Abstract
BackgroundChronic lymphocytic leukemia (CLL) is an incurable malignancy of mature B-lymphocytes, characterized as being a heterogeneous disease with variable clinical manifestation and survival. Mutational statuses of rearranged immunoglobulin heavy chain variable (IGVH) genes has been consider one of the most important prognostic factors in CLL, but despite of its proven value to predict the course of the disease, the regulatory programs and biological mechanisms responsible for the differences in clinical behavior are poorly understood.MethodsIn this study, (i) we performed differential gene expression analysis between the IGVH statuses using multiple and independent CLL cohorts in microarrays platforms, based on this information, (ii) we constructed a simplified protein-protein interaction (PPI) network and (iii) investigated its structure and critical genes. This provided the basis to (iv) develop a Boolean model, (v) infer biological regulatory mechanism and (vi) performed perturbation simulations in order to analyze the network in dynamic state.ResultsThe result of topological analysis and the Boolean model showed that the transcriptional relationships of IGVH mutational status were determined by specific regulatory proteins (PTEN, FOS, EGR1, TNF, TGFBR3, IFGR2 and LPL). The dynamics of the network was controlled by attractors whose genes were involved in multiple and diverse signaling pathways, which may suggest a variety of mechanisms related with progression occurring over time in the disease. The overexpression of FOS and TNF fixed the fate of the system as they can activate important genes implicated in the regulation of process of adhesion, apoptosis, immune response, cell proliferation and other signaling pathways related with cancer.ConclusionThe differences in prognosis prediction of the IGVH mutational status are related with several regulatory hubs that determine the dynamic of the system.Electronic supplementary materialThe online version of this article (doi:10.1186/s12976-015-0008-z) contains supplementary material, which is available to authorized users.
Highlights
Chronic lymphocytic leukemia (CLL) is an incurable malignancy of mature B-lymphocytes, characterized as being a heterogeneous disease with variable clinical manifestation and survival
Understanding the pathological mechanisms of CLL has helped to divide the disease into two risk categories that have a strong impact on prognosis and treatment: 1) patients with minimal clinical manifestations and 2) an aggressive form characterized by high mortality, whose immunoglobulin heavy chain variable (IGHV) genes can be somatically mutated or unmutated, respectively
We inquired into the impact of differentially expressed genes (DEG) between the immunoglobulin heavy chain variable (IGVH) statuses by mapping them onto the protein-protein interaction (PPI) network
Summary
Chronic lymphocytic leukemia (CLL) is an incurable malignancy of mature B-lymphocytes, characterized as being a heterogeneous disease with variable clinical manifestation and survival. Understanding the pathological mechanisms of CLL has helped to divide the disease into two risk categories that have a strong impact on prognosis and treatment: 1) patients with minimal clinical manifestations and 2) an aggressive form characterized by high mortality, whose IGHV genes can be somatically mutated or unmutated, respectively. Due to the importance of IGVH status in the determination of the course of the disease, several expression studies have focused on the comparison of CLL type mutated IGVH vs IGVH unmutated. These studies have identified genes that are not functionally related and cannot elucidate biological mechanisms to distinguish between risk categories
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