PXD044885-2

PXD044885 is an original dataset announced via ProteomeXchange.

Title	Label-free quantitative data dependent (DDA) nano-LC-MS/MS analysis of proteomic changes in the mesenteric lymph harvested from healthy (control) and DSS-fed mice models of colitis
Description	The gastrointestinal mucosa constitutes a critical barrier where millions of microbes and environmental antigens can interact with the host immune system. Intestinal barrier defects have been linked to a broad range of pathological states, including autoimmune, cancer and neurodegenerative diseases. Accordingly, it has been proposed as a leading therapeutic target. This research aimed to investigate the qualitative and quantitative changes in the proteomes of pre- and post-nodal mesenteric lymph at steady state and following inflammatory disruption of the intestinal barrier which could lead to the identification the antigenic and inflammatory load draining to the mesenteric lymph nodes, in both healthy and DSS-feed mice models of colitis and inflammatory bowel disease (IBD). To achieve this goal, we employed label-free quantitative (LFQ) bottom-up proteomics analysis of pre- and post-nodal mesenteric lymph. To map changes in the lymph composition following inflammatory damage, mice were fed dextran sulfate sodium (DSS), a sulfated polysaccharide which causes ulcerative colitis-like pathologies and as an additional inflammatory effect on the ileum mucosa. DSS-mediated inflammation in mice mediated significant qualitative and quantitative proteomic changes mapped to the release of damage-associated molecular pattern (DAMPS) in the afferent lymph, mostly generated from the damaged epithelia. In addition, molecular signatures of colitis/enteritis, organ injury and gastrointestinal inflammation were further found by the proteomics analysis. Importantly, enzymes normally confined to the gut, such as chymotrypsin, peptidases, phospholipases, elastases were mapped in the afferent lymph, consistent with the proteolysis and lipolysis observed following breaking down of the gut barrier.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_06:53:59.606.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD044885
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; deaminated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2023-08-26 16:44:24	ID requested
1	2024-08-09 05:26:57	announced
⏵ 2	2024-10-22 06:54:01	announced	2024-10-22: Updated project metadata.

10.1016/j.celrep.2024.114311;

10.6019/PXD044885;

Nanaware PP, Khan ZN, Clement CC, Shetty M, Mota I, Seltzer ES, Dzieciatkowska M, Gamboni F, D'Alessandro A, Ng C, Nagayama M, Lichti CF, Soni RK, Jacob B Geri, Matei I, Lyden D, Longman R, Lu TT, Wan X, Unanue ER, Stern LJ, Santambrogio L, Role of the afferent lymph as an immunological conduit to analyze tissue antigenic and inflammatory load. Cell Rep, 43(6):114311(2024) [pubmed]

submitter keyword: mouse mesenteric lymph

DDA nano-LC/MS/MS

Laura Santambrogio
contact affiliation	Radiation Oncology Department Weill Cornell Medicine College 1300 York Avenue, NY, NY 10065
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/2024/08/PXD044885

PRIDE project URI

• PRIDE
  1. PXD044885
     1. Label: PRIDE project
     2. Name: Label-free quantitative data dependent (DDA) nano-LC-MS/MS analysis of proteomic changes in the mesenteric lymph harvested from healthy (control) and DSS-fed mice models of colitis