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MetabolomicsMetabolomics profiling (GC-MS and LC-MS) for time-course differentiation of pre-B cells-like (B3 cell line) under the controlled induction of the transcription factor Ikaros (STATegra Project)
The main goal of the project is to develop a new generation of bioinformatics resources for the integrative analysis of multiple types of 'omics data. These resources include both novel statistical methodologies as well as user-friendly software implementations. STATegra methods address many aspects...
2016-12-15 | MTBLS283 | MetaboLights
ProteomicsNIMA-related kinase 9–mediated phosphorylation of the microtubule-associated LC3B protein at Thr-50 suppresses selective autophagy of p62/sequestosome 1
We found that LC3B is phosphorylated in vitro by STK3, STK4, NEK9, and PKCζ. To identify phosphorylation sites following in vitro phosphorylation, GST-LC3B was overexpressed in E. coli, purified using glutathione-Sepharose 4 Fast Flow beads and incubated in kinase assays with recombinant kinases or ...
ORGANISM(S): Homo sapiens (Human) 
2020-01-23 | PXD016681 | Pride
Microtubule-associated lc3b protein Autophagy In vitro phosphorylation 
TranscriptomicsEndosome-associated lc3b mRNA is translated in axons and the protein contributes to endosomal clearance
The primary objective of this project was to identify transcripts in close proximity to endosomes using the APEX-seq approach. To achieve this, we employed SH-SY5Y cells expressing APEX2-NES, APEX2-RAB5A, or 2xFYVE-APEX2 constructs. Biotinylation of RNAs was validated by dot blot, and biotinylated R...
ORGANISM(S): Mus musculus 
2026-09-01 | E-MTAB-15783 | biostudies-arrayexpress
UnknownThe ubiquitin isopeptidase USP10 deubiquitinates LC3B to increase LC3B levels and autophagic activity.
Not available
S-EPMC7960534 | biostudies-literature
GenomicsTranscriptome changes in the retinal pigment epithelial cells of Microtubule-Associated Protein 1 Light Chain 3B gene knockout mouse (LC3b-/-)
Transcriptome changes in the retinal pigment epithelial cells of Microtubule-Associated Protein 1 Light Chain 3B gene knockout mouse (LC3b-/-)
PRJNA935311 | ENA
ProteomicsOpportunistic pathogen Porphyromonas gingivalis targets the LC3B-ceramide complex and mediates lethal mitophagy resistance in oral tumors
Mechanisms by which Porphyromonas gingivalis (P. gingivalis) infection enhances oral tumor growth or resistance to cell death remain elusive. Here, we determined that P. gingivalis infection mediates therapeutic resistance via inhibiting lethal mitophagy in cancer cells and tumors. Mechanistically, ...
ORGANISM(S): Porphyromonas gingivalis Homo sapiens (Human) 
2024-06-23 | PXD051568 | Pride
Therapeutic resistance Oral cancers Ceramide  ceramide-dependent mitophagy  sphingolipid metabolism  oral infection  oral microbiota 
ProteomicsHDX-MS analysis of IRGQ in the presence of GABARAP-L2 and LC3B
The autophagy-lysosome system directs the degradation of a wide variety of cargo and is also involved in tumor progression. Here we show that immunity-related GTPase family Q protein (IRGQ) acts in the quality control of MHC-I molecules and directs misfolded MHC-I for lysosomal degradation through i...
ORGANISM(S): Homo sapiens (Human) Escherichia coli 
2024-11-26 | PXD045212 | Pride
Hdx-ms Irgq Ligand binding 
GenomicsEndosome-associated lc3b mRNA is translated in axons and the protein contributes to endosomal clearance
Endosome-associated lc3b mRNA is translated in axons and the protein contributes to endosomal clearance
PRJEB101068 | ENA
ProteomicsProximity proteomics of phagophore-associated proteins using APEX2-LC3B in VPS37A KO U-2 OS cells
We utilized an APEX2-mediated proximity biotinylation approach to label proteins on LC3-positive membranes that accumulate in VPS37A-knockout (KO) U-2 OS cells. AP, APEX2 control; WT, APEX2-LC3B.
ORGANISM(S): Homo sapiens (Human) 
2024-12-03 | PXD057301 | Pride
Human Vps37a ko u-2 os cells Autophagosomal membrane Phagophore Apex2-lc3b 
GenomicsAutophagy driven by a master regulator of hematopoiesis
Developmental and homeostatic remodeling of cellular organelles is mediated by a complex process termed autophagy. The cohort of proteins that constitute the autophagy machinery function in a multistep biochemical pathway. Though components of the autophagy machinery are broadly expressed, autophagy...
ORGANISM(S): Homo sapiens 
2011-09-30 | E-GEOD-32491 | biostudies-arrayexpress
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