Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1089821 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28393049_1.fastq.gz | Fastqsanger.gz | |||
| SRR28393049_2.fastq.gz | Fastqsanger.gz | |||
| SRR28393050_1.fastq.gz | Fastqsanger.gz | |||
| SRR28393050_2.fastq.gz | Fastqsanger.gz | |||
| SRR28393051_1.fastq.gz | Fastqsanger.gz |
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Project description:Individuals with genetic elimination of MLKL exhibit an increased susceptibility to neurodegenerative diseases like Alzheimer’s disease (AD). However, the specific mechanism behind this relationship is not yet fully understood. Here, we initially observed significant compromise in autophagy in the brains of MLKL knockout (KO) mice, as evidenced by the down-regulation of autophagy-initiation proteins Beclin1 and ULK1. To elucidate the mechanism by which MLKL, primarily a cytosolic protein, regulates the protein levels of Beclin1 and ULK1, we performed a proteomic screening of MLKL-association proteins and identified UBA52 as the binding partner under physiological conditions. Loss of MLKL induces a decrease in ubiquitin levels by preventing UBA52 from producing ubiquitin and the C-terminal ribosomal protein L40. Furthermore, we demonstrated that in the brain, the deubiquitinase (DUB) USP7 mediates the processing of UBA52, which is regulated by MLKL. Knock down (KD) of USP7 or UBA52 showed similar effects on autophagy and ubiquitin levels as MLKL KD/KO. Moreover, our results indicated that the reduction of Beclin1 and ULK1 upon MLKL loss is attributed to a decrease in their lysine 63 (K63)-linked polyubiquitination. Additionally, single-nucleus RNA sequencing revealed that the loss of MLKL resulted in the disruption of multiple neurodegenerative disease-related pathways, including those associated with AD. These results were consistent with the observation of cognitive impairment in MLKL KO mice and exacerbation of AD pathologies in an AD mouse model with MLKL deletion. Taken together, our findings demonstrate that MLKL-USP7-UBA52 signaling is required for autophagy in brain through maintaining ubiquitin homeostasis, and highlight the contribution of MLKL loss-induced ubiquitin deficits to the development of neurodegeneration. Thus, the maintenance of adequate levels of ubiquitin may provide a novel perspective to protect individuals from multiple neurodegenerative diseases through regulating autophagy.
2025-01-29 | GSE270139 | GEO
Project description:The AMP-activated protein kinase (AMPK) is a master sensor of the cellular energy status and is crucial for the adaptive response to limited energy availability. AMPK is implicated in the regulation of many cellular processes, including autophagy. However, the precise mechanisms by which AMPK controls these processes and the identities of relevant substrates are not fully understood. With a protein microarrays we identified Cyclin Y as novel AMPK substrate that is phosphorylated at S326 both in vitro and in cells. Phosphorylation of Cyclin Y at S326 promotes its interaction with the cyclin-dependent kinase 16 (CDK16), thereby stimulating its catalytic activity. When expressed in cells, Cyclin Y/CDK16 is sufficient to promote autophagy. Moreover, Cyclin Y/CDK16 is necessary for efficient AMPK-dependent activation of autophagy. This functional interaction is mediated by AMPK phosphorylating S326 of Cyclin Y. Collectively, we define Cyclin Y/CDK16 as downstream effector of AMPK for inducing autophagy.
2020-02-17 | PXD009968 | Pride
Project description:AMP-activated protein kinase (AMPK) stabilizes tubular cell metabolism and protects against renal fibrosis through promoting autophagy and mitochondrial homeostasis. Liver kinase B1 (LKB1) is the key regulator for AMPK activation. However, the direct activators of LKB1 are scarce in commercial. In this study, we report a novel LKB1 activator, the piericidin analogue S14 (PA-S14), which was isolated from the culture broth of a marine-derived Streptomyces strain by our group. PA-S14 binds with residue D176 in LKB1 kinase domain, and then induces LKB1 phosphorylated activation and its complex formation with MO25 and STRADα. Furthermore, PA-S14 promotes AMPK activation to enhance LC3B-II/LC3B-I ratio, trigger autophagosome formation and increase autophagic flux. PA-S14 exhibits perfect protective effects on stabilizing mitochondrial homeostasis, inhibiting tubular cell senescence, and retarding fibrogenesis in various CKD models (UUO, UIRI and adriamycin nephropathy models) and TGF-β-stimulated tubular cell culture. Transcriptomics sequencing and site-specific mutation analysis further prove that PA-S14 is a novel lead compound of LKB1 activator, which perfectly protects against renal fibrosis through inducing AMPK-mediated autophagy and mitochondrial homeostasis.
2022-10-26 | GSE193072 | GEO
Project description:AMP-activated protein kinase (AMPK) stabilizes tubular cell metabolism and protects against renal fibrosis through promoting autophagy and mitochondrial homeostasis. Liver kinase B1 (LKB1) is the key regulator for AMPK activation. However, the direct activators of LKB1 are scarce in commercial. In this study, we report a novel LKB1 activator, the piericidin analogue S14 (PA-S14), which was isolated from the culture broth of a marine-derived Streptomyces strain by our group. PA-S14 binds with residue D176 in LKB1 kinase domain, and then induces LKB1 phosphorylated activation and its complex formation with MO25 and STRADα. Furthermore, PA-S14 promotes AMPK activation to enhance LC3B-II/LC3B-I ratio, trigger autophagosome formation and increase autophagic flux. PA-S14 exhibits perfect protective effects on stabilizing mitochondrial homeostasis, inhibiting tubular cell senescence, and retarding fibrogenesis in various CKD models (UUO, UIRI and adriamycin nephropathy models) and TGF-β-stimulated tubular cell culture. Transcriptomics sequencing and site-specific mutation analysis further prove that PA-S14 is a novel lead compound of LKB1 activator, which perfectly protects against renal fibrosis through inducing AMPK-mediated autophagy and mitochondrial homeostasis.
2022-10-26 | GSE193067 | GEO
Project description:PIP2 enhances MLKL channel activity in a direct interaction manner and this gain of function promotes both necroptosis and inflammation. Previous studies have reported that phospholipids assisted MLKL recruitment and translocation which facilitates its mediated function like liposome leaking. Here, our result support MLKL act as ion channel and is finely tuned by PIP2. In the immune process especially, PIP2, as an important modulator, promotes intracellular potassium depletion and trigger inflammation which mediated bythrough MLKL channel function. Defining the role of MLKL channel function in MLKL-induced necroptosis or other potential necroptotic models will extend our understanding of the programmed cell death and critically inform the development and testing of new disease-specific, Anti-inflammatory, therapeutic strategies.
2022-11-05 | PXD030814 | Pride
Project description:For survival, autophagy is a crucial intracellular self-degradation process to provide energy sources, helping adapt to nutrient deprivation. Although nutrient availability is a key determinant of autophagy initiation, it remains elusive underlying mechanism(s) of perceiving nutritional scarcity by which cells timely turn on autophagy as the last self-destructive process for energy supply. Here, we showed that PKA-dependent lipolysis can block the initiation of futile autophagy during short-term nutritional deprivation by repressing AMPK. Using Raman microscopy imaging and metabolomics, we found that autophagy occurred by reduction in available free fatty acids (FFAs) for energy sources. By modulating genes involved in lipolysis and fatty acid oxidation, we found that the use of lipolysis-derived FFAs precedes autophagy initiation. The dysregulated autophagy suppression during short-term fasting decreased motility and lifespan extension of worms. Taken together, these data suggest that PKA is a pivotal factor to orchestrate sophisticated catabolic pathways, preferring the use of PKA-mediated lipolytic products to repress futile autophagic degradation during short-term fasting through AMPK inhibition.
2022-04-27 | ST002206 | MetabolomicsWorkbench
Project description:Here, we show that autophagy is activated in the intestinal epithelium in murine and human colorectal cancer and that the conditional inactivation of Atg7 in intestinal epithelial cells inhibits the formation of pre-cancerous lesions in Apc+/- mice by enhancing anti-tumor responses. The antibody-mediated depletion of CD8+ T cells showed that these cells are essential for the antitumoral responses mediated by the inhibition of autophagy. We show that Atg7 deficiency leads to intestinal dysbiosis and that the microbiota is required for anti-cancer responses. In addition, Atg7 deficiency resulted in a stress response accompanied by metabolic defects, AMPK activation and p53-mediated cell cycle arrest in tumor cells but not in normal tissue. This study reveals that the inhibition of autophagy within the epithelium may prevent the development and progression of colorectal cancer in genetically-predisposed patients.
2015-05-26 | GSE56337 | GEO
Project description:Autophagy is an evolutionarily conserved mechanism of cellular self-digestion in which proteins and organelles are degraded through delivery to lysosomes. Defects in this process are implicated in numerous human diseases including cancer. To further elucidate regulatory mechanisms of autophagy, we performed a functional screen in search of microRNAs (miRNAs), which regulate the autophagic flux in breast cancer cells. In this study we identified the tumor suppressive miRNA, miR-101, as a potent inhibitor of basal, etoposide- and rapamycin-induced autophagy. Through transcriptome profiling, we identified three novel miR-101 targets, STMN1, RAB5A and ATG4D. siRNA-mediated depletion of these genes phenocopied the effect of miR-101 overexpression, demonstrating their importance in autophagy regulation. Importantly, overexpression of STMN1 could partially rescue cells from miR-101-mediated inhibition of autophagy, indicating a functional importance for this target. Finally, we show that miR-101-mediated inhibition of autophagy can sensitize breast cancer cells to 4-hydroxytamoxifen (4-OHT) mediated cell death. Collectively, these data establish a novel link between two highly important and rapidly growing research fields and present a new role for miR-101 as a key regulator of autophagy. MCF-7 cells were seeded in 6-cm plates and independent triplicate transfections were performed the following day with 50 nM miR-101 or scramble control using Lipofectamine 2000. Total RNA was harvested 24 h after transfection using Trizol reagent. There are a total of six arrays included in this experiment, including three biological replicates of mRNA expression after miR-101 over-expression and three scramble controls in MCF-7 cells.
2011-08-19 | E-GEOD-31397 | biostudies-arrayexpress
Project description:Ionizing radiation promotes cytosolic DNA sensing and consequent antitumor immune responses. But how tumor cell-intrinsic cytosolic DNA sensing is initiated by radiation remains poorly defined. Here, we demonstrated that STING-mediated type I interferon production in tumor cells after radiation relied on the engagement of MLKL-mediated necroptosis, which was elicited by the ZBP1-RIPK3 signaling axis. Physiologically, tumor cell-intrinsic ZBP1-MLKL cascade augmented antitumor immune responses after radiation largely by regulating STING signaling. Mechanistically, ZBP1-MLKL-dependent necroptosis maintained the enrichment of mitochondria DNA inside the cytosol of tumor cells after radiation in a cell-density dependent fashion, contributing to type I interferon responses. In contrast, ablation of caspase-8 unleashed ZBP1-MLKL cascade to gain enhanced cytosolic DNA sensing, and in turn potentiated therapeutic effects of radiation. Thus, our findings uncover an unanticipated mechanism that ZBP1-MLKL-dependent necroptosis drives cytosolic DNA sensing-mediated antitumor immunity after radiation, and provide new strategy to improve radiotherapy by inhibiting caspase-8 cascade.
2021-10-13 | GSE168016 | GEO
Project description:Necroptosis is a form of regulated necrotic cell death which promotes inflammation. In cells undergoing necroptosis, the activated RIPK1 kinase mediates the formation of RIPK1/RIPK3/MLKL complex to promote MLKL oligomerization and execution of necroptosis. RIPK1 kinase activity also promotes cell-autonomous activation of proinflammatory cytokine production in necroptosis. However, the signaling pathways downstream of RIPK1 kinase in necroptosis and how RIPK1 kinase activation controls inflammatory response induced by necroptosis are still largely unknown. Here we quantitatively measured the temporal dynamics of over 7000 confident phosphosites during necroptosis using mass spectrometry. Our study defined a RIPK1-dependent phosphorylation pattern in late necroptosis that is associated with a proinflammatory component marked by p-S473 TRIM28. We show that the activation of p38 MAPK mediated by oligomerized MLKL promotes the phosphorylation of S473 TRIM28, which in turn mediates inflammation during late necroptosis. Taken together, our study illustrates a mechanism by which p38 MAPK may be activated by oligomerized MLKL to promote inflammation in necroptosis.
2021-04-01 | GSE171214 | GEO