neurons, that was undetected in gene edited neurons. Taken together, these results represent a novel finding for disease pathogenesis showing dramatic ER structural damage and function in FRDA. In addition, these results validate the efficacy profile of our FXN gene editing approach, in a disease relevant model improving mitochondrial and cellular, and supporting our approach as an effective strategy for therapeutic intervention for Friedreich’s ataxia.
2024-01-29 | GSE244886 | GEO
Project description:The goal of the experiment was to identify which genes are differentially expressed between the unedited and SPI1-edited populations. The RS4:11 cell line was edited both mono and biallelicaly via electroporation with guides and Cas9. Following editing, RNA from unedited (SPI1 +/+), mono (SPI1 +/-) and biallellicaly edited (SPI1 -/-) cells were extracted through the Direct-zol RNA Microprep kit. cDNA libraries for sequencing were then prepared using the TruSeq Stranded mRNA Library Prep Kit and the IDT for Illumina-TruSeq RNA UD Indexes (Illumina). Samples were then sequenced on the Illumina NovaSeq platform.
2021-03-24 | E-MTAB-8677 | biostudies-arrayexpress
Project description:The goal of the experiment was to understand the epigenetic effects of PU.1 haploinsufficiency on pro-B cells. The RS4:11 cell line was edited both mono and biallelicaly via electroporation of Cas9 and guides. Following editing, aliquots of unedited (SPI1 +/+), mono (SPI1 +/-) and biallellicaly edited (SPI1 -/-) cells were lysed before undergoing the transposition reaction. After transposition, the ATAC-seq libraries were purified and then amplified via PCR. Libraries were sequenced using the Illumina Novaseq platform.
2021-03-24 | E-MTAB-8676 | biostudies-arrayexpress
Project description:The inherited neurodegenerative disease Friedreich’s ataxia (FRDA) is caused by hyperexpansion of GAA•TTC trinucleotide repeats within the first intron of the FXN gene, encoding the mitochondrial protein frataxin. Long GAA•TTC repeats causes heterochromatin-mediated silencing and loss of frataxin in affected individuals. We report the derivation of induced pluripotent stem cells (iPSCs) from FRDA patient fibroblasts through retroviral transduction of transcription factors. FXN gene repression is maintained in the iPSCs, as are the mRNA and miRNA global expression signatures reflecting the human disease. GAA•TTC repeats uniquely in FXN in the iPSCs exhibit repeat instability similar to patient families, where they expand and/or contract with discrete changes in length between generations. The mismatch repair enzyme Msh2, implicated in repeat instability in other triplet repeat diseases, is highly expressed in the iPSCs, occupies FXN intron 1, and shRNA silencing of Msh2 impedes repeat expansion, providing a possible molecular explanation for repeat expansion in FRDA.
2010-07-02 | GSE22651 | GEO
Project description:Expansion of triplex-forming GAA/TTC repeats in the first intron of FRDA gene is known to cause Friedreich’s ataxia. Besides FRDA, there are a number of other highly polymorphic GAA/TTC loci in the human genome where the size variations so far were considered to be a neutral event. Using yeast as a model system, we demonstrate that expanded GAA/TTC repeats represent a threat to eukaryotic genome integrity by triggering double-strand breaks and gross chromosomal rearrangements. The fragility potential strongly depends on the length of the track and orientation of the repeats relative to the replication origin which correlates with their propensity to adopt secondary structure and to block replication progression. We show that fragility is mediated by mismatch repair machinery and requires the MutS(beta) and endonuclease activity of MutL(alpha). We suggest that the mechanism of GAA/TTC-induced chromosome aberrations defined in yeast can also operate in human carriers with expanded tracks. Keywords: CGH-array
2008-05-14 | GSE11425 | GEO
Project description:WS iPSC (iWS780) is a WRN-null iPSC line derived from AG00780 fibroblast. This iPSC line showed normal 46,XY karyotype. iWS780 was gene-edited by CRIPSR/Cas9 to correct the WRN point mutation. Two clones (C21 & C24) were characterized and showed expression of wild-type WRN protein after gene editing. The iPSC lines (isogenic) were subsequently differentiated into mesenchymal stem cells (MSC). RNA-seq was performed on these MSC.
2019-09-24 | GSE137856 | GEO
Project description:Expansion of triplex-forming GAA/TTC repeats in the first intron of FRDA gene is known to cause Friedreich’s ataxia. Besides FRDA, there are a number of other highly polymorphic GAA/TTC loci in the human genome where the size variations so far were considered to be a neutral event. Using yeast as a model system, we demonstrate that expanded GAA/TTC repeats represent a threat to eukaryotic genome integrity by triggering double-strand breaks and gross chromosomal rearrangements. The fragility potential strongly depends on the length of the track and orientation of the repeats relative to the replication origin which correlates with their propensity to adopt secondary structure and to block replication progression. We show that fragility is mediated by mismatch repair machinery and requires the MutS(beta) and endonuclease activity of MutL(alpha). We suggest that the mechanism of GAA/TTC-induced chromosome aberrations defined in yeast can also operate in human carriers with expanded tracks. Keywords: CGH-array Genomic DNA from each of 15 strains was competitively hybridized to DNA from the parent diploid strain (Cy3/green). Gains of genomic segments in the survivors were detected as continuous regions of positive Log2 Red:Green ratios, while losses were detected as negative Log2 Red:Green ratios.
2008-05-14 | E-GEOD-11425 | biostudies-arrayexpress
Project description:CRISPR-edited human induced pluripotent stem cell (iPSC)-derived glioma models provide a robust platform to investigate the biology of these aggressive tumors in an isogenic background or to test possible treatments in preclinical settings. We created iPSC12 lines that carry different combinations of glioma driver mutations using CRISPR/Cas9 genome editing technology, including TP53-/-, ATRX-/-, IDH1-R132H/WT, PTEN-/-, CDKN2A/B-/-, TERT promoter(TERTp) C228T/WT, MTAP-/-, and overexpression (OE) of EGFRvIII oncogenic isoform. Edited iPSCs were then differentiated into neural progenitor cells (NPC) using a small molecule protocol. We cultured the edited NPCs in 3D organoid with an FBS-containing differentiation medium. After 14 days, different genotypes of NPCs formed organoids were harvest and RNAs were isolated and subjected to RNA-seq analysis. To create an in vivo model system, NPCs with different genotypes were intracranially transplanted into athymic mice. Mice were sacrificed when pathologic symptoms developed resulting from tumor burden or 120 days post brain transplantation. RNAs were extracted from the tumor region of brain tissue sections and subjected to RNA-seq analysis. Our study showed that the iPSC-based model of gliomas displayed distinct mutation-dependent variation in transcriptome, which recapitulated the gene expression signatures of human gliomas.
2024-05-15 | GSE212671 | GEO
Project description:Lymphoblast cells from a patient with Freidriech's Ataxia were incubated with pyrrole-imidazole polyamides targeted to the GAA triplet repeat in the intron 1. The polyamides were shown in cell culture to increase levels of endogenous frataxin mRNA. A normal sibling derived lymphoblast cell line was used as a control. Keywords: human lymphoblast cells
2006-06-14 | GSE5040 | GEO
Project description:Transcriptome-wide analysis of CRISPR-edited iPSC-derived glioma models
| PRJNA876721 | ENA