The Mutational and Signaling Landscape of Multiple Myeloma Varies Dependent upon Translocation Cyclin D (TC) Subgroup

Introduction

The spectrum and frequency of mutations in newly diagnosed and relapsed MM has been reported and exhibits a pattern which is distinct from other peripheral lymphoid disorders. A number of data sources have suggested that MM is not a single disease, but rather a collection of molecularly diverse entities which present as malignancies of plasma cells with different clinical courses and response to therapy. To test this hypothesis we examined the spectrum of common mutations and their associations with gene expression in etiological subgroups defined by a simplified TC classification based on translocation subgroup and the deregulation of a D group cyclin.

Materials and methods

We examined a set of gene expression data from 907 newly diagnosed MM patients and classified them according to an updated TC model. An additional set of 482 cases underwent both sequencing by the FoundationOne Heme targeted panel and gene expression profiling. Mutational data were analyzed for significant associations with gene expression data within five primary TC subgroups: D1, D2, CCND (translocated 11q13 or 6p21), MMSET, and MAF.

Results

Gene expression signatures of GEP70 risk status, chromosomal aberrations [1q+, 1p-, 13q-, 17p-, HRD], proliferation index, NF-kB activation, and BCL2/MCL1 ratio were not distributed evenly across the TC subgroups, consistent with distinct biological differences amongst groups. Having noted differential expression patterns between subgroups, we hypothesized that distinct patterns of mutation may also exist across TC subgroups.

Mutations in RB1 and CDKN2C, seen primarily in the D2 and MMSET subgroups, were mutually exclusive yet both associated with increased proliferation and HR status. Thus two paths to extreme proliferation emerge through either ahomozygous deletion of CDKN2C (with low expression of CDKN2C) or an RB1 alteration (with high expression of CDKN2C).

Mutations in KRAS, NRAS, and BRAF were not evenly distributed across subgroups and were significantly inversely associated with an NF-kB signature. RRAS2 was also significantly inversely associated with MAPK mutations in the D1 and D2 subgroups, while genes encoding sprouty-related proteins, SPRED1 and SPRED2, were positively associated with MAPK mutations in the CCND-11q13 subgroup.

Overall, MAPK mutations were most significantly associated with elevated expression of DKK1, a known Wnt antagonist, and DUSP6, a known inhibitor of the pathway. These gene expression patterns were primarily localized in the D1, D2, and CCND-11q13 subgroups. In contrast, the MMSET and MAF subgroups had a unique patterns of expression not seen in the D1, D2, or CCND subgroups.

A gene set enrichment analysis showed that the DNA replication and cell cycle pathways were significantly enriched in the MMSET and MAF subgroups in the presence of MAPK pathway mutations. Within the MMSET subgroup, MAPK mutations were positively associated with GEP70 HR, proliferation index, and membership of the UAMS-PR subtype, while being negatively associated with FGFR3 expression. This result indicates that the reliance on FGFR3 signaling as an oncogenic driver is lost in the presence of a MAPK activating mutation.

Conclusions

In MM proliferative signals are delivered via the RAS and NF-kB pathways and activation of these two pathways appears to offer mutually exclusive pathways to disease progression since the majority of cases exhibit a reciprocal relationship between these two signaling pathways.

The MMSET and MAF subgroups lack a strong association between NF-kB and MAPK signaling pathways, which may indicate that their initiating translocation event and subsequent genetic patterns provide a unique background in which MAPK alterations accelerate progression.

As mutational interactions are differential across TC subgroups, we propose a comprehensive approach to MM classification that includes the etiologic designation by simplified TC subgroups and the subsequent use of genetic and biological markers characteristic of acquired features associated with disease progression, such as MAPK or NF-kB activation.

Distinct patterns of RNA expression are associated with DNA mutations in myeloma when contextualized by etiologic subgroups. This indicates that the cellular background in which a mutation occurs has a distinct impact on downstream expression patterns-this observation is particularly relevant to the MMSET and MAF subgroups.