Acute myeloid leukemia (AML) often presents as an oligoclonal disease whereby multiple genetically distinct subclones can co-exist within patients. Differences in signaling and drug sensitivity of such subclones complicates treatment and warrants tools to identify them and track disease progression. We previously identified over 50 AML-specific plasma membrane (PM) proteins and seven of these (CD82, CD97, FLT3, IL1RAP, TIM3, CD25 and CD123) were implemented in routine diagnostics in patients with AML (n=256) and MDS (n=33). We developed a pipeline termed CombiFlow in which expression data of multiple PM markers is merged, allowing a Principle Component-based analyses to identify distinctive marker expression profiles and to generate single cell tSNE landscapes to longitudinally track clonal evolution. Positivity for one or more of the markers after 2 courses of intensive chemotherapy predicted a shorter relapse-free survival supporting a role of these markers in measurable residual disease (MRD) detection. CombiFlow also allowed the tracking of clonal evolution in paired diagnosis and relapse samples (n=12). Extending the panel to 36 AML-specific markers further refined the CombiFlow pipeline. In conclusion, CombiFlow provides a valuable tool in the diagnosis, MRD detection, clonal tracking, and the understanding of clonal heterogeneity in AML.

Here, we demonstrated that the knockdown of non-T cell activation linker (NTAL) in acute myeloid leukemia (AML) cells was linked to reduced cell proliferation and survival in vitro and in vivo. In addition, we identified NTAL interactors in AML using label-free protein quantification. NTAL interactors presented a high expression in patients with AML, being associated with a leukemic granulocyte-macrophage progenitor-like state. Finally, NTAL interactors were capable to predict survival in a large subset of patients with AML. These data provide evidence that NTAL and its interactors could represent potential therapeutic targets for granulocytemacrophage progenitor-like leukemias. Highlights• NTAL knockdown in AML cells decreased cell proliferation and survival.• We discovered 49 NTAL interactors presents in AML cells.• Patients with de novo AML displayed a high expression of NTAL and its interactors.• NTAL and its interactors were associated with overall survival in patients with AML.

Summary Many cancers, including leukemias, are dynamic oligoclonal diseases. Tools to identify and prospectively isolate genetically distinct clones for functional studies are needed. We describe our CombiFlow protocol, which is a combinatorial flow cytometry-based approach to identify and isolate such distinct clones. CombiFlow enables the visualization of clonal evolution during disease progression and the identification of potential relapse-inducing cells at minimal residual disease (MRD) time points. The protocol can be adapted to various research questions and allows functional studies on live sorted cell populations. For complete details on the use and execution of this protocol, please refer to de Boer et al. (2018) .