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ProteomicsExtending the Comprehensiveness of Immunopeptidome Analyses Using Isobaric Peptide Labeling
Defining the repertoire of peptides presented by the major histocompatibility complex class I (MHC I) is a key step towards the identification of relevant antigens for cancer immunotherapy. However, the identification of the cancer-specific antigens is a significant analytical challenge in view of t...
ORGANISM(S): Homo sapiens (Human) 
2020-11-16 | PXD017918 | Pride
Tmt Minor antigens Mhc Tumor specific antigens Faims 
ProteomicsNRS1, a nitrogen source-regulated microprotein, confers an alternative mechanism of G1/S transcriptional activation in budding yeast
Commitment to cell division at the end of G1 phase, termed Start in the budding yeast Saccharomyces cerevisiae, is strongly influenced by nutrient availability. To identify newdominant activators of Start that might operate under different nutrient conditions, we screened a genome-wide ORF overexpr...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2021-08-25 | PXD018681 | Pride
G1/s transcription Start Quantitative microscopy Nutrient limitation Evolution Microprotein Genetic screen Transcription factor Saccharomyces cerevisiae 
ProteomicsImipridones cause cellular toxicity in human cells and bacteria by ectopic activation of the ClpP protease
Ectopic activation of the conserved ClpP protease by chemical activators causes toxicity in bacteria and human cells due to unrestrained proteolysis. The imipridone ONC201 has been ascribed multiple mechanisms of action and is currently in cancer clinical trials. To systematically investigate the ge...
ORGANISM(S): Homo sapiens (Human) Staphylococcus aureus 
2020-03-26 | PXD016119 | Pride
Imipridones Clpp protease 
ProteomicsA rapid and efficient method for the extraction of histone proteins
Current protocols used to extract and purify histones are notoriously tedious, especially when using yeast cells. Here, we describe the use of a simple filter-aided sample preparation approach enabling histone extraction from yeast and mammalian cells using acidified ethanol, a condition that not on...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-08-10 | PXD041524 | Pride
N-terminal clipping Histone extratction Fasp 
ProteomicsAbemaciclib differentially reshapes the immunopeptidome of breast cancer subtypes
The cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) Abemaciclib has demonstrated transformative potential in the treatment of hormone receptor-positive (HR+) breast cancer. Beyond its established role in cell cycle arrest, we reveal its capacity to enhance tumor immunogenicity by remodeling the immu...
ORGANISM(S): Homo sapiens (Human) 
2026-02-25 | PXD060684 | Pride
Breast cancer Abemaciclib Tumor antigens Mass spectrometry Cancer immunotherapy Immunopeptidomics 
ProteomicsK29-linked unanchored polyubiquitin chains disrupt ribosome biogenesis and direct ribosomal proteins to the Intranuclear Quality control compartment (INQ)
Ribosome assembly requires precise coordination between the production and assembly of ribosomal components. Mutations in ribosomal proteins that inhibit the assembly process orribosome function are often associated with Ribosomopathies, some of which are linked to defects in proteostasis. In this ...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2023-08-10 | PXD042259 | Pride
Intranuclear quality control compartment Ribosomopathies Unconventional k29-linked unanchored polyubiquitin chains Protein aggregation Dub-e3 ligase interplay Ubiquitin homeostasis Ribosome assembly stress response 
Proteomicsp38γ and p38δ modulate innate immune response by regulating MEF2D activation
Evidence implicating p38γ and p38δ (p38γ/p38δ) in inflammation are mainly based on experiments using p38γ/p38δ deficient (p38γ/δ-/-) mice, which show low levels of TPL2, the kinase upstream of MKK1-ERK1/2 in myeloid cells. This could obscure p38γ/p38δ roles, since TPL2 is essential for regulating in...
ORGANISM(S): Mus musculus (Mouse) 
2023-08-10 | PXD042626 | Pride
Inflammation Mef2d P38δ Phosphorylation P38γ 
ProteomicsIntracellular pH regulates the ubiquitin-mediated degradation of the atypical MAP kinase ERK3
The atypical mitogen-activated protein kinase ERK3 is known for its instability and degradation via the ubiquitin-proteasome system (UPS). However, the specific environmental factors regulating ERK3 turnover have remained unclear. In this study, we demonstrate that intracellular pH (pHi) plays a cru...
ORGANISM(S): Homo sapiens (Human) 
2025-10-07 | PXD056239 | Pride
Map kinases  erk3  ph  protein stability 
ProteomicsRhes, a striatal enriched protein regulates post-translational Small-Ubiquitin like-Modifier (SUMO) Modification of nuclear proteins and alters gene expression
Rhes (Ras homolog enriched in the striatum) is a multifunctional protein that orchestrates striatal toxicity, motor behaviors and abnormal movements associated with dopaminergic signaling, Huntington disease and Parkinson disease signaling in the striatum. Rhes engineers membranous tunneling nanotub...
ORGANISM(S): Homo sapiens (Human) 
2024-06-10 | PXD023394 | Pride
Perinuclear membrane Morphology Brain Medium spiny neurons Differentiation Gene regulation Sumo e3-ligase Signaling 
ProteomicsO-GlcNAcylation of FOXK1 orchestrates the E2F pathway
Gene transcription is a highly regulated process, and deregulation of transcription factors activity underlie numerous pathologies including cancer. FOXK1 and FOXK2 (FOXK1/2) transcription factors have recently emerged as important regulators of cell metabolism, autophagy and cell differentiation. W...
ORGANISM(S): Homo sapiens (Human) 
2024-06-10 | PXD050014 | Pride
E2f pathway O-glcnacylation Foxk1 
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