RT Journal Article
SR Electronic
T1 The HLA Ligand Atlas. A resource of natural HLA ligands presented on benign tissues
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 778944
DO 10.1101/778944
A1 Ana Marcu
A1 Leon Bichmann
A1 Leon Kuchenbecker
A1 Linus Backert
A1 Daniel J. Kowalewski
A1 Lena Katharina Freudenmann
A1 Markus W. Löffler
A1 Maren Lübke
A1 Juliane S. Walz
A1 Julia Velz
A1 Holger Moch
A1 Luca Regli
A1 Manuela Silginer
A1 Michael Weller
A1 Andreas Schlosser
A1 Oliver Kohlbacher
A1 Stefan Stevanović
A1 Hans-Georg Rammensee
A1 Marian C. Neidert
YR 2019
UL http://biorxiv.org/content/early/2019/09/25/778944.abstract
AB The human leukocyte antigen (HLA) complex regulates the adaptive immune response by showcasing the intracellular and extracellular protein content to the immune system, where T cells are able to distinguish between self and foreign. Therefore, a comprehensive map of the entirety of both HLA class I- and class II-presented peptides from different tissues, is a highly sought after resource1, as it enables the investigation of basic immunological questions beyond the exome level. In this work, we describe the HLA Ligand Atlas, a comprehensive collection of matched HLA class I and class II ligandomes from 29 non-malignant tissues and 13 human subjects (208 samples in total), covering 38 HLA class I, and 17 HLA*DRB alleles. Nearly 50% of HLA ligands have not been previously described. The generated data is relevant for basic research in diverse fields such as systems biology, general immunology, and molecular biology. Furthermore, the HLA Ligand Atlas provides essential information for translational applications by supporting the development of effective cancer immunotherapies. The characterization of HLA ligands from benign tissues, in particular, is necessary in informing proteogenomic HLA-dependent target discovery approaches. Thus, this data set provides a basis for novel insights into immune-associated processes in the context of tissue and organ transplantation and represents a valuable tool for researchers exploring autoimmunity. The HLA Ligand Atlas is publicly available as a raw data resource but also in the form of a user-friendly web interface that allows users to quickly formulate complex queries against the data set. Both downloadable data and the query interface are available at www.hla-ligand-atlas.org.ACNAcetonitrileAGCAutomatic gain controlCIDCollision-induced dissociationDaDaltonFAFormic acidFDRFalse discovery rateHCDHigher-energy collisional dissociationHLAHuman leukocyte antigenIEDBImmune epitope database and analysis toolLCLiquid chromatographyMSMass spectrometryMS/MSTandem mass spectrometryNATNon-malignant adjacent tissuePBSPhosphate-buffered salineppmParts per millionTFATrifluoroacetic acidUHPLCUltra-high performance liquid chromatography