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July 8, 2021 by Brittany Enzmann, PhD 3 min read

Publication Highlight: Personalized Single-Cell Proteogenomics to Distinguish Acute Myeloid Leukemia from Nonmalignant Clonal Hematopoiesis

Paper:
Dillon L.W., et al. Personalized single-cell proteogenomics to distinguish acute myeloid leukemia from nonmalignant clonal hematopoiesis. Blood Cancer Discov. 2021 May 2:1-7. doi: 10.1158/2643-3230.BCD-21-0046.

Background:
Clonal hematopoiesis of indeterminate potential (CHIP), also called age-related clonal hematopoiesis, is a condition in which hematopoietic stem cells (HSCs) with certain somatic mutations clonally expand into subpopulations. CHIP is a non-malignant condition but has the potential of transforming into a hematologic malignancy, such as acute myeloid leukemia (AML). The mutations typical of CHIP — epigenetic regulators such as DNMT3A, TET2, and ASXL1 (together referred to as DTA mutations) — are also found in AML. Because these mutations present in both CHIP and AML clones, it is often difficult to distinguish the two. This challenge is particularly relevant for the identification of minimal/ measurable residual disease (MRD) in AML patients following treatment. Traditional methods of MRD identification (genetic sequencing and flow cytometry) are often discordant. In this paper, Dillon et al. use proteogenomic profiling to investigate the genetic and immunophenotypic features of CHIP and malignant clones in three relapsed AML patients in an attempt to identify leukemia MRD.

Question:
Is it possible to distinguish AML from CHIP clones using single-cell proteogenomic profiling? 

Methods:
This study used Mission Bio’s Tapestri Platform to perform single-cell DNA sequencing (scDNA-seq) with antibody-oligo conjugates to simultaneously investigate genotype and immunophenotype of bone marrow mononuclear cells (BMMCs) and peripheral blood mononuclear cells (PBMCs) in three patients with relapsed AML. Patient-specific DNA probes (designed using whole-genome sequencing) were used in scDNA-seq to target mutations and chromosome aberrations. Antibody-oligonucleotide sequencing was performed in the same cells as targeted DNA sequencing and compared to multiparameter flow cytometry.

Main Results:
The authors were able to confidently distinguish AML and CHIP clones using genotypic and immunophenotypic from the same cells. They determined that one case where AML arose independently from CHIP and two cases where AML developed from precursor CHIP cells. 

For Patient 1, five genetically defined clones were found in PBMCs. The pathognomonic inversion of chromosome 16 was detected in 13% of cells and was mutually exclusive from clones containing DTA-associated mutations. Some of the cells containing a chromosome 16 inversion also contained trisomy 8. Leukemic genotypes were found in cells with a more mature myeloid immunophenotype. In contrast, CHIP subclones containing DTA mutations were not restricted to myeloid or lymphoid lineages. Importantly, flow cytometry only identified about half the cells with a malignant genotype as also having a malignant phenotype. 

Patients 2 and 3 had AML that likely arose from precursor CHIP cell populations. scDNA-seq of BMMCs from Patient 2 revealed a clone (20% of cells) containing leukemia-defining features in addition to some DTA-associated mutations that were within but not specific to that clone. Similarly, scDNA-seq of BMMCs from Patient 3 revealed 26% of cells containing DTA-associated mutations represented a CHIP founder population. This cell population had diverse immunophenotypes spanning both myeloid and lymphoid lineages. Malignant cells had both DTA and leukemia-defining mutations. 

Conclusion:
Traditionally, AML MRD is identified through either genetic sequencing or flow cytometry. However, when using either of these methods alone, one can not confidently identify residual disease, especially in cases where patients also have non-malignant CHIP clones. Conventional bulk NGS cannot distinguish whether DTA mutations are harbored by CHIP or AML clones since it averages mutation frequencies across cells in a sample. On the other hand, conventional flow cytometry risks underrepresenting true genetically-defined MRD.  

This study overcomes these limitations by combining genotypic and immunophenotypic analysis through single-cell proteogenomic profiling. Using this approach, the authors were able to confidently resolve the clonal architecture of three patients and distinguish CHIP and AML clones. Single-cell DNA + protein multi-omics using Mission Bio’s Tapestri Platform offers considerable potential for precision medicine for hematologic malignancies like AML. 

Check out the paper here!

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