Immunopeptidomics of cutaneous leishmaniasis patients reveals the natural antigenic landscape

Abstract

Introduction: Cutaneous leishmaniasis (CL) is a skin disease caused by Leishmania infection, for which no licensed human vaccine exists. Protective immunity is largely T cell–mediated and depends on antigen presentation by MHC molecules, yet the naturally presented epitopes during human disease remain poorly defined. Methods: To address this gap, we performed mass spectrometry–based immunopeptidomics on lesional biopsies from 27 Ethiopian CL patients spanning the full clinical spectrum. Results: We newly identified 333 MHC-I and 247 MHC-II epitopes from 398 L. aethiopica proteins, including 19 peptides and 51 antigens recurrently presented across patients of which several were also epitope-rich. Some peptides were also detected during early infection in a L. aethiopica–infected THP-1 monocyte model, highlighting their relevance from disease onset. Notably, despite the broad predictive coverage of NetMHCpan and NetMHCIIpan, these tools missed 20–70% of the naturally presented epitopes while predicting millions of candidates, underscoring the limitations of prediction-only vaccine pipelines. Discussion: This first comprehensive map of the Leishmania immunopeptidome in human disease reveals conserved and prevalent antigens that can inform rational vaccine design and deepen our understanding of protective T cell responses in leishmaniasis.