Gene expression profiling of chronic myeloid leukemia with variant t(9;22) reveals a different signature from cases with classic translocation
© Albano et al.; licensee BioMed Central Ltd. 2013
Received: 13 February 2013
Accepted: 29 April 2013
Published: 4 May 2013
The t(9;22)(q34;q11) generating the BCR/ABL1 fusion gene represents the cytogenetic hallmark of chronic myeloid leukemia (CML). About 5–10% of CML cases show variant translocations with the involvement of other chromosomes in addition to chromosomes 9 and 22. The molecular bases of biological differences between CML patients with classic and variant t(9;22) have never been clarified.
In this study, we performed gene expression microarray analysis to compare CML patients bearing variant rearrangements and those with classic t(9;22)(q34;q11). We identified 59 differentially expressed genes significantly associated with the two analyzed groups. The role of specific candidate genes such as TRIB1 (tribbles homolog 1), PTK2B (protein tyrosine kinase 2 beta), and C5AR1 (complement component 5a receptor 1) is discussed.
Our results reveal that in CML cases with variant t(9;22) there is an enhancement of the MAPK pathway deregulation and show that kinases are a common target of molecular alterations in hematological disorders.
KeywordsChronic myeloid leukemia Variant t(9;22) rearrangements Gene expression profiling Protein kinases Cellular pathways
Chronic myeloid leukemia (CML) is a myeloproliferative disorder derived from hematopoietic stem cell transformation and characterized by heterogeneous biological and clinical features. The CML molecular marker is BCR/ABL1 fusion gene generation as a consequence of a reciprocal t(9;22)(q34;q11)[1, 2]. In most cases, the Philadelphia (Ph) chromosome is cytogenetically detectable but about 5–10% of CML patients show variant t(9;22)(q34;q11) rearrangements with the involvement of additional chromosomes[3, 4]. In these cases the BCR/ABL1 fusion gene can be revealed by Fluorescence in situ hybridization (FISH) or reverse transcriptase-polymerase chain reaction. The occurrence of genomic microdeletions proximally to ABL1 or distally to BCR has been reported in CML cases with variant translocations with a greater frequency (30-40%) than in cases with classic t(9;22) (10-18%)[6, 7]. The prognostic significance of variant t(9;22) was unclear and debated in the pre-imatinib era, whereas recent studies of large CML series have reported that the presence of variant translocations has no impact on the cytogenetic and molecular response or on prognosis[6, 8]. However, the molecular bases of biological differences between CML patients with classic and variant t(9;22) have never been elucidated.
In this study, we performed gene expression profiling (GEP) by microarrays to identify a signature discriminating CML patients bearing variant rearrangements from those with classic t(9;22)(q34;q11). A list of 59 genes was found to be significantly associated with the two analyzed groups showing a differential expression. We applied network analysis to evaluate potential pathways involved in CML heterogeneity. An overall deregulation of genes encoding for protein kinases and involved in crucial cellular pathways such as MAPK (mitogen-activated protein kinase) signaling was found, unveiling the biological basis of differences in the CML patients subgroup with variant rearrangements.
Upregulation of kinases genes
Querying the Database for Annotation, Visualization and Integrated Discovery (DAVID) showed that the enhanced biological process in our gene set involved the intracellular protein kinases cascade, a series of reactions in which a signal is passed within the cell by sequential protein phosphorylation. This enhancement was significant (p = 0.003) and associated to a value of 7.6. In detail, the kinases list included 5 genes: TRIB1 (tribbles homolog 1), STK17B (serine/threonine kinase 17b), PTK2B (PTK2B protein tyrosine kinase 2 beta), C5AR1 (complement component 5a receptor 1) and ZFP36 (zinc finger protein 36, C3H type, homolog). Interestingly, TRIB1 resulted one of the highest expressed genes showing a 2.9-fold change in GEP experiments. The upregulation of all 5 kinases was confirmed by quantitative real-time polymerase chain reaction experiments (qRT-PCR) analysis, with statistically significant expression levels ranging from 2.20 to 8.02.
Involvement of kinases in the RAS/MAPK pathway
To date several profiling studies in CML have been reported focusing mainly on predicting response to imatinib therapy and identifying a gene-specific signature for different stages of the disease[13, 14]. Our GEP analysis performed on CML cases with variant t(9;22) may improve the understanding of the biological mechanisms at the basis of the CML heterogeneity. Overall, our results reveal that in CML cases with variant t(9;22) there is an enhancement of the MAPK pathway deregulation already known to underlie the CML pathogenesis and point out the role of interesting candidate genes, such as TRIB1, PTK2B, and C5AR1. These findings show that kinases are a common target of molecular alterations in hematological disorders and reinforce the idea that a perturbed action of signal transduction pathways is one of the hallmarks of cancer.
Chronic myeloid leukemia
Fluorescence In Situ Hybridization
Gene expression profiling
Mitogen-activated protein kinase
Database for Annotation, Visualization and Integrated Discovery
Tribbles homolog 1
B serine/threonine kinase 17b
PTK2B protein tyrosine kinase 2 beta
Complement component 5a receptor 1
Zinc finger protein 36, C3H type, homolog
Quantitative real-time polymerase chain reaction experiments
Ingenuity Pathways Analysis
Extracellular signal-regulated kinases
p38 mitogen-activated protein kinase
c-Jun N-terminal kinase
RAC-alpha serine/threonine-protein kinase
Mitogen activated protein kinase kinase
CCAAT⁄enhancer binding protein alpha
Mitogen-activated ERK kinase 1
MAP kinase kinase 4
Poly(rC) binding protein 2.
The authors would like to thank Ms. MVC Pragnell, B.A. for language revision of the manuscript.
This work was supported by “Fondazione Cassa di Risparmio di Puglia” and “Associazione Italiana contro le Leucemie (AIL)-BARI”.
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