Multiple myeloma (MM) is an incurable malignancy of antibody secreting plasma B-cells whose etiology is still poorly understood. We used whole genome sequencing (WGS) and deep-read capture validation to thoroughly characterize the mutation landscape in four newly diagnosed MM patients and further examined mutation recurrence in 89 additional MM patients. WGS cases were selected to be racially diverse and represent both hyperdiploid and non-hyperdiploid MM with otherwise “simple” karyotypes. All studies to date have used peripheral blood as controls, however, abnormal B cells and circulating tumor cells frequently contaminate the peripheral blood of MM patients and these studies may have missed the early genetic events potentially important in disease pathogenesis. We therefore chose to use matched skin samples as normal controls. The use of skin DNA controls and deep read count capture validation of single nucleotide variants (SNV) allowed us, for the first time, to demonstrate clear separation between normal and malignant cell populations. Our analysis pipeline detected both somatic SNVs and structural variants (SV, ie. translocations, deletions, insertions). In all four patients, we observed chromosomal translocations at the Ig heavy chain locus, VDJ recombination, and Ig locus somatic hypermuation. We found somatic mutations affecting the E3 ubiquitin ligase HUWE1 in 4% (4/94) of cases, as well as recurring deletions affecting the Rho pathway regulator DIAPH2 (recurrence data will be presented). RNA sequencing was preformed for 3 of the WGS patients to explore transcriptional effects of mutations observed. Statistical analysis identified significantly mutated genes, i.e. mutation hotspots, including ROBO2, BCL6 and cadherin/catenin genes. Genes involved in cell polarity, cell adhesion and axon guidance were affected in all four WGS patients. Chromosomal translocations present in all four WGS patients involved both known oncogenes (CCND1, MYC and MAFB) and putative oncogenes. A novel translocation implicated KCNT2, encoding a sodium-activated potassium channel, as a potential oncogene in MM. Recurrent point mutations were relatively rare in MM, suggesting that SVs are more common driver mutations and/or that SNVs in MM disrupt a diverse array of genes to affect key pathways. For genomic studies in MM moving forward, our results emphasize the importance of matched normal controls uncontaminated by tumor cells, and suggest that careful analysis of SVs be included to find novel oncogenes and important clinical correlations.
No relevant conflicts of interest to declare.
Asterisk with author names denotes non-ASH members.