Abstract
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.
Footnotes
Abbreviations
- ACN
- Acetonitrile
- AGC
- Automatic gain control
- CID
- Collision-induced dissociation
- Da
- Dalton
- FA
- Formic acid
- FDR
- False discovery rate
- HCD
- Higher-energy collisional dissociation
- HLA
- Human leukocyte antigen
- IEDB
- Immune epitope database and analysis tool
- LC
- Liquid chromatography
- MS
- Mass spectrometry
- MS/MS
- Tandem mass spectrometry
- NAT
- Non-malignant adjacent tissue
- PBS
- Phosphate-buffered saline
- ppm
- Parts per million
- TFA
- Trifluoroacetic acid
- UHPLC
- Ultra-high performance liquid chromatography