Single-Cell Mutational Profiling Describes the Molecular Heterogeneity of Clonal Evolution in MDS during Therapy and Relapse

Background: Myelodysplastic syndromes (MDS) are a collection of clonal diseases of dysfunctional hematopoietic stem cells, characterized by ineffective hematopoiesis, cytopenias, and dysplasia. Increased understanding of the mutational landscape of MDS has led to initial improvements in prognostic models based on clinical and cytogenetic variables. However, bulk sequencing techniques are limited in their ability to delineate clonal complexity and identify rare drug resistant subclones. To better understand clonal heterogeneity and clonal evolution of MDS we applied a high-throughput single cell sequencing technique to both diagnostic and longitudinal MDS samples.

Methods: Samples were examined for 5 patients with MDS at diagnosis and, when available, progression. Mutational bulk sequencing was performed by NGS panel sequencing and exon sequencing was available in select cases. Single cell processing was performed using the Tapestri (Mission Bio) platform. Briefly, individual cells were isolated using a microfluidic approach, followed by barcoding and genomic DNA amplification for individual cancer cells confined to droplets. Barcodes are then used to reassemble the genetic profiles of cells from next generation sequencing data. We applied this approach to individual MDS samples, genotyping the most clinically relevant loci across upwards of 10,000 individual cells.

Results: Single-cell sequencing was able to be performed successfully on all samples tested and recapitulated bulk sequencing data. We observed high concordance between bulk variant allele frequencies (VAFs) and sample level VAFs derived from single cell sequencing data (r2 = 0.98). Additionally, single cell analysis allowed for resolution of subclonal architecture and tumor phylogenetic evolution beyond what was predicted from bulk sequencing alone. Single-cell SNVs were able to resolve host and donor cell populations after bone marrow transplant and accurately predict chimerism and disease relapse. Furthermore, we were able to resolve the co-occurance of molecular alterations within subclones and establish zygosity of individual mutations at a single cell level. Rare subclones associated with disease relapse, were able to be identified in initial diagnostic samples that were frequently under the limit of detection of bulk NGS.

Conclusions: Our results suggest more molecular complexity in MDS tumor samples than implied from bulk sequencing methods alone and indicates utility of single-cell sequencing for identification of resistant clones and longitudinal therapy monitoring.