Similar Datasets
Project description:Primary Hyperoxaluria Type 1 (PH1) is a rare inherited metabolic disorder characterized by oxalate overproduction in the liver, resulting in renal damage. It is caused by mutations in the AGXT gene. Combined liver and kidney transplantation is currently the only permanent curative treatment. We combined locus-specific gene correction and hepatic direct cell reprogramming to generate autologous healthy induced hepatocytes (iHeps) from PH1 patient-derived fibroblasts. First, site-specific AGXT corrected cells were obtained by homology directed repair (HDR) assisted by CRISPR/Cas9, following two different strategies: accurate point mutation (c.853T>C) correction or knock-in of an enhanced version of AGXT cDNA. Then, iHeps were generated, by overexpression of hepatic transcription factors. Generated AGXT-corrected iHeps showed hepatic gene expression profile and exhibited in vitro reversion of oxalate accumulation compared to non-edited PH1-derived iHeps. This strategy set up a potential alternative cellular source for liver cell replacement therapy and a personalized PH1 in vitro disease model.
2024-03-27 | GSE226019 | GEO
Project description:The therapeutic use of adeno-associated viral vector (AAV)-mediated gene disruption using CRISPR-Cas9 is limited by potential off-target modifications and the risk of uncontrolled integration of vector genomes into CRISPR-mediated double-strand breaks. To address these concerns, we explored the use of AAV-delivered paired Staphylococcus aureus nickases (D10ASaCas9) to target the Hao1 gene for the treatment of primary hyperoxaluria type 1 (PH1). Our study demonstrated effective Hao1 gene disruption, a significant decrease in glycolate oxidase expression, and a therapeutic effect in PH1 mice. The assessment of undesired genetic modifications through CIRCLE-seq and CAST-Seq analyses revealed neither off-target activity nor chromosomal translocations. Importantly, the use of paired-D10ASaCas9 resulted in a significant reduction in AAV integration at the target site compared to SaCas9 nuclease. Additionally, our study highlights the limitations of current analytical tools in characterizing modifications introduced by paired D10ASaCas9, necessitating the development of a custom pipeline for more accurate characterization. These results describe a positive advance towards a safe and effective potential long-term treatment for PH1 patients.
2023-11-10 | GSE245791 | GEO
Project description:This study aims to investigate a wheat recombination hotspot (H1) in comparison with a “regular” recombination site (Rec7) on the sequence and epigenetic level in conditions with functional and non-functional Ph1 locus.
2022-12-14 | GSE220598 | GEO
Project description:Primary hyperoxaluria type I (PH1) is a genetic disease caused by a deficiency in the peroxisomal alanine:glyoxylate aminotransferase (AGT) activity. Mutations in AGT mostly cause protein mistargeting and enhanced aggregation, although the molecular and structural basis of these mechanisms are unknown. In this work, we use hydrogen-deuterium exchange monitored by mass spectrometry (HDX-MS) to provide novel insight into these pathogenic mechanisms. We characterize the wild-type (WT) protein, the LM variant (containing the mutations P11L and I340M, a haplotype more frequent in PH1 patients) and the LM G170R (the most common genotype in PH1, introducing the G170R mutation on the LM background). Our study provides the first experimental analysis of the local stability and dynamics of AGT, showing that stability is heterogeneous in the native state and providing a blueprint for frustrated regions with potentially functional relevance. The LM and LM G170R variants destabilize locally the structure. Enzymatic transamination of the PLP bound to AGT hardly affects stability. Our study thus supports that AGT misfolding is not caused by dramatic effects on the stability and dynamics of the holo-protein.
2024-01-25 | PXD046749 | Pride
Project description:Ovarian cancer is a difficult-to-treat malignancy with a high recurrence rate of 70–80% in the late stage and 20–25% in the early stage. Primary debulking surgery (PDS) or interval debulking surgery (IDS), followed by platinum-based adjuvant chemotherapy, is the standard of care for ovarian cancer. Patients with ovarian cancer who underwent PDS or IDS for a newly diagnosed disease, diagnostic laparoscopy, or secondary debulking for a recurrent disease at the Yonsei Cancer Center, Seoul, Republic of Korea, were prospectively recruited between October 2019 and March 2022 (NCT 05504174). For the non-cancer control group, patients who underwent surgery for a suspicious ovarian mass with a CA-125 level of > 35 U/mL were enrolled. Patients with ovarian cancer received adjuvant therapy based on the current standard of care as clinicians were blinded to the ctDNA results. We aimed to assess the clinical utility of ctDNA testing using tumor-naïve, small-sized next-generation sequencing (NGS) panels. A total of 296 patients, including 201 with ovarian cancer and 95 with benign or borderline disease, were enrolled. Patients received adjuvant therapy based on the current standard of care. Cell-free DNA was extracted and sequenced using an NGS panel of nine genes: TP53, BRCA1, BRCA2, ARID1A, CCNE1, KRAS, MYC, PIK3CA, and PTEN.
2023-11-23 | E-MTAB-13555 | biostudies-arrayexpress
Project description:In this study, a whole-genome CRISPRi library was developed in Y. lipolytica and applied for enforcing the tolerance to furfural and acetic acid. Several novel gene targets were discovered through NGS before and after screening. And to analyze the tolerance mechanism caused by transcriptional repression of the most prominent gene targets, the transcriptome and proteomics were performed.
2024-03-31 | PXD051116 | iProX
Project description:Transcriptional adaptation of yeast (BY4743 homozygous deletion mutant of HO) cells to long-term sustained exposure to rapamycin is investigated against the transcriptional profile of untreated cells. Cells were inoculated into 2nM rapamycin containing medium and were grown until mid-exponential phase. Both treated and untreated cells were grown in fermenters where the pH was controlled at 5.5 (pH1) or monitored (pH0), and dissolved oxygen saturation was controlled at >90% (air1) or monitored (air0) in a 2 x 2 factorial design. All experiments were conducted in duplicates (R1 and R2).
2018-11-20 | E-MTAB-6628 | biostudies-arrayexpress