Frequent Igh Fusion Transcripts with Clinical Impact in Multiple Myeloma

Background: Significant heterogeneity has been described in Multiple Myloma (MM), especially at the genomic level. Frequent gains and losses of DNA along with various mutations have been observed, and differential allelic expression is being characterized. Fusion proteins are common and maybe associated with cell transformation, growth and lethality of tumor cells. However, unlike in leukemia, no consistent fusion gene product has been consistently identified. As IgH-related translocations have an important role in myeloma, we have investigated fusion genes involving IgH, to understand their biology and explore a possible effect on survival in MM.

Methods: We performed deep RNA-Seq on purified MM cells from 430 newly-diagnosed MM patients and analyzed gene expression profiles, isoform signatures and both novel and known fusion genes using two common algorithms: TopHat and MapSplice. We also correlated genomic data with patient data including cytogenetics and FISH, as well as survival.

Results: We primarily focused on fusions involving the IGH gene (chromosome 14) and found that about one fourth of the patients (57 out of 430) presented an IGH fusion gene (97 patients according to TopHat, 303 according to Mapsplice, 57 according to both). These included the well described t(4,14) fusion involving the MMSET gene (found in 47 patients by both algorithms, 49 by Tophat, 54 by Mapsplice). Additionally we observed fusions involving chromosomes 14 and chromosomes 1, 4, 11, 12, and 16. The counterpart genes involved in the IgH fusions included PDE3A (chromosome 12 - 4 patients); HFM1 (chromosome 1, 2 patients); NFKB1, FGFR3, CIITA, WWOX and MRPL21 (chromosomes 4, 16, and 11, 1 patient). As RNA-Seq data allows the precise localization of the breakpoints, we were able to identify that out of the 47 t(4,14) patients, 62% were MB4-1, 9.5% were MB4-2 and 28.5% were MB4-3. Interestingly, we did not see fusion products involving IgH and other known parts on Chromosomes 8 and 20. We studied event-free survival in a subset of 265 patients with available survival data and found that, as predicted, patients with an IgH-MMSET fusion had significantly lower survival than others. However, patients with a fusion gene involving IGH and any other partner have a significantly better prognosis as a group. Moreover, the poor prognosis of IgH-MMSET fusion appears to be driven by MB4-3 patients. Importantly, the fusions identified using RNA-seq were also validated by FISH analysis. All t(4,14) fusions were characterized by a very high MMSET expression (FPKM greater than 20) while patients with other fusions presented a lower MMSET expression (FPKM lower than 10).

Conclusion: Our study suggests that IgH-related translocations in myeloma may impact tumor biology by a number of mechanism, one of which is the generation of fusion proteins with functional consequences. It also highlights a possible clinical impact that requires validation in larger cohorts.