Dataset Information

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

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Lymph

DISEASE(S): Inflammatory Bowel Disease

SUBMITTER: Cristina Clement

LAB HEAD: Laura Santambrogio

PROVIDER: PXD044885 | Pride | 2024-08-09

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20220104_LSantambrogio_lymph_Afferent_C1.mgf	Mgf
	20220104_LSantambrogio_lymph_Afferent_C1.mzxml	Mzxml
	20220104_LSantambrogio_lymph_Afferent_C1.raw	Raw
	20220104_LSantambrogio_lymph_Afferent_C2.mgf	Mgf
	20220104_LSantambrogio_lymph_Afferent_C2.mzxml	Mzxml

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Publications

Role of the afferent lymph as an immunological conduit to analyze tissue antigenic and inflammatory load.

Nanaware Padma P PP Khan Zohaib N ZN Clement Cristina C CC Shetty Madhur M Mota Ines I Seltzer Ethan S ES Dzieciatkowska Monika M Gamboni Fabia F D'Alessandro Angelo A Ng Charles C Nagayama Manabu M Lichti Cheryl F CF Soni Rajesh K RK Jacob B Geri Matei Irina I Lyden David D Longman Randy R Lu Theresa T TT Wan Xiaoxiao X Unanue Emil R ER Stern Lawrence J LJ Santambrogio Laura L

Cell reports 20240605 6

The lymphatic fluid is the conduit by which part of the tissue "omics" is transported to the draining lymph node for immunosurveillance. Following cannulation of the pre-nodal cervical and mesenteric afferent lymphatics, herein we investigate the lymph proteomic composition, uncovering that its composition varies according to the tissue of origin. Tissue specificity is also reflected in the dendritic cell-major histocompatibility complex class II-eluted immunopeptidome harvested from the cervica ...[more]

PMID: 38848214

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Project description:Inflammatory bowel disease (IBD) is a complex and relapsing inflammatory disease, and patients with IBD exhibit a higher risk of developing colorectal cancer (CRC). Epithelial barrier disruption is one of the major causes of inflammatory bowel disease (IBD) in which epigenetic modulations are pivotal elements. However, the epigenetic mechanisms underlying the epithelial barrier integrity regulation remain largely unexplored. Here, we investigated how SETD2, a histone H3K36 trimethyltransferase, maintains intestinal epithelial homeostasis under inflammatory conditions. GEO public database and IBD tissues were used to investigate the clinical relevance of SetD2 in IBD. To define the role of SetD2 in the colitis, we generated mice with epithelial-specific deletion of Setd2 (Setd2Vil-KO mice). Acute colitis was induced by 2% dextran sodium sulfate (DSS), and colitis-associated CRC was induced by injecting azoxymethane (AOM), followed by three cycles of 2% DSS treatments. Colon tissues were collected from mice and analyzed by histology, immunohistochemistry and immunoblots. Organoids were generated from Setd2Vil-KO and control mice, and were stained with 7-AAD to detect apoptosis. We isolated intestinal epithelial cells (IECs), performed RNA-seq and H3K36me3 ChIP-seq analysis to uncover the mechanism. Results were validated in functional rescue experiments by N-acetyl-l-cysteine (NAC) treatment and transgenes expression in IECs. SETD2 expression was decreased in IBD patients and DSS-treated colitis mice. Setd2Vil-KO mice had abnormal loss of mucosa-producing goblet cells and antimicrobial peptide (AMP)-producing Paneth cells, and promoted early intestinal inflammation development. Consistent with the reduced SETD2 expression in IBD patients, Setd2Vil-KO mice exhibited increased susceptibility to DSS-induced colitis, accompanied by more severe epithelial barrier disruption. Intestinal permeability was markedly increased in Setd2Vil-KO mice. Setd2 ablation drived inﬂammation-associated CRC. Deletion of Setd2 resulted in excess reactive oxygen species (ROS), which led to cellular apoptosis and the defects in barrier integrity. N-acetyl-l-cysteine (NAC) treatment in Setd2Vil-KO mice rescued epithelial barrier injury and apoptosis. Moreover, overexpression of antioxidase PRDX6 in Setd2Vil-KO IECs largely alleviated the overproductions of ROS and improved the cellular survival. Deficiency of Setd2 specifically in the intestine aggravates epithelial barrier disruption and inflammatory response in colitis via a mechanism dependent on oxidative stress. More importantly, we show that Setd2 depletion results in excess ROS by directly down-regulating PRDX6, an antioxidant protein that inhibit excess ROS. Thus, our results highlight an epigenetic mechanism by which Setd2 mediates oxidative stress to modulate intestinal epithelial homeostasis.