Single-Cell Transcriptomic Profiling of Leukemic Stem Cell Populations in Acute Myeloid Leukemia

Abstract

Leukaemic stem cells have been defined by an immunophenotype for nearly three decades. Single-cell sequencing shows that definition failing in both directions at once: it contains normal stem cells that should not be there, and misses leukaemic ones that lie outside the gate. Objectives: To review the published evidence from single-cell transcriptomic profiling of leukaemic stem cell populations in acute myeloid leukaemia: what cellular states have been resolved, how they relate to the immunophenotypic definition, what they reveal about chemoresistance, and whether the findings support a universal marker or a patient-specific one.
Material and Methods: Narrative review of single-cell sequencing studies, functional xenograft work, stemness score derivations and cellular hierarchy analyses indexed in PubMed and the major haematology and genomics journals. Studies were eligible if they characterised leukaemic stem or progenitor populations in acute myeloid leukaemia by single-cell methods, or established the phenotypic and functional definitions those methods have tested. No new patient data were generated and no patients were recruited; every finding quoted is one published by the original investigators. Results: Integrating single-cell mutation detection with transcriptomes across sixteen patients resolved six malignant cell types resembling normal counterparts along the differentiation axis, from stem-cell-like through progenitor, granulocyte-monocyte progenitor, promonocyte and monocyte to dendritic-cell-like, with
strikingly heterogeneous abundance between tumours: some comprised one or two types, others a full range. Leukaemic stem cells constitute under 10 per cent of malignant CD34-positive blasts. A quiescent immature stem-cell-like population was identified carrying raised AP-1 transcription factor expression and reduced class II major histocompatibility expression. A previously described surface marker was upregulated in only one of four patients examined. In thirteen paired pre- and post-chemotherapy paediatric samples, approximately half of leukaemic stem and progenitor populations actively expressed stem cell and oxidative phosphorylation signatures and showed enhanced metabolic programmes under treatment. Conclusion: The historical CD34-positive CD38-negative definition encompasses normal haematopoietic stem cells while missing leukaemic cells outside that compartment. Marker expression appears patient-specific rather than universal, which constrains what any single-marker targeting strategy can achieve.
Abbreviations: AML – Acute Myeloid Leukaemia, LSC – Leukaemic Stem Cell, HSC – Haematopoietic Stem Cell, LSPC – Leukaemic Stem and Progenitor Cell, scRNA-seq – Single-Cell RNA Sequencing, GMP – Granulocyte-Monocyte Progenitor, cDC – Conventional Dendritic Cell, OXPHOS – Oxidative Phosphorylation, MHC – Major Histocompatibility Complex, AP-1 – Activator Protein 1, MRD – Measurable Residual Disease, NOD/SCID – Non-Obese Diabetic Severe Combined Immunodeficiency.