Transcriptional changes by PARP7 inhibitor in cancer cell lines

PARP7 is a monoPARP that catalyzes the transfer of single units of ADP-ribose onto substrates to change their function. PARP7 expression is increased by aromatic hydrocarbons and cellular stress, and the PARP7 gene is amplified in cancers, especially in those of the upper aerodigestive tract. PARP7 is a negative regulator of nucleic acid sensing in tumor cells. Inhibition of PARP7 restores Type I IFN signaling responses to nucleic acids in tumor models. Restored signaling can directly inhibit cell proliferation and activate the immune system, both of which contribute to tumor regression. RBN-2397 is a potent and selective inhibitor of PARP7. To further investigate the mechanism of action of RBN-2397 and identify potential biomarkers we investigated transcriptional changes after RBN-2397 treatment in two PARP7 inhibitor sensitive cell lines, NCI-H1373 and NCI-H647, by RNA sequencing. NCI-H1373 and NCI-H647 were treated with 2 different PARP7 inhibitors (RBN-2397 and RBN012337) at 3 concentrations around the IC25, IC50 and IC90 (RBN-2397: 10, 30, 300 nM and RBN012337 3, 10, 100 nM) for 6 or 24 hours. RNA was isolated from triplicate experiments using the MagMAX™-96 for Microarrays Total RNA Isolation Kit (Thermo Fisher Scientific, #AM1839) per manufacturer’s instructions. RNA concentration was determined using a NanoDrop 8000 (ThermoFisher Scientific, Waltham, MA). Paired-end sample libraries consisting of 60 bp with 6 nucleotide indices were prepared for measuring high-throughput 3’ digital gene expression based on a previously published protocol (Massachusetts Institute of Technology, Cambridge, MA) (Soumillon, 2014). Vehicle (DMSO) treated cells were used as control.