Gene Expression Profiling of CD34+/Lin- Cells of Patients with Chronic Myeloid Leukemia at Diagnosis and after 12 Months of Nilotinib
Authors: Trojani Alessandra , Lodola Milena , Di Camillo Barbara , Rossi Giuseppe , Capucci Adele , Perego Alessandra , Pogliani Enrico Maria , Orlandi Ester , Iurlo Alessandra , Malato Simona , Corradini Paolo , Cairoli Roberto , Bregni Marco , Artale Salvatore , Morra Enrica , Pungolino Ester 
Published: October 2019

Abstract
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.