Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteogenomic analysis of Human acute myeloid leukemia

ABSTRACT: Here, we used OpenCustomDB, a web-based tool that uses both sample-specific RNAseq data to identify genomic variants and the OpenProt resource that annotates alternative proteins in addition to canonical proteins. We tested OpenCustomDB with a cohort of 17 patients with acute myeloid leukemia and detected 3026 peptides from alternative proteins, including 208 variants in LC-MS/MS.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Cell, Blood

DISEASE(S): Acute Leukemia

SUBMITTER: Noé Guilloy

LAB HEAD: Xavier Roucou

PROVIDER: PXD029240 | Pride | 2023-05-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Publications

OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases.

Guilloy Noé N Brunet Marie A MA Leblanc Sébastien S Jacques Jean-François JF Hardy Marie-Pierre MP Ehx Grégory G Lanoix Joël J Thibault Pierre P Perreault Claude C Roucou Xavier X

Journal of proteome research 20230324 5

Proteomic diversity in biological samples can be characterized by mass spectrometry (MS)-based proteomics using customized protein databases generated from sets of transcripts previously detected by RNA-seq. This diversity has only been increased by the recent discovery that many translated alternative open reading frames rest unannotated at unsuspected locations of mRNAs and ncRNAs. These novel protein products, termed alternative proteins, have been left out of all previous custom database gen ...[more]

PMID: 36961377

Similar Datasets

A novel class of CLK kinases inhibitors that target SRSF10 and promote p53mediated cytotoxicity on human colorectal cancer cells

Project description:The elevated expression of the splicing regulator SRSF10 in metastatic colorectal cancer (CRC) stimulates the production of the pro-tumorigenic Bclaf1-L splice variant. We discovered a group of small molecules with an aminothiazole carboxamide core (GPS167, GPS192 and others) that decrease production of Bclaf1-L. While additional alternative splicing events regulated by SRSF10 are affected by GPS167/192 in HCT116 cells (e.g., in MDM4, WTAP, SLK1 and CLK1), other events are shifted in a SRSF10-independent manner (e.g., in MDM2, NAB2 and TRA2A). GPS167/192 increased the interaction of SRSF10 with the CLK1 and CLK4 kinases, leading us to show that GPS167/192 are CLK kinase inhibitors preferentially impacting the activity of SRSF10. Notably, GPS167 impairs the growth of CRC cell lines and organoids, inhibits anchorage-independent colony formation, cell migration, and promotes cytoxicity that requires SRSF10 and p53. In contrast, GPS167 only minimally affects normal colonocytes and normal colorectal organoids. Thus, GPS167 reprograms the tumorigenic activity of SRSF10 in CRC cells to elicit p53-dependent apoptosis.

2021-09-09 | PXD022333 | Pride

Optimized Sample Preparation Workflow for Improved Identification of Ghost Proteins

Project description:Large scale proteomic strategies rely on database interrogation. Thus, only referenced proteins can be identified. Recently, Alternative Proteins (AltProts) translated from nonannotated Alternative Open reading frame (AltORFs) were discovered using customized databases. Because of their small size which confers them peptide-like physicochemical properties, they are more difficult to detect using standard proteomics strategies. In this study, we tested different preparation workflows for improving the identification of AltProts in NCH82 human glioma cell line. The highest number of identified AltProts was achieved with RIPA buffer or boiling water extraction followed by acetic acid precipitation.

2021-02-15 | PXD024134 | Pride

Global profiling and functional characterization of post-translational modifications of the fission yeast RNA exosome

Project description:The RNA exosome is a multi-subunit complex essential for processing and degradation of many classes of RNA. Although many of the functions of the RNA exosome are well established, how the activity of this complex is regulated remains poorly understood. Here we report a comprehensive proteomic analysis of the RNA exosome complex from the fission yeast Schizosaccharomyces pombe and identified 39 post-translational modifications (PTMs), including phosphorylation, methylation, and acetylation. Interestingly, most of the modifications were identified in Dis3 and Rrp6, the catalytic subunits of the RNA exosome, as well as in the exosome-associated RNA helicase, Mtr4. Functional characterization of residues found to be modified in distinct exosome subunits revealed specific substitutions that affected cell growth and RNA exosome functions. Notably, phosphomimetic substitutions of phosphorylation sites Ser-809 and Tyr-814 in S. pombe Dis3 resulted in striking loss-of-function phenotype in vivo. Biochemical analysis of the Ser-809 and Tyr-814 phosphomimetic versions of Dis3 revealed proper assembly in vivo, but a marked decrease in degradation capacity in vitro. Given that Ser-809 and Tyr-814 are positioned in the vicinity of the catalytic centre of Dis3, our data suggest that site-specific phosphorylation of the RNA exosome represents a mechanism to control its activity in vivo.

2019-01-21 | PXD009529 | Pride

Subcellular proteomics analysis of different stages of colorectal cancer cell lines

Project description:Studying cell differentiation and transformation allows a better understanding of the mechanisms involved in the initiation and the evolution of cancer. The role of proteins which participate in these processes is dependent on their location within the cell. Determining the subcellular localization of proteins or the changes in localization is, therefore, paramount in elucidating their role. Using quantitative mass spectrometry, we characterized the protein expression and subcellular localization of nearly 5,000 proteins from seven different colorectal cancer (CRC) cell lines, as well as normal colon fibroblasts and intestinal epithelial cells. This cellular characterization allowed the identification of colon cancer-associated proteins with differential expression patterns as well as deregulated protein networks and pathways. Indeed, our results demonstrate differential expression of proteins involved in cell adhesion, cytoskeleton, and transcription in colon cancer cells compared to normal colon-derived cells. Pathway analyses identified different cellular functions, including endocytosis and eIF2 signaling, whose deregulation correlates with mutations found in the different CRC phenotypes. Our results provide an unbiased, quantitative and high-throughput approach to measure changes in protein expression and subcellular protein locations in different colorectal cancer cell lines.

2017-04-19 | PXD004879 | Pride

BMP2K is an inhibitor of erythroid differentiation that restricts endocytosis and SEC16A-dependent autophagy

Project description:Coordination of membrane-related processes inside the cells is facilitated by proteins regulating multiple vesicular trafficking pathways. Bone morphogenetic protein 2-inducible kinase (BMP2K) is a poorly studied ubiquitous protein with the highest expression in the erythroid lineage. We hypothesized that this kinase, potentially implicated in endocytosis and autophagy, could integrate various trafficking routes. By proximity biotinylation (BioID), we revealed differential association of two BMP2K splicing variants with regulators of clathrin-mediated endocytosis (CME) and with components of early secretory pathway (ESP). We found the longer variant (BMP2K-L) to interact with markers of clathrin-coated pits, REPS1 and phosphorylated μ2 adaptin, and the shorter variant (BMP2K-S) to associate with early secretory compartments positive for ARFGAP1 and SEC16A proteins. Splicing variant-specific RNAi approach in K562 erythroleukemia cells showed that BMP2K-L controls μ2 phosphorylation while BMP2K-S post-transcriptionally maintains SEC16A protein levels. Depleting all BMP2K splicing variants promoted autophagic degradation via a functional crosstalk with SEC16A, enhanced transferrin endocytosis, and erythroid differentiation. We propose that, owing to alternative splicing, BMP2K gene products restrict erythroid differentiation coordinating endocytosis and SEC16A-dependent autophagy.

2019-07-31 | PXD013542 | Pride

AP-MS of GFP-MCM2 in the cellular response to etoposide induced DNA damage.

Project description:SILAC quantitative proteomics using immunoprecipitation of GFP-tagged fusion proteins to identify proteins interacting with the MCM complex, and quantify changes in interactions in response to DNA damage. U2OS cells expressing GFP-MCM2 were used to purify the MCM complex following treatment or not with etoposide, a topoisomerase II inhibitor causing DNA damage.

2017-12-06 | PXD001949 | Pride

Proximity-dependent biotinylation by TurboID to identify protein-protein interaction networks in yeast

Project description:The use of proximity-dependent biotinylation assays coupled to mass spectrometry (PDB-MS) has changed the field of protein-protein interactions (PPI) studies. Yet, despite the recurrent and successful use of BioID-based PPI screening in mammalian cells, the implementation of PDB-MS in yeast has not been effective. Here we report a simple and rapid approach in yeast to effectively screen for proximal and interacting proteins in their natural cellular environment by using TurboID, a recently described version of the BirA biotin ligase. Using the protein arginine methyltransferase Rmt3 and the RNA exosome subunits, Rrp6 and Dis3, the application of PDB-MS in yeast by using TurboID was able to recover protein-protein interactions previously identified using other biochemical approaches and provided complementary information for a given protein bait. The development of a rapid and effective PDB assay that can systematically analyze PPIs in living yeast cells opens the way for large-scale proteomics studies in this powerful model organism.

2019-05-16 | PXD013183 | Pride

Mislocalization of pathogenic RBM20 variants in dilated cardiomyopathy is caused by loss-of-interaction with Transportin-3

Project description:Severe forms of dilated cardiomyopathy (DCM) are associated with point mutations in the alternative splicing regulator RBM20 that are frequently located in the arginine/serine-rich domain (RS-domain). Such mutations can cause defective splicing and cytoplasmic mislocalization, which leads to the formation of detrimental cytoplasmic granules. Successful development of personalized therapies requires identifying the direct mechanisms of pathogenic RBM20 variants. Here, we decipher the molecular mechanism of RBM20 mislocalization and its specific role in DCM pathogenesis. We demonstrate that mislocalized RBM20 variants retain their splice regulatory activity, which reveals that aberrant cellular localization drives the pathological phenotype. A genome-wide CRISPR knock-out screen combined with image-enabled cell sorting identified Transportin-3 (TNPO3) as the main nuclear importer of RBM20. We show that the direct RBM20-TNPO3 interaction involves the RS-domain, disrupted by pathogenic variants. Re-localization of pathogenic RBM20 variants to the nucleus restores alternative splicing and dissolves cytoplasmic granules in cell culture and animal models. These findings provide proof-of-principle for developing therapeutic strategies to restore RBM20’s nuclear localization in RBM20-DCM patients.

2023-06-19 | PXD038790 | Pride

Probing the Function of Alternative Proteins in Cell Reprogramming by Large Scale Proteomics and Cross - Linking Mass Spectrometry

Project description:Many proteins are lacking from reference databases because they are issued from alternative ORFs neither respecting the rules decreed for the genome annotation or for the protein translation from mRNA. It was evidenced that not only a single protein is therefore translated from an mRNA. However, the function of these Alternative Proteins (AltProts) remain largely unknown. Here, we were interested by looking to the function of AltProts in the context of cancer cell reprogramming. We have developed a large scale approach based on shot-gun proteomics and cross-linking mass spectrometry (XL-MS) to identify the regulation of the reference proteins (RefProts) versus the AltProts and find the their interaction partners. The study was conducted from NCH82 human glioma cells which were stimulated by the protein kinase A (PKA) activator Forskolin upon 16H, 24H and 48H to induce cell differentiation and epithelial-mesenchymal transition (EMT). The data have shown to enable tracing back the function of the AltProts by combining experimental data to in silico analysis using cytoscape with ClueGo for GO Term annotation and enrichment of pathways with String. Very interestingly many AltProts demonstrate to be involved in the regulation of tRNA through their interaction with aaRS proteins and of the cellular mobility.

2021-02-15 | PXD014642 | Pride

Timeline of changes in spike conformational dynamics in emergent SARS-CoV-2 variants reveal progressive stabilization of trimer stalk with altered NTD dynamics

Project description:SARS-CoV-2 emergent variants are characterized by increased viral fitness and each shows multiple mutations predominantly localized to the spike (S) protein. Here, amide hydrogen/deuterium exchange mass spectrometry has been applied to track changes in S dynamics from multiple SARS-CoV-2 variants. Our results highlight large differences across variants at two loci with impacts on S dynamics and stability. A significant enhancement in stabilization first occurred with the emergence of D614G S followed by smaller, progressive stabilization in subsequent variants. Stabilization preceded altered dynamics in the N-terminal domain, wherein Omicron BA.1 S showed the largest magnitude increases relative to other preceding variants. Changes in stabilization and dynamics resulting from S mutations detail the evolutionary trajectory of S in emerging variants. These carry major implications for SARS-CoV-2 viral fitness and offer new insights into variant-specific therapeutic development.

2023-03-14 | PXD040717 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data