Clonal evolution in tyrosine kinase inhibitor-resistance: lessons from in vitro-models

Abstract

IntroductionResistance in anti-cancer treatment is a result of clonal evolution and clonal selection. In chronic myeloid leukemia (CML), the hematopoietic neoplasm is predominantly caused by the formation of the BCR::ABL1 kinase. Evidently, treatment with tyrosine kinase inhibitors (TKIs) is tremendously successful. It has become the role model of targeted therapy. However, therapy resistance to TKIs leads to loss of molecular remission in about 25% of CML patients being partially due to BCR::ABL1 kinase mutations, while for the remaining cases, various other mechanisms are discussed.MethodsHere, we established an in vitro-TKI resistance model against the TKIs imatinib and nilotinib and performed exome sequencing.ResultsIn this model, acquired sequence variants in NRAS, KRAS, PTPN11, and PDGFRB were identified in TKI resistance. The well-known pathogenic NRAS p.(Gln61Lys) variant provided a strong benefit for CML cells under TKI exposure visible by increased cell number (6.2-fold, p < 0.001) and decreased apoptosis (-25%, p < 0.001), proving the functionality of our approach. The transfection of PTPN11 p.(Tyr279Cys) led to increased cell number (1.7-fold, p = 0.03) and proliferation (2.0-fold, p < 0.001) under imatinib treatment.DiscussionOur data demonstrate that our in vitro-model can be used to study the effect of specific variants on TKI resistance and to identify new driver mutations and genes playing a role in TKI resistance. The established pipeline can be used to study candidates acquired in TKI-resistant patients, thereby providing new options for the development of new therapy strategies to overcome resistance.

Chromosomal Copy Number Variation Predicts EGFR-TKI Response and Prognosis for Patients with Non-Small Cell Lung Cancer

“…Consistent with this, an acquired sequence variant in the NRAS gene on chromosome 1 was identified in an in vitro TKI-resistant model involving imatinib and nilotinib. 37 The emergence of TKI resistance may involve MET or HER2 amplification on chromosome 7 and BRAF mutation. 7 Refer to Table 3 for a subset of chromosome 1 and 7 genes associated with TKI resistance.…”

Synthesis of Novel Nilotinib Analogues and Biological Evaluation of Their Antiplatelet Activity and Functionality towards Cancer Cell Proliferation In Vitro

“…Throughout the years, many resistances have been identified in cancer therapy, specifically in chronic myelogenous leukemia (CML) [ 10 , 11 ]. CML is a myeloproliferative neoplasm, and its distinctive characteristic is the Philadelphia chromosome (Ph), formed by the translocation of the chromosomes 9 and 22, that results in Bcr-Abl kinase formation [ 10 , 12 , 13 , 14 ].…”

“…The deadliest mutation, and in fact a frequent one, that develops resistance to nilotinib is the “gatekeeper” mutation T315I, where isoleucine replaces threonine in position 315 of Bcr-Abl [ 10 , 13 ]. Commonly, the resistances are due to mutations within the kinase domain of Bcr-Abl, and thus it is an interesting target in cancer therapy that showed important cancer-specific activity [ 10 , 11 ].…”