Therapeutic Repurposing of Brincidofovir in Natural Killer/T-Cell Lymphoma Reveals Potent Induction of Replication Stress, Sting Pathway Activation and Immunogenic Cell Death

Abstract

Introduction Natural killer/T-cell lymphoma (NKTCL) is an aggressive subtype of non-Hodgkin lymphoma associated with Epstein-Barr virus (EBV) infection. Brincidofovir (BCV), a lipid conjugated form of cidofovir, is a biologically active acyclic nucleoside phosphonate known for both antiviral and antiproliferative properties. Methods We investigated BCV in a panel of NKTCL cell lines (n=11) and mouse xenograft models. The mechanism of action was examined using bulk and single cell RNA sequencing (10X Chromium 3' Gene Expression Profiling), and validated in orthogonal assays. Results BCV evoked a dose- and time-dependent inhibition of cell viability in all NKTCL cell lines, independent of EBV presence. Exquisite sensitivity was observed in 4 cell lines KAI-3, NK-S1, NK-92 and KHYG-1 (IC50 range, 36.0 to 303.6 ng/ml), accompanied by increase in sub-G1 fraction and S-phase arrest on cell cycle analyses. Bulk RNA sequencing of BCV-treated cell lines (KAI-3 and NK-S1) revealed pervasive downregulation of MYC target pathways, along with upregulation of immune-related and DNA repair pathways. Single cell RNA sequencing revealed distinct temporal cell states evoked by BCV. In KAI-3 cells, a significant shift in transcriptomic cell states occurred upon BCV treatment for 48h, with appearance of cell clusters enriched for type I interferon and cytokine signaling pathways, as well as activation of p53 and apoptosis pathways. Cell cycle and DNA repair pathways were also evident. At 72h post-BCV treatment, type II interferon signaling and endoplasmic reticulum stress response pathways were prominent. Similarly in NK-S1 cells, cell clusters enriched for immune signals, including interleukin-18 and cytokine pathways emerged, as did cell cycle, DNA repair, and apoptosis pathways. Western blot demonstrated increase in replication stress markers (p-CHK1 S317 and S345, RRM2, p-RPA2 S33), p-H2AX (DNA double strand break) and p-TBK1 (STING pathway activation). In keeping with this result, BCV triggered micronuclei formation, DNA fragmentation, and cytoplasmic DNA release. Gene expression levels of type I (IFNA, IFNB1) and II (IFNY) interferons and cytokines (CCL5, CXCL10) were upregulated following BCV treatment, as did the proportion of calreticulin-expressing cells and amount of extracellular HMGB1 released, indicative of immunogenic cell death. Notably, nuclear and membranous protein expression of the immune checkpoint protein PD-L1 also markedly increased. Intraperitoneal administration of BCV (40 mg/kg, twice per week) inhibited tumor volume in NOD/SCID mouse xenografts of NKTCL, compared with vehicle alone (p=0.0005, two-tailed t-test). On immunohistochemistry, PD-L1 was significantly overexpressed in BCV-treated tumor xenografts compared with control, with a 1.9-fold higher median H-score (p=0.0007, Mann-Whitney test). Conclusions Taken together, these results demonstrate a novel repurposed role of BCV in the treatment of NKTCL. The activation of DNA damage-induced STING pathway and immune-related signals suggests a further potential for combination with checkpoint immunotherapy.