HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy

Abstract

BackgroundThe human leucocyte antigen (HLA) complex controls adaptive immunity by presenting defined fractions of the intracellular and extracellular protein content to immune cells. Understanding the benign HLA ligand repertoire is a prerequisite to define safe T-cell-based immunotherapies against cancer. Due to the poor availability of benign tissues, if available, normal tissue adjacent to the tumor has been used as a benign surrogate when defining tumor-associated antigens. However, this comparison has proven to be insufficient and even resulted in lethal outcomes. In order to match the tumor immunopeptidome with an equivalent counterpart, we created the HLA Ligand Atlas, the first extensive collection of paired HLA-I and HLA-II immunopeptidomes from 227 benign human tissue samples. This dataset facilitates a balanced comparison between tumor and benign tissues on HLA ligand level.MethodsHuman tissue samples were obtained from 16 subjects at autopsy, five thymus samples and two ovary samples originating from living donors. HLA ligands were isolated via immunoaffinity purification and analyzed in over 1200 liquid chromatography mass spectrometry runs. Experimentally and computationally reproducible protocols were employed for data acquisition and processing.ResultsThe initial release covers 51 HLA-I and 86 HLA-II allotypes presenting 90,428 HLA-I- and 142,625 HLA-II ligands. The HLA allotypes are representative for the world population. We observe that immunopeptidomes differ considerably between tissues and individuals on source protein and HLA-ligand level. Moreover, we discover 1407 HLA-I ligands from non-canonical genomic regions. Such peptides were previously described in tumors, peripheral blood mononuclear cells (PBMCs), healthy lung tissues and cell lines. In a case study in glioblastoma, we show that potential on-target off-tumor adverse events in immunotherapy can be avoided by comparing tumor immunopeptidomes to the provided multi-tissue reference.ConclusionGiven that T-cell-based immunotherapies, such as CAR-T cells, affinity-enhanced T cell transfer, cancer vaccines and immune checkpoint inhibition, have significant side effects, the HLA Ligand Atlas is the first step toward defining tumor-associated targets with an improved safety profile. The resource provides insights into basic and applied immune-associated questions in the context of cancer immunotherapy, infection, transplantation, allergy and autoimmunity. It is publicly available and can be browsed in an easy-to-use web interface at https://hla-ligand-atlas.org.

Immunopeptidomics toolkit library (IPTK): a python-based modular toolbox for analyzing immunopeptidomics data

“…6 ). As seen in the figure, compartment related to extracellular exomes, protein secretions and recycling are highly enriched, which is in agreement with previous findings [ 44 ] and with the biological rule of HLA-II proteins as presenters of endosomal and lysosomal proteins.

Fig.

…”

“…As a first case study, we started by analyzing data from the HLA-ligand atlas [ 44 ] database using the library. Given that different tissues have different processing capabilities, for example, by expressing different sets of digestive enzymes, we started first by looking at the sequences located upstream and downstream of the identified peptides in their inferred parent proteins.…”

“…Previously, Chen et al [ 42 ] have identified gene expression as a major contributing factor in shaping HLA-II immunopeptidome. To this end, we used IPTK to integrate the immunopeptidomes of different tissues available on the HLA-ligand atlas [ 44 ] with the transcriptome of these tissues using the Human protein Atlas [ 41 ] to analyze the impact of gene expression on shaping HLA-II peptidomes. As shown in Additional file 1 : Fig.…”

Unsupervised mining of HLA-I peptidomes reveals new binding motifs and substantial false positives in community database

“…A combined dataset of mass spectrometry raw data of mono-allelic HLA class I peptidomes (399 raw files, 88 HLA alleles) were obtained from two prior studies 8,17 (MSV000080527 and MSV000084172). List of reported antigen-HLA pairs were obtained from the Immune Epitope Database 15 (IEDB, downloaded December 2020), the HLA Ligand Atlas 32 (downloaded June 2020), and from peptidomics analyses of multi-allelic patient samples 8,33 . It should be noted that these recent studies of patient samples not only reported new data but also provided compilations of multi-allelic peptidomics data from earlier studies.…”

Is the Immunopeptidome Getting Darker?: A Commentary on the Discussion around Mishto et al., 2019

“…It is also time as a field that we decide how we debate these issues and in my opinion time to stop subjectively re-searching others data but to design and implement our own experiments to more definitely corroborate or repudiate various sources of antigenic peptides in the immunopeptidome. Our field has made great strides and can look back at great community initiatives: the human immunopeptidome project ( 46 ) that strives to advance the documentation of peptides available for immune recognition in a variety of healthy and diseased states; minimal information requirements for an immunopeptidomics experiment ( 47 ) and HLA peptide atlases ( 48 , 49 ) and data repositories ( 50 ) that have driven improvements in predictive algorithms and will provide the data required for the next generation of AI-based informatic tools ( 25 ). Let’s use this same spirit to explore the immunopeptidome and illuminate its dark side as a community united in this purpose.…”