Transcriptomic dataset of neural progenitors differentiated from Parkinson's disease patient induced pluripotent stem cells with heterozygous PARK2 junction mutations transduced with a lentivector containing PARK2 cDNA.
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA844165 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19487283_1.fastq.gz | Fastqsanger.gz | |||
| SRR19487283_2.fastq.gz | Fastqsanger.gz | |||
| SRR19487284_1.fastq.gz | Fastqsanger.gz | |||
| SRR19487284_2.fastq.gz | Fastqsanger.gz | |||
| SRR19487285_1.fastq.gz | Fastqsanger.gz |
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Project description:Parkinson's disease (PD) is a neurodegenerative pathology caused by progressive loss of dopaminergic neurons in the substantia nigra. Juvenile PD is known to be strongly associated with mutations in the PARK2 gene encoding E3 ubiquitin ligase Parkin. Despite numerous studies, molecular mechanisms that trigger PD still remain unknown. Here, we presented the transcriptome profile for neural progenitors (NP) which were obtained from iPSCs of Parkinson's disease patient, transduced with lentiviral particles carrying the full-length copy of cDNA PARK2. Transcriptome profiles were generated on an NextSeq 500 System (Illumina). A comparative transcriptome analysis of this data along with transcriptome profiles for NP of healthy donors and other patients with PD will allow determining the contribution of mutations of the PARK2 gene to PD pathogenesis and identifying genes whose expression depends on PARK2 overexpression.
2022-06-03 | GSE205235 | GEO
Project description:Parkinson's disease (PD) is a complex systemic disease caused by neurodegenerative processes in the brain, in which the death of dopaminergic neurons (DN) of the substantia nigra is primarily noted. 50% of cases of familial PD are associated with mutations in the PARK2 gene. Induced pluripotent stem cells (iPSCs) and their neuronal derivatives are powerful tool for disease modeling. Here, we presented the transcriptome profiles for neural progenitors (NP) and neurons, presumably DN, differentiated from iPSC lines of healthy donors and PARK2 mutations-associated PD patients generated on an NextSeq 500 System (Illumina). A comparative transcriptome analysis of neuronal derivatives of healthy donors and patients with PD will allow determining the contribution of mutations of the PARK2 gene to PD pathogenesis upon neuronal differentiation.
2021-08-19 | GSE181029 | GEO
Project description:Mutation of the gene PARK2 is the most common cause of early-onset Parkinson's Disease (PD)1,2. PARK2 encodes a gene product with E3 ubiquitin ligase activity3. In a search for multisite tumor suppressors, we identified PARK2 as a frequently targeted gene on chromosome 6q25.2-q27 in cancer. Here, we describe inactivating somatic mutations and frequent intragenic deletions of PARK2 in human malignancies. The PARK2 mutations in cancer occur in the same domains, and sometimes, at the same residues as the germline mutations causing familial PD. Cancer-specific mutations abrogate the growth suppressive effects of PARK2. PARK2 mutations in cancer decrease the gene product's E3 ligase activity, compromising its ability to ubiquitinate cyclin E and resulting in mitotic instability. These data strongly point to PARK2 as a tumor suppressor on 6q25.2-q27. PARK2, a gene that causes neuronal dysfunction when mutated in the germline, may instead contribute to oncogenesis when altered in non-neuronal somatic cells. Human colorectal samples were profiled on Agilent 244K aCGH arrays per manufacturer's instructions. Pooled reference normal DNA was used as the reference.
2010-06-22 | E-GEOD-18638 | biostudies-arrayexpress
Project description:We have generated human induced Pluripotent Stem cells (hiPSc) from Parkinson's Disease patients, using retrovirus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to dopaminergic neuronal clutures and downstream functional assays. Fernandes H.J.R., Hartfield E.M., Badger J., Christian H. C., Emmanoulidou E., Vowles J., Evetts S., Vekrellis K., Talbot K., Hu M.T., James W., Cowley S.A., and Wade-Martins, R. Heterozygous glucocerebrosidase mutations in Parkinson's increase autophagic demand, but decrease capacity, in induced pluripotent stem cell-derived dopaminergic neuronal cultures. submitted for publication human iPSc lines were derived from human dermal fibroblasts from 2 Parkinson's Disease patients with heterozygous glucocerebrosidase mutations (GBA N370S) mutations, and 2 idiopathic Parkinson's Disease patients. SNP datasets from the 2 control individuals used in this study have been published previously [PMID 23951090; A mature physiological cellular model of human dopaminergic neurons Hartfield E.M., Yamasaki-Mann M., Fernandes H.J., Vowles., James W.S., Cowley S.A, and Wade-Martins R. In revision]
2013-12-18 | E-GEOD-53425 | biostudies-arrayexpress
Project description:Parkinson’s disease (PD) is the second most common neurodegenerative disease worldwide and the first involving motor symptoms. Deep brain stimulation (DBS) neurosurgery treatment through electrodes implanted to the subthalamic nucleus (STN) improves dramatically the debilitating motor symptoms of the disease due to yet unknown molecular mechanisms. Affymetrix human junction prototype microarrays (HJAY) of blood leukocytes mRNA from PD patients prior to, and following DBS neurosurgery treatment on electrical stimulation were compared to these of age- and gender-matched healthy control volunteers. About 95% of all human genes undergo alternative splicing, and alternative splicing is involved in human diseases and specifically in neurodegenerative diseases. Thus, the goal of this study was to detect alternatively spliced genes in PD patients prior to, and following DBS and to predict the effect of these on the functional level of change at the transcript level (such as exon inclusion, intron retention and nonsense-mediated decay events). Understanding the role of alternative splicing in neurodegenerative diseases will open new avenues to future novel approaches for early detection and neuroprotective treatment enabled by the development of future genetic therapeutics targeted at specific modified splice variants. A total of 11 blood leukocytes mRNA samples were analyzed: four from Parkinson's Disease (PD) patients pre-DBS treatment, three from PD patients tested again post-DBS (while being on electrical stimulation), three from age- and gender-matching healthy control (HC) volunteers, and one PD sample pre-DBS sample was re-stained and rescanned .
2015-05-22 | E-GEOD-37591 | biostudies-arrayexpress
Project description:Mutation of the gene PARK2 is the most common cause of early-onset Parkinson's Disease (PD)1,2. PARK2 encodes a gene product with E3 ubiquitin ligase activity3. In a search for multisite tumor suppressors, we identified PARK2 as a frequently targeted gene on chromosome 6q25.2-q27 in cancer. Here, we describe inactivating somatic mutations and frequent intragenic deletions of PARK2 in human malignancies. The PARK2 mutations in cancer occur in the same domains, and sometimes, at the same residues as the germline mutations causing familial PD. Cancer-specific mutations abrogate the growth suppressive effects of PARK2. PARK2 mutations in cancer decrease the gene product's E3 ligase activity, compromising its ability to ubiquitinate cyclin E and resulting in mitotic instability. These data strongly point to PARK2 as a tumor suppressor on 6q25.2-q27. PARK2, a gene that causes neuronal dysfunction when mutated in the germline, may instead contribute to oncogenesis when altered in non-neuronal somatic cells.
2009-10-21 | GSE18638 | GEO
Project description:We have generated human induced Pluripotent Stem cells (hiPSc) from Parkinson's Disease patients, using retrovirus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to dopaminergic neuronal clutures and downstream functional assays. human iPSc lines were derived from human dermal fibroblasts from 2 Parkinson's Disease patients with heterozygous glucocerebrosidase mutations (GBA N370S) mutations, and 2 idiopathic Parkinson's Disease patients. SNP datasets from the 2 control individuals used in this study have been published previously [PMID 23951090; A mature physiological cellular model of human dopaminergic neurons Hartfield E.M., Yamasaki-Mann M., Fernandes H.J., Vowles., James W.S., Cowley S.A, and Wade-Martins R. In revision]
2013-12-18 | E-GEOD-53424 | biostudies-arrayexpress
Project description:HITI junction characterization
| PRJNA666453 | ENA
Project description:Early-onset Parkinson's disease can be caused by mutations in the gene PARK7. Many functions have been proposed for PARK7, but in vivo evidence is largely lacking or conflicting with enzymological data. Here, we provide unequivocal evidence that PARK7 and its orthologues can prevent damage of proteins and metabolites inflicted by the glycolytic intermediate 1,3-bisphosphoglycerate, without changing the abundance of this metabolite. In the absence of PARK7, several glycerate-modified metabolites, as well as numerous glycerate- or phosphoglycerate-modified proteins accumulate in human cell lines, mouse brain and flies. This gives an explanation for the pleiotropic effects of PARK7, indicates that spontaneous metabolic damage contributes to the development of hereditary Parkinson's disease, and opens new roads for future therapeutic approaches. Submitted here are the proteomics analyses, where we identify and quantify glyceroyl- and phosphoglyceroyl-modifications of lysine residues in 5 different experimental models. 1. The human colorectal cancer cell line HCT116 was analyzed in four different conditions: a. Wild type cells transduced with an empty recombinant empty lentivirus b. PARK7 knockout cells transduced with an empty recombinant empty lentivirus c. PARK7 knockout cells transduced with a recombinant lentivirus driving expression of PARK7. 2. Brain samples from wild type and PARK7 knockout mice. 3. Red blood cell lysates from wild type and PARK7 knockout mice 4. Whole body extracts from wild type and DJ1beta knockout Drosophila melanogaster 5. In vitro reactions where 1,3-bisphosphoglycerate was produced either by GAPDH or PGK, in the presence and absence of PARK7. Samples were a. Enzymes in the absence of any cofactors (i.e. no 1,3-BPG production) b. Production via GAPDH (using glyceraldehyde 3-phosphate, phosphate and NAD+ as substrates) in the presence or absence of PARK7 c. Production via PGK (using 3-phosphoglycerate and ATP as substrates) in the presence or absence of PARK7.
2022-01-26 | PXD029410 | Pride
Project description:We have generated human induced Pluripotent Stem cells (hiPSc) from Parkinson's Disease patients, using retrovirus-mediated delivery of reprogramming factors. hiPSc lines have been screened using SNP array to assess chromosomal stability (alongside the fibroblast lines from which they derived), and validation of the pluripotency of the hiPSc lines is provided by Pluritest assessment of transcriptome datasets, prior to differentiation to dopaminergic neuronal clutures and downstream functional assays. Fernandes H.J.R., Hartfield E.M., Badger J., Christian H. C., Emmanoulidou E., Vowles J., Evetts S., Vekrellis K., Talbot K., Hu M.T., James W., Cowley S.A., and Wade-Martins, R. Heterozygous glucocerebrosidase mutations in Parkinson's increase autophagic demand, but decrease capacity, in induced pluripotent stem cell-derived dopaminergic neuronal cultures. submitted for publication
2013-12-18 | GSE53425 | GEO