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Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs
Mark Yarmarkovich1, Quinlen F Marshall1, John M Warrington1
1Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Abstract:
The majority of oncogenic drivers are intracellular proteins, thus constraining their immunotherapeutic targeting to mutated peptides (neoantigens) presented by individual human leukocyte antigen (HLA) allotypes1. However, most cancers have a modest mutational burden that is insufficient to generate responses using neoantigen-based therapies2,3. Neuroblastoma is a paediatric cancer that harbours few mutations and is instead driven by epigenetically deregulated transcriptional networks4. Here we show that the neuroblastoma immunopeptidome is enriched with peptides derived from proteins that are essential for tumourigenesis and focus on targeting the unmutated peptide QYNPIRTTF, discovered on HLA-A*24:02, which is derived from the neuroblastoma dependency gene and master transcriptional regulator PHOX2B. To target QYNPIRTTF, we developed peptide-centric chimeric antigen receptors (CARs) using a counter-panning strategy with predicted potentially cross-reactive peptides. We further hypothesized that peptide-centric CARs could recognize peptides on additional HLA allotypes when presented in a similar manner. Informed by computational modelling, we showed that PHOX2B peptide-centric CARs also recognize QYNPIRTTF presented by HLA-A*23:01 and the highly divergent HLA-B*14:02. Finally, we demonstrated potent and specific killing of neuroblastoma cells expressing these HLAs in vitro and complete tumour regression in mice. These data suggest that peptide-centric CARs have the potential to vastly expand the pool of immunotherapeutic targets to include non-immunogenic intracellular oncoproteins and widen the population of patients who would benefit from such therapy by breaking conventional HLA restriction.
Insights
This study introduces peptide-centric chimeric antigen receptors (CARs) to target intracellular neuroblastoma oncoproteins, overcoming limitations of neoantigen therapies and expanding treatment options for patients with specific human leukocyte antigen (HLA) types.
Area of Science:
- Immunology
- Oncology
- Biotechnology
Background:
- Most cancer immunotherapies target mutated peptides (neoantigens) presented by human leukocyte antigen (HLA) molecules.
- Cancers with low mutational burden, like neuroblastoma, are poorly targeted by neoantigen-based therapies.
- Neuroblastoma is driven by epigenetic deregulation rather than mutations, presenting a challenge for current immunotherapies.
Purpose of the Study:
- To develop a novel immunotherapeutic strategy for neuroblastoma targeting intracellular oncoproteins.
- To engineer peptide-centric chimeric antigen receptors (CARs) capable of recognizing specific tumor-associated peptides.
- To overcome human leukocyte antigen (HLA) restriction in CAR T-cell therapy.
Main Methods:
- Identification of a neuroblastoma-specific peptide (QYNPIRTTF) derived from PHOX2B presented on HLA-A*24:02.
- Development of peptide-centric CARs using a counter-panning strategy.
- Computational modeling to predict cross-reactivity with other HLA allotypes.
- In vitro and in vivo validation of CAR T-cell efficacy against neuroblastoma cells.
Main Results:
- Peptide-centric CARs successfully targeted the PHOX2B-derived peptide QYNPIRTTF.
- CARs demonstrated cross-reactivity, recognizing the peptide presented by HLA-A*23:01 and HLA-B*14:02.
- Potent and specific killing of neuroblastoma cells expressing these HLAs was observed in vitro.
- Complete tumor regression was achieved in mouse models.
Conclusions:
- Peptide-centric CARs offer a promising approach to target intracellular oncoproteins previously inaccessible to immunotherapy.
- This strategy broadens the applicability of CAR T-cell therapy by overcoming conventional HLA restriction.
- The findings suggest a potential for wider patient benefit in neuroblastoma and other cancers with low mutational burden.
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