PXD010808

PXD010808 is an original dataset announced via ProteomeXchange.

Title	B cell Lymphomas present Immunoglobulin Neoantigens
Description	Immunoglobulin gene rearrangement and somatic hypermutation have the potential to create neoantigens in non-Hodgkin B cell lymphoma. However, the presentation of these putative immunoglobulin neoantigens by B cell lymphomas has not been proven. We used MHC immunoprecipitation followed by liquid chromatography and tandem mass spectrometry (LC-MS/MS) to define antigens presented by follicular lymphomas (FL), chronic lymphocytic leukemias (CLL), diffuse large B cell lymphoma (DLBCL) and mantle cell lymphomas (MCL). We found presentation of the clonal immunoglobulin molecule, including neoantigens by both class I and class II MHC, though more commonly in class II MHC. To determine whether B cell activation could promote presentation of immunoglobulin neoantigens, we used a toll-like receptor 9 (TLR9) agonists to upregulate expression of MHC-II. This resulted in enhanced class II MHC presentation of the immunoglobulin variable region including neoantigens. These findings demonstrate that immunoglobulin neoantigens are presented across most subtypes of B cell lymphomas. Activation of lymphoma cells to upregulate antigen presentation boosts presentation of immunoglobulin neoantigens and represents a strategy for augmenting lymphoma immunotherapies.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:11:03.495.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Niclas Olsson
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	cysteinylation (disulfide with free L-cysteine); phosphorylated residue; monohydroxylated residue; deamidated residue
Instrument	Orbitrap Fusion Lumos; LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-08-17 06:47:24	ID requested
1	2019-01-07 05:15:42	announced
⏵ 2	2024-10-22 04:11:04	announced	2024-10-22: Updated project metadata.

Khodadoust MS, Olsson N, Chen B, Sworder B, Shree T, Liu CL, Zhang L, Czerwinski DK, Davis MM, Levy R, Elias JE, Alizadeh AA, B-cell lymphomas present immunoglobulin neoantigens. Blood, 133(8):878-881(2019) [pubmed]

10.1182/blood-2018-06-845156;

curator keyword: Biological

submitter keyword: lymphoma, neoantigens,MHC, Orbitrap

Joshua E Elias
contact affiliation	Department of Chemical & Systems Biology, Stanford University, USA
contact email	josh.elias@stanford.edu
lab head
Niclas Olsson
contact affiliation	Calico Life Sciences
contact email	nic.e.olsson@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/2019/01/PXD010808

PRIDE project URI

• PRIDE
  1. PXD010808
     1. Label: PRIDE project
     2. Name: B cell Lymphomas present Immunoglobulin Neoantigens