Preliminary attempt to inhibit proliferation of NUT carcinoma cell lines using antisense oligonucleotides targeting NUTM1

NUT carcinoma is an aggressive cancer driven by NUTM1 fusion proteins. This study evaluated antisense oligonucleotides (ASOs) targeting NUTM1 as a potential therapeutic approach. Three ASOs targeting NUTM1 and scrambled controls were tested at 10-50 nM doses in three NUT carcinoma cell lines (TC-797, 10-15, 14169) and one control line (293T). ASOs were delivered both gymnotically and using a transfection reagent. Cell viability was assessed at 48 and 72 hours using a luminescence-based assay. No ASOs showed selective inhibition of NUT carcinoma cell viability compared to controls across all conditions tested. Thus, this pilot study did not identify ASOs with activity against NUT carcinoma cells. However, it did establish preliminary protocols and generated data to inform future ASO optimization efforts targeting NUTM1 in NUT carcinoma. Further refinement of ASO design and delivery methods is needed to identify therapeutic candidates. Graphical Abstract Hypothesis This experiment was performed as a pilot experiment to generate data to inform future work, which should include formal hypothesis testing with a reduced number of conditions. The hypothesis of this pilot experiment was that one or more of the non-scrambled antisense oligonucleotides (ASOs) targeting NUTM1 will selectively decrease proliferation and/or viability of NUT carcinoma cells, indicated by a reduction in luminescence (as compared to treated non-NUT carcinoma and untreated NUT carcinoma control cells) using the CellTiter-Glo Luminescent Cell Viability Assay.