A compendium of DIS3 mutations and associated transcriptional signatures in plasma cell dyscrasias

Abstract

DIS3 is a catalytic subunit of the human exosome complex, containing exonucleolytic (RNB) and endonucleolytic (PIN) domains, recently found mutated in multiple myeloma (MM), a clinically and genetically heterogeneous form of plasma cell (PC) dyscrasia. We analyzed by next-generation sequencing (NGS) the DIS3 PIN and RNB domains in purified bone marrow PCs from 164 representative patients, including 130 cases with MM, 24 with primary PC leukemia and 10 with secondary PC leukemia. DIS3 mutations were found respectively in 18.5%, 25% and 30% of cases. Identified variants were predominantly missense mutations localized in the RNB domain, and were often detected at low allele frequency. DIS3 mutations were preferentially carried by IGH-translocated/nonhyperdiploid patients. Sequential analysis at diagnosis and relapse in a subset of cases highlighted some instances of increasing DIS3 mutation burden during disease progression. NGS also revealed that the majority of DIS3 variants in mutated cases were comparably detectable at transcriptional level. Furthermore, gene expression profiling analysis in DIS3-mutated patients identified a transcriptional signature suggestive for impaired RNA exosome function. In conclusion, these data further support the pathological relevance of DIS3 mutations in plasma cell dyscrasias and suggest that DIS3 may represent a potential tumor suppressor gene in such disorders.

Keywords: DIS3; multiple myeloma; next-generation sequencing; plasma cell leukemia.

Figure 1. Frequency of SNVs and in-frame deletions in DIS3 coding region in MM, including information from literature

In the lower part of the figure, a schematic diagram of the DIS3 gene is reported, based on exon-intron organization of the longer transcript variant, NM_014953.4. Exons are numbered under the boxes, filled with black in the coding region. Exons sequenced in this study (i.e., exons 1–4 and exons 10–18) encompass respectively the entire PIN (cd09862, amino acids 9–197) and RNB domain (pfam00773, amino acids 467–791), plus portions of the flanking regions, as indicated by the blue and red dashed lines connecting the diagram of the gene to the scheme of the DIS3 protein, in the upper part of the figure. Here, somatic mutations identified in the present series and reported in the main MM datasets [3, 4, 6, 7, 13] are depicted.

Figure 2. Changes of DIS3 mutational burden during disease progression

For patients found mutated at diagnosis and/or relapse, allele frequencies of variants reported in the legend are plotted at both timepoints.

Figure 3. DIS3 mutations detected on genomic DNA and cDNA

A. Percentages of variant DIS3 sequencing reads identified by NGS analyses of genomic DNA and retrotranscribed total RNA. B. Correlation between VAFs detected on genomic DNA and cDNA.

Figure 4. Heatmap of the 28 differentially expressed genes identified at q-value = 0 by SAM two-class analysis of 102 MM patients stratified based on the presence of DIS3 mutations

In the heatmap, the color-scale bar represents the relative gene expression changes normalized by the standard deviation, and the color changes in each row represent gene expression level relative to the mean across the samples.