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RNA-seq of HCT116 cells upon downregulation of PINK1

ABSTRACT: RNA-seq of HCT116 cells upon downregulation of PINK1

PROVIDER: PRJEB62023 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR11420819_1.fastq.gz	Fastqsanger.gz
	ERR11420819_2.fastq.gz	Fastqsanger.gz
	ERR11420820_1.fastq.gz	Fastqsanger.gz
	ERR11420820_2.fastq.gz	Fastqsanger.gz
	ERR11420821_1.fastq.gz	Fastqsanger.gz

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RNA-seq of HCT116 cells upon downregulation of PINK1

Project description:This experiment is aimed at studying the changes in transcript levels when PINK1, a key regulator of autophagy, is downregulated.

2023-09-01 | E-MTAB-12946 | biostudies-arrayexpress

Whole Blood RNA Expression in Pink1-/- and Wildtype Rats

Project description:Early-onset pathology and reliable disease biomarkers for diagnostics are poorly understood for progressive degenerative disorders such as Parkinson disease (PD). PD is the second most common age-related degenerative disorder. The Pink1-/- rat is a mitochondrial dysfunction model of prodromal PD. In this study, we used RNA sequencing to examine gene expression within whole blood samples of young and old Pink1-/- rats as compared to age-matched wildtype controls.

2023-08-23 | GSE213543 | GEO

Tom20 gates PINK1 activity and mediates its tethering of the TOM and TIM23 translocases upon mitochondrial stress

Project description:Mutations in PTEN-induced putative kinase 1 (PINK1) cause autosomal recessive early onset Parkinson disease (PD). PINK1 is a Ser/Thr kinase that regulates mitochondrial quality control by triggering mitophagy mediated by the ubiquitin ligase Parkin. Upon mitochondrial damage, PINK1 accumulates on the outer mitochondrial membrane (OMM) forming a high molecular weight complex with the translocase of the outer membrane (TOM). PINK1 then phosphorylates ubiquitin, which enables recruitment and activation of Parkin followed by autophagic clearance of the damaged mitochondrion. Thus, Parkin-dependent mitophagy hinges on the stable accumulation of PINK1 on the TOM complex. Yet, the mechanism linking mitochondrial stressors to PINK1 accumulation and whether the translocases of the inner membrane (TIMs) are also involved, remain unclear. Herein, we demonstrate that mitochondrial stress induces the formation of a PINK1-TOM-TIM23 supercomplex in human cultured cell lines, dopamine neurons, and midbrain organoids. Moreover, we show that PINK1 is required to stably tether the TOM to TIM23 complexes in response to stress, such that the supercomplex fails to accumulate in cells lacking PINK1. This tethering is dependent on an interaction between the PINK1 NT-CTE module and the cytosolic domain of the Tom20 subunit of the TOM complex, the disruption of which, by either designer or PD-associated PINK1 mutations, inhibits downstream mitophagy. Together, the findings provide key insight into how PINK1 interfaces with the mitochondrial import machinery, with important implications for the mechanisms of mitochondrial quality control and PD pathogenesis.

2024-03-02 | PXD047765 | Pride

Changes in proteome upon deletion of UBE2S/UBE2C in HCT116 cells

Project description:The proteome of HCT116 cells deleted of UBE2S and/or UBE2C was compared to the proteome of wild-type HCT116 cells.

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Transcriptional profile of pink1 mutant flies

Project description:Global analysis of transcriptional changes in Drosophila pink1 mutants.

2013-12-02 | E-MEXP-3645 | biostudies-arrayexpress

Neuronal mitochondria transport Pink1 mRNA via Synaptojanin 2 to support local mitophagy

Project description:PTEN-induced kinase 1 (PINK1) is a very short-lived protein that is required for the removal of damaged mitochondria through Parkin translocation and mitophagy. Because the short half-life of PINK1 limits its ability to be trafficked into neurites, local translation is required for this mitophagy pathway to be active far from the soma. The Pink1 transcript is associated with and cotransported with neuronal mitochondria. In concert with translation, the mitochondrial outer membrane protein Synaptojanin 2 Binding Protein (SYNJ2BP) and Synaptojanin 2 (SYNJ2) are required for tethering Pink1 mRNA to mitochondria via an RNA-binding domain in SYNJ2. This neuron-specific adaptation for local translation of PINK1 provides distal mitochondria with a continuous supply of PINK1 for activation of mitophagy.

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mRNA-seq of HCT116 RNF40 knockdown cells upon TNF-alpha stimulation

Project description:mRNA-seq of HCT116 RNF40 knockdown cells upon TNF-alpha stimulation

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Insulin signaling regulates Pink1 mRNA localization via modulation of AMPK activity to support PINK1 function in neurons

Project description:Mitochondrial quality control failure is frequently observed in neurodegenerative diseases. The detection of damaged mitochondria by stabilization of PTEN-induced kinase 1 (PINK1) requires transport of Pink1 mRNA by tethering it to the mitochondrial surface. Here, we report that inhibition of AMPK by activation of the insulin signaling cascade prevents Pink1 mRNA binding to mitochondria. Mechanistically, AMPK phosphorylates the RNA anchor complex subunit SYNJ2BP within its PDZ domain, a phosphorylation site that is necessary for its interaction with the RNA-binding protein SYNJ2. Interestingly, loss of mitochondrial Pink1 mRNA association upon insulin addition is required for PINK1 protein activation and its function as a ubiquitin kinase in the mitophagy pathway, thus placing PINK1 function under metabolic control. Induction of insulin-resistance in vitro by the key genetic Alzheimer-risk factor apolipoprotein E4 retains Pink1 mRNA at the mitochondria and prevents proper PINK1 activity especially in neurites. Our results thus identify a metabolic switch controlling Pink1 mRNA localization and PINK1 activity via insulin and AMPK signaling in neurons and propose a mechanistic connection between insulin resistance and mitochondrial dysfunction.

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Project description:Loss of function in the PTEN-induced kinase 1 gene (Pink1) causes an early-onset, autosomal recessive form of PD. The translational Pink1-/- rat shows cranial sensorimotor deficits including: declines in ultrasonic vocalization, negative impacts on social vocal function, and alterations to thyroarytenoid muscle structure. The aim of this study was to identify differentially expressed genes using RNA-sequencing and bioinformatic analysis of the thyroarytenoid muscle of male Pink1-/- rats compared to wildtype controls. To construct gene co-expression networks and gene modules, a WGCNA was used to identify biological networks of interest including where Pink1 was a central node with interconnecting genes. Data are congruent with previous findings demonstrating changes to thyroarytenoid muscle structure. These data are consistent with the hypothesis that differences in peripheral biology may influence the early pathogenesis of vocalizations at the level of the thyroarytenoid muscle.

2020-05-27 | GSE151209 | GEO

Effect of deficiency of PINK1 on gene expression during 4-month and 24-month.

Project description:To investigate the PINK1 regulates mitochondrial function, we performed the gene expression data for two independent libraries for Pink1-/- and Pink1+/+ mice, at two different time points, 4 and 24 months.

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