Identification of Collaborating Oncogeneic Events Leading to Disease Progression in Myeloma Cases with a t(4;14) and t(11;14) Using SNP and Gene Expression Arrays.
Authors: Jenner Matthew W. , Walker Brian A. , Leone Paola E. , Gonzalez David , Ross Fiona M. , Li Cheng , Davies Faith E. , Morgan Gareth J. 
Published: April 2020

Abstract
Immunoglobulin heavy chain translocations are an initiating genetic event in the pathogenesis of 50% of multiple myeloma cases. The t(4;14) and t(11;14) translocations each occur in approximately 15% of cases but have distinct clinical outcomes with t(4;14) being associated with a poor prognosis. This may reflect the patterns of genes deregulated by the translocation but also by additional genetic events acquired later in the disease natural history collaborating with the initial translocation. Previous analysis has shown that the t(4;14) results in overexpression of both FGFR3 and MMSET, whereas the t(11;14) results in dysregulation of cyclin D1. In order to identify collaborating genes important in disease progression, we have used the Affyemtrix 50K SNP mapping array to determine chromosomal copy number and loss of heterozygosity (LOH), and the Affymetrix U133 plus 2 array to determine gene expression levels, in t(4;14) and t(11;14) cases. CD138 plasma cells were selected from 22 newly diagnosed myeloma cases, and the presence of the translocation and hyperdiploid status were determined by FISH (9 t(4;14) cases, 13 t(11;14) cases, all cases non-hyperdiploid using the FISH ploidy index). In keeping with our previous studies both t(4;14) and t(11;14) had distinct gene expression profiles characterized by overexpression of FGFR3, MMSET, cyclin D1 and cyclin D2 using hierarchical clustering programmes. A significant percentage of cases lacking a t(4;14) also appeared to have dysregulation of MMSET and its splice variants, as using the array specific hybridization patterns and RT-PCR there was overexpression of the C terminal exons of MMSET but a lack of IgH-MMSET fusions. There was a good correlation between the hyperdiploid status of the cells using FISH and SNP arrays, although some chromosomes that were not tested by FISH showed the presence of chromosomal trisomies in the SNP array. All of the t(4;14) cases had numerous large regions of chromosomal amplification and deletion, some of which were associated with LOH whereas a number of the t(11;14) cases showed diploid SNP calls with no regions of LOH, suggesting greater genomic instability in t(4;14). There was 90% correlation between the presence of a t(4;14) and deletion of chromosome 13q. Chromosome 1 has been suggested to be the site of important collaborating genes previously and in keeping with this we identified 1p amplifications in 12/22 cases, 1q amplifications in 7/22 cases and 1p deletions in 2/22 cases. These abnormalities were equally distributed across both translocation groups suggesting that they are common events in myeloma which are not associated with any particular translocation. In contrast, deletion of regions 16q appear to be specific to a subgroup of t(11;14) cases, with loss in 5 of 13 t(11;14) cases and none being seen in the t(4;14) cases. Current studies comparing the abnormalities detected with high resolution SNP array to gene expression profiles will help to determine how the expression of genes within these key regions of gain and loss are altered and how they may contribute to myeloma pathogenesis.