Search of new prognostic markers of efficacy of therapy with tyrosine kinase inhibitors in chronic myeloid leukemia patients using exome sequencing
Background. Chronic myeloid leukemia (CML) is a common myeloproliferative disease characterized by pathologic activity of the fusion gene BCR/ABL, which encodes a tyrosine kinase that stimulates uncontrolled cell proliferation and DNA instability. Up to 20% of CML patients demonstrate primary resistance or non-optimal response to targeted tyrosine-kinase inhibitors (TKI) therapy. Objective. To find new potential genetic markers of TKI resistance by whole exome sequencing. Materials and methods. The study included eight patients with Ph+ CML in the chronic phase (CF). After 6 months of follow-up period patients were divided into two groups: four with an optimal response to TKI therapy and four with a non- optimal response. The validation group included 62 patients (32 with optimal and 30 with non-optimal response to therapy). Exome sequencing was performed using the Ion Torrent PGM platform. Alignment was performed on the human genome (GRCh37). Sanger sequencing was conducted on an ABI PRISM 3500xl. Statistical processing of the results was carried out using MS Office Excel and SPSS21. Results and conclusion. Exome sequencing revealed seven single-nucleotide variants (SNVs) associated with therapy outcomes: ANKRD35-rs11579366, DNAH9-rs1990236, MAGEC1-rs 176037, TOX3-rs10653661, THSD1 -rs3803264, MORN2-rs3099950, and PTCRA-rs9471966. Validation of these variants in 62 patients did not confirm prognostic role of any of the individual SNVs or their combinations. An additional analysis of the number of SNVs in 9000 genes revealed 75 genes with significant differences in the number of SNVs. Enrichment analysis showed that these genes are involved in cell adhesion, cell contacts, T-cell antigen activation, and inhibition of IFNα-mediated antiproliferative signaling. Many of these genes are also associated with a variety of cancers (renal, lung and breast cancer). Possible multifactorial nature of the efficacy of therapy complicates the search of new prognostic markers.