Identification of Distinct Subtypes in Immune Tolerance after Hematopoietic Cell Transplantation Using the Prospective ABLE1.0 Pediatric Study Cohort

The lack of immune tolerance after hematopoietic cell transplantation (HCT) can result in chronic graft-versus-host disease (cGvHD), which is the primary nonrelapse limitation of successful HCT. To date, immune tolerance has been considered a single biological entity, but we hypothesized that post-HCT immune tolerance could develop through multiple pathways. Using the ABLE network database, which comprises measurements of 75 cell populations, 10 cytokines and chemokines, lymphocyte population telomere length, KRECs and TRECs, and 132 metabolites from the largest pediatric cGvHD cohort (n = 241), we applied clustering analysis to patients with primary immune tolerance (PIT; no acute GvHD [aGvHD] or cGvHD) and patients with secondary immune tolerance (SIT; previous aGvHD and no cGvHD) to test whether subtypes could be identified. The evaluation of PIT identified 3 subtypes. PIT-1, associated with postpubertal age, lower thymic output, and increased ST2 compared to PIT-2 and PIT-3, is effector memory T cell-predominant. PIT-2, associated with prepubertal age, normal thymic output, increased B cell development, and longer lymphocyte telomeres, has a naïve T cell-predominant pattern. PIT-3, associated with postpuberty, higher thymic output, and malignancy, is dominated by increased PD1⁺ regulatory T cells and helper T cells and decreased long-chain acylcarnitine. We partially replicated these PIT subtypes using metabolomic data from a separate pediatric cohort of the Children's Oncology Group trial ASCT0031 (n = 24 PIT patients). Previously resolved aGvHD had a minimal impact on the overall patterns of SIT-1 and SIT-2 compared to PIT-1 and PIT-2, except for time delays in the expansion of some immune cells. PIT-3 and SIT-3 were dominated by late increases in phosphatidylcholines (lysophosphatidylcholine precursors) and long-chain lysophosphatidylcholines (LYSOC20:4 and LYSOC16:2), respectively. This is the first time that distinct biological patterns of immune reconstitution after HCT are identified, which on validation and potentially could aid the development of future strategies for tolerance induction.