Single-Cell Multi-Omics Identifies Measurable Residual Disease Targets Among Myelodysplasia- and Clonal Hematopoiesis-Related Genes in Acute Myeloid Leukemia

Background: In acute myeloid leukemia (AML), the most sensitive measurable residual disease (MRD) methods are single-gene approaches, but these are applicable only in ~60% of AML cases. Methods: We applied multi-omics single-cell analysis on diagnostic and first remission samples to identify leukemia-specific molecular markers for subsequent MRD monitoring in six AML patients lacking AML-defining variants. Results: Five selection criteria were defined to identify suitable MRD markers. Markers of primordial leukemic clones were identified by combining data from single-cell sequencing and immunophenotyping. Specific markers suitable for use in MRD follow-up were identified in 6/6 patients, in some cases in myelodysplasia-related genes and clonal hematopoiesis-related genes usually not recommended for use in MRD determinations. Patient-specific ddPCR (limits of detection: 0.06–0.0011%) or EC-NGS assays correlated with therapeutic responses: 0/4 markers displayed molecular relapses in three non-relapsing patients, contrary to 4/4 markers of three relapsing patients. Of these, 3/4 and 1/4 markers detected molecular relapses earlier than or simultaneous with conventional methods, respectively (−115 to −338 days). Conclusions: Our results demonstrate that single-cell subclonal mapping at diagnosis and during first remission enables selection of reliable MRD targets for personalized disease surveillance in patients lacking conventional MRD markers.