Reprogramming of nucleotide metabolism by interferon confers dependence on the replication stress response pathway in pancreatic cancer cells

Abstract

Highlights d Interferon signaling biomarkers are enriched in a subset of PDAC tumors d Phosphoproteomics and chemical genomics identify ATR as an interferon-induced codependency in PDAC cells d Blocking ATR in combination with interferon signaling limits nucleotide pools d ATR inhibitors restrict the growth of PDAC tumors in which interferon signaling is driven by STING

Purine nucleoside phosphorylase enables dual metabolic checkpoints that prevent T cell immunodeficiency and TLR7-associated autoimmunity

“…(F) Cell Titer Glo analysis of CEM-YFP and CEM-SAMHD1 cells treated with 5 μM dG with or without 1 μM PNPi and 1 μM dCKi (mean ± SD; n = 4; 1-way ANOVA corrected for multiple comparisons). ****P < 0.0001. lines and was further increased by IFN-β exposure (Supplemental Figure 2F), consistent with SAMHD1 being an IFN-stimulated gene (25). PNPi/dG elicited dCK-dependent proliferation inhibition in SAMHD1-deficient M230 and M418 cells, while having no effects against SAMHD1-proficient M297 cells (Supplemental Figure 2G).…”

“…As SAMHD1 expression was undetectable in a subset of CCLE melanoma cell lines ( Supplemental Figure 2A ), we extended our analysis to a panel of melanoma cell lines derived at UCLA. We identified 2 lines (M230 and M418) in which SAMHD1 expression was undetectable both at baseline ( Supplemental Figure 2E ) and after type I IFN (IFN-β) treatment; in contrast, SAMHD1 was expressed at baseline in M297, M257, and M296 lines and was further increased by IFN-β exposure ( Supplemental Figure 2F ), consistent with SAMHD1 being an IFN-stimulated gene ( 25 ). PNPi/dG elicited dCK-dependent proliferation inhibition in SAMHD1-deficient M230 and M418 cells, while having no effects against SAMHD1-proficient M297 cells ( Supplemental Figure 2G ).…”

“…This factor is present in sera from C57BL/6 mice and CM from murine bone marrow stromal cells and BMDMs but not in sera from humanized mice or CM from human bone marrow stromal cells. We focused on nucleosides as potential resistance factors, as previous work by us and others has shown that stromal cells release these metabolites ( 25 , 28 ). LC-MS/MS-MRM analyses revealed that resistance-conferring MS5 CM contained substantially more nucleosides uridine, cytidine, and deoxycytidine (dC) than the HS5 CM ( Figure 3E and Supplemental Figure 3A ).…”

“…As SAMHD1 expression was undetectable in a subset of CCLE melanoma cell lines (Supplemental Figure 2A), we extended our analysis to a panel of melanoma cell lines derived at UCLA. We identified 2 lines (M230 and M418) in which SAM-HD1 expression was undetectable both at baseline (Supplemental Figure 2E) and after type I IFN (IFN-β) treatment; in contrast, SAMHD1 was expressed at baseline in M297, M257, and M296 these metabolites (25,28). LC-MS/MS-MRM analyses revealed that resistance-conferring MS5 CM contained substantially more nucleosides uridine, cytidine, and deoxycytidine (dC) than the HS5 CM (Figure 3E and Supplemental Figure 3A).…”

Drug-induced adaptation along a resistance continuum in cancer cells

“…As expected, control cells were enriched for functions related to a proliferative and metabolically active phenotype (E2F targets, oxphos, mTOR signaling) when compared with the adapted cells, which, under drug treatment, slow down proliferation. Module A is enriched for interferon response genes, an endogenous signature induced upon replication stress (34) and DNA-damaging agents (35–37). As previously noted at the gene level analysis, cells related to modules A and B retain epithelial features (keratinization), while a spectrum of EMT enrichment from modules B to E was observed.…”