PXD073349

PXD073349 is an original dataset announced via ProteomeXchange.

Title	Molecular characterization of patient-derived Follicular Lymphoma and Chronic Lymphocytic Leukemia B cell receptor variable domain glycans
Description	Follicular lymphoma (FL) is a systemic, lymphoid tissue-derived neoplasm of germinal center phenotype B cells that have undergone a t(14;18) chromosomal translocation. A remarkable feature of B cell receptors (BCRs) expressed by FL B cells is the presence of variable domain N-linked glycosylation sites, which are introduced during a process called somatic hypermutation. These novel glycosylation sites are preferentially located in specific ‘hotspot’ sites and are suggested to play a role in the survival of FL B cells, feasibly via the interactions between the N-glycans that occupy these sites and environmental lectins. Thus far, in-depth, molecular characterization of patient-derived, primary FL BCR variable domain glycans (VDGs) has not been performed. In this report, using liquid chromatography-mass spectrometry, we assess the glycosylation profiles of 14 VDG sites from 9 unique patient-derived tumors, and as a comparator, include 3 patient-derived chronic lymphocytic leukemia B cell clones, each harboring a VDG site. We show that FL BCR heavy chain VDG are enriched in oligomannose-type glycans and show using molecular dynamics simulations, that the level of glycan processing correlates with the accessibility of glycosidase ERManI to the glycosylation site and is additionally affected by steric hindrance from neighboring glycans.
HostingRepository	PRIDE
AnnounceDate	2026-01-23
AnnouncementXML	Submission_2026-01-23_02:34:34.341.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rayman Tjokrodirijo
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: NEWT:9606;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2026-01-21 07:50:57	ID requested
⏵ 1	2026-01-23 02:34:34	announced

Dataset with its publication pending

submitter keyword: BCR, IgM, IgG, N-glycans, Follicular Lymphoma

Peter A. van Veelen
contact affiliation	Head Proteomics Group, Leiden University Medical Center, Center for Proteomics and Metabolomics, PO Box 9600, Postal zone P1-Q, 2300 RC Leiden, The Netherlands
contact email	P.A.van_Veelen@lumc.nl
lab head
Rayman Tjokrodirijo
contact affiliation	Leiden University Medical Center, Proteomics group
contact email	r.t.n.tjokrodirijo@lumc.nl
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/2026/01/PXD073349

PRIDE project URI

• PRIDE
  1. PXD073349
     1. Label: PRIDE project
     2. Name: Molecular characterization of patient-derived Follicular Lymphoma and Chronic Lymphocytic Leukemia B cell receptor variable domain glycans