PXD024239

PXD024239 is an original dataset announced via ProteomeXchange.

Title	Label-free comparative data dependent (DDA) nanoLC-MS/MS analysis of redox mediated posttranslational modifications (PTMs) in the proteomes from mouse primary dendritic cells (DC) isolated from control B6 and obese (Ob/Ob) mice
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.
HostingRepository	PRIDE
AnnounceDate	2021-03-21
AnnouncementXML	Submission_2021-03-21_14:57:46.180.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD024239
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	dihydroxylated residue; carboxylated residue; phosphorylated residue; formylated residue; monohydroxylated residue; acetylated residue; iodoacetic acid derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-02-18 10:03:16	ID requested
⏵ 1	2021-03-21 14:57:47	announced

Clement CC, Nanaware PP, Yamazaki T, Negroni MP, Ramesh K, Morozova K, Thangaswamy S, Graves A, Kim HJ, Li TW, Vigano' M, Soni RK, Gadina M, Tse HY, Galluzzi L, Roche PA, Denzin LK, Stern LJ, Santambrogio L, Pleiotropic consequences of metabolic stress for the major histocompatibility complex class II molecule antigen processing and presentation machinery. Immunity, 54(4):721-736.e10(2021) [pubmed]

submitter keyword: control B6 and Ob/Ob mice dendritic cells, bottom-up proteomics on QEHF and Velos Orbitrap

Laura Santambrogio M.D. Ph.D, Associate Director Precision Immunology
contact affiliation	Englander Institute of Precision Medicine Professor Radiation Oncology Professor Physiology and Biophysics Weill Cornell Medicine 1300 York Avenue Room E215 New York, NY 10065 tel 646-962-2160
contact email	las4011@med.cornell.edu
lab head
Cristina Clement
contact affiliation	Weill Cornell Medicine
contact email	ccc4002@med.cornell.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2021/03/PXD024239

PRIDE project URI

• PRIDE
  1. PXD024239
     1. Label: PRIDE project
     2. Name: Label-free comparative data dependent (DDA) nanoLC-MS/MS analysis of redox mediated posttranslational modifications (PTMs) in the proteomes from mouse primary dendritic cells (DC) isolated from control B6 and obese (Ob/Ob) mice