Molecular Characterization of Human Multiple Myeloma Cell Lines by Genome-Wide Profiling Identifies Kinase Pathway Alterations.

Abstract

Multiple Myeloma (MM) is a malignancy depicted by clonal expansion of plasma cells in the bone marrow. There are two broad genetic subtypes of multiple myeloma as defined as hyperdiploid multiple myeloma (H-MM), characterized by trisomies of chromosomes 3, 5, 7, 9, 11, 15, 19, and 21, and nonhyperdiploid multiple myeloma (NH-MM) associated with primary translocations involving the immunoglobulin heavy chain (IgH). These two subtypes of multiple myeloma have two different molecular pathogenesis given that characteristic changes of each have been already observed. In order to contribute to the understanding of this malignancy and to unveil the different molecular pathogenesis, our interest is focused on Human Multiple Myeloma Cell lines (HMCLs), as a model, and a broad but specific group of enzymatic proteins: the Kinases. Kinase hyperactivity or lack of it often results in disregulation of cellular pathways involved in proliferation and survival. In our study, we describe the patterns of genetic lesions and molecular pathogenesis of 11 HMCLs with Single Nucleotide Polymorphism (SNP)-based mapping arrays from Affymetrix Human Mapping 500K array set. This technique allows the examination and identification of copy number changes, bi-allelic deletions and the identification of loss of heterozygosity (LOH) due to loss and uniparental disomy, as well as gene localization and identification. The 11 HMCLs utilized are characterized for their structural alterations and not by hyperdiploidy. In addition, so as to fulfill the selection criteria, a minimum of 3 cell lines must present the alterations cited below. The most frequently identified alterations were located as follows: Previously described gains were observed in 1q, 7q, 8, 11q, 18, 19, and 20q; but also found at 4q. The bi-allelic deletions were ascertained on 3p. Similarly, we identified the regions of hemizygotic deletions on 1, 2q, 6q, 8q, 9p, 11q, 12, 13q, 14q, 17p, and 20p. In addition, described regions of homozygotic deletions were detected on 1p, 6q, 8p, 13q, 16q, and 22q, and furthermore located on 2q, 3, 4q, 9, 10q, 12p, and 20p. Finally, the uniparental disomies (UPDs) obtained were traced on 1q, 4q, 8q, 10q, and 22q. These identified alterations are affecting a series of enzymatic genes belonging to targeted pathways. Within the chromosomes 1, 10, 11, 14, and 16 we have localized kinases that are part of the PI3K/AKT pathway, which affect to a number of intracellular and extracellular myeloma growth cytokines. In the chromosomes 1, 6, 12, and 19 we identified a series of Cyclin-Dependent Kinases that are critical regulators of cell cycle progression and RNA transcription, since they regulate and control the cyclins, cell cycle regulatory proteins, which can provoke dysregulation and abnormally accelerated cell cycle progression. And finally on chromosomes 1, 2, 14, 21, and 22 we observed certain Aurora and related kinases, as another family of the cell cycle regulators and often aberrantly activated in human tumor cells, they facilitate transit from G2 through cytokinesis. These mutated kinases may be potential targets for therapeutics. Our data demonstrates the genomic complexity of multiple myeloma enhancing our understanding of the molecular pathogenesis of the disease and the importance of the HMCLs as a model.