Coordinated Immune Cell Networks in the Bone Marrow Microenvironment Define the Graft versus Leukemia Response with Adoptive Cellular Therapy

Understanding how intra-tumoral immune populations coordinate to generate anti-tumor responses following therapy can guide precise treatment prioritization. We performed systematic dissection of an established adoptive cellular therapy, donor lymphocyte infusion (DLI), by analyzing 348,905 single-cell transcriptomes from 74 longitudinal bone-marrow samples of 25 patients with relapsed myeloid leukemia; a subset was evaluated by protein-based spatial analysis. In acute myelogenous leukemia (AML) responders, diverse immune cell types within the bone-marrow microenvironment (BME) were predicted to interact with a clonally expanded population of ZNF683+GZMB+ CD8+ cytotoxic T lymphocytes (CTLs) which demonstrated in vitro specificity for autologous leukemia. This population, originating predominantly from the DLI product, expanded concurrently with NK and B cells. AML nonresponder BME revealed a paucity of crosstalk and elevated TIGIT expression in CD8+ CTLs. Our study highlights recipient BME differences as a key determinant of effective anti-leukemia response and opens new opportunities to modulate cell-based leukemia-directed therapy. ### Competing Interest Statement K.M., C.Y.P, E.A., and C.J.W. are inventors on a licensed, pending international patent application, having serial number USP Serial No. 63/586,686, filed by Dana-Farber Cancer Institute, directed to certain subject matter related to the CD8+ ZNF683Hi CTL population described in this manuscript. C.J.W. is an equity holder of BioNTech, Inc. and receives research funding from Pharmacyclics. P.B. reports equity in Agenus, Amgen, Johnson & Johnson, Exelixis, and BioNTech; and receives research support from Allogene Therapeutics. D.N. received personal fees from Pharmacyclics, served as consultant to the American Society of Hematology Research Collaborative, and has stock ownership in Madrigal Pharmaceuticals. JR receives research funding from Kite/Gilead, Novartis and Oncternal Therapeutics and serves on Advisory Boards for Clade Therapeutics, Garuda Therapeutics, LifeVault Bio, Novartis and Smart Immune. K.J.L. reports equity in Standard BioTools Inc. and serves on scientific advisory board for MBQ Pharma Inc. R.J.S. serves on the Board of Directors for Be the Match/National Marrow Donor Program and DSMB for BMS; reports personal fees from Vor Biopharma, Smart Immune, Neovii, Astellas, Amgen, Bluesphere Bio, and Jasper. The remaining authors declare no competing interests.