Single-Nucleotide Variations, Insertions/Deletions and Copy Number Variations in Myelodysplastic Syndrome during Disease Progression Revealed by a Single-Cell DNA Sequencing Platform
by
, , , , , and
Paul Lee
1,†
,
Rita Yim
1,†,
Sin-Hang Fung
2,†,
Kai-Kei Miu
2,†,
Zhangting Wang
2,
Ka-Chun Wu
3,
Lester Au
1,
Garret Man-Kit Leung
1,
Victor Ho-Fun Lee
3 and
Harinder Gill
1,* 1
Department of Medicine, School of Clinical Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
2
School of Biomedical Sciences, Faculty of Medicine, Chinese University of Hong Kong, Hong Kong, China
3
Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, University of Hong Kong, Hong Kong, China
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Int. J. Mol. Sci. 2022, 23(9), 4647; https://doi.org/10.3390/ijms23094647
Submission received: 25 March 2022
/
Revised: 12 April 2022
/
Accepted: 21 April 2022
/
Published: 22 April 2022
(This article belongs to the Special Issue Progress of Tumor-Targeted Drugs)
Simple Summary
Myelodysplastic syndrome (MDS) is a myeloid neoplasm associated with complex clonal architecture. The application of single-cell sequencing is capable of revealing the clonal dynamics of MDS during disease progression and treatment resistance. This has advantages over bulk-tumor sequencing which is limited by its resolution. In this study, we evaluated two patients with MDS for the clonal dynamics of pathogenic mutations at the single-cell level of disease progression and resistance to hypomethylating agents (HMAs). There were two key observations. First, changes in the clonal heterogeneity of the pathogenic FLT3-ITD, IDH2, EZH2, or GATA2 mutations was associated with disease progression and resistance to HMA. Secondly, disease progression and resistance to HMA was accompanied by the acquisition of copy number variations of DNMT3A, TET2, and GATA2.
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 of patients and is indicative of 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 fails 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 with bulk tumor sequencing. Rare cell clones with mutations that are undetectable by bulk tumor sequencing were detected by sc-DNA sequencing. In addition to SNVs and short INDELs, this study also revealed the presence of a clonal copy number loss of DNMT3A, TET2, and GATA2 as standalone events or in association with the small SNVs or INDELs detected during HMA resistance and disease progression.
