Multiple myeloma-associated hDIS3 mutations cause perturbations in cellular RNA metabolism and suggest hDIS3 PIN domain as a potential drug target

Abstract

hDIS3 is a mainly nuclear, catalytic subunit of the human exosome complex, containing exonucleolytic (RNB) and endonucleolytic (PIN) active domains. Mutations in hDIS3 have been found in ∼10% of patients with multiple myeloma (MM). Here, we show that these mutations interfere with hDIS3 exonucleolytic activity. Yeast harboring corresponding mutations in DIS3 show growth inhibition and changes in nuclear RNA metabolism typical for exosome dysfunction. Construction of a conditional DIS3 knockout in the chicken DT40 cell line revealed that DIS3 is essential for cell survival, indicating that its function cannot be replaced by other exosome-associated nucleases: hDIS3L and hRRP6. Moreover, HEK293-derived cells, in which depletion of endogenous wild-type hDIS3 was complemented with exogenously expressed MM hDIS3 mutants, proliferate at a slower rate and exhibit aberrant RNA metabolism. Importantly, MM mutations are synthetically lethal with the hDIS3 PIN domain catalytic mutation both in yeast and human cells. Since mutations in PIN domain alone have little effect on cell physiology, our results predict the hDIS3 PIN domain as a potential drug target for MM patients with hDIS3 mutations. It is an interesting example of intramolecular synthetic lethality with putative therapeutic potential in humans.

Collaborative Control of Cell Cycle Progression by the RNA Exonuclease Dis3 and Ras Is Conserved Across Species

“…Elimination of dis3 function in yeast, flies, and vertebrate cells appears to reduce cell growth and division (Ohkura et al 1988;Kiss and Andrulis 2010;Tomecki et al 2014; and this article), but de novo, tumor-specific, apparently hypomorphic mutations in dis3 are found recurrently in multiple myeloma (Chapman et al 2011;Walker et al 2012;Lohr et al 2014), a cancer of plasma B cells, suggesting that dis3 promotes progression of this cancer. To explore this possibility, we examined the phenotype of flies transheterozygous for dis3 1 , dis3 2 , or a deficiency of the region and dis3 G5039 , a P-element insertion of the P[EP] type (Rorth 1996) in dis3's 59 UTR, here referred to as dis3 P .…”

“…In vitro studies of the most common dis3 mutations in multiple myeloma appear to reduce but not eliminate dis3 function (Tomecki et al 2014). Thus, we sought to test whether reducing dis3 function increased proliferation in a relevant B cell context in the presence of proliferative signals and increased ERK activation.…”

“…reduction of Dis3 exonuclease function retards cell growth; elimination of Dis3 function appears incompatible with cell growth (Tomecki et al 2014). Except for the observation that RNAi-mediated depletion of dis3 function leads to early larval arrest and reduces tissue growth in Drosophila (Hou et al 2012;Towler et al, 2015), the role of dis3 has not been rigorously explored in higher eukaryotic model systems.…”

“…In multiple myeloma, a malignancy of plasma B cells, whole genome sequencing approaches uncover dis3 as one of the most frequently mutated genes in this cancer (Chapman et al 2011;Walker et al 2012;Lohr et al 2014). Essentially all multiple myeloma-specific dis3 mutations are missense mutations that cluster in its RNB domain and appear to reduce but not eliminate dis3 function in the tumor cells: dis3 mutations that are associated with loss of heterozygosity appear to simply reduce Dis3 exonuclease activity, whereas those mutations found associated with a wild-type copy of dis3 in the tumor appear to largely eliminate exonuclease activity for the variant allele product (Chapman et al 2011;Walker et al 2012;Lohr et al 2014;Tomecki et al 2014). Within multiple myeloma tumors, dis3 mutations have been found simultaneously clonal with activating mutations in k-ras (Lohr et al 2014).…”

Functional characterization of a chr13q22.1 pancreatic cancer risk locus reveals long-range interaction and allele-specific effects onDIS3expression

“…Perhaps the most striking example is multiple myeloma (MM), which shows a 10-18.5% somatic mutation rate in different studies (15,16,20,21). DIS3 ribonuclease II (RNB) domain mutations observed in MM were shown to be synthetic lethal with catalytic mutations in the PIN domain, suggesting a possible drug target (22). Furthermore, a trend towards shorter survival was observed in MM patients with DIS3 mutations (16).…”