RETRACTED ARTICLE: Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs

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.

Chimeric Antigen Receptors Directed at Mutant KRAS Exhibit an Inverse Relationship Between Functional Potency and Neoantigen Selectivity

“…The possibilities for improving the potency/selectivity of CARs directed at mutant KRAS pMHCs include: (i) higher diversity of the initial and/or optimization binder libraries [24]; (ii) more complex, diverse counter-screens during binder selection; (iii) structure-based design [25]; and, (iv) higher throughput functional screens. Indeed, TCR optimization via phage display has been associated with at least one case of off-target reactivity that caused fatal toxicity in the clinic [23].…”

Using chimeric antigen receptor T-cell therapy to fight glioblastoma multiforme: past, present and future developments

“…WT1 is known to be over-expressed in many malignancies, including GBM [ 101 ], offering broad tumor therapeutic potential. Expanding on this strategy to target MHC-presented peptides from key intracellular oncoproteins, Yamarkovich M. et al have recently created a peptide-centric CAR (PC-CAR) that can target neuroblastoma dependency gene and intracellular transcriptional regulator PHOX2B and induce remission in a murine model of neuroblastoma [ 102 ].…”

Current Status of CRISPR/Cas9 Application in Clinical Cancer Research: Opportunities and Challenges

“…Some cancers lack the tumor mutational burden and MHC expression, which hinders the application of conventional CARs. Very recently, a synthetic peptide-centric CARs (PC-CARs) approach has been proposed to target some tumor specific oncoproteins [ 35 ].…”