The utilities of next-generation sequencing in myeloid malignancies

Abstract

Human myeloid malignancies, including acute myeloid leukemia (AML) and myeloproliferative neoplasm (MPN), are clonal diseases of the hematopoietic stem or progenitor cells. Recent advents in next-generation sequencing (NGS) have accelerated our understanding of the genetic basis of myeloid malignancies and generated discoveries that are important for clinical application. In this study, I utilised NGS platforms including targeted sequencing and whole exome sequencing (WES) to provide insights into the genetic basis of myeloid malignancies and the relevance to clinical management of patients.

In Project 1, genetic landscape of AML carrying core-binding factor (CBF) was examined. The clinical response of this subtype to conventional chemotherapy is heterogeneous and while most patients respond favourably at induction, leukemia relapse may occur and genetic mutations may modify disease outcome. Mutation spectrum and clinical outcome of a consecutive cohort of CBF-AML patients aged 18–60 years old from six regional hospitals in Hong Kong were examined. NGS based on a myeloid gene panel showed that mutations of genes involved in cell signaling and DNA methylation, as exemplified by KIT activation loop (AL) domain and TET2 mutations, were associated with inferior leukemia-free survival (LFS), suggesting that these mutations might result in leukemia relapse. In Project 2, WES was performed in treatment naïve and resistant samples from FLT3-ITD AML patients receiving sorafenib monotherapy who achieved remission and eventually progressed to the resistant stage, with a view to understand the clonal changes of leukemia progression. Clones carrying FLT3 tyrosine kinase domain (TKD D835) mutation, which has been shown to confer resistance to sorafenib, expanded at resistant stage. On the other hand, isochromosome 17q, mutations in TP53, RAS genes and solute carrier members (SLC15A1 and SLC12A4) were also shown to expand at resistance, underscoring their potential roles in drug resistance and leukemia progression. In Project 3, WES was performed in a family with familial MPN and ZNF467 nonsense variant was identified as a potential predisposing factor to MPN in two generations. The variant was shown to escape nonsense-mediate decay pathway and impaired nuclear localization of the protein. The results have provided important leads for mechanistic study of ZNF467 in myeloid oncogenesis. These observations underscored the emerging role of NGS in leukemia biology research as well as clinical management of patients with myeloid malignancies.