PXD026068

PXD026068 is an original dataset announced via ProteomeXchange.

Title	Nano LC-MS/MS DDA mass spectrometry profiling of I-Ab MHCII immunopeptidome eluted from B6 mice on normal and high fructose/high fat (HFHF) diet
Description	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 B6 mice on normal or high fat/high fructose (HFHF) diet and analyzed MHC-II-associated peptides by nano LC-MS/MS using data-dependent (DDA) acquisition approaches. Our results show that the environment-driven lipotoxicity and glucotoxicity induced an MHC-class-II immunopeptidome enriched in peptides derived from proteins involved in cellular metabolism, oxidative phosphorylation, and responses to redox mediated cellular stress. The quantitative analysis of the I-Ab-eluted immunopeptidomes pinpoint important differences in peptide presentation and epitope selection in mice subjected to a diet rich in saturated fat and carbohydrates, which in turn, could be responsible for inducing a low-grade chronic inflammation in several organs including nonalcoholic steatohepatitis.
HostingRepository	PRIDE
AnnounceDate	2022-08-22
AnnouncementXML	Submission_2022-08-22_11:31:27.249.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD026068
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Cristina Clement
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	monohydroxylated residue; deamidated residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-05-18 01:43:37	ID requested
⏵ 1	2022-08-22 11:31:28	announced

Clement CC, Osan J, Buque A, Nanaware PP, Chang YC, Perino G, Shetty M, Yamazaki T, Tsai WL, Urbanska AM, Calvo-Calle JM, Ramsamooj S, Ramsamooj S, Vergani D, Mieli-Vergani G, Terziroli Beretta-Piccoli B, Gadina M, Montagna C, Goncalves MD, Sallusto F, Galluzzi L, Soni RK, Stern LJ, Santambrogio L, PDIA3 epitope-driven immune autoreactivity contributes to hepatic damage in type 2 diabetes. Sci Immunol, 7(74):eabl3795(2022) [pubmed]

submitter keyword: mouse I-Ab immunopeptidome

DDA nanoLC-MS/MS

Orbitrap Fusion Tribrid mass spectrometer

Laura Santambrogio; Cristina C Clement
contact affiliation	Department: Radiation Oncology; Weill Cornell Medicine: Englander Institute of Precision Medicine; USA.
contact email	las4011@med.cornell.edu
lab head
Cristina Clement
contact affiliation	Weill Cornell Medicine
contact email	ccc4002@med.cornell.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD026068
     1. Label: PRIDE project
     2. Name: Nano LC-MS/MS DDA mass spectrometry profiling of I-Ab MHCII immunopeptidome eluted from B6 mice on normal and high fructose/high fat (HFHF) diet