Proteomics

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Characterization of I-Ab MHCII immunopeptidome eluted from control and obese (Ob/Ob) mice using a combination of data-dependent (DDA) and data-independent acquisition (DIA) nanoLC mass spectrometry


ABSTRACT: In Dendritic cells (DC), the MHC II eluted immunopeptidome reflects the antigenic composition of the microenvironment. Proteins are transported and processed into peptides in endosomal MHC II compartments through autophagy or phagocytosis; extracellular peptides can also directly bind MHC II proteins at the cell surface. Altogether, these mechanisms allow DC to sample both the intra and extracellular environment. With an increase in mass spectrometry sensitivity and accuracy, we can now finally tackle important questions on the nature and plasticity of the MHC-II immunopeptidome in health and disease. Presented epitopes, neoepitopes, and PTM-modified epitopes can be quantitatively and qualitatively analyzed to provide a comprehensive picture of DC role in immunosurveillance. To determine whether the redox metabolic conditions induce an altered spectrum of presented peptides, we eluted immunoaffinity-purified I-Ab from conventional dendritic cells isolated from control B6 or obese Ob/Ob mice, and analyzed MHC-II-associated peptides by LC/MS/MS using combined data-dependent (DDA) and data-independent acquisition (DIA) approaches. We analyzed the DIA data by employing a reference spectral library consisting of all peptides identified by database matching in the pool of spectra from combined DDA dataset, thus allowing a direct label-free quantitation of relative abundances between the two sample categories. The quantitative analysis of the I-Ab-eluted immunopeptidomes pinpoint important differences in peptide presentation and epitope selection in obese mice.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Dendritic Cell

DISEASE(S): Disease Of Metabolism

SUBMITTER: Cristina Clement  

LAB HEAD: Laura Santambrogio and Lawrence J.Stern

PROVIDER: PXD023581 | Pride | 2021-03-21

REPOSITORIES: Pride

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Publications


Hyperglycemia and hyperlipidemia are often observed in individuals with type II diabetes (T2D) and related mouse models. One dysmetabolic biochemical consequence is the non-enzymatic reaction between sugars, lipids, and proteins, favoring protein glycation, glycoxidation, and lipoxidation. Here, we identified oxidative alterations in key components of the major histocompatibility complex (MHC) class II molecule antigen processing and presentation machinery in vivo under conditions of hyperglycem  ...[more]

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