The genomic landscape of structural variations and complex events in multiple myeloma

Introduction: Multiple Myeloma (MM) initiation and progression is driven by recurrent cytogenetic events, i.e. multiple trisomies or translocations within the immunoglobulin locus. Gene mutations have been extensively studied, and they are generally involved in late phases of disease development. On the contrary, very little is known about structural variations (SV), which are increasingly emerging as critical driver in several cancers. Methods: We performed whole genome sequencing (WGS) on 67 CD138+ purified bone marrow MM samples from 30 patients (median of 2 samples per patient; range 1-4), to which we added 22 previously published cases (Chapman et al, Nature 2011) for a total of 89 tumour samples. We defined SVs as inversions, translocations, internal tandem duplications and deletions, which we analysed using publicly available tools developed at the Wellcome Trust Sanger Institute. Events with > 3 independent SVs involved in distinct copy-number abnormalities (CNAs) were defined as “complex”. Results: We found a stunning 1887 unique SVs in the whole cohort, with a heterogeneous distribution across the entire series (median 29 per patients, range 0-156). IGH and MYC translocations were the most frequent recurrent events and accounted for only 5.3% of the entire SV catalogue. Integrating data on SV and CNAs we found that a SV was responsible for ~90% of CNAs where a breakpoint could be mapped. Furthermore, 93% of patients carried multiple CNAs across different chromosomes all sustained by the same complex SV. Our analysis thus offers a pathogenic explanation of many recurrent CNAs in MM.Overall, 136 complex events were observed in 43/52 patients (83%). We found 34 instances of chromotripsis (Korbel J.O. et al., Cell 2013) in 18/52 patients. The vast majority (30/34) were clonal and conserved during evolution, suggesting a potential early role in MM pathogenesis. In addition, we observed 5 chromoplexy (Korbel J.O. et al., Cell 2013) events acquired in 5 patients. More interestingly, in 13 patients we found an entirely novel complex event characterized by multiple concatenated translocations causing small CNAs on more than 2 different chromosomes, that we named template insertion (TI). Interestingly, 77% of TIs resulted in a translocation involving an important MM oncogene (8 MYC and 2 CCND1), suggesting that this is a novel relevant driver mechanism in MM. Reconstructing their order of acquisition, we show that SVs and complex events are at the nodes of initiation and subclonal diversification during MM life history, with high variability of timing from patient to patient, confirming their driver role in MM pathogenesis. Conclusions: In this study, we described for the first time the landscape of MM SV and complex events, showing their critical role in MM pathogenesis. Overall these data suggested a new pathogenetic model where MM evolution is driven by few clonal sweeps promoted by heterogeneous and private structural events.