Chromothripsis and Chromoplexy Are Associated with DNA Instability and Adverse Clinical Outcome in Multiple Myeloma

Introduction: Chromothripsis and chromoplexy are gross structural events that deregulate multiple genes simultaneously and may help explain rapid changes in clinical behavior. Previous screening studies in multiple myeloma (MM) using copy number arrays have identified chromothripsis at a low frequency (1.3%) and suggested it adversely impacts prognosis. Here, using whole genome sequencing (WGS) data we have identified a higher frequency of these events, suggesting they are more common than previously thought.

Methods: 10X ChromiumWGS (10XWGS) from 76 newly diagnosed MM (NDMM) patients were analyzed for structural rearrangements using Longranger. Oxford Nanopore long read sequencing was performed on 2 samples. Long insert WGS data from 813 NDMM patient samples from the Myeloma Genome Project (MGP) were analyzed for structural rearrangements using Manta. Whole exome sequencing was available for 712 samples. RNA-seq was available for 643 samples. Chromothripsis was determined by manual curation of breakpoint and copy number data. Chromoplexy was defined as rearrangements within 1 Mb of one another involving 3 or more chromosomes.

Results: Chromoplexy was detected in 33/76 (46%) cases using 10XWGS data, and cross validated in the MGP WGS dataset being found in 30% (247/813) of samples and was most frequent on chromosomes 8 (11.7% of samples), 14 (10.6%), 11 (9.6%), 1 (9.5%), 6 (8.0%), 22 (7.6%), 12 (6.7%), and 17 (6.7%). The gene regions most involved in chromoplexy events were MYC (chr8; 7.3%), IGH (chr14, 8.8%), IGL (chr22; 4.6%), CCND1 (chr11; 3.9%), TXNDC5 (chr6; 1.7%), FCHSD2 (chr11; 1.4%), FAM46C (chr1; 1.2%), MMSET (chr4; 1.2%), and MAP3K14 (chr17; 0.7%).

Chromoplexy samples involved pairings of super-enhancer donors (IGH, IGL, FAM46C, TXNDC5) and oncogenic receptors (CCND1, MMSET, MAP3K14, MYC) implicating transcriptional deregulation. To confirm, RNASeq showed an elevation of expression over median in the oncogenic receptors when paired with a donor: CCND1 (median expression = 12.0 vs. median expression with donor = 17.9), MAP3K14 (10.8 vs. 14.7), MYC (12.7 vs. 14.1) and MMSET (11.9 vs. 16.7). We also identified elevated expression of PAX5 (8.23 vs. 13.79) and two cases where BCL2 (13.32 vs. 14.68) partnered with MYC, one involved IGH similar to follicular lymphoma.

To determine if chromoplexy events were happening on the same allele, we performed long read sequencing using Oxford Nanopore on a sample with a t(2;6;8;11) event. We observed a read mapped to chromosome 2, with secondary alignment to chromosomes 6 and 8. This single 32 kb read was a continuous t(2;6;8) event, proving these events occurred on the same allele. However, despite close proximity, the data did not put the t(8;11) in the same read meaning this event occurred on a different allele or sub-clone, suggesting ongoing genomic instability.

Chromothripsis was detected in 16/76 (21%) cases using 10XWGS, and was consistent in MGP data, (170/813; 21%). Chromothripsis occurred on all chromosomes but at different frequencies where chromosome 1 had most events (5.1%), followed by 14 (2.4%), 11 (2.3%), 12 (2.2%), 20 (1.9%), 17 (1.9%), and 8 (1.9%).

We hypothesized the presence of both chromoplexy and chromothripsis could be associated with ineffective DNA repair and indeed, using WES data, patients with both events show more mutations in TP53 (19% vs. 5%) and ATM (10% vs. 4%) implicating homologous recombination deficiency as an etiologic mechanism. Gene set enrichment analysis showed significant enrichment and positive normalized enrichment score (NES) for the DNA Repair (P = 0.01; NES = 1.7) and MYC pathways (P = 0.01; NES = 3.2) consistent with previous results.

In relation to prognosis, chromoplexy and chromothripsis have a negative impact on progression free survival (28.6 months vs. 42.8 months, P=0.03 and 28.6 months vs. 40.7 months P=0.01, respectively). When patients with both chromoplexy and chromothripsis (9%) were examined there was a pronounced effect on PFS (40.7 months vs. 22.7 months, P<0.001).

Conclusion: Complex structural events are seen frequently in MM and could help explain disease progression. Severe cases with both chromoplexy and chromothripsis are associated with acquired genomic instability and an adverse impact on prognosis either directly or due to their association with DNA repair abnormalities. This opens the possibility of specifically therapeutically targeting the underlying DNA abnormalities.