Overcoming Resistance to CAR-T Cell Therapy by Targeting the HLA Immunopeptidome

Chimeric antigen receptor T cells directed against the CD19 protein have shown marked clinical efficacy in patients with B cell malignancies. Despite a high response rate, relapse is common with most patients losing expression of CD19 at time of recurrence. This phenomenon of CD19 negative relapse remains an unmet clinical challenge. Current evidence has shown that CD19 is misfolded, causing it to lose surface expression as well as the epitope recognized by the CAR antibody.

As opposed to traditional antibodies used in CAR T cell constructs, which are only able to bind surface proteins, TCR-like antibodies recognize peptides presented on MHC molecules. This increases the target repertoire to include intracellular proteins. We hypothesized that in CD19 negative relapse CD19 is processed and presented as short peptides on MHC molecules, and that these MHC/peptide complexes may serve as an alternative target for immunotherapy.

We have identified MHC-bound-CD19-derived peptides in CD19-negative relapse cell lines through peptide elution. TCR-like antibodies specifically targeting the CD19-derived peptide-MHC complex were isolated using phage display. Antibodies were used to create CAR constructs which were subsequently transduced into donor-derived T cells. These engineered T cells are currently being tested in vitro against leukemia cell lines. This will be followed by assays using patient-derived samples and eventually by in-vivo testing. We expect that T cells armed with the TCR-like-CARs will cause effective killing of leukemia even once surface expression of CD19 is lost. This may offer sequential, personalized therapy for patients with relapse following conventional CAR T cell therapy.