Immunopeptidomics of cutaneous leishmaniasis patients reveals the natural antigenic landscape

Nicky De Vrij¹Elise Pepermans²Louise Laurijssen¹Thao-Thy Pham³Lauren Thijs²Kurt Boonen²Kadrie Ramadan³Ilse Maes³Yetemwork Aleka⁴Mekibib Kassa⁴Tigist Mekonnen⁴Mezgebu Silamsaw Asres⁴Mikias Woldetensay⁴Seid Hassen⁵Fentaw Bialfew⁵Feleke Tilahun Zewdu⁵Seid Getahun Abdela⁵Malgorzata Anna Domagalska³Bart Cuypers¹Saskia Caroline Van Henten³Johan Van Griensven³Pieter Meysman¹Geert Baggerman¹Kris Laukens¹Wim Adriaensen^3*

• ¹Universiteit Antwerpen, Antwerp, Belgium
• ²ImmuneSpec, Niel, Belgium
• ³Institute of Tropical Medicine Antwerp, Antwerp, Belgium
• ⁴University of Gondar, Gondar, Ethiopia
• ⁵Boru meda hospital, Dessie, Ethiopia

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. To address this gap, we performed mass spectrometry–based immunopeptidomics on lesional biopsies from 27 Ethiopian CL patients spanning the full clinical spectrum. 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. 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.