Personal and Shared Tumor-Antigen Prioritization in Diffuse Large B Cell Lymphoma Patients Undergoing CD19 CAR T Cell Treatment
Authors: Karagkouni Dimitra , Katopodi Xanthi Lida , Cheloni Giulia , Ma Yuling , Miles Brodie , Tiwari Gayatri , Kim Jenny J. , Mattie Mike , Rosenblatt Jacalyn , Avigan David , Vlachos Ioannis 
Published: December 2023

Backgroun d: Durable response to Axi-cel CD19 CAR T cell therapy is associated with activation and clonotypic expansion of the host T cell repertoire (Cheloni et al Blood, ASH, 2022). The characterization of the tumor microenvironment (TME) and the identification of tumor antigens associated with therapeutic efficacy is a critical area of investigation.
Aim: We sought to determine the association between the host immune activation in response to tumor-associated and tumor-specific antigens and the clinical response to CAR-T cell treatment in diffuse large B cell lymphoma patients.
Methods: RNAseq was performed on FFPE lymphoma samples collected before CAR T cell infusion (N=16). Patients were divided into 3 distinct cohorts: stable progressive disease at 1 month post-CAR T (non-responders, n=2), disease relapse within 6 months post-CAR T (relapsed, n=3), and on-going response lasting greater than 1 year (long-term responders, n=11). For neoantigens, mutations were retrieved following the GATK best practices for RNAseq data and annotated with Variant Effect Predictor (VEP). Tumor-specific antigens and tumor-associated antigens were detected by prioritizing 9-11mer amino acid sequences, preferentially presented by class I molecules, observed solely or primarily in tumor samples, respectively, as compared to a pool of healthy controls derived from 250 RNAseq samples, corresponding to 29 tissues (GTEx Portal). Antigen prioritization was performed following weighted scoring considering RNA expression, translation potential, peptide-MHC binding affinity, predicted immunogenicity, physicochemical properties, and clonality, in the case of neoantigens. Using deconvolution methods and canonical marker expression, we characterized the major immune cell types within the TME.
Results: Higher cell proportions of lymphocytes and innate immune cells, including NK, and activated dendritic cells were observed in long-term responders, suggesting that a higher infiltration of these cell types in the tumor bed is associated with a better response to CAR T cell therapy. Notably, a positive correlation between the mutational burden and the a/b clonotypic expansion of peripheral blood cytotoxic T cell populations, detected from single-cell immunoprofiling (Cheloni et al Blood, ASH, 2022) was observed in eight long-term responders, consistent with prior studies highlighting the significance of neoantigens in eliciting robust and durable immune response against cancer cells. A high occurrence of neoantigens originating from the Titin ( TTN) gene in two long-term responders with the highest mutational burden was observed, and from ACTB and ACTG1, mutated genes associated with lymphoid cancers. A substantial enrichment of shared tumor antigens originating from retroelements was observed in long-term responders, suggesting the presence of common epitopes that drive an antigen-specific response.
Conclusion: These findings shed light on the potential immunogenicity of specific neoantigens and shared antigens derived from repetitive elements, which could serve as promising targets for immunotherapeutic strategies in lymphoma patients. Understanding the tumor immune landscape and antigenic features associated with long-term response to CAR T cell therapy may pave the way for the development of personalized and effective combinatorial treatments for lymphoid cancers.