Apobec Family Mutational Signatures Are Associated with Poor Prognosis Translocations in Multiple Myeloma

Abstract

Aberrant chromosomal translocations are seen in ~40% of presenting patients and predominantly involve the IGH locus at 14q32. The five main translocations involving the IGH locus are t(4;14), t(6;14), t(11;14), t(14;16) and t(14;20), which result in over-expression of MMSET/FGFR3, CCND3, CCND1, MAF and MAFB, respectively. In previous clinical trials we have shown that the t(4;14), t(14;16) and t(14;20) are associated with a poor prognosis. In initial sequencing studies of myeloma it has been noted that the spectrum of mutations fall into two groups, one of which is characterised by an APOBEC signature. This signature comprises of C>T, C>G and C>A mutations in a TpC context and comprises only a subset of samples, with the rest having a rather generic mutation signature representing an intrinsic mutational process occurring as a result of the spontaneous deamination of methylated cytosine to thymine. Whole exome sequencing was performed on 463 presentation patients enrolled into the UK Myeloma XI trial. DNA was extracted from germline DNA and CD138+ plasma cells and whole exome sequencing was performed using SureSelect (Agilent). In addition to capturing the exome, extra baits were added covering the IGH, IGK, IGL and MYCloci in order to determine the breakpoints associated with translocations in these genes. Tumor and germline DNA were sequenced to a median of 60x and data processed to generate copy number, acquired variants and translocation breakpoints in the tumor. Progression-free and overall survival was measured from initial randomization and median follow up for this analysis was 25 months. These combined data allow us to examine the effect of translocations on the mutational spectra in myeloma and determine any associations with progression-free or overall survival. Translocations were detected in 232 (50.1%) patients of which 59 patients (12.7%) had a t(4;14), 86 patients (18.6%) a t(11;14), 17 patients (3.7%) a t(14;16), 5 patients (1%) a t(6;14) and 4 patients (0.9%) a t(14;20). MYC translocations were found in 85 patients (18.4%). Using the tiled regions we were able to detect a mutational signature, kataegis, where regional clustering of mutations can be indicative of somatic genomic rearrangements. We found the hallmarks of kataegis in 15 samples (3.2%), where there was enrichment for TpCpH mutations with an inter-mutational distance <1 kb. Where we detected kataegis surrounding MYC there was also an inter-chromosomal translocation involving either IGK or IGL. Interestingly, the partner chromosomes also showed signs of kataegis e.g. in the t(2;8) kataegis was found at IGK and MYC and in the t(8;22) kataegis was found at MYC and IGL. APOBECs are thought to be involved in the generation of kataegis and as such this co-localisation is indicative of APOBEC involvement in the generation of MYCbreakpoints. We found mutation of translocation partner oncogenes, in particular CCND1 was mutated in 10 patients with the t(11;14). There was an association of mutated CCND1 with a poor prognosis when compared with non-mutated t(11;14) patients (OS median of 20.2 months vs. not reached, p=0.005). Mutations were also seen in FGFR3, MAF and MAFB but only in the samples with the respective translocations. The mutations are likely due to somatic hypermutation mediated by AID, an APOBEC family member. We found that t(14;16) and t(14;20) samples have a significantly higher number of mutations compare to the other translocation groups (p=1.65x10-5). These mutations were enriched for those with an APOBEC signature (T(C>T)A, p=9.1x10-5; T(C>T)T, p=0.0014; T(C>G)A, p=0.001; T(C>G)T, p=0.0064), indicating that the ‘maf’ translocation groups are characterized by APOBEC signature mutations, specifically APOBEC3B. When samples are assigned to either an APOBEC or non-APOBEC group the ‘maf’ translocations account for 66.6% of samples in the APOBEC group but only 1.3% of the non-APOBEC group. Here we show three different mutational signatures mediated by the APOBEC family: translocation partner mutation by AID, APOBEC signature mediated by APOBEC3B, and kataegis mediated by an unknown APOBEC family member. We also show for the first time a clinical impact of APOBEC mutations and their association with a poor prognosis. The poor prognosis of this mutational signature is inextricably linked to a high mutation load and the adverse t(14;16) and t(14;20) translocation subgroups. Disclosures Walker: Onyx Pharmaceuticals: Consultancy, Honoraria.

Timing the initiation of multiple myeloma

“…Two of these were characterized by high mutation burden and >20% contribution from APOBEC (SBS2 +SBS13). Both patients had IGH translocations involving MAFB and MAFA, confirming the known association between these IGH translocations and high APOBEC mutational activity (Supplementary Data 1) 26,27 . Interestingly, these two cases were the only ones without detectable non-canonical activationinduced deaminase (AID) (SBS9) activity.…”

“…1c, d) 6,7,9,17,[24][25][26] . APOBEC (SBS2 and SBS13) was also confirmed as an essential mutational process, absent in only 9 patients (17%) 17,25,27,28 . While SBS2 was always the most common APOBEC signature (43/52; 83%), SBS13 activity was observed in 6 cases (11.5%) (Supplementary Data 2).…”

Overexpression of B‐cell lymphoma 6 alters gene expression profile in a myeloma cell line and is associated with decreased DNA damage response

“…AID is implicated in oncogenic mutations and chromosomal translocations, especially those involving immunoglobulin genes, which results in B‐cell and plasma cell tumorigenesis . It has been reported that the AID/APOBEC‐mediated mutational signature is associated with poor prognosis of myeloma patients . Taken together, BCL6‐dependent AID upregulation is a threat to the genomic integrity of myeloma cells and thus may affect disease progression.…”

Toward personalized treatment in multiple myeloma based on molecular characteristics

“…[12][13][14][15] Dozens of myeloma driver genes have been identified. The most common occur in the RAS and NF-kB families, 12,14,16 with many mutations associated with the primary myeloma molecular subgroups suggesting the underlying background initiating event drives the acquisition of subsequent molecular abberations. 13 A number of these new technologies are now Clinical Laboratory Improvement Amendments certified and available for diagnostic use, while additional techniques such as DNA methylation analysis remain confined to research laboratories.…”

“…These subgroups are also associated with a mutational signature (a characteristic combination of mutation types) associated with the activity of the mRNA editing enzyme APOBEC and have an increased number of mutations. 16 MAF and MAFb protein have been demonstrated to mediate resistance to proteasome inhibitors, 22,23 perhaps contributing to this subgroup's adverse outcome seen in most, 2,24,25 though not all, 26 studies. Images from left to right show G-band karyotyping, FISH, GEP data, SNP array data, and NGS data.…”