Gene Expression Profiling of CD34+/Lin- Cells of Patients with Chronic Myeloid Leukemia at Diagnosis and after 12 Months of Nilotinib

• Published in: Blood 2014-12, Vol.124 (21), p.5177-5177
• Main 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
• Format: Article
• Language: English
• ISSN: 0006-4971; 1528-0020
• DOI: 10.1182/blood.V124.21.5177.5177

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 pat