Implementation of DNA-barcoded pMHC-I multimer reagents and single cell immune profiling with feature barcoding technology to accelerate tumor neoantigen-specific T cell receptor (TCR) identification for adoptive T cell therapies
The Alliance contributes to the development of broad patient-tailored T cell monitoring and TCR discoveries for therapeutic purposes.
Tumor neoepitopes that arise from somatic mutations in cancer cells represent ideal targets for T cell-based immunotherapeutic interventions due to their lack of expression in healthy tissues and surveillance by immune tolerance.
To this end the development and routine application of personalized T cell receptor (TCR) gene-engineered adoptive T cell therapies (ACT) targeting individual- as well as shared patient-derived neoepitopes is important. Based on a state-of-the-art tumor mutagenome analysis as well as in silico T cell epitope prediction pipeline that is combined with a highly sensitive pMHCmultimer-guided antigen-specific T cell discovery workflow, the Alliance project members have already identified and validated several neoepitope-specific TCRs across various solid tumor entities. By incorporating DNA-barcoded pMHC-I multimer reagents into the workflow, they link multiplexed tumor antigen recognition with their associated TCR repertoire and cell phenotype at a single cell resolution, which further accelerates the selection of TCRs / antigen pairs for validation prior to their usage in an ACT.
Using the Alliance Explore!Tech opportunity, the project members were able to test the DNA-barcoded pMHC-I multimer reagents for guided single-cell sequencing of T cells from patients suffering from breast adenocarcinoma, liposarcoma and melanoma, respectively, and able to test and verify tumor neoantigen-as well as tumor-associated (NY-ESO-1)-specific T cell receptors in all three cases. In addition, they developed a novel technically accessible peptide-receptive MHC multimer production platform termed MediMer, which we also tested in combination with DNA-barcoding. The entire workflow including the development of the MediMer system and implementation of the reagents (dCODE U-Load® (10x) system, immudex) for the assembly of a DNA-barcoded pMHC-I multimer library was published recently (01/2024) in Frontiers in Immunology (https://doi.org/10.3389/fimmu.2023.1294565).
Coordination: Marten Meyer, Medical Faculty Heidelberg, Heidelberg University/ DKFZ, Frank Momburg, DKFZ, Pornpimol Charoentong, Medical Faculty Heidelberg, Heidelberg University, Yanhong Lyu, DKFZ, Patrick Schmidt, DKFZ, Paula Roberti, DKFZ, Selina Börsig, Medical Faculty Heidelberg, Heidelberg University/DKFZ, Nadja Bulbuc, DKFZ, Inka Zörnig, Medical Faculty Heidelberg, Heidelberg University & Dirk Jäger, Medical Faculty Heidelberg, Heidelberg University/DKFZ
Platform partner involved: David Ibberson, Deep Sequencing Core Facility, Heidelberg University