Molecular Karyotyping by High Resolution Arrray CGH Uncovers New Deleted and Amplified Genomic Regions That Contain Genes of Biological Interest in Multiple Myeloma Cells.

Multiple Myeloma (MM) is a malignancy characterized by clonal expansion of plasma cells. In 50% of the cases, the neoplastic transformation begins with a chromosomal translocation that juxtaposes the IGH gene locus to an oncogene. After defining the IGH-translocations present in a panel of MM cell lines, we conducted expression-profiling analysis. Supervised analysis identified 166 genes significantly differentially expressed among the cell lines harboring MMSET/FGFR3 (4p16), MAF (16q) and CCND1 (11q13) rearrangements. Besides translocations, gene copy number changes are also frequent in MM but far less characterized than in other neoplasias. We conducted array Comparative Genomic Hybridization (arrayCGH) with the same cDNA platform that was used for the expression analysis with the double purpose of characterizing the amplified genome regions and identifying the amplified and overexpressed (A/O) genes within these regions. We focused in five chromosomes recurrently affected by gains/amplifications in primary samples and cell lines where we found 60 A/O genes. Among them, twenty-five (42%) were only overexpressed when amplified, and six, CHI3L1, ELMO1, BNIP3L, PLAG1, LOC157567, and VPS28, showed a significant association between overexpression and gain/amplification.

In a second step, we are conducting a high resolution analysis of copy number changes in flow sorted CD138 myeloma cells from patients with normal karyotype, as stated by conventional cytogenetics. We are using the Human Genome CGH Microarray 44A platform from Agilent Technologies (Palo Alto, CA), which contains 44.000 60-mer oligonucleotides covering the human genome with an average resolution of 40 Kb. As expected, this genomic approach, performed on selected cells, allowed the identification of a high number of deletions and gains. We have found small regions (below 500 Kb of size) that were rearranged as follows: