Search

Background Targeted therapy with Tyrosine-Kinase-Inhibitors (TKIs) totally modified the course of treatment of Chronic Myeloid Leukemia (CML). The objectives and the needs of treatment have been modified during the last years and the discontinuation of therapy is now a feasible aim. However, a lot of biological data acquired in the last twenty years, showed that degree and mechanisms of Leukemic Stem Cells (LSCs) clearance during TKI treatment are not clearly established as well as the predictive criteria for a stable and prolonged Treatment Free Remission (TFR). The multicentre, prospective, single-arm PhilosoPhi34 study (EudraCT: 2012-005062-34) was designed by the Rete Ematologica Lombarda (REL), to verify the in-vivo activity and time-course of first-line Nilotinib (NIL) therapy on Bone Marrow (BM) CD34+/lin-Ph+ cells clearance. An exploratory Gene Expression Profiling (GEP) study of CD34+/lin- cells at diagnosis and at 12 months (mos) of treatment, for the first 30 evaluable pts, was included. Preliminary GEP data suggested a correlation between different NFKBIA expression at diagnosis and at 12 mos and the achievement of a deeper Molecular Response (MR) (Pungolino et al, AJH 2018). We report here some results of GEP analysis on all enrolled evaluable pts and their possible correlation with clinical data. Methods BM cells were collected and stored at diagnosis and at 12 mos of treatment. CD34+/lin- cells were purified with a Diamond CD34 Isolation Kit Miltenyi (97% of purity). For GEP analysis we used Affymetrix HG-U133 Plus 2.0 microarray and Genechip platform (Affymetrix) and the Affymetrix GeneChip Scanner 3000. Data was pre-processed and normalized using the Robust Multi-array Average (RMA) algorithm. The Significant Analysis of Microarrays (SAM) was used to identify genes with statistically significant changes in expression. P-values were corrected for multiple testing using false discovery rate, for differentially expressed genes confirmation. We chose to analyse different expression of NFKBIA (the inhibitor of NF-kB onco-gene) in order to confirm the preliminary data reported on the first 30 analysed pts. Pts were monitored according to ELN-recommendation. Biological data were correlated with MR at 3, 12 and 36 mos of therapy. We use Fishers test to compare unbalanced group. Results Out of the 87 enrolled pts, 80 completed the first 12 mos of treatment and 78 (1 failure and 77 CCyR) were evaluable for GEP analysis. We observed 2726 genes symbol differentially expressed of which 1868 are coding genes. Among these, JAK-2 showed a down regulation at 12 mos (p: .024). JAK-2 expression ranged from 2.62 to 4.95 at diagnosis and from 1.48 to 5.58 at 12 mos. Only 26/78 pts increased JAK-2 expression that was > 4 in 1/26 pts, at diagnosis; 2/26 (7.69%) pts showed a H Sokal. Other 52/78 pts decreased JAK-2 expression that was ≥ 4 in 21/52 pts, at diagnosis; 10/52 (19.23%) pts and 6/21 (28,57%) pts showed a H Sokal. Similarly, when we compared low JAK-2 expression (< 3.5) vs vary high expression (≥ 4) 2/21 vs 6/22 pts had H Sokal (9.52% vs 27.27%; p: .0057). Considering the role of JAK-2 and NFKBIA in cell regulation and survival, we evaluated how the combination of their different expression impact on MR (i.e. NFKBIA increased expression/JAK-2 decreased expression vs NFKBIA decreased expression/JAK-2 increased expression). Data are reported in Table 1 and 2. Conclusion GEP analysis showed a down regulation of JAK-2 expression after 12 mos of first line NIL treatment, in 78 early chronic phase CML pts. Data suggest that high expression of JAK-2, at diagnosis, correlate with H Sokal score. However, H Sokal pts with a JAK-2 down regulation, obtain during treatment similar MR compared to L Sokal pts. Additionally, the study confirms our preliminary observation on 30 pts , concerning the role of NKBIA up - regulation in increasing percentage of earlier and deeper MR . The better condition of NFKBIA and JAK-2 expression (up regulation of NFKBIA and down regulation of JAK-2) is associated with a higher percentage of early MR3 and optimal responses over time, despite the higher number of H Sokal pts in this group. A study with NIL as first line treatment combined with low dose of JAK-2 inhibitor and a natural inhibitor of NF-kB (such as curcuma), during the first year of treatment, to increase the deeper MR rate and the probability of TFR is warrented. Disclosures Rossi: Sandoz: Honoraria; Jazz: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Gilead: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Roche: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; BMS: Honoraria; Teva: Membership on an entity's Board of Directors or advisory committees; Mundipharma: Honoraria; Novartis: Honoraria; Pfizer: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees.

BACKGROUND: Chronic myeloid leukemia (CML) is a clonal myeloproliferative disorder with heterogeneous biological and clinical features. The biomolecular mechanisms of CML response to tyrosine-kinase inhibitors are not fully defined. OBJECTIVE: We undertook a gene expression profiling (GEP) study of selected bone marrow (BM) CD34+/lin-cells of chronic-phase CML patients at diagnosis and after 12 months of TKI nilotinib to investigate molecular signatures characterizing both conditions. METHODS:We selected and counted BM CD34+/lin- cells of 30 CML patients at diagnosis and during 3, 6 and 12 months of first-line nilotinib treatment. GEP was performed between CD34+/lin- cells of patients at diagnosis and the same patients after 12 months of nilotinib. RESULTS: The number of BM CD34+/lin- cells dramatically decreased after 3, 6 and 12 months of nilotinib. GEP detected 264 statistically significant differentially expressed genes at diagnosis vs. 12 months of nilotinib. Functional enrichment analysis revealed groups of genes belonging to 14 pathways differentially active during nilotinib treatment. CONCLUSIONS: In conclusion, lipid, glucose and sphingolipid metabolism, insulin resistance, complement and coagulation, platelet activation, cytoscheleton, cell adhesion, transport, B cell differentiation, RAS-signaling pathway, proliferation, growth factors, and apoptosis were significantly deregulated between CML patients at diagnosis and after 12 months of nilotinib.

Introduction Chronic myeloid leukemia (CML) is a stem cell disease characterized by the constitutive activity of the oncoprotein BCR-ABL that activates multiple signal transduction pathways. Tyrosine-kinase inhibitor (TKI) nilotinib successfully inhibits the activation and the proliferative function of BCR-ABL in patients with CP-CML. Despite the success of nilotinib, some patients become refractory suggesting the presence of a population of Philadelphia positive (Ph+) quiescent stem cells escaping the drug activity. Thus, the molecular mechanisms underlying CML remain poorly understood. In this study, we enrolled 87 CP-CML patients (Pungolino et. al. Am J Hematol. 2018). Samples were collected on the behalf of the Rete Ematologica Lombarda (REL) the PhilosoPhi34 study (EudraCT: 2012-005062-34), which included 15 centers from Italy. We undertook gene expression profiling (GEP) of selected bone marrow (BM) CD34+/lin- cells of 80 patients at diagnosis vs. the same patients after 12 months of nilotinib to investigate gene expression changes induced by the treatment. Methods We isolated CD34+/lin- cells from BM samples in 87 patients at diagnosis whereas the same cells were also selected from 80/87 patients after 3, 6 and 12 months of nilotinib (Trojani et. al. Cancer Biomark. 2017). BM mononuclear cells (MNCs) as well as BM CD34+/lin- cells of all 80 CML patients were counted at diagnosis and during the treatment with nilotinib (at 3, 6, and 12 months, respectively). Standard FISH tested isolated BM CD34/lin- cells for the 87 patients at diagnosis, and for 80/87 patients after 3, 6 and 12 months of nilotinib treatment, respectively. Therefore, we performed GEP analyses of selected BM CD34+/lin- cells of 80/87 patients at diagnosis vs. the same patients after 12 months of nilotinib treatment. Then, we executed bioinformatic preprocessing and correction for batch effects on raw microarray data. Finally, we conducted differential expression analysis and significantly perturbed genes were subjected to functional clustering. Results We observed a wide variability of the number of BM MNCs as well as the number of the BM CD34+/lin- cells among the 80 CP-CML patients at diagnosis and after 3, 6 and 12 months of nilotinib for each patient (Table 1). Figure 1 showed that the number of the BM CD34+/lin- cells dramatically decreased between the diagnosis and after 3 as well as 6 months of nilotinib. We noticed that the BM CD34+/lin- cells slightly increased between 6 and 12 months of nilotinib which might be caused by the gradual repopulation of the normal CD34+/lin- cells in the bone marrow as FISH results suggested. FISH analysis detected CD34+/lin- Ph+ cells in 87 CP-CML patients at diagnosis. No positive Ph+ nuclei were detected on CD34+/lin- cells of 79/80 patients after 12 months of treatment (to categorize a sample as negative, at least 200 nuclei were examined). All of these 79 patients achieved at least complete cytogenetic response. 1/80 patient relapsed at 12 months. We conducted GEP analyses on 78 subjects because, due to experimental issues, two patients were not considered for differential expression analyses, as the microarray CEL files of the 12 months' samples were corrupted and missed probe intensities for most of the probes. GEP analyses determined 2,959 significantly differently expressed probes between diagnosis and after 12 months of nilotinib treatment. Functional clustering identified some pathways significantly enriched between diagnosis and 12 months of nilotinib. Among these pathways, we found that ABCC4, ABCC5, and ABCD3 genes associated with ATP-binding cassette (ABC) transporters were up regulated at diagnosis. GEP results highlighted that 26 genes belonging to cell cycle, mitosis, DNA damage and repair were over expressed at diagnosis. Moreover, GEP data demonstrated that JAK-STAT signaling pathway was deregulated: JAK2, IL7, STAM, PIK3CA, PTPN11, RAF1, SOS1 were over expressed whereas IL22RA1 was under expressed at diagnosis vs. 12 months of nilotinib, respectively. Conclusions In summary, we reported that BM CD34+/lin- cells from CP-CML patients after 12 months of nilotinib were characterized by changes of expression of genes involved in cell cycle checkpoints and mitosis, ABC transporters genes that pump drugs outside form the cells, and JAK-STAT signaling pathway genes responsible for the proliferation, differentiation and cell survival in CML. Disclosures Rossi: Teva: Membership on an entity's Board of Directors or advisory committees; Sanofi: Membership on an entity's Board of Directors or advisory committees; Abbvie: Membership on an entity's Board of Directors or advisory committees; Pfizer: Membership on an entity's Board of Directors or advisory committees; Jazz: Membership on an entity's Board of Directors or advisory committees; Novartis: Honoraria; Mundipharma: Honoraria; BMS: Honoraria; Sandoz: Honoraria; Gilead: Membership on an entity's Board of Directors or advisory committees; Amgen: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees; Roche: Membership on an entity's Board of Directors or advisory committees.

The study analyzed 30 chronic phase CML patients at diagnosis and at 3, 6 and 12 months of first-line nilotinib treatment. As optimal molecular response was achieved at 3, 6 and 12 months after nilotinib in all the 30 patients (figure 1), we established cut off values of molecular response (MR) to define groups of CML patients (n =30), and to investigate differences of gene expression profiles between patients at diagnosis based on the MR achieved after 3, 6 and 12 months of nilotinib, respectively. We used the following cut off values: 1% IS at 3 months of nilotinib, 0.1% IS at 6 months of nilotinib, and 0.01% IS at 12 months of nilotinib. Patients were divided into 2 groups based on MR values of each patient at 3 months of nilotinib: group A (n =24) with MR ≤1.0% IS and group B (n =6) with MR >1% IS. Based on the values of MR at 6 months of nilotinib, patients were divided into 2 groups: group C (n =22) with MR ≤0.1% IS and group D (n =8) with MR >0.1% IS. At 12 months of nilotinib, patients were divided into the following groups: group E (n =18) with MR ≤0.01% IS and group F (n =12) with MR >0.01% IS. Gene expression profiling (GEP) on the selected bone marrow (BM) CD34+/lin- cells of 30 CML patients at diagnosis was performed using Affymetrix GeneChip HTA 2.0. GEP data was preprocesses using RMA. SAMR and GSEA were used to detect differentially expressed genes and pathways (i.e. MSigDB Canonical pathways and GOBP gene sets) associated with the different groups, respectively. In both cases, correction for multiple testing was performed using the false discovery rate procedure with a threshold 0.05 for SAMR and 0.25 for GSEA as suggested by the software developers. GSEA detected significant differences in the transcriptional signature between group A and group B associated with the MR at 3 months as well as between group C and group D in respect to the MR at 6 months of nilotinib, whereas no genes were identified as significantly differentially expressed. Based on the MR at 3 months, we identified Reactome pathways "P130 cascade" and "GRB2 SOS linkage to MAPK signaling for integrins" significantly upregulated in group A compared to group B. FGA, FGB, FGG, APBB1IP, ITGA2B and CRK genes contributed to call the pathways upregulated. In vitro studies (Ding J et al. PloS One, 2013) demonstrated that nilotinib induced dephosphorilation of the BCR-ABL1 target CRK oncogene which acts in the CML hematopoietic stem cells like an adaptor in diverse signaling pathways and cellular processes playing an apoptotic role in CML. Our GEP results highlighted that the Reactome pathway involved in MAPK signaling (CRK gene) wasover expressed in CML patients with a better MR ≤1% IS at 3 months of nilotinib. Pathway "aminoacid and amine transport across the plasma membrane" was also significantly over expressed, whereas "lipid metabolism" was significantly down regulated (genes AKR1C1 and ANGPTL3) in group A compared to group B, respectively. Based on the MR at 6 months, GEP results showed that "positive regulation of cytokine secretion" and "interleukin 1 secretion" were significantly upregulated in group C compared to group D, involving PYCARD8, NLRP2, NLRC4, NLRP3 and CARD8 genes. Of note, PYCARD and CARD8 represent key mediators, which promote caspase-mediated apoptosis processes involving the recruitment of certain recognition receptors, such as NLRP2, NLRP3 and NLRC4. In addition, CARD8 and PYCARD promote apoptosis inhibiting NFKB activation. In conclusion, the study showed that MAPK signaling for integrins and amine transport across the plasma membrane were significantly over expressed in CML patients with a MR ≤1.0% IS while lipid metabolism was significantly over expressed in CML patients with a MR >1% IS after 3 months of nilotinib. After 6 months of nilotinib, positive regulation of cytokine secretion and interleukin 1 secretion were significantly over expressed in CML patients with a MR ≤0.1 IS compared to patients with a MR >0.1% IS. We identified distinct sets of genes involved in apoptotic processes differentially expressed in 30 CML patients based on the MR at 3 months as well as 6 months of first-line nilotinib treatment. Studies in a larger cohort of CML patients are ongoing to define the expression, role and functions of the genes regulating apoptosis CRK, PYCARD and CARD8 as candidate prognostic factors for molecular response to first-line nilotinib treatment. Disclosures No relevant conflicts of interest to declare.

This study aimed to determine the gene expression profiling (GEP) of bone marrow (BM) CD34+/lin- cells of CML patients at diagnosis and after nilotinib treatment.Microarray was performed on 30 CML patients at diagnosis as well as 8 patients after 12 months of nilotinib treatment using the latest generation Affymetrix GeneChip HTA 2.0 to further investigate genomic complexity. Bone marrow blood (in a range of 5-20 ml) samples were collected from patients at diagnosis and after 3, 6 and 12 months of nilotinib treatment. BM mononuclear cells were purified by density gradient centrifugation at 800 rpm for 20 min and soon after CD34+/lin- cells were isolated using Diamond CD34 Isolation Kit (Miltenyi Biotec). The purity of CD34+/lin-cells was about 97% as determined by flow citometry and the cells were counted at diagnosis and after the treatment with nilotinib (at 3, 6, and 12 months). BM CD34+/lin- cells of 30 patients at diagnosis and after 3 and 6 months of nilotinib were resuspended in RNAlater (Ambion, Life Technologies) and stored at -20°C until RNA extraction was performed. Total RNA was extracted from BM CD34+/lin- cells using MagMAX 96 Total RNA Isolation Kit (Ambion). BM CD34+/lin- cells were counted and a range of 100,000-800,000 has been noted at diagnosis. cRNA was prepared according to OvationPico WTA System V2 kit followed by Encore Biotin Module Kit (NuGEN). Ultimately, cRNA was hybridized to HTA 2.0 and signals were scanned by Affymetrix GeneChip Scanner 3000 following the manufacturer’s instructions. We observed that the number of CD34+/lin- cells dramatically decreased at 3 months (1,000-600,000), after 6 months (1,000-260,000) and after 12 months (100-130,000). In particular, CD34+/lin- cells were even less than 1000 after 12 months of nilotinib. If the number of CD34+/lin- cells after 12 months of nilotinib was less than 1000, we directly resuspended the cells in Prelude direct Lysis module (NuGEN) and microarray experiments were performed without RNA extraction. In this case, cRNA was prepared using Ovation One Direct System kit followed by Encore Biotin Module Kit (Nugen) and finally hybridized to the HTA 2.0. Microarray experiments were performed on CD34+/lin- cells of 30 CML patients at diagnosis with HTA 2.0. Moreover, we performed microarray experiments on CD34+/lin- cells of 8 CML patients at diagnosis vs. 8 CML patients after 12 months of nilotinib using HTA 2.0. Data was preprocessed and normalized using Robust Multi-array Average (RMA) algorithm. The Significant Analysis of Microarrays (SAM) was used to identify genes with statistically significant changes in expression in CML patients at diagnosis and at 12 months of treatment. P-values were corrected for multiple testing using false discovery rate. In conclusion, as far as we know, this is the first study which has isolated BM CD34+/lin-cells from CML patients at diagnosis and after nilotinib treatment. We observed a wide variety of the number of CD34+/lin- cells in 30 CML patients at diagnosis as well as after 3, 6 and 12 months of nilotinib. In particular, CD34+/lin- cells of CML patients at diagnosis were over 100.000. RNA was extracted and cRNA was prepared with OvationPico WTA System V2 kit followed by Encore Biotin Module Kit (NuGEN) and finally hybridized to HTA 2.0. On the other hand, the number of CD34+/lin- cells of CML patients after 12 months of nilotinib markedly decreased as low as 100 cells. In this case, we decided to avoid RNA extraction from the cells and we directly prepared cRNA using Ovation One Direct System kit and Encore Biotin Module Kit (Nugen) followed by the hybridization to the HTA 2.0 Array. To increase the statistical power in biomarker identification, we combined samples pre-processed with different experimental protocols (NuGEN) using ComBat, an empirical Bayes framework that adjusts data for batch effects and is robust to outliers in small datasets. Principal component analysis applied to the expression data before and after ComBat adjustment shows that the adopted normalization procedure effectively removes the systematic bias introduced by different protocols. Disclosures No relevant conflicts of interest to declare.

Chronic myeloid leukemia (CML) is a disease of stemming from genetic damage to a hematopoietic stem cell. Despite nilotinib being a very effective drug for the treatment of CML, drug resistance can emerge. In the contest of the REL-PhilosoPhi34 study on behalf of the Rete Ematologica Lombarda, we performed an exploratory study aimed to identify the gene expression signature of bone marrow (BM) CD34+/lin- cells of CML patients at diagnosis as well as after 12 months of nilotinib to investigate the genes and pathways responsible for the response or resistance to nilotinib. Microarray experiments were performed using the latest generation Affymetrix GeneChip HTA 2.0 to further investigate genomic complexity. The study was developed in two steps as follows: In the first step we analyzed 30 CML patients and from the comparison between the BM CD34+/lin- cell counts from each patient at diagnosis and after 3 and 6 months of nilotinib, patients were divided into 2 classes: class 1 (n=24) showed highly reduced levels of CD34+/lin- cells while class 2 (n=6) demonstrated increasing levels of CD34+/lin- cells after 3 and 6 months of nilotinib, respectively (Fig.1). The 30 patients can be divided into 6 groups showing different patterns of CD34+/lin- cellularity (Figure 1). Data was preprocessed and normalized using Robust Multi-array Average (RMA) algorithm. The Significant Analysis of Microarrays (SAM) was used to identify genes with statistically significant changes in expression in CML patients. P-values were corrected for multiple testing using false discovery rate. No transcripts were selected as differentially expressed using this threshold. However, if a nominal significance level alpha equal to 0.05 is adopted together with a fold-change threshold equal to 2 (absolute value), 56 transcripts were selected in the comparison between the 2 groups of CML patients. Among them, we focused on NFKBIAgene which was over expressed in class 1 compared to class 2.NFKBIA is involved in 68 pathways regulating apoptosis (PI3K,NF-kB) and encodes IkBα protein belonging to the NF-kB pathway which is a potential downstream target of BCR-ABL1 due to its role in regulating cell survival and proliferation. Of note, 31/56 transcripts are located on chromosome 15 suggesting that this region could be crucial for transcriptional regulation of CML correlated to nilotinib response. The second step analyzed the GEP of CD34+/lin- cells of 8 patients at diagnosis (class 1) vs. the same 8 patients after 12 months of nilotinib (class 2) to investigate the gene expression changes and the pathways induced by nilotinib treatment. Data was preprocessed and analyzed as described above. 247 probes (corresponding to 51 genes and 180 non-annotated transcripts) were selected with a p-value lower than 0.05 after multiple testing correction and using a fold-change threshold equal to 3 (absolute value). Functional enrichment analysis was performed using DAVID and highlighted the following pathways and genes: ¯ Defense response and immune system: CAMP, CRISP3, CYBB, RGS1, CEACAM8, LTF (cell growth and differentiation), MNDA and HP (positive regulation of apoptosis) were over expressed in class 2 with high fold changes of 7.65, 9.95, 4.40, 3.47, 4.28, 3.61, 3.60, 3.95, respectively ¯ Transcriptional regulation and cell cycle: MMP8was under expressed in class 1 with the high fold change of 8,94 ¯ S100A12, S100A8, S100A9 (regulation of the cell cycle and differentiation) were over expressed in class 2 with the FC of 8.68, 3.96, 4.49, respectively ¯ RNA5S-ribosomal pseudogenes 310-311-312-313-314-315-316-317-320-363 were downregulated in class 2 ¯ 10 small-nuclear-RNAs and 11 small-nucleolar RNA were differently deregulated between the 2 classes ¯ APOC1, PLBD1 (lipid metabolism) were overexpressed and underexpressed in class 1, respectively In conclusion, this is the first study of GEP of CD34+/lin- cells with HTA 2.0 which demonstrated that 51 genes mostly involved in immune system, transcriptional regulation and cell cycle were significantly differently expressed from the comparison between CML patients at diagnosis and after 12 month of nilotinib. Ongoing studies are focused on examining the genetic and biologic mechanisms underlying nilotinib response or resistance to predict response or failure providing new insights into the molecular mechanisms in CML. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.