The remission status of AML patients after allo-HCT is associated with a distinct single-cell bone marrow T-cell signature

Abstract

Acute myeloid leukemia (AML) is a hematologic malignancy for which allogeneic stem cell transplantation (alloSCT) often remains the only curative therapeutic approach. However, incapability of T cells to recognize and eliminate residual leukemia stem cells (LSCs) might lead to an insufficient graft-versus-leukemia (GvL) effect and relapse. Here, we performed single-cell RNA-sequencing on bone marrow (BM) T lymphocytes and CD34+ cells of six AML patients 100 days after alloSCT to identify T cell signatures associated with either imminent relapse (REL) or durable complete remission (CR). We observed a higher frequency of cytotoxic CD8+ effector and gamma delta (γδ) T cells in CR versus REL samples. Pseudotime and gene regulatory network analyses revealed that CR CD8+ T cells were more advanced in maturation and had a stronger cytotoxicity signature, while REL samples were characterized by inflammatory TNF/NF-κB signaling and an immunosuppressive milieu. We identified ADGRG1/GPR56 as a surface marker enriched in CR CD8+ T cells and confirmed in a CD33-directed chimeric antigen receptor (CAR)-T/AML co-culture model that GPR56 becomes upregulated on T cells upon antigen encounter and elimination of AML cells. We show that GPR56 continuously increases at the protein level on CD8+ T cells after alloSCT and confirm faster IFNγ secretion upon re-exposure to matched, but not unmatched recipient AML cells in the GPR56+ versus GPR56- CD8+ T cell fraction. Together, our data provide a single-cell reference map of BM-derived T cells post alloSCT and propose GPR56 expression dynamics as a surrogate for antigen encounter post alloSCT.

Integrative single-cell analysis of longitudinal t(8;21) AML reveals heterogeneous immune cell infiltration and prognostic signatures

“…The prognostic efficiency of 14TGS was further validated in other AML cohorts, and 14TGS demonstrated robust predictive value. Interestingly, one recent study published in Blood reported a distinct single-cell T-cell signature associated with stem cell transplantation outcome in AML patients; one of the included genes was GPR56 , a biomarker of alloreactive CD8+ T cells ( 55 ). This further suggested that cluster_2 T cells are a novel subset that has different phenotypes and mechanisms of action.…”

Role of Stem-Like Cells in Chemotherapy Resistance and Relapse in pediatric T Cell Acute Lymphoblastic Leukemia

“…TR supervised computational analysis. AM helped with the set-up of the SCENIC pipeline 14,15,41 and run initial SCENIC analyses. JZ supervised the set-up of the SCENIC pipeline 14,15,41 .…”

“…AM helped with the set-up of the SCENIC pipeline 14,15,41 and run initial SCENIC analyses. JZ supervised the set-up of the SCENIC pipeline 14,15,41 . MS, GE, CE provided patients samples and data for the analyses.…”