Exonuclease 1 Drives Growth and Genomic Instability in Multiple Myeloma through Interaction with CAD, a Key Protein Involved in De Novo Pyrimidine Biosynthesis

Human exonuclease 1 (Exo1) plays important roles in DNA replication and repair including the resection of DNA ends during homologous recombination (HR). Based on our previous data demonstrating the role of HR in genomic instability and growth of cancer cells, we investigated role of EXO1 in multiple myeloma (MM). Expression of EXO1 and pRPA32 (a marker of DNA end resection) was elevated in all myeloma cell lines tested (N=10) relative to normal peripheral blood mononuclear (PBMC) cell samples. We developed a fluorescence-based EXO1 activity assay and observed elevated (~1.5- to > 5-fold; p < 0.05) Exo1 activity in all twelve MM cell lines tested relative to normal PBMCs. Moreover., elevated expression of EXO1 correlated with poor overall and event-free survival in MM patients (MMRF dataset; p < 1x10^-5). Transgenic suppression of EXO1 in MM cell lines caused a time-dependent loss in cell viability. Evaluation at day 5 after selection indicated that, relative to control cells, EXO1 suppression in RPMI, MM1S, MM1R and U266 cells was associated with ∼95%, 85%, 60% and 40% cell death, respectively. Apoptosis, as evaluated by annexin-labeling, was detected in ~50% of EXO1-knockdown cells compared to 11.9% of control MM1S cells. Conditional knockdown in H929 cells evaluation at 48 h after adding doxycycline demonstrated apoptosis in 18% of EXO1-suppressed cells vs. 4.9% of control cells.

To investigate the mechanisms by which EXO1 impacts MM cell viability, the proteins interacting with EXO1 in MM cell lines (MM1S and H929) were identified using Exo1 pull-down and mass spectrometry. Interaction of EXO1 with CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase), a trifunctional protein involved in the first three steps of de novo pyrimidine biosynthesis, was identified and its binding confirmed with co-immunoprecipitation. We found that EXO1 overexpression increased the growth rate of non-cancerous cell types (HS5 - bone marrow stromal cells and normal fibroblasts), whereas suppression of CAD inhibited the spontaneous and EXO1-mediated increase in growth rate as well as DNA replication in both normal cell types. Consistently, the CAD-knockdown increased apoptosis in HS5 cells by ∼5-fold, whereas EXO1 overexpression reduced it by ~2-fold. Conversely, suppression of CAD also increased apoptosis in EXO1-overexpressing cells by 3-fold. In normal diploid fibroblast cells with a limited lifespan, EXO1 overexpression increased DNA replication by 32%, whereas CAD-knockdown reduced it by ∼65%. Importantly, CAD-knockdown in EXO1-overexpressing cells also reduced DNA replication by 26%. These data indicate that CAD is involved in EXO1-dependent cell proliferation and survival.

Investigating the molecular events associated with EXO1, we observed that its suppression in MM cells inhibits DNA end resection, DNA breaks, HR activity and genomic instability (as assessed by a micronucleus assay); whereas overexpression in normal cells increased those activities. Moreover, inhibition of CAD reduced spontaneous as well as EXO1-induced HR activity and genomic instability in both hematopoietic and solid tumor cell types. Since CAD is involved in the first three steps of pyrimidine biosynthesis, our data suggest that interaction with CAD enables EXO1 to drive DNA replication, HR and associated genomic instability. Functional relevance of this interaction and possible regulation of de novo pyrimidine biosynthesis by EXO1 is being further investigated. Inhibitors of CAD may provide a novel therapeutic target in myeloma as well as other Exo1 overexpressing malignancies.

Munshi:GSK: Consultancy; Takeda Oncology: Consultancy; Bristol-Myers Squibb: Consultancy; Janssen: Consultancy; Amgen: Consultancy; Oncopep: Consultancy, Current equity holder in publicly-traded company, Other: scientific founder, Patents & Royalties; Novartis: Consultancy; Adaptive Biotechnology: Consultancy; Pfizer: Consultancy; Abbvie: Consultancy; Celgene: Consultancy; Karyopharm: Consultancy; Legend: Consultancy.