Acute myeloid leukemia (AML) is a molecularly heterogeneous disorder of the bone marrow with poor long-term clinical outcomes due to a high risk of relapse after initial therapy. Relapse is thought to occur from minimal residual disease (MRD) consisting of leukemic blasts present below the limit of morphologic detection. Genomic sequencing studies have suggested complex subclonal architecture of AML, however bulk sequencing techniques may not fully resolve individual subclones present at diagnosis, remission and relapse. Here, we use a high-throughput single cell sequencing technique to delineate the subclonal structure of AML and identify clones present at diagnosis and at time of remission associated with disease relapse.Matched diagnosis, remission, and relapse samples were examined for 20 de novo AML cases including 15 relapsed and 5 non-relapsed controls. Mutational bulk sequencing was performed by NGS panel sequencing and exome sequencing was available in select cases. Single cell processing was performed using the Tapestri platform (Mission Bio, inc). Briefly, individual cells were isolated using a microfluidic approach, followed by barcoding and genomic DNA amplification for individual cancer cells confined to droplets. Barcodes were then used to reassemble the genetic profiles of cells from next generation sequencing data. We applied this approach to individual AML samples, for accurate single nucleotide variant (SNV) and indel calling for up to 300 multiplexed loci from up to 10,000 cells in a single run.Targeted single-cell sequencing was able to recapitulate all mutations identified by bulk sequencing. Additionally, single cell analysis allowed for resolution of subclonal architecture and tumor phylogenetic evolution beyond what was predicted from bulk sequencing alone. We identified rare subclonal populations associated with relapse at time of diagnosis and remission. Additionally, single-cell sequencing unambiguously resolved pre-leukemic/clonal hematopoiesis-associated clones, which persisted following treatment. Analysis of paired samples at diagnosis and relapse identified subclonal populations below detection of standard bulk sequencing methods. These included rare single-cell populations associated with treatment resistance including independent subclones with IDH1 and IDH2 mutations, co-occurring RAS and FLT3 mutations, as well as persistent low level clones associated with MRD positivity and disease relapse. Our results suggest a greater degree of subclonal heterogeneity in de novo AML samples than inferred from bulk sequencing methods alone and shows the utility of single-cell sequencing for treatment monitoring, MRD identification, and understanding of disease resistance mechanisms.

Citation Format: Alexey Aleshin, Robert Durruthy-Durruthy, Ryan Corces, Michaela Liedtke, Dennis Eastburn, Ravindra Majeti. Single-cell mutational profiling of paired AML samples at diagnosis, remission and relapse: Implications for therapeutic resistance and MRD detection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5130.