Dataset Information

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

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 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.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Dendritic Cell

DISEASE(S): Obesity,Disease Free

SUBMITTER: Cristina Clement

LAB HEAD: Laura Santambrogio; Cristina C Clement

PROVIDER: PXD026068 | Pride | 2022-08-22

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	CC_SyntheticPeptides_PDIA3_2_PDIA_3_1_Date_050621.sky	Other
	CC_SyntheticPeptides_mix_sample_s1-s4.sky	Other
	CC_fusion_S2_4HPeptideMix_DDA.mgf	Mgf
	CC_fusion_S2_4HPeptideMix_DDA.raw	Raw
	CC_fusion_S3_4HPeptideMix_DDA.mgf	Mgf

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Publications

PDIA3 epitope-driven immune autoreactivity contributes to hepatic damage in type 2 diabetes.

Clement Cristina C CC Osan Jaspreet J Buque Aitziber A Nanaware Padma P PP Chang Yoke-Chen YC Perino Giorgio G Shetty Madhur M Yamazaki Takahiro T Tsai Wanxia Li WL Urbanska Aleksandra M AM Calvo-Calle J Mauricio JM Ramsamooj Shakti S Ramsamooj Shakti S Vergani Diego D Mieli-Vergani Giorgina G Terziroli Beretta-Piccoli Benedetta B Gadina Massimo M Montagna Cristina C Goncalves Marcus DaSilva MD Sallusto Federica F Galluzzi Lorenzo L Soni Rajesh K RK Stern Lawrence J LJ Santambrogio Laura L

Science immunology 20220819 74

A diet rich in saturated fat and carbohydrates causes low-grade chronic inflammation in several organs, including the liver, ultimately driving nonalcoholic steatohepatitis. In this setting, environment-driven lipotoxicity and glucotoxicity induce liver damage, which promotes dendritic cell activation and generates a major histocompatibility complex class II (MHC-II) immunopeptidome enriched with peptides derived from proteins involved in cellular metabolism, oxidative phosphorylation, and the s ...[more]

PMID: 35984892

Similar Datasets

Project 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. 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.

Project description:Proteomic modifications linked to non-enzymatic glycation and glycoxidation are common in all tissues under hyperglycemic conditions, as present in metabolic syndrome, type 2 diabetes (T2D), mice bearing a homozygous mutation in leptin (so-called Ob/Ob mice, a common model of obesity and T2D) and mice subjected to a high fat diet (HFD). It has been already shown that the circulating levels of glycated or glycoxidated proteins (e.g., glycated hemoglobin or albumin) are commonly employed as a reliable indicator of overall glycemic status. Albeit these initial non-enzymatic reactions are reversible, following a series of chemical rearrangements protein glycation and glycoxidation become irreversible, generating the so-called advanced glycation end-products (AGEs). AGEs are commonly detected in tissue proteins with an extended half-life, including dermal collagens as well as extracellular matrix proteins. In these proteins, Nϵ-carboxymethyllysine (CML), pentosidins, and glucosepane represent the most prevalent AGEs. As an additional, novel mechanism linking protein PTMs to altered immunity, the research presented herein highlights that several components of the MHC class II antigen processing and presentation machinery are glycated in metabolic conditions associated with increased oxidative stress, leading to qualitative and quantitative changes in the MHC class II immunopeptidome. To investigate the impact of T2D and metabolic syndrome on the proteome of antigen presenting cells (APCs) we isolated dendritic cells (DCs, which are key for the initiation of antigen-specific immunity) from the lymph nodes of Ob/Ob mice and syngeneic, age-matched control C57BL/6 (B6) mice and mapped the oxidized proteins at the molecular and cellular level by employing label-free mass spectrometry using at least three biologically independent whole lysates of DCs. Analysis of the type of post-translational modifications (PTMs) accumulated in the proteome from the combined three biological Ob/Ob samples ranked the formyl-lysine and site-specific carboxymethylation on lysine (CML) as the most abundant AGEs found in the glycated proteome; with CML having about two-fold increase in their total PTM-modified spectral counts in the Ob/Ob vs control dendritic cell proteome. Additional glycoxidation-specific PTMs, that mapped only on the Ob/Ob proteome, albeit at a smaller amount than CML and formyl lysine, were glyceryl lysine and 3-deoxyglucosone. Finally, a separate proteomic analysis, performed on gradient purified late endosomes also mapped an increased number of PTM-modified proteins in the Ob/Ob organelles. Ingenuity pathway analysis (IPA) analysis identified metabolic pathways as well as phagocytosis, antigen processing and presentation and phagosome maturation amongst the top pathways including a higher number of proteins modified by AGEs or carbonylation in primary DCs from Ob/Ob vs. control mice. The site-specific amide-AGE modifications that we detected also mapped to proteins involved in response to DC signaling, immune cell trafficking, actin and cytoskeleton signaling, cell movement, and carbohydrate, nucleic acids and protein metabolism. Overall, these findings indicate that the DC proteome of Ob/Ob mice has an increased number of carbonyl PTMs and AGEs as compared to DC of C57BL/6 mice. The results presented herein are one of the first to map the redox mediated PTM in the primary mouse DC in healthy vs T2DM type syndrome physiological conditions.