PXD003469

PXD003469 is an original dataset announced via ProteomeXchange.

Title	Functional Proteogenomics Reveals Biomarkers and Therapeutic Targets in Lymphomas
Description	The proteomic and posttranslational modification signatures of most cancers are unknown. N-linked glycosylation is a post-translational modification that targets proteins for membrane expression or secretion making this class of proteins attractive cancer biomarkers and therapeutic targets. Using an unbiased mass spectrometry (MS)-based approach we generated a compendium of 1,155 N-linked glycoproteins (2,160 N-glycosites) from 44 human primary lymphomas and malignant lymphoma cell lines. Hierarchical clustering highlighted distinct subtype signatures which included several novel subtype-specific biomarkers. Orthogonal immunologic studies in 671 primary lymphoma tissue biopsies, 36 lymphoma-derived cell lines or 8 patient-derived circulating tumor cell samples corroborated MS-based glycoproteomic data and authenticated selected proteins as tissue biomarkers. Functional targeting using a toxin-conjugated ligand in vitro and RNAi-mediated silencing targeting subtype-specific glycoproteins abrogated lymphoma growth in vivo. Our results demonstrate the utility of global N-glycoproteomics discovery of cancer biomarkers and targets for precision therapeutics.
HostingRepository	PRIDE
AnnounceDate	2017-10-24
AnnouncementXML	Submission_2017-10-24_04:55:36.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Damian Fermin
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	glycosylated residue; oxidation; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap XL

Revision	Datetime	Status	ChangeLog Entry
0	2016-01-15 05:54:38	ID requested
1	2017-06-19 01:59:32	announced
2	2017-06-20 00:20:33	announced	Updated project metadata.
⏵ 3	2017-10-24 04:55:37	announced	Updated project metadata.

Rolland DCM, Basrur V, Jeon YK, McNeil-Schwalm C, Fermin D, Conlon KP, Zhou Y, Ng SY, Tsou CC, Brown NA, Thomas DG, Bailey NG, Omenn GS, Nesvizhskii AI, Root DE, Weinstock DM, Faryabi RB, Lim MS, Elenitoba-Johnson KSJ, Functional proteogenomics reveals biomarkers and therapeutic targets in lymphomas. Proc Natl Acad Sci U S A, 114(25):6581-6586(2017) [pubmed]

curator keyword: Biomedical

submitter keyword: MS/MS,B-cell lymphoma, glycoproteomics

Kojo Elenitoba-Johnson
contact affiliation	Department of Pathology and Laboratory Medicine University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
contact email	Kojo.Elenitoba-Johnson@uphs.upenn.edu
lab head
Damian Fermin
contact affiliation	Pathology
contact email	damian.fermin@gmail.com
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/2017/06/PXD003469

PRIDE project URI

• PRIDE
  1. PXD003469
     1. Label: PRIDE project
     2. Name: Functional Proteogenomics Reveals Biomarkers and Therapeutic Targets in Lymphomas