Monitoring of Neoantigens and Adoptively Transferred Personalized Neotcr T Cell Populations in the Tumor and PBMCs of Patients with Solid Tumors

Background: NeoTCR-P1 is a personalized autologous T cell therapy for treatment of patients with solid tumors. Neoantigen-specific T cell receptors (neoTCRs) were isolated from the patients’ circulating CD8 T cells followed by non-viral precision genome engineering into autologous apheresis-derived T cells for infusion back into the patient. We present comprehensive immune monitoring data for 2 patients treated in a first-in-human Phase 1 clinical trial (NCT03970382). Each patient was infused with their own personalized cell therapy product consisting of 3 unique neoTCRs targeting neoantigens identified as truncal in screening biopsies. Methods: We identified infused neoTCR specific T cells in the blood by using patient-specific peptide HLA reagents with single cell RNA seq and in the tumor using RNA scope probes or bulk transcriptome analysis. Results: Patient 0503, a patient with MSS colorectal cancer, was treated with 3 unique neoTCRs (1.3x109 neoTCR+ cells) which targeted 2 distinct neoantigens presented by HLA-B*39:01 or HLA-C*12:02. Analysis of longitudinal biopsies confirmed that targeted mutations were truncal, with both neoantigens present pre- and post-dosing. NeoTCR+ T cells were identified in the tumor by RNA seq and imaging, with neoTCR+ T cells also expressing Granzyme B. Furthermore, single cell RNA seq of neoTCR+ T cells from the pre-infusion product as compared neoTCR T cells isolated from the patients’ blood 2 months post-infusion demonstrated evidence of antigen engagement in 1 out of 3 neoTCR T cell products, with a shift from a predominantly Tcm/Tem-like phenotype pre-infusion to a Teff-like state post-infusion. This neoTCR T cell product also increased slightly in the blood from 1.1 to 3.4% between month 1 and 2, while the other 2 T cell products remained predominantly in the Tcm-like phenotype and remained stable in the blood between month 1 and 2. Patient 0612, a patient with melanoma, was treated with 3 unique neoTCRs (4.0x109 neoTCR+ cells) which targeted 3 distinct neoantigens presented by HLA-B*08:01 or HLA-C*07:02. Longitudinal biopsies support the assessment that 2/3 mutations were truncal and 1 targeted mutation was sub-clonal based on their presence in each biopsy. Retrospective analysis showed HLA loss of heterozygosity at HLA-C07:02 in all 3 biopsies, affecting 2/3 infused TCR products. The remaining TCR showed evidence of a shift from a predominantly Tcm-like phenotype pre-infusion to more differentiated Teff/Tcm-em phenotypes post-infusion compared to the 2 TCRs targeting mutations expressed by the lost HLA allele. Conclusion: These case studies illustrate for the first time tracking of 3 unique personalized T cell products within a single patient. Shifts in the T cell phenotype of the neoTCR T cell products post-infusion for some, but not all, of the products suggest early signs of T cell engagement with the target. Citation Format: Susan Foy, Cliff Wang, Benjamin Yuen, Sara Said, Boi Quach, Jonathan Hoover, Saparya Nayak, Theresa Hunter, Zheng Pan, Chad Smith, Tyler Borrman, Eric Stawiski, Alphonsus H. C. Ng, Yue Lu, James Heath, Stefanie Mandl. Monitoring of neoantigens and adoptively transferred personalized neoTCR T cell populations in the tumor and PBMCs of patients with solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 901.