Dataset Information

Label-free comparative data independent (DIA) nanoLC-MS/MS analysis of protein expression profiles of mouse primary dendritic cells (DC) from B6 mice on normal and high fructose/high fat (HFHF) diet

ABSTRACT: A diet rich in saturated fat and carbohydrates causes a low-grade chronic inflammation in several organs including nonalcoholic steatohepatitis. The environment-driven lipotocicity and glucotoxicity induce tissue damage, which promotes dendritic cell adjuvanticity, and supports an MHC-class-II immunopeptidome enriched in peptides derived from proteins involved in cellular metabolism, oxidative phosphorylation and molecular cellular responses to oxidative stress. To investigate the impact of metabolic syndrome on the whole cellular proteome of antigen presenting cells (APCs) we isolated six biological replicates consisted of total proteomic extracts DCs lysates from B6 mice on normal and high fructose/high fat (HFHF) diet and employed a quantitative label-free data independent (DIA) nanoLC-MS/MS analysis of redox stress mediated changes in the protein expression profiles in HFHF vs normal diet. The LFQ DIA analysis of cellular proteomics changes induced by HFHF diet in the DCs highlighted the involvement of proteins associated with cellular pathways involved in lipid and carbohydrate metabolism, oxidative phosphorylation, cell death and inflammation. Altogether depicting an image of cells under metabolic and oxidative stress with up-regulated inflammatory pathways.

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: PXD026190 | Pride | 2022-08-22

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Cristina_Fusion_S10_20210118110521.mgf	Mgf
	Cristina_Fusion_S10_20210118110521.raw	Raw
	Cristina_Fusion_S11_20210118131132.mgf	Mgf
	Cristina_Fusion_S11_20210118131132.raw	Raw
	Cristina_Fusion_S12_20210118151745.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

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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.