The Supplementary Figures file includes Figures S1 to S13.
Figure S1: Gating strategy for the evaluation of LSC frequencies pre and post enrichment.
Figure S2: Amino acid distribution within LSC and AML bulk immunopeptidomes.
Figure S3: HLA class I immunopeptidomics.
Figure S4: Abundance of AML- and AML/LSC-associated HLA class I ligands within the immunopeptidome.
Figure S5: Identification of AML- and AML/LSC-associated HLA class II antigen targets by comparative immunopeptidome profiling.
Figure S6: Abundance of AML- and AML/LSC-associated HLA class II peptides within the immunopeptidome.
Figure S7: Spectral validation of HLA class I-restricted AML- and AML/LSC-associated peptides.
Figure S8: Spectral validation of HLA class II-restricted AML- and AML/LSC-associated peptides.
Figure S9: Magnitude and functionality of in vitro primed CD8+ T cells.
Figure S10: Characterization of memory T cell responses detected in ELISpot assays.
Figure S11: Further characterization of HLA class II-restricted antigens.
Figure S12: In-depth characterization and phenotyping of HLA class II AML/LSC-specific CD4+ T cells by single-cell RNA sequencing and multi-color flow cytometry.
Figure S13: Impact of immunopeptidome diversity and peptide-specific immune responses on patient survival.
Funding
Deutsche Forschungsgemeinschaft (DFG)
Federal Ministry of Education and Research
German Cancer Consortium
Ernst Jung Prize for Medicine
Landesforschungspreis of Baden-Württemberg
Wilhelm Sander-Stiftung (Wilhelm Sander Foundation)
Jose Carreras Leukämie Stiftung
Deutsche Krebshilfe (German Cancer Aid)
Swiss National Science Foundation
European Research Council
Else Kröner-Fresenius-Stiftung (EKFS)
Fortüne Programm of the University of Tübingen
Fortüne Program of the University of Tübingen
ARTICLE ABSTRACT
Therapy-resistant leukemia stem and progenitor cells (LSC) are a main cause of acute myeloid leukemia (AML) relapse. LSC-targeting therapies may thus improve outcome of patients with AML. Here we demonstrate that LSCs present HLA-restricted antigens that induce T-cell responses allowing for immune surveillance of AML. Using a mass spectrometry–based immunopeptidomics approach, we characterized the antigenic landscape of patient LSCs and identified AML- and AML/LSC-associated HLA-presented antigens absent from normal tissues comprising nonmutated peptides, cryptic neoepitopes, and neoepitopes of common AML driver mutations of NPM1 and IDH2. Functional relevance of shared AML/LSC antigens is illustrated by presence of their cognizant memory T cells in patients. Antigen-specific T-cell recognition and HLA class II immunopeptidome diversity correlated with clinical outcome. Together, these antigens shared among AML and LSCs represent prime targets for T cell–based therapies with potential of eliminating residual LSCs in patients with AML.
The elimination of therapy-resistant leukemia stem and progenitor cells (LSC) remains a major challenge in the treatment of AML. This study identifies and functionally validates LSC-associated HLA class I and HLA class II–presented antigens, paving the way to the development of LSC-directed T cell–based immunotherapeutic approaches for patients with AML.See related commentary by Ritz, p. 430.This article is featured in Selected Articles from This Issue, p. 419
