Unique single-nucleotide variations, insertions/deletions and copy number variations in myelodysplastic syndrome during treatment resistance and progression revealed by a single-cell DNA sequencing platform

Abstract Myelodysplastic syndrome (MDS) is a clonal myeloid neoplasm characterized by ineffective hematopoiesis, cytopenia, dysplasia and clonal instability leading to leukemic transformation. Hypomethylating agents are the mainstay of treatment in higher-risk MDS. However, treatment resistance and disease transformation into acute myeloid leukemia (AML) is observed in the majority patients and portend a dismal outcome. The residual cell clones resistant to therapy or cell clones acquiring new genetic aberrations are two of the key events responsible for drug resistance. Bulk tumor sequencing often fail to detect these rare subclones that confer resistance to therapy. In this study, we employed a single-cell DNA (sc-DNA) sequencing approach to study the clonal heterogeneity and clonal evolution in two MDS patients refractory to HMA. In both patients, different single nucleotide variations (SNVs) or insertions and deletions (INDELs) were detected concordant with bulk tumor sequencing. Rare cell clones with mutations undetectable on bulk tumor sequencing, were detected on single-cell DNA sequencing. In addition to SNVs and short INDELs, this study also revealed the presence clonal copy number loss of DNMT3A, TET2, and GAT2 as standalone events or in associated with the small SNVs or INDELs detected during HMA resistance and disease progression.