Abstract 3253: A high-throughput platform to produce neoE-HLA libraries for capturing neoE-specific T cells from the peripheral blood of patients with solid tumors
Authors: Dalmas Olivier , Pan Zheng , Shieh Christine , Xu Allison , Kwa Jason , Heeringa Katharine , Ma Yan , Collins John , An Duo , Peng Songming , Franzusoff Alex 
Published: September 2020

A critical step in the development of personalized neoTCR-T cell therapies is operational selection of tumor-exclusive neoantigen peptide targets (neoepitopes or neoE) presented by each person's own HLA proteins (neoE-HLA targets). We have developed a high-throughput, automated process for the cloning, expression and purification of soluble proteins comprising neoE peptide with beta2m and the HLA heavy chain fused into a single polypeptide (neoE-HLA proteins).

Of the 13 thousand HLA alleles in the human population, with 6 HLA alleles expressed in each person, our HLA catalog enables rapid production of neoE-HLA protein candidate libraries, representing &gt;4 of 6 HLAs for ≥95% of all patients, regardless of ethnicity. We apply our proprietary bioinformatics pipeline to predict and prioritize tumor-exclusive neoE-HLA candidates for each patient. We then generate neoE-HLA libraries in single production runs for up to several hundred neoE-HLA candidates per patient. These soluble neoE-HLA proteins are then assembled into barcoded snare multimers. These barcoded snare libraries are used to interrogate matched PBMCs from that patient to capture rare (&gt;1 per 106) to abundant antigen-experienced CD8 T cells which specifically bind the cognate neoE-HLA tumor targets, using the imPACT Isolation Technology®.

This platform is capable of producing barcoded snares predicted to represent high affinity (≤500 nM) and low affinity (&gt;500nM) neoE binding to their cognate HLAs. These capabilities permit deep and broad interrogation of the tumor-targeted neoE-specific T cell repertoire in the blood of patients with solid cancers. Data shown here demonstrate that &gt;85% of patients with different cancer types, indeed, harbor a surprising repertoire of tumor-targeted neoE-specific T cells. These antigen-experienced T cells reveal the pre-existing immune response to each person's cancer, and how that repertoire evolves in longitudinal analyses of patients that respond/do not respond to their cancer therapies.

In summary, PACTs proprietary neoE-HLA prediction pipeline and the proprietary high-throughput neoE-HLA protein production platform enables the discovery of tumor-targeted, neoE-specific T cells from patients. We leverage the neoTCRs cloned from these captured T cells to engineer fresh T cells from the patient into a full dose of tumor-targeted personalized neoTCR-T cells (NeoTCR-P1 T cell therapy). This fully personalized NeoTCR-P1 cell therapy is manufactured in fully enclosed, automatable systems for each individual patient with solid tumors. These breakthrough technologies support the on-going Phase 1 clinical trial of personalized engineered autologous NeoTCR-P1 T cell therapies for patients with six different solid tumor types (NCT03970382).

Citation Format: Olivier Dalmas, Zheng Pan, Christine Shieh, Allison Xu, Jason Kwa, Katharine Heeringa, Yan Ma, John Collins, Duo An, Songming Peng, Alex Franzusoff. A high-throughput platform to produce neoE-HLA libraries for capturing neoE-specific T cells from the peripheral blood of patients with solid tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3253.