Trial in Progress: A Phase 1 Umbrella Study of TCR-Engineered T Cells That Target HA-1 (TSC-100) and HA-2 (TSC-101) to Treat Residual Leukemia after Hematopoietic Cell Transplantation

Background: Engineered T cell therapies targeting the lineage-specific antigens CD19 (B cells) or BCMA (plasma cells) are highly effective in patients with lymphoid malignancies and feasible because depleting normal B cells or plasma cells can be tolerated by patients. Targeting lineage antigens in myeloid malignancies is not feasible, however, since depleting normal myeloid cells like neutrophils would lead to serious complications such as febrile neutropenia. To address myeloid malignancies with T cell therapies, one solution is to target antigens that are expressed on the hematopoietic cells of patients undergoing allogeneic hematopoietic cell transplantation (HCT), but not expressed on their donor's cells. Hematopoietic lineage-specific minor histocompatibility antigens (MiHAs) can be targeted by T cell receptors (TCRs), but not chimeric antigen receptors, because they most frequently represent single-amino acid changes in intracellular proteins that are presented on the cell surface by human leukocyte antigen (HLA) binding. TScan has developed the engineered T cell products TSC-100 and TSC-101 that express TCRs targeting MiHAs HA-1 and HA-2 respectively, both presented by HLA-A*02:01. By choosing HCT patients who are HA-1 or HA-2 positive and donors who are mismatched on either the MiHA or HLA-A*02:01, TSC-100 and TSC-101 can eliminate all recipient hematopoietic cells while leaving donor hematopoietic cells untouched. These products are being developed in patients with AML, ALL and MDS undergoing HCT to eliminate any residual hematopoietic cells after HCT and prevent disease relapse that affect ~40% of patients. We describe the clinical trial design and translational assays to generate early evidence of biological activity. Preliminary clinical safety and translational data will be presented.

Study Design and Methods: Study NCT05473910 is a multi-center, multi-arm, non-randomized controlled Phase 1 umbrella study evaluating the feasibility, safety and preliminary efficacy of TSC-100 and TSC-101. Key inclusion criteria include adult patients with AML, MDS or ALL who are eligible for reduced intensity conditioning (RIC)-based haploidentical donor transplantation. HLA-A*02:01-positive patients are assigned to the treatment arms, undergo HA-1/ HA-2 testing and receive either TSC-100 or TSC-101 in addition to standard HCT. HLA-A*02:01-negative patients are assigned to the control arm and receive standard HCT alone. Donors in treatment arms undergo two rounds of leukapheresis, one to manufacture TSC-100/101 and one after mobilization to collect stem cells. Patients undergo RIC, peripheral blood stem cell infusion followed by post-transplant cyclophosphamide. Upon count recovery, patients begin treatment with TSC-100 or TSC-101. In Dose Level 1, patients receive a single dose of 5x10⁶ cells/kg. In Dose Level 2, patients receive two doses of 5x10⁶ cells/kg given 40 days apart. In Dose Level 3, patients receive one dose of 5x10⁶ cells/kg and asecond dose of 2x10⁷ cells/kg given 40 days later. Primary endpoints include adverse event profiles of TSC-100/ 101 and dose limiting toxicities. Secondary endpoints measure efficacy including relapse rates, disease-free survival and overall survival. Exploratory endpoints include persistence of TSC-100/ TSC-101, surrogates of efficacy including minimal residual disease (MRD) rates before/ after transplantation, donor chimerism kinetics and rates post-transplantation and markers of T cell activation on TSC-100/ 101.

Novel translational assays have been developed for the exploratory endpoints. TSC-100/ 101 persistence is measured by flow cytometry with lower limit of quantification <0.1% of total T cells. MRD is measured by flow cytometry and next-generation sequencing (NGS) the combination of which detects MRD with greater sensitivity than either assay alone. Donor chimerism is measured by standard STR-based assays with a limit of detection of 1-2% and a novel NGS-based assay called Alloheme with a limit of detection of 0.04%. T-cell activation markers on TSC-100/ 101 are measured by flow cytometry, cytokine profiling and single-cell RNA sequencing. Together these translational assays measure elimination of the target hematopoietic cell population, malignant or normal, and provide evidence of potential biological activity well before frank clinical relapses occur.

Reshef:Atara Biotherapeutics: Consultancy, Research Funding; Gilead Science: Consultancy, Research Funding; J&J: Research Funding; Immatics: Research Funding; Incyte: Consultancy, Research Funding; Pharmacyclics: Consultancy, Research Funding; Precision Biosciences: Research Funding; Shire: Research Funding; Takeda: Research Funding; Bristol-Myers Squibb: Consultancy; Jasper: Consultancy; Novartis: Consultancy; Regeneron: Consultancy; Synthekine: Consultancy; TScan: Consultancy; Bayer: Consultancy; Kite: Consultancy, Research Funding; Magneta: Consultancy; Pfizer: Consultancy; Celgene: Research Funding. Kothari:CareDx, Inc.: Current Employment, Current equity holder in publicly-traded company. Bell:CareDx, Inc.: Current Employment, Current equity holder in publicly-traded company. Boudot:TScan Therapeutics: Current Employment, Current equity holder in publicly-traded company. Wang:TScan Therapeutics: Current Employment, Current equity holder in publicly-traded company. Abelowitz:TScan Therapeutics: Current Employment, Current equity holder in publicly-traded company. Murray:TScan Therapeutics: Current Employment, Current equity holder in publicly-traded company. Macbeath:TScan Therapeutics: Current Employment, Current equity holder in publicly-traded company. Barton:NKILT therapeutics: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Arovella Therapeutics: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees; TScan Therapeutics: Current Employment, Current equity holder in publicly-traded company. Chattopadhyay:TScan Therapeutics: Current Employment, Current equity holder in publicly-traded company.