Gene Expression Signatures Associated with Treatment and Resistance to Imatinib Mesylate in Chronic Myeloid Leukemia Patients.
Authors: Oehler Vivian , Branford S. , Pogosova-Agadjanyan E. , Shah N. , Sawyers C. , Mao M. , Linsley P. , Hughes T. , Radich J. 
Published: April 2020

Abstract
Imatinib mesylate (IM) has dramatically changed the treatment approach for patients with chronic myeloid leukemia (CML). However, ~20% of chronic phase (CP) patients are initially resistant to IM, and among patients who achieve a complete cytogenetic response (CCyR), a small minority relapse back into CP or progress to advanced disease. Abl tyrosine kinase domain mutations are the major cause of secondary resistance. Oligonucleotide microarray analysis was used to study gene expression patterns associated with primary IM resistance and relapse after initial successful response to IM. Samples included total RNA from diagnostic samples of 25 CML CP patients within 6 months of diagnosis and at the time of failure (7 patients); total RNA from 18 patients who relapsed after initial CCyR with documented Abl point mutations (12 CP and 6 BC); and 10 myeloid progenitor samples (sorted by CD34 and CD38 status) from an IM naïve and IM resistant (R) patient, both in blast crisis.
Results: For primary IM resistance, analysis of paired samples before and after treatment revealed that primary failure was associated with the differential expression of genes associated with RNA post-transcriptional modification, protein synthesis, cellular growth and proliferation, and cell death. Two genes with the highest differential expression included the apotosis resistance genes API5 and TRAF5. TRAF5 was also increased in patients who relapsed after initial CCyR, while API5 showed significantly increased expression in sorted CD34+ cells from an IMR patient. In secondary resistance patients, a set of drug transporters including ABCA2, ABCA3, MDR1, and ABCC3 had increased expression and hOCT1 decreased expression relative to 42 IM naïve CP patients. In vitro experiments compared K562 resistant (R) and sensitive (S) cell lines over time exposed to IM. The K562 IMR cell line showed a 1.5 log higher expression of ABCG2 and a 1 log higher expression of TRAF5 compared to the K562 IMS cells. However, sequential clinical samples of 16 IM non-responders vs. 14 CCyR patients showed no change in ABCG2 expression, possibly because ABCG2 is expressed only in early progenitor cells, not differentiated cells. The importance of using CD34+ cells was demonstrated in 7 array studies comparing gene expression in CD34+ selected cells from an IMR patient compared to an IM naïve patient. IM resistance was associated with increased expression of genes associated with cell cycle, DNA recombination and repair, and proliferation. Genes associated with apoptosis resistance included increased expression of API5, survivin, and decreased expression of BAK1. Protein serine/threonine and tyrosine kinases associated with cell proliferation/survival and tumor progression with increased expression in the IMR patient included: AURKB, AKT3, BUB1B, CDC2, CHEK1, MAPK9, STK6, TTK, and WEE1.
Conclusion: Gene expression studies suggest that
primary resistance to IM therapy is associated with resistance to apoptosis; relapse on IM is associated with activation of drug transporter genes and genes associated with disease progression; in studying disease response and resistance, primitive hematopoetic cells are critical for analysis.