Single-cell genomics in AML: extending the frontiers of AML research

Abstract

The era of genomic medicine has allowed acute myeloid leukemia (AML) researchers to improve disease characterization, optimize risk-stratification systems, and develop new treatments. Although there has been significant progress, AML remains a lethal cancer because of its remarkably complex and plastic cellular architecture. This degree of heterogeneity continues to pose a major challenge, because it limits the ability to identify and therefore eradicate the cells responsible for leukemogenesis and treatment failure. In recent years, the field of single-cell genomics has led to unprecedented strides in the ability to characterize cellular heterogeneity, and it holds promise for the study of AML. In this review, we highlight advancements in single-cell technologies, outline important shortcomings in our understanding of AML biology and clinical management, and discuss how single-cell genomics can address these shortcomings as well as provide unique opportunities in basic and translational AML research.

Graphical abstract

Figure 1.

Stem cell model of normal and malignant hematopoiesis. Hematopoietic stem cells (HSCs) are capable of self-renewal (semicircular arrow) and reside at the apex of healthy polyclonal hematopoiesis (black). The acquisition of mutations in HSCs (m₁) can create preleukemic HSCs (pHSCs; purple) that can drive clonal hematopoiesis (shaded purple). Clonal evolution through additional mutation acquisition (m_{2, 3, …x}) or other molecular processes can further transform pHSCs into LSCs (red). These LSCs reside at the apex of the AML cellular hierarchy and are capable of (re)generating frank leukemia (brown).

Figure 2.

Clinical course for a patient with AML who is refractory or eventually relapses. (A) Patients with AML present with high leukemia blast burden (brown), receive induction chemotherapy, and often enter complete remission. Some patients have refractory disease, and most patients who achieve complete remission ultimately relapse. Patients who are refractory to induction therapies never clear their disease, as assessed by morphology. Those who enter complete remission often have persistent measurable residual disease (MRD), below levels detectable by morphologic analysis. These patients relapse, with variable clonal dynamics, but often have an expanded LSC (red) compartment. Those who relapse late may have had persistent pHSCs (purple) that reevolved into AML. (B) MRD can be assessed by morphology using microscopy (detection limit, 10⁻² cells), cytogenetics (10⁻² cells), multiparameter flow cytometry (10⁻⁴ cells), or mutation-specific polymerase chain reaction (PCR) or next-generation sequencing (NGS; 10⁻⁶ cells). FISH, fluorescence in situ hybridization; FITC, fluorescein isothiocyanate; PE, phycoerythrin.

Figure 3.

Multiomic analysis of single cells. Current single-cell methods can quantify numerous analytes, including scDNA-seq, messenger RNA (scRNA-seq), chromosome accessibility (assay for transposase-accessible chromatin using sequencing [scATAC-seq]), DNA methylation, intracellular proteins using mass spectrometry, and surface proteins using antibody-derived tags (ADTs). Additionally, barcoding methods coupled with both scRNA-seq and scATAC-seq can facilitate lineage-tracing studies.

Figure 4.

Single-cell assessment of MRD. Multiomic evaluation of MRD at remission may provide not only the underlying clonal architecture but also the cellular state of each clone, potential cellular fates, and cell-cell ecosystems within the bone marrow environment. Comparing these observations with those from diagnosis and relapse and the patient’s eventual clinical outcome may provide valuable insight into the clinical significance of the detected MRD.