PXD031804

PXD031804 is an original dataset announced via ProteomeXchange.

Title	Proteomics of Mouse Endothelial Cell Dysfunction in Sepsis
Description	An early aspect of sepsis is dysregulated activation of endothelial cells (EC), initiating a cascade of inflammatory signaling leading to leukocyte adhesion/migration and organ damage. Therapeutic targeting of ECs has been hampered by concerns regarding ECs heterogeneity from different organs. Using a combination of in vitro and in silico analysis, we present a comprehensive analysis of proteomic changes in mouse lung, kidney and liver ECs following exposure to a clinically relevant cocktail of proinflammatory cytokines. Mouse lung, liver and kidney ECs were incubated with TNFα/IL-1β/IFNγ for 4 or 24 hrs to model inflammatory responses during sepsis. Quantitative label-free global proteomics was performed on the ECs to identify differentially expressed proteins (DEP). Proteins with an abundance ratio >2.0 or <0.5 and an adjusted p<0.05 were characterized as upregulated or downregulated respectively. Gene Ontology (GO) classification was used to determine biological processes that regulate EC function during sepsis and PANTHER was used to classify the molecular function of the identified proteins. Finally, an interactive pathway was developed to investigate signaling within ECs and across organs. Proteomic analysis identified both unique and shared DEPs between the ECs specific to lung, liver and kidney. Using GO, 5 Biological Processes (BP) for each of the organ specific ECs were identified. Interestingly, 4 of the top 5 GO BPs were observed in all 3 ECs at 4 and 24 hrs: defense response to other organism, innate immune response, response to bacterium and response to cytokine. However, these BPs were found to be differentially regulated. For example, at 4 and 24 hrs, lung ECs which have the highest number and highest fold expression of upregulated proteins (189 and 316 respectively), also have higher numbers of unique upregulated proteins (124 vs 194) compared to liver (98 vs 121) and kidney ECs (109 vs 136). The liver showed the greatest number of conserved proteins between 4 and 24 hrs (56) compared to lung (50) and kidney (51). The number of common proteins between all three ECs increases from 38 at 4 hrs to 79 at 24 hrs, indicating more uniformity in ECs proteomic expression during the progression of sepsis. The PANTHER database was used to classify proteins in different functional groups (e.g. defense/immunity) at 4 and 24 hrs. Thus, BPs and PANTHER hits can provide insight into why some organs are more susceptible to sepsis early on and show that as sepsis progresses, some protein expression patterns become more uniform while additional organ specific proteins are expressed. Proteomic analysis of organ-specific ECs provides further understanding of how sepsis affects multiple organs across time and supports future proteomic, temporal studies of EC dysfunction.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:33:21.670.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD031804
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Carmen Merali
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2022-02-21 05:40:14	ID requested
1	2022-10-14 21:13:18	announced
⏵ 2	2023-11-14 08:33:26	announced	2023-11-14: Updated project metadata.

Rossi MT, Langston JC, Singh N, Merali C, Yang Q, Merali S, Prabhakarpandian B, Kilpatrick LE, Kiani MF, Molecular Framework of Mouse Endothelial Cell Dysfunction during Inflammation: A Proteomics Approach. Int J Mol Sci, 23(15):(2022) [pubmed]

10.6019/PXD031804;

submitter keyword: inflamation,Proteomics, sepsis, endothelium

Salim Merali, Ph.D.
contact affiliation	Temple University School of Pharmacy, Department of Pharmaceutical Sciences, Temple University, Philadelphia, PA, USA
contact email	smerali@temple.edu
lab head
Carmen Merali
contact affiliation	Temple University
contact email	clmerali@temple.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD031804
     1. Label: PRIDE project
     2. Name: Proteomics of Mouse Endothelial Cell Dysfunction in Sepsis