Single-cell analysis reveals the chemotherapy-induced cellular reprogramming and novel therapeutic targets in relapsed/refractory acute myeloid leukemia

Abstract

Chemoresistance and relapse are the leading cause of AML-related deaths. Utilizing single-cell RNA sequencing (scRNA-seq), we dissected the cellular states of bone marrow samples from primary refractory or short-term relapsed AML patients and defined the transcriptional intratumoral heterogeneity. We found that compared to proliferating stem/progenitor-like cells (PSPs), a subpopulation of quiescent stem-like cells (QSCs) were involved in the chemoresistance and poor outcomes of AML. By performing longitudinal scRNA-seq analyses, we demonstrated that PSPs were reprogrammed to obtain a QSC-like expression pattern during chemotherapy in refractory AML patients, characterized by the upregulation of CD52 and LGALS1 expression. Flow cytometric analysis further confirmed that the preexisting CD99+CD49d+CD52+Galectin-1+ (QSCs) cells at diagnosis were associated with chemoresistance, and these cells were further enriched in the residual AML cells of refractory patients. Interaction of CD52-SIGLEC10 between QSCs and monocytes may contribute to immune evading and poor outcomes. Furthermore, we identified that LGALS1 was a promising target for chemoresistant AML, and LGALS1 inhibitor could help eliminate QSCs and enhance the chemotherapy in patient-derived primary AML cells, cell lines, and AML xenograft models. Our results will facilitate a better understanding of the AML chemoresistance mechanism and the development of novel therapeutic strategies for relapsed/refractory AML patients.

Leukemic stem cells hijack lineage inappropriate signalling pathways to promote their growth

“…GATA2 expression was also up-regulated, with increased binding to its enhancers thus setting up an auto-regulatory loop (Figures S6H and S6I). GATA2 is a key regulator of stem cell maintenance 23 and we and others have shown that GATA2 is expressed in LSCs (Figure 1) 36 . To examine whether the increase in GATA2 binding after AP-1 inhibition would lead to a reactivation of LSC-specific genes we first examined transcription factor binding at LSC or blast cell specific genes as defined in Figure 1 with and without dnFOS induction in Kasumi-1 cells (Figure 6E).…”

Recent advances in CAR‐T cell therapy for acute myeloid leukaemia

“…CD99 is a transmembrane glycoprotein and is strongly expressed in the majority of AML. CD99 is a marker expressed on the surface of leukaemic stem cells but not normal haematopoietic stem cells, thus can be a promising therapeutic target for AML 16,93 . Previous studies show that expression of CD99 can separate LSCs from functionally normal HSCs in AML and have higher CD99 levels in relapse AML blasts 94 .…”

Targeting and Monitoring Acute Myeloid Leukaemia with Nucleophosmin-1 (NPM1) Mutation

“…Similarly, the application of single-cell technology is continuously under development for MRD monitoring for improved resolution. Both DNA and conventional RNA single-cell sequencing have been employed in MRD monitoring in AML but are not routinely used due to cost and the high requirement for sample preparation [ 74 , 75 ]. With the inclusion of surface marker staining, single-cell multi-omic analysis further increases the resolution of the MRD in NPM1 mutated AML patients [ 76 ].…”