Discovery of Prolyl-tRNA Synthetase As a Novel Target in Multiple Myeloma

Aminoacyl-tRNA synthetases (aaRSs) are essential enzymes that charge tRNAs with their cognate amino acids. Recent studies have revealed that the expression of aaRSs is dynamically altered in response to cellular stresses, and that specific isoforms play pivotal roles in carcinogenesis and tumor progression. Despite emerging interest in aaRSs in cancer, the biologic sequelae of aaRSs in multiple myeloma (MM) have not yet been elucidated. We first examined RNA expression levels of aaRSs in tumor cells from MM patients. Gene expression analyses revealed that most aaRSs were upregulated in MM patients compared to healthy donors. Importantly, expression of 4 aaRSs, including glutamyl-prolyl-tRNA synthetase (EPRS), correlated with worse clinical prognosis: high EPRS expression correlated with disease progression (GSE6477; P< 0.001) and shorter survival (CoMMpass; P = 0.007). Consistent with clinical data, ERPS knockdown in MM cells (AMO1, RPMI 8226, and MM.1S) triggered significant cell growth inhibition, suggesting that EPRS is a growth and survival factor in MM cells.

Halofuginone (HF) is an inhibitor of the prolyl-tRNA-synthetase (PRS) activity of EPRS and potently inhibits MM growth. However, HF is proline (Pro) competitive and increased levels of Pro abrogates the effect of HF, including the Pro-rich tumor microenvironment. To overcome this limitation, we developed a novel ATP competitive and Pro non-competitive PRS inhibitor, NCP26. NCP26 potently decreased growth in MM cell lines, including drug (Dox, Dex, PI, IMiDs) resistant isogenic derivatives, and patient MM cells (EC50 ≈ 500 nM), without significant toxicity to peripheral blood mononuclear cells. Neither anti-apoptotic cytokines (i.e., IL-6) nor co-culture with bone marrow (BM) stromal cells abrogated NCP26-induced MM cell death. Importantly, unlike HF, NCP26-induced cell growth inhibition was not altered by an excess of exogenous Pro. Since aaRSs inhibition results in accumulation of uncharged tRNAs sensed by the amino acid response (AAR), we next examined whether NCP26 activates the AAR pathway in MM cells. As expected, NCP26 increased both p-GCN2 and p-eIF2α, associated with upregulation of ATF4 and CHOP expression. Moreover, NCP26 treatment induced G0/G1 cell cycle arrest followed by apoptotic cell death, evidenced by cleavage of caspases and PARP. We also evaluated in vivo efficacy of NCP26 in the AMO1 xenograft mouse model: NCP26 (10 mg/kg, q.d.) significantly inhibited tumor growth (P = 0.005) and prolonged host survival (P < 0.001) compared to control, without affecting body weight. To further characterize the biological impact of NCP26 in MM cells, we performed single-cell RNA-seq using BM samples from MM patients. While both HF and NCP26 treatment reduced MM, NCP26 triggered more sustained and robust activation of integrated stress response, evidenced by induction of GCN2, CHOP, and IRE1, compared to HF. Gene set enrichment analysis also revealed significant alteration in chromatin processes, besides proteostasis, such as translation, signal peptide, and stress response, after NCP26 treatment.

Since previous studies suggested that translation of genes bearing high Pro-Pro (PP) motifs is more susceptible to EPRS inhibition than non-PP-bearing genes, we next performed a quantitative proteomic analysis in AMO1 cells treated with NCP26: of 7,366 proteins, 84 were upregulated and 363 were downregulated after 6-hour treatment. We also performed in silico bioinformatic analysis to uncover PP-bearing genes, and incorporated CRISPR-screening data to identify genetic dependencies in MM. By overlapping the three datasets, we identified a group of 55 PP motif-containing proteins which play essential roles in MM cell pathogenesis, including MYC, PIM2, and CCND1/2. We also confirmed that PP motif-containing proteins were significantly downregulated by NCP26 treatment in MM cells both in vitro and in vivo.

In conclusion, our results identify EPRS as a biomarker of poor prognosis and a novel therapeutic target in MM. NCP26, a novel ATP-competitive and Pro non-competitive EPRS inhibitor, induces MM cytotoxicity both in vitro and in vivo by triggering AAR and EPRS-Pro-rich proteins pathways. Our data provide the preclinical rationale for development of NCP26-based clinical candidates to improve patient outcomes in MM.