PXD020942

PXD020942 is an original dataset announced via ProteomeXchange.

Title	Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation
Description	Abstract: The role of pro-inflammatory macrophage activation in cardiovascular disease (CVD) is a complex one amenable to network approaches. While an indispensible tool for elucidating the molecular underpinnings of complex diseases including CVD, the interactome is limited in its utility as it is not specific to any cell type, experimental condition or disease state. We introduced context-specificity to the interactome by combining it with co-abundance networks derived from unbiased proteomics measurements from activated macrophage-like cells. Each macrophage phenotype contributed to certain regions of the interactome. Using a network proximity-based prioritization method on the combined network, we predicted potential regulators of macrophage activation. Prediction performance significantly increased with the addition of co-abundance edges, and the prioritized candidates captured inflammation, immunity and CVD signatures. Integrating the novel network topology with transcriptomics and proteomics revealed top candidate drivers of inflammation. In vitro loss-of-function experiments demonstrated the regulatory role of these proteins in pro-inflammatory signaling.
HostingRepository	PRIDE
AnnounceDate	2020-08-18
AnnouncementXML	Submission_2020-08-17_22:33:14.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sasha Singh
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2020-08-17 02:45:23	ID requested
⏵ 1	2020-08-17 22:33:16	announced

Halu A, Wang JG, Iwata H, Mojcher A, Abib AL, Singh SA, Aikawa M, Sharma A, Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation. Elife, 7():(2018) [pubmed]

Iwata H, Goettsch C, Sharma A, Ricchiuto P, Goh WW, Halu A, Yamada I, Yoshida H, Hara T, Wei M, Inoue N, Fukuda D, Mojcher A, Mattson PC, Barab, á, si AL, Boothby M, Aikawa E, Singh SA, Aikawa M, PARP9 and PARP14 cross-regulate macrophage activation via STAT1 ADP-ribosylation. Nat Commun, 7():12849(2016) [pubmed]

submitter keyword: THP-1 cells, TMT, macrophages,

Masanori Aikawa
contact affiliation	Brigham and Women's Hospital
contact email	maikawa@bwh.harvard.edu
lab head
Sasha Singh
contact affiliation	Brigham and Women's Hospital, Harvard Medical School
contact email	sasingh@bwh.harvard.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/2020/08/PXD020942

PRIDE project URI

• PRIDE
  1. PXD020942
     1. Label: PRIDE project
     2. Name: Context-enriched interactome powered by proteomics helps the identification of novel regulators of macrophage activation