Integration of Gene Mapping and Expression Arrays Identifies Mechanisms by Which Genes Are Dysregulated as a Result of Copy Number Loss and Gain Associated with IgH Translocations in Multiple Myeloma.
Authors: Jenner Matthew W. , David Gonzalez , Leone Paola E. , Walker Brian A. , Johnson David C. , Dickens Nicholas J. , Ross Fiona M. , Davies Faith E. , Morgan Gareth J. 
Published: April 2020

Abstract
We have previously shown that integration of gene expression and SNP based mapping arrays can identify genes dysregulated as a result of copy number loss and gain in multiple myeloma. Using FISH, it has been possible to identify that gain and loss frequently occurs in association with primary IgH translocations, such as loss of FGFR3 and gain of CCND1 in a proportion of t(4;14) and t(11;14) cases. The aim of this study was to determine the frequency and size of such copy number change associated with IgH translocations and to identify the genes dysregulated as a consequence of these. FISH was performed on CD138 selected plasma cells from 80 newly diagnosed myeloma cases to identify cases with primary IgH translocations. Affymetrix 500K mapping arrays were used to determine copy number change using paired tumor and constitutional DNA and Affymetrix U133 plus 2.0 expression arrays were used to determine global gene expression. Samples were analyzed in dChip and CNAG. Thirty eight of 80 cases (47.5%) had primary IgH translocations: 7 t(4;14), 1 t(6;14), 16 t(11;14), 3 t(14;16), 2 t(14;20) and 9 with an unknown translocation partner. Of 29 cases with a known translocation partner, 11 had gain or loss of all or part of the derivative chromosome. Three of 7 t(4;14) cases had loss of FGFR3 by FISH, confirmed by mapping array as being due to deletion of the derivative 14, with loss of 4p16.3-pter and the remainder of chromosome 14 excluding IgH. The region on 4p commenced at FGFR3 and extended to the telomere. Gene expression analysis showed that there was underexpression of FGFR3 and 4 other genes in the deleted region in the 4p16 deleted cases. In 6 of 16 t(11;14) cases, the translocation was associated with an additional copy of CCND1 by FISH. Mapping arrays revealed in all cases the gain commenced at the presumed translocation breakpoint: in 4 cases there was gain of 11q13.3-qter and in 2 there was gain of a small region of 11q13 only. In most cases there was isolated gain of a variable sized region of 14q32 suggesting a sequence whereby translocation was followed by gain then by deletion of a portion of the derivative chromosome. Gene expression analysis identified 4 genes overexpressed on 11q in t(11;14) cases with 11q gain. In a single t(6;14) case there was a complex rearrangement involving gain of 6p21.1-pter and IgH with loss of the derivative 6, again suggesting translocation followed by gain then loss. In one t(14;16) case there was UPD of 16q except for 16q23-qter with associated gain of IgH alone. This complex pattern suggests a sequence whereby deletion is followed by IgH translocation then by duplication of the untranslocated 16q. This study has shown that loss and gain of translocated regions is a frequent occurrence, present in 11/29 cases with known IgH translocations. Using mapping arrays it is possible to demonstrate that in the majority of cases, the translocation is the initial event, followed by subsequent gain or loss as a later event. We have shown the variable size of these regions and have identified genes dysregulated as a result of the deletions of 4p in t(4;14) cases and gains of 11q in t(11;14) cases. These findings provide evidence of collaborating mechanisms that may be responsible for disease progression in these cases.