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Related Experiment Video

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A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations
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CombiFlow: combinatorial AML-specific plasma membrane expression profiles allow longitudinal tracking of clones.

Roos Houtsma1, Nisha K van der Meer1, Kees Meijer2

  • 1Department of Hematology, and.

Blood Advances
|September 20, 2021
PubMed
Summary

A new tool, CombiFlow, aids in diagnosing acute myeloid leukemia (AML) by analyzing plasma membrane proteins. It tracks clonal evolution and predicts relapse-free survival, improving measurable residual disease detection.

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Area of Science:

  • Hematology
  • Oncology
  • Immunophenotyping

Background:

  • Acute myeloid leukemia (AML) is often an oligoclonal disease with coexisting, genetically distinct subclones.
  • Subclonal heterogeneity complicates AML treatment due to differences in signaling and drug sensitivity.
  • Identifying and tracking these subclones is crucial for effective disease management.

Purpose of the Study:

  • To develop and validate a computational pipeline (CombiFlow) for analyzing multiple acute myeloid leukemia-specific plasma membrane (PM) markers.
  • To assess the utility of CombiFlow in diagnosing AML, detecting measurable residual disease (MRD), and tracking clonal evolution.
  • To evaluate the prognostic value of PM marker expression in predicting relapse-free survival.

Main Methods:

  • Development of the CombiFlow pipeline integrating expression data from multiple PM markers.
  • Principal component analysis and single-cell t-distributed stochastic neighbor embedding for analyzing marker profiles and clonal evolution.
  • Validation in patients with AML (n=256) and myelodysplastic syndrome (n=33), including paired diagnosis and relapse samples.

Main Results:

  • CombiFlow successfully identified distinctive marker expression profiles and tracked clonal evolution longitudinally.
  • Positivity for one or more PM markers after chemotherapy predicted shorter relapse-free survival, indicating utility in MRD detection.
  • Extending the marker panel to 36 AML-specific markers further enhanced the pipeline's capabilities.

Conclusions:

  • CombiFlow is a valuable tool for diagnosing AML, detecting MRD, and tracking clonal heterogeneity.
  • The pipeline facilitates understanding of clonal evolution in AML patients.
  • PM marker analysis via CombiFlow aids in predicting patient outcomes and guiding treatment strategies.