Abstract
Despite the effectiveness of tyrosine kinase inhibitors (TKIs) against chronic myeloid leukemia (CML), they are not usually curative as some patients develop drug-resistance or are at risk of disease relapse when treatment is discontinued. Studies have demonstrated that primitive CML cells display unique miRNA profiles in response to TKI treatment. However, the utility of miRNAs in predicting treatment response is not yet conclusive. Here, we analyzed differentially expressed miRNAs in CD34+ CML cells pre- and post-nilotinib (NL) therapy from 58 patients enrolled in the Canadian sub-analysis of the ENESTxtnd phase IIIb clinical trial which correlated with sensitivity of CD34+ cells to NL treatment in in vitro colony-forming cell (CFC) assays. We performed Cox Proportional Hazard (CoxPH) analysis and applied machine learning algorithms to generate multivariate miRNA panels which can predict NL response at treatment-naïve or post-treatment time points. We demonstrated that a combination of miR-145 and miR-708 are effective predictors of NL response in treatment-naïve patients whereas miR-150 and miR-185 were significant classifiers at 1-month and 3-month post-NL therapy. Interestingly, incorporation of NL-CFC output in these panels enhanced predictive performance. Thus, this novel predictive model may be developed into a prognostic tool for use in the clinic.
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Introduction
Chronic myeloid leukemia (CML) is a myeloproliferative stem cell disease characterized by the fusion oncoprotein BCR-ABL1 [1, 2]. Tyrosine kinase inhibitors (TKIs) that selectively target BCR-ABL1, such as Imatinib Mesylate (IM), and second generation TKIs Dasatinib (DA) and Nilotinib (NL), have demonstrated remarkable clinical efficacy in the treatment of chronic phase (CP) CML [3,4,5,6,7,8,9]. For example, a 10-year follow up of the ENESTnd clinical trial evaluating long-term outcomes of NL and IM, demonstrated that NL had increased rates of treatment-free remission (TFR) eligibility and overall survival compared to IM treatment [10, 11]. The extension of the ENESTnd clinical trial, ENESTxtnd, further supported the use of NL as a front-line therapy, with 81% of CP-CML patients achieving major molecular remission (MMR) by 24 months [12]. These advances in TKI therapy have improved cancer-free survival rates and resulted in faster and deeper levels of molecular response in these patients. However, TKI treatments are not usually curative as some patients develop drug-resistance or are at risk of disease relapse when treatment is discontinued [13,14,15,16,17]. Thus, it has been of interest to develop predictive biomarkers to accurately predict whether patients may achieve a deep molecular response with first-line TKI, require a switch to second generation TKIs or can discontinue treatment safely. Patient material from a variety of sources has been profiled using microarrays, RNA-sequencing and, more recently, single cell RNA-sequencing [18,19,20,21]. Some studies have identified parameters that may indicate poor TKI response in CML patients, such as the detection of additional chromosomal abnormalities in BCR-ABL1+ cells at diagnosis or observing a slow rate of change in BCR-ABL1 transcript levels in the first 3 months of TKI therapy, among others [22,23,24]. It was also reported that IM response could be predicted in treatment-naïve CD34+ stem/progenitor cells by an in vitro CFC assay [25]. Moreover, analysis of differential gene expression between IM-nonresponders and responders has offered predictive potential: a 17-gene panel quantified via qRT-PCR to classify patients as high-risk or low-risk was able to predict early molecular response failure, based on BCR-ABL1 transcript levels at 3 months in CP-CML patients treated with IM or NL [26]. However, differences in the cell types profiled, the technologies used, and the inherent complexity associated with the interpretation of molecular data pose challenges in identifying reliable biomarkers with clinical utility.
MicroRNAs (miRNA) are single-stranded non-coding RNAs of about 18–25 nucleotide length that are aberrantly expressed in various malignancies and regulate numerous biological processes including cell differentiation and survival [27,28,29,30]. Some miRNA tumor suppressors regulating BCR-ABL1 were reported to be downregulated in CML cells whereas oncogenic miRNAs (oncomiRs) modulated by BCR-ABL1 were found to be overexpressed [31,32,33]. Additionally, BCR-ABL1-dependent and -independent miRNA expression profiles were observed in CML patient cells at different stages of the disease [32, 34]. Interestingly, the expression of some of these miRNAs was reported to change in response to TKI-treatment and may therefore be good indicators of TKI-resistance [34,35,36,37,38]. Recently, we generated global transcriptome profiles on treatment-naïve CD34+ CML cells with known subsequent IM responses and identified several differentially expressed miRNAs, including miR-185 and miR-145, in IM-nonresponders as compared to IM-responders [39].
In this study, we aimed to generate an effective, combinational predictive model consisting of miRNAs and in vitro TKI CFC data by analyzing miRNA expression profiles in CD34+ cells from 58 patients (retrospectively classified as NL-responders or NL-nonresponders) and the sensitivity of these cells to TKIs. Through Cox Proportional Hazard (CoxPH) analysis and machine learning approaches, we identified and evaluated two predictive miRNA panels in treatment-naïve or post-NL treatment in CML patients. Interestingly, incorporation of in vitro CFC data into either panel improved the predictive power at each time point. To our knowledge, this is the first study to utilize miRNA expression profiles, CFC data, and clinical response data from matched patient samples to develop a predictive model of response to NL treatment.
Methods
Study design and treatment
Heparin-anticoagulated peripheral blood (PB) samples were obtained from 62 newly diagnosed CML patients enrolled in the Canadian sub-analysis arm of the ENESTxtnd phase IIIb clinical trial (https://clinicaltrials.gov/ct2/show/NCT01254188, Supplementary Table 1). Four patients were excluded due to insufficient enrichment of CD34+ cells (<65%), leaving a total of 58 patient samples. These patients were newly diagnosed (within 6 months) CP-CML patients who had not been previously treated with IM. PB samples were obtained prior to therapy (BL), 1 month (M1) and 3 months (M3) after 300 mg or 400 mg BID nilotinib (NL) therapy [11, 40]. Clinical responses of patients were classified as either NL-responders (R) or NL-nonresponders (NR) at 12 months (46 R, 12 NR) after treatment based on BCR-ABL1 transcript levels following the European Leukemia Net treatment guidelines [41]. Informed consent was obtained in accordance with the Declaration of Helsinki, and all procedures performed were approved by the University of British Columbia Clinical Research Ethics Board (certificate H20-00421).
Colony-forming cell (CFC) assay
CD34+ cells (>90%) were enriched immunomagnetically using EasySep CD34 selection kits (STEMCELL Technologies) and analyzed using a fluorescence-activated cell sorter (FACS). CFC assays were performed as previously described and in a double-blinded approach, with results subsequently linked to each patient’s clinical response to NL [25]. Briefly, 3000 primary CD34+ cells were mixed with MethoCult™ H4230 (STEMCELL Technologies) and growth factor cocktail in the presence or absence of inhibitors: 10 µM NL (Novartis), 150 nM DA (Bristol-Myers Squibb), 5 µM IM (Novartis). Colonies were counted after 14 days.
Microfluidic quantitative PCR
Microfluidic quantitative PCR (qPCR) was conducted as previously described [39]. Briefly, pooled RT primer mix containing 47 distinct miRNA stem-loop and RNU48 primers were prepared and mixed with total RNA extracted from CD34+ CML cells. Amplified cDNA from these reactions was mixed with Taqman master mix and loaded to sample inlets of a Fluidigm 48 ×48 Dynamic array device. High-throughput quantitative real-time PCR was then performed using the BioMark HD system (Fluidigm) to produce image-based fluorescent signals and raw Ct values. The raw Ct values were normalized to the RNU48 endogenous control (ΔCt method).
Statistical analysis
For CFC data, a Student’s two-tailed t-test was used to test for differential colony output between responders and nonresponders. The HTqPCR R package was used to perform data quality control and normalization. Normalization to the endogenous RNU48 control achieved the closest to normal distribution (Supplementary Fig. 1) and was therefore selected as the normalization method in this study. Two samples were excluded as they showed unusual variation in RNU48 Ct values that were >1.5-fold above the interquartile range. Univariate Cox Proportional Hazard (CoxPH) analyses were performed using individual normalized miRNA expression levels to determine the hazard-ratio (HR) of each miRNA. As CoxPH analysis performs best on categorical data, four different cut-offs were applied: median, 1st quartile, 3rd quartile and maximally selected rank statistics [42]. While the maximally selected rank statistics calculated cut-off from the survival (v3.3-1) R package was the method we later adopted in our modeling, only miRNAs that were significantly associated with NL nonresponse for at least two of the four applied cut-offs in the univariate CoxPH analysis were selected for further analysis. Overall, only miRNAs that fulfilled the following criteria were selected for the subsequent multivariate analysis step: significant association with NL nonresponse (Welch t-test), differential expression between NL-responder and NL-nonresponder samples at BL, and unidirectional association with NL nonresponse over time (either increased or decreased hazard at both M1 and M3). Predictive performance of the remaining candidates was evaluated in multivariate CoxPH, random forest (RF) and Naïve-Bayes (NB) machine learning algorithms (R caret v6.0-91 and MLeval v0.3). All models were tenfold cross-validated and predictive performance was assessed based on area-under-curve (AUC) values from receiver operating characteristic (ROC) and precision recall (PR) curves. The R scripts used to generate the presented data are available upon request.
Results
Treatment-naïve CD34+ CML cells from NL-responders and NL-nonresponders generate significantly different CFC outputs during in vitro Nilotinib treatment
We previously demonstrated that CFC assays in IM-supplemented cultures can classify CML patients into IM-responders and IM-nonresponders, based on the colony output from treatment-naïve CD34+ stem/progenitor cells obtained at diagnosis [25]. To determine whether a similar method can be applied to NL, we performed in vitro CFC assays with and without TKI treatments on CD34+ cells from 58 newly diagnosed CML patients enrolled in the ENESTxntd trial. NL-responders (R) had 3-log-fold or greater reduction in BCR-ABL1 transcripts (<0.1%) at month 12 of NL therapy, while those that failed to achieve this response were classified as NL-nonresponders (NR, Supplementary Table 1). As expected, we observed an overall reduction in CFC outputs generated from CD34+ cells upon NL, DA or IM treatment compared to untreated controls. Furthermore, NL-response in patient CFC data correlated with DA-CFC and IM-CFC counts from the same patient sample (DA: Pearson’s R = 0.06831, p < 0.0001; IM: R = 0.7243, p < 0.0001; Fig. 1A). However, while most retrospectively classified responders produced overall fewer colonies upon any TKI treatment, we observed a more diverse pattern for nonresponders, clustering into two response fractions in CFC assays. Some of the nonresponder samples responded poorly and produced high numbers of colonies upon NL or DA or IM treatment, but a few samples produced similar numbers of colonies as CD34+ cells from responders (Fig. 1B). Nevertheless, a significant difference in CFC output was observed between responder and nonresponder samples for NL (p = 0.014) but not for IM or DA (Fig. 1B). To determine if CFC output was significantly associated with nonresponse, each patient was categorized as CFC low or high based on maximally selected rank statistics calculated cut-offs (NL = 46.2%, DA = 26.9%, IM = 34.3%). Univariate CoxPH analysis showed that CFC outputs from all three TKIs were significant classifiers in predicting NL clinical response status (p ≤ 0.019, Table 1) and displayed hazard-ratios (HR) < 1, associating higher colony output with NL nonresponse.
Expression of miR-145 and miR-708 in treatment-naïve CML cells predicts patient response and accuracy is further improved by incorporation of in vitro NL-CFC data
We recently published a miRNA-sequencing study highlighting 47 differentially expressed miRNAs identified in CD34+ stem/progenitor cells between normal bone marrow (NBM) and CML patient samples, particularly between IM-responders and IM-nonresponders [39]. In the present study, we collected microfluidic qRT-PCR expression data for this panel of 47 miRNAs in CD34+ cells obtained at diagnosis (BL), 1-month (M1) and 3-month (M3) post-NL treatment from 58 CML patients. Interestingly, univariate CoxPH analysis identified that expression of 17/47 miRNAs was significantly associated with NL nonresponse (four miRNAs at BL, nine miRNAs at M1, and ten miRNAs at M3; p < 0.05, Fig. 2A and Supplementary Table 2). Some of these miRNAs were significantly associated with nonresponse across all the three time points and overall, 9/47 miRNAs were differentially expressed between NL-responder and NL-nonresponder patients at any time point (BL, M1, M3; p ≤ 0.047, Fig. 2B).
To evaluate their predictive capacity, we next combined miRNAs that demonstrated significant association with NL nonresponse and fulfilled all additional selection criteria (see Materials and Methods) into multivariate models for each individual time point of sample collection. At the treatment-naïve state (BL), increased miR-145 expression (HR 6.95, p = 0.013) and decreased miR-708 expression (HR 0.13, p = 0.009) were associated with NL-nonresponse in multivariate CoxPH modeling (Fig. 3A). ROC-AUC values generated by trained random forest (RF)- and Naïve-Bayes (NB)- machine learning models also indicated predictive performance of miR-145 and miR-708 (ROC-AUC: RF = 0.58, NB = 0.67; Fig. 3C and Supplementary Fig. 2A). We next tested if the model accuracy could be further improved through incorporation of the TKI-CFC response data (NL, IM, and DA). Indeed, multivariate CoxPH models incorporating CFC output (HR 0.15, p = 0.003) but not IM or DA showed superior Concordance in predicting NL nonresponse compared to models based on miRNA expression alone (Ci = 0.8 vs. Ci = 0.89) (Fig. 3B). Most interestingly, results from our trained RF and NB machine learning models showed that inclusion of NL-CFC increased the ROC-AUC and PR-AUC values by 1.2-fold (RF) and 1.9-fold (NB) (Fig. 3D and Supplementary Fig. 2B). Of note, no other clinical factors except for NL-CFC, including WBC count and BCR-ABL1 transcript levels at BL and 12 months, were identified as important features in machine learning or associated with patient response (Supplementary Table 3). Thus, we could identify the combination of miR-145 and miR-708 expression as a predictive indicator of NL response at the treatment-naïve state and we have observed that inclusion of NL-CFC data further enhanced predictive performance.
MiR-150 and miR-185 expression levels in post-NL CML samples predict treatment response and accuracy is further improved by incorporation of in vitro NL-CFC data
Since our model performed well in treatment-naïve patient cells, we next tested if a similar predictive panel could be generated at the M1 and M3 post-NL treatment. From the nine miRNAs that showed significant association with nonresponse in univariate CoxPH analyses, four miRNAs (miR-145, miR-365, miR-150, miR-185) displayed HR values that remained consistent between M1 and M3 and were therefore selected for further analysis. Overall, combination of miR-150 and miR-185 expression levels into multivariate CoxPH and machine learning models, achieved the best performance (ROC-AUC: RF = 0.76, NB = 0.73; Ci = 0.8; Fig. 4A, C and Supplementary Fig. 2C). Addition of NL-CFC to the M1 model improved Concordance (Ci = 0.88) and overall accuracy (ROC-AUC RF = 0.84, NB = 0.88, Fig. 4B, C and Supplementary Fig. 2C), overall by up to 1.3-fold (Fig. 4D and Supplementary Fig. 2D). Applying the same panel to data collected at M3 validated the predictive potential of miR-150 and miR-185 in multivariate CoxPH analysis (Fig. 5A) but underperformed in the machine learning evaluation with lower-than-expected ROC-AUC values (RF = 0.52, NB = 0.51; Ci = 0.74) (Fig. 5A, C and Supplementary Fig. 2E). However, predictive performance was again greatly improved when NL-CFC was included to the M3 model, enhancing Concordance (Ci = 0.84) and increasing ROC-AUC values by 2-fold (RF = 0.72, NB = 0.68; Fig. 5C, D and Supplementary Fig. 2E, F). After NL treatment, both at M1 and M3, expression levels of miR-150 and miR-185 were identified as potential classifiers of treatment response and incorporation of NL-CFC data yielded significantly improved predictive accuracy, particularly after 1 month of treatment.
Discussion
TKI therapies induce high rates of initial hematological and molecular responses in CP-CML patients, but TKI resistance and disease progression continue to pose a challenge for some patients. Current clinical scoring systems cannot accurately predict the heterogeneous treatment outcomes that are observed. From our analyses of CML patient samples at the treatment-naïve and post-NL treatment states from 58 patients, we propose two panels of NL-nonresponse predictors: The first panel consists of NL-CFC, miR-145 and miR-708, which predicts NL-nonresponse at diagnosis. The second panel of NL-CFC, miR-150 and miR-185 predicts NL-nonresponse at M1 and M3 post-NL treatment. Although miRNA signatures have alluded to TKI response prediction in CML, this study shows merit for combining matched miRNA expression profiles with in vitro CFC output to predict NL-specific response.
Previously, we demonstrated that IM response could be predicted in treatment naïve CD34+ cells by an in vitro CFC assay in a small cohort study [25]. Here, we show that CFC output data from patient CD34+ cells obtained at diagnosis can also predict NL response in a larger cohort. Since singular predictive variables alone may not be sufficient to predict response due to cellular variations and molecular complexity among patients, we generated a multivariate predictive panel based on a combination of expression of specific miRNAs and patient’s NL-CFC response. This combination improved the predictive value of using miRNA levels alone, as demonstrated by improved Concordance, ROC-AUC and PR-AUC at all time points. It has been well-documented that CML stem cells and their progenitor cells are the least TKI responsive and are responsible for disease recurrence when TKIs are discontinued [2, 43,44,45,46,47]. Notably, BCR-ABL1 transcript and protein levels are significantly elevated in CD34+ cells and even more so in the CD34+CD38− stem cell-enriched population compared to the bulk CD34− population [45, 48]. Therefore, it has been of interest to determine whether distinguishing features of CD34+ leukemic stem/progenitor cells from CML patients might vary amongst patients in correlation with the subsequent clinical response to TKI therapy. Our studies of primitive CD34+ CML cells from individual CP patients show that they indeed display cellular and molecular differences. In particular, clinically defined responders and nonresponders differ significantly from each other with respect to the growth response of their pre-treatment CFC to NL, and their miRNA expression changes. Our two newly identified predictive panels based on stably down- and up-regulated miRNAs whose expression levels differ significantly and associate with treatment response pre- and post-NL therapy might therefore form the basis of prospective tests for predicting early treatment response and ultimately for optimizing CML patient management.
In this study, we highlight miR-145 and miR-708 as potential predictive biomarkers in treatment naïve patients. MiR-145 expression changes were significantly different between IM-responders and IM-nonresponders in CD34+ CML cells obtained at diagnosis [39], adding to previous reporting that miR-145 is differentially expressed between CML peripheral blood patient samples and normal hematopoietic progenitor cells and between AP-CML versus CP-CML cells [38, 39]. NL treatment also seems to be able to increase expression of miR-145 in BCR-ABL1+ cell lines [36]. Although overall miR-145 expression in CD34+ cells differed significantly between NL-responders and NL-nonresponders in this study, we observed that the variation in miR-145 expression level among responders is relatively high with some responder patient cells expressing levels similar to NL-nonresponders; a trend that was also observed in other miRNAs in this study. These observations indicate heterogeneous and differential expression of miRNAs in individual CML patients even before NL treatment. Thus, it is critical to use advanced multivariable statistical and bioinformatics tools to precisely identify useful miRNA predictors among other clinical, biological and molecular parameters. Mechanistically, the role of miR-145 in CML has yet to be fully explored. However, miR-145 was found to be downregulated and was suggested to sensitize resistant cancer cells to treatment by modulating drug efflux and apoptotic pathways in solid tumors [49, 50]. A conflicting report shows that miR-145 is overexpressed in later stage breast cancer and supports cancer cell survival by promoting epithelial to mesenchymal transition and hypermethylating apoptotic genes [51]. However, miRNA expression is highly context-dependent and downstream effects can differ greatly between tumor types. While expression of miR-708 was found to be significantly reduced in CD34+ CML cells compared to normal CD34+ bone marrow cells, there is a lack of understanding of miR-708 in CML and other myeloid leukemias [39]. MiR-708 has been studied most extensively in lymphoblastic leukemias like acute lymphoblastic leukemia (ALL) where it is speculated to have both oncogenic and tumor suppressive functions depending on the subtype of ALL [52]. Clinically, ALL patients with low miR-708 levels were reported to have an increased risk of relapse [52]. Based on our analysis, reduced miR-708 expression in NL-nonresponder cells may also be indicative of more aggressive and drug-resistant properties.
In CD34+ CML cells obtained 1-month and 3-month post-NL treatment, we observed that NL-nonresponder patients had increased levels of miR-150 and decreased levels of miR-185 compared to NL-responders. Combining both miRNAs into multivariate models predicted NL-nonresponse at both time points. Interestingly, both miR-150 and miR-185 have been demonstrated to have tumor suppressive properties in CML [39, 53,54,55]. MiR-150 was suggested to be negatively regulated by BCR-ABL1 via MYC which in turn increases MYB expression and contributes to CML pathogenesis [53]. CML patients who were able to achieve early treatment response (ETR) after IM treatment were observed to have higher miR-150 levels [54, 55]. MiR-185 can be repressed by BCR-ABL1 in IM-nonresponder patients, which contributes to leukemic stem cell survival and TKI-resistance through increased PAK6 and OXPHOS mechanisms [39]. Furthermore, restoration of miR-185 could sensitize IM-resistant cells to TKIs [39]. In summary, these studies suggest that both miR-150 and miR-185 are key players in CML pathogenesis and rationalize their association with TKI-resistance.
The differences in significant miRNA classifiers among our two predictive panels, generated at the treatment naïve and post-NL treatment state, are likely attributed to dynamic changes in miRNA expression in response to NL treatment. Our observation of increased miR-150 expression in NL-nonresponder patients appears to conflict with other studies that reported miR-150 to be downregulated in CML and that its increased expression following IM treatment is an early positive predictor for IM response [54]. This discrepancy may be due to our use of enriched CD34+ stem/progenitor cells as opposed to unpurified peripheral blood and bone marrow cells or because miRNA expression may be modulated differently between NL and IM treatments [21]. Furthermore, it is not uncommon for miRNAs to possess conflicting roles, e.g. serving as oncogenic and tumor suppressive properties in the same cancer type, mainly owed to their ability to regulate expression of multiple target genes, which in turn also include both oncogenes and tumor suppressors [56]. Therefore, independent validation of these proposed predictive panels using greater numbers of patient samples and further exploration of the mechanistic roles of these select miRNAs in CML is warranted to facilitate their utility as prognostic tools in the clinic. Unique to this study, we combined miRNA expression data with patient-matched in vitro CFC outputs. In both BL and M1/M3 models, we found that inclusion of NL-CFC data in the multivariate panels improved predictive performance compared to miRNAs alone. It is widely agreed that treatment response may be affected by multiple factors not just related to biological mechanisms, such as pharmacokinetic variations between CML patients. Thus, prognostic algorithms that rely on genetic signatures alone may not be sufficient to model these extrinsic factors, highlighting the need for multifaceted molecular panels to improve predictive accuracy. The ability to develop rapid and robust tests to predict individual patients’ response to TKI therapy could ultimately have a profound impact on CML patient management, providing a foundation for more effective treatment decisions.
References
Rowley JD. Letter: a new consistent chromosomal abnormality in chronic myelogenous leukaemia identified by quinacrine fluorescence and Giemsa staining. Nature 1973;243:290–3.
Holyoake TL, Vetrie D. The chronic myeloid leukemia stem cell: stemming the tide of persistence. Blood 2017;129:1595–606.
Druker BJ, Guilhot F, O’Brien SG, Gathmann I, Kantarjian H, Gattermann N, et al. Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. N. Engl J Med. 2006;355:2408–17.
Druker BJ, Tamura S, Buchdunger E, Ohno S, Segal GM, Fanning S, et al. Effects of a selective inhibitor of the Abl tyrosine kinase on the growth of Bcr-Abl positive cells. Nat Med. 1996;2:561–6.
Weisberg E, Manley PW, Breitenstein W, Bruggen J, Cowan-Jacob SW, Ray A, et al. Characterization of AMN107, a selective inhibitor of native and mutant Bcr-Abl. Cancer Cell. 2005;7:129–41.
Shah NP, Tran C, Lee FY, Chen P, Norris D, Sawyers CL. Overriding imatinib resistance with a novel ABL kinase inhibitor. Science 2004;305:399–401.
Ross DM, Hughes TP. Treatment-free remission in patients with chronic myeloid leukaemia. Nat Rev Clin Oncol. 2020;17:493–503.
Shah NP, Garcia-Gutierrez V, Jimenez-Velasco A, Larson S, Saussele S, Rea D, et al. Dasatinib discontinuation in patients with chronic-phase chronic myeloid leukemia and stable deep molecular response: the DASFREE study. Leuk Lymphoma. 2020;61:650–9.
Rea D, Nicolini FE, Tulliez M, Guilhot F, Guilhot J, Guerci-Bresler A, et al. Discontinuation of dasatinib or nilotinib in chronic myeloid leukemia: interim analysis of the STOP 2G-TKI study. Blood 2017;129:846–54.
Caldemeyer L, Akard LP. Rationale and motivating factors for treatment-free remission in chronic myeloid leukemia. Leuk Lymphoma. 2016;57:2739–51.
Kantarjian HM, Hughes TP, Larson RA, Kim DW, Issaragrisil S, le Coutre P, et al. Long-term outcomes with frontline nilotinib versus imatinib in newly diagnosed chronic myeloid leukemia in chronic phase: ENESTnd 10-year analysis. Leukemia 2021;35:440–53.
Hughes TP, Munhoz E, Aurelio Salvino M, Ong TC, Elhaddad A, Shortt J, et al. Nilotinib dose-optimization in newly diagnosed chronic myeloid leukaemia in chronic phase: final results from ENESTxtnd. Br J Haematol. 2017;179:219–28.
Vetrie D, Helgason GV, Copland M. The leukaemia stem cell: similarities, differences and clinical prospects in CML and AML. Nat Rev Cancer. 2020;20:158–73.
Quintas-Cardama A, Kantarjian HM, Cortes JE. Mechanisms of primary and secondary resistance to imatinib in chronic myeloid leukemia. Cancer Control. 2009;16:122–31.
Jabbour EJ, Cortes JE, Kantarjian HM. Resistance to tyrosine kinase inhibition therapy for chronic myelogenous leukemia: a clinical perspective and emerging treatment options. Clin Lymphoma Myeloma Leuk. 2013;13:515–29.
Rousselot P, Charbonnier A, Cony-Makhoul P, Agape P, Nicolini FE, Varet B, et al. Loss of major molecular response as a trigger for restarting tyrosine kinase inhibitor therapy in patients with chronic-phase chronic myelogenous leukemia who have stopped imatinib after durable undetectable disease. J Clin Oncol. 2014;32:424–30.
Mahon FX, Rea D, Guilhot J, Guilhot F, Huguet F, Nicolini F, et al. Discontinuation of imatinib in patients with chronic myeloid leukaemia who have maintained complete molecular remission for at least 2 years: the prospective, multicentre Stop Imatinib (STIM) trial. Lancet Oncol. 2010;11:1029–35.
Warfvinge R, Geironson L, Sommarin MNE, Lang S, Karlsson C, Roschupkina T, et al. Single-cell molecular analysis defines therapy response and immunophenotype of stem cell subpopulations in CML. Blood 2017;129:2384–94.
Giustacchini A, Thongjuea S, Barkas N, Woll PS, Povinelli BJ, Booth CAG, et al. Single-cell transcriptomics uncovers distinct molecular signatures of stem cells in chronic myeloid leukemia. Nat Med. 2017;23:692–702.
Chen Y, Li S. Molecular signatures of chronic myeloid leukemia stem cells. Biomark Res. 2013;1:21.
Krishnan V, Kim DDH, Hughes TP, Branford S, Ong ST. Integrating genetic and epigenetic factors in chronic myeloid leukemia risk assessment: toward gene expression-based biomarkers. Haematologica 2022;107:358–70.
Clark RE, Apperley JF, Copland M, Cicconi S. Additional chromosomal abnormalities at chronic myeloid leukemia diagnosis predict an increased risk of progression. Blood Adv. 2021;5:1102–9.
Song HY, Noh H, Choi SY, Lee SE, Kim SH, Kee KM, et al. BCR-ABL1 transcript levels at 4 weeks have prognostic significance for time-specific responses and for predicting survival in chronic-phase chronic myeloid leukemia patients treated with various tyrosine kinase inhibitors. Cancer Med. 2018;7:5107–17.
Glauche I, Kuhn M, Baldow C, Schulze P, Rothe T, Liebscher H, et al. Quantitative prediction of long-term molecular response in TKI-treated CML - Lessons from an imatinib versus dasatinib comparison. Sci Rep. 2018;8:12330.
Jiang X, Forrest D, Nicolini F, Turhan A, Guilhot J, Yip C, et al. Properties of CD34+ CML stem/progenitor cells that correlate with different clinical responses to imatinib mesylate. Blood 2010;116:2112–21.
Kok CH, Yeung DT, Lu L, Watkins DB, Leclercq TM, Dang P, et al. Gene expression signature that predicts early molecular response failure in chronic-phase CML patients on frontline imatinib. Blood Adv. 2019;3:1610–21.
Si W, Shen J, Zheng H, Fan W. The role and mechanisms of action of microRNAs in cancer drug resistance. Clin Epigenetics. 2019;11:25.
Peng Y, Croce CM. The role of MicroRNAs in human cancer. Signal Transduct Target Ther. 2016;1:15004.
O’Brien J, Hayder H, Zayed Y, Peng C. Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation. Front Endocrinol (Lausanne). 2018;9:402.
Bissels U, Bosio A, Wagner W. MicroRNAs are shaping the hematopoietic landscape. Haematologica 2012;97:160–7.
Litwinska Z, Machalinski B. miRNAs in chronic myeloid leukemia: small molecules, essential function. Leuk Lymphoma. 2017;58:1297–305.
Alves R, Goncalves AC, Jorge J, Marques G, Luis D, Ribeiro AB, et al. MicroRNA signature refine response prediction in CML. Sci Rep. 2019;9:9666.
Ciccone M, Calin GA. MicroRNAs in myeloid hematological malignancies. Curr Genomics. 2015;16:336–48.
Machova Polakova K, Lopotova T, Klamova H, Burda P, Trneny M, Stopka T, et al. Expression patterns of microRNAs associated with CML phases and their disease related targets. Mol Cancer. 2011;10:41.
Venturini L, Battmer K, Castoldi M, Schultheis B, Hochhaus A, Muckenthaler MU, et al. Expression of the miR-17-92 polycistron in chronic myeloid leukemia (CML) CD34+ cells. Blood 2007;109:4399–405.
Ferreira AF, Moura LG, Tojal I, Ambrosio L, Pinto-Simoes B, Hamerschlak N, et al. ApoptomiRs expression modulated by BCR-ABL is linked to CML progression and imatinib resistance. Blood Cells Mol Dis. 2014;53:47–55.
San Jose-Eneriz E, Roman-Gomez J, Jimenez-Velasco A, Garate L, Martin V, Cordeu L, et al. MicroRNA expression profiling in imatinib-resistant chronic myeloid leukemia patients without clinically significant ABL1-mutations. Mol Cancer. 2009;8:69.
Flamant S, Ritchie W, Guilhot J, Holst J, Bonnet ML, Chomel JC, et al. Micro-RNA response to imatinib mesylate in patients with chronic myeloid leukemia. Haematologica 2010;95:1325–33.
Lin H, Rothe K, Chen M, Wu A, Babaian A, Yen R, et al. The miR-185/PAK6 axis predicts therapy response and regulates survival of drug-resistant leukemic stem cells in CML. Blood 2020;136:596–609.
Hochhaus A, Saglio G, Hughes TP, Larson RA, Kim DW, Issaragrisil S, et al. Long-term benefits and risks of frontline nilotinib vs imatinib for chronic myeloid leukemia in chronic phase: 5-year update of the randomized ENESTnd trial. Leukemia 2016;30:1044–54.
Hochhaus A, Baccarani M, Silver RT, Schiffer C, Apperley JF, Cervantes F, et al. European LeukemiaNet 2020 recommendations for treating chronic myeloid leukemia. Leukemia 2020;34:966–84.
Hothorn T, Lausen B. On the exact distribution of maximally selected rank statistics. Computational Stat Data Anal. 2003;43:121–37.
Corbin AS, Agarwal A, Loriaux M, Cortes J, Deininger MW, Druker BJ. Human chronic myeloid leukemia stem cells are insensitive to imatinib despite inhibition of BCR-ABL activity. J Clin Invest. 2011;121:396–409.
Jiang X, Saw KM, Eaves A, Eaves C. Instability of BCR-ABL gene in primary and cultured chronic myeloid leukemia stem cells. J Natl Cancer Inst. 2007;99:680–93.
Jiang X, Zhao Y, Smith C, Gasparetto M, Turhan A, Eaves A, et al. Chronic myeloid leukemia stem cells possess multiple unique features of resistance to BCR-ABL targeted therapies. Leukemia 2007;21:926–35.
Turhan AG, Hugues P, Sorel N, Desterke C, Bourhis JH, Bennaceur-Griscelli A, et al. Evidence of BCR-ABL1-positive progenitor spread in blood during molecular recurrence after TKI discontinuation in chronic myeloid leukemia (CML). Leuk Lymphoma. 2020;61:1719–23.
Abraham SA, Hopcroft LE, Carrick E, Drotar ME, Dunn K, Williamson AJ, et al. Dual targeting of p53 and c-MYC selectively eliminates leukaemic stem cells. Nature 2016;534:341–6.
Jamieson CH, Ailles LE, Dylla SJ, Muijtjens M, Jones C, Zehnder JL, et al. Granulocyte-macrophage progenitors as candidate leukemic stem cells in blast-crisis CML. N. Engl J Med. 2004;351:657–67.
Xu WX, Liu Z, Deng F, Wang DD, Li XW, Tian T, et al. MiR-145: a potential biomarker of cancer migration and invasion. Am J Transl Res. 2019;11:6739–53.
Xu W, Hua Y, Deng F, Wang D, Wu Y, Zhang W, et al. MiR-145 in cancer therapy resistance and sensitivity: A comprehensive review. Cancer Sci. 2020;111:3122–31.
Manvati S, Mangalhara KC, Kalaiarasan P, Chopra R, Agarwal G, Kumar R, et al. miR-145 supports cancer cell survival and shows association with DDR genes, methylation pattern, and epithelial to mesenchymal transition. Cancer Cell Int. 2019;19:230.
Monteleone NJ, Lutz CS. miR-708-5p: a microRNA with emerging roles in cancer. Oncotarget 2017;8:71292–316.
Srutova K, Curik N, Burda P, Savvulidi F, Silvestri G, Trotta R, et al. BCR-ABL1 mediated miR-150 downregulation through MYC contributed to myeloid differentiation block and drug resistance in chronic myeloid leukemia. Haematologica 2018;103:2016–25.
Habib EM, Nosiar NA, Eid MA, Taha AM, Sherief DE, Hassan AE, et al. MiR-150 expression in chronic myeloid leukemia: relation to imatinib response. Lab Med. 2022;53:58–64.
Di Stefano C, Mirone G, Perna S, Marfe G. The roles of microRNAs in the pathogenesis and drug resistance of chronic myelogenous leukemia (Review). Oncol Rep. 2016;35:614–24.
Svoronos AA, Engelman DM, Slack FJ. OncomiR or tumor suppressor? The duplicity of MicroRNAs in cancer. Cancer Res. 2016;76:3666–70.
Acknowledgements
We thank the Stem Cell Assay Laboratory staff for processing patient samples, Josephine Leung and Kyi Min Saw for excellent technical assistance, members of the Leukemia/Bone Marrow Transplant Program of British Columbia and the Hematology Cell Bank of British Columbia for patient samples, the Terry Fox Laboratory FACS Facility for cell sorting and STEMCELL Technologies for culture reagents.
Funding
This work was supported by the Canadian Cancer Society, the Leukemia & Lymphoma Society of Canada, the Canadian Institutes of Health Research (CIHR) and the Collings Stevens Chronic Leukemia Research Fund (XJ). RY received a Four-Year Fellowship from UBC and a CIHR Frederick Banting and Charles Best Canada Graduate Scholarship; SG is supported by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation—project 446251518), Michael Smith Health Research BC and the Lotte & John Hecht Memorial Foundation (project RT-2020-0578); AW and JS received MITACS Accelerate Fellowships; KR was a MITACS Elevate Postdoctoral Fellow.
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DLF, CE and XJ developed the concept and designed the experiments; RY performed data analyses and statistical and bioinformatics analyses; SG provided expertise in complex statistical and data analyses and insightful discussions; HL, HN, JS, KR, AW performed q-RT-PCR, CFC experiments and data analyses; DLF provided the clinical data and insightful discussions; AW, RY, SG, JS, and XJ wrote the manuscript and all authors commented on it.
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Research funding: Novartis Canada (DLF, CE, and XJ). Other authors declare no conflicts of interests.
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Yen, R., Grasedieck, S., Wu, A. et al. Identification of key microRNAs as predictive biomarkers of Nilotinib response in chronic myeloid leukemia: a sub-analysis of the ENESTxtnd clinical trial. Leukemia 36, 2443–2452 (2022). https://doi.org/10.1038/s41375-022-01680-4
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DOI: https://doi.org/10.1038/s41375-022-01680-4
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