TY  - JOUR
AU  - Murcia Pienkowski, Victor
AU  - Boschert, Tamara
AU  - Skoczylas, Piotr
AU  - Sanecka-Duin, Anna
AU  - Jasiński, Maciej
AU  - Król-Józaga, Bartłomiej
AU  - Mazzocco, Giovanni
AU  - Stachura, Sławomir
AU  - Bunse, Lukas
AU  - Kaczmarczyk, Jan
AU  - Green, Edward
AU  - Blum, Agnieszka
TI  - Computational identification of cross-reactive TCR epitopes with ARDitox.
JO  - Journal of cancer research and clinical oncology
VL  - 151
IS  - 12
SN  - 0301-1585
CY  - Heidelberg
PB  - Springer
M1  - DKFZ-2025-02256
SP  - 311
PY  - 2025
N1  - #LA:D170#
AB  - Cellular immunotherapies, such as those utilizing T lymphocytes expressing native or engineered T cell receptors (TCRs), have demonstrated therapeutic efficacy. However, some engineered high-affinity TCRs have caused fatal off-target immunotoxicity due to targeting epitopes later found to be expressed by both tumor cells and healthy tissues. Unfortunately, TCRs can be cross-reactive to epitopes with highly distinct sequences, making prediction difficult, and the exquisite sequence specificity of TCRs means that safety studies in mice miss human-specific epitopes.To address this issue, we developed ARDitox, a novel in silico method based on computational immunology and artificial intelligence (AI) for predicting and analyzing potential TCR off-target toxicities. We tested the performance of ARDitox on four TCRs reported to target tumor-associated antigens, two of which are known to cause clinical immunotoxicity (MAGEA3112-120 and MAGEA3168-176 epitopes), one of which has experimentally identified off-target antigens (AFP158-166 epitope), and the last one for which no cross-reactive epitopes are known (NY-ESO-1157-165).ARDitox confirmed the previously identified immunotoxic epitopes. We then expanded our analyses to a novel TCR targeting the tumor-associated antigen NLGN4X, frequently upregulated in gliomas. For this target, ARDitox identified a cross-reactive peptide that would not have been found using mouse models, highlighting the value of our computational approach.Our findings underscore the value of the ARDitox in silico method for the early and reliable identification of off-target epitopes for further preclinical evaluation. This platform strongly supports the development of safer TCR-mediated immunotherapies.
KW  - Humans
KW  - Epitopes, T-Lymphocyte: immunology
KW  - Cross Reactions: immunology
KW  - Receptors, Antigen, T-Cell: immunology
KW  - Computational Biology: methods
KW  - Antigens, Neoplasm: immunology
KW  - Mice
KW  - Animals
KW  - Computer Simulation
KW  - Artificial Intelligence
KW  - T-Lymphocytes: immunology
KW  - 3R (Other)
KW  - Cell therapy (Other)
KW  - Cross-reactivity (Other)
KW  - Off-target toxicity (Other)
KW  - Safety (Other)
KW  - TCR (Other)
KW  - Epitopes, T-Lymphocyte (NLM Chemicals)
KW  - Receptors, Antigen, T-Cell (NLM Chemicals)
KW  - Antigens, Neoplasm (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:41175267
DO  - DOI:10.1007/s00432-025-06330-7
UR  - https://inrepo02.dkfz.de/record/305606
ER  -