Label-free quantitative data dependent (DDA) and independent (DIA) analysis of the I-Ab-MHCII peptidomes eluted from cervical and mesenteric dendritic cells (DCs) of B6 mice.

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. To understand the contribution of the lymph proteome to the MHC-II immunopeptidome we eluted I-Ab complexes from DCs harvested from the deep cervical or mesenteric nodes and investigated whether the I-Ab presented peptidome reflects the anatomical distribution of the proteomes carried by the lymph collected from the same anatomical districts. Heatmap representation and cluster analysis indicated differences among the two immunopeptidome. Similarly, regression analysis showed a much higher regression coefficient among MHC II immunopeptidomes eluted from the same anatomical district (r=0.699) as compared to the one eluted from the two different anatomical districts (deep cervical, average r = 0.877 and mesenteric, average r = 0.937). Overall, all analyzed peptides displayed the expected I-Ab binding motives, binding affinity and expected range of peptide length. A combination of data dependent (DDA) and data independent (DIA) analysis indicated that around 36% of the eluted peptides were shared by both the cervical and mesenteric lymph nodes. The rest of the eluted peptides were distinct to each lymph node reflecting the qualitatively different proteome associated with each of the two anatomical districts: peptides unique to the cervical lymph nodes displayed many proteins known to be enriched in brain tissue, whereas those unique to mesenteric lymph nodes were enriched in mesenteric organ proteins. As such, the quantitative analysis of the I-Ab-eluted immunopeptidomes pinpoint important differences in peptide presentation and epitope selection in distinct anatomical districts.

INSTRUMENT(S): Orbitrap Fusion Lumos, Orbitrap Fusion

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Cristina Clement   Laura Santambrogio  

PROVIDER: MSV000094761 | MassIVE | Tue May 14 21:16:00 BST 2024

SECONDARY ACCESSION(S): PXD052267

REPOSITORIES: MassIVE