RNA-seq data for LS180 and NCI-H358 Cancer cell lines

Despite exciting developments in cancer immunotherapy, its broad application is limited by the paucity of targetable antigens on the tumor cell surface. As an intrinsic cellular pathway, nonsense-mediated decay (NMD) conceals neoantigens through the destruction of the RNA products from genes harboring truncating mutations. We developed and conducted a high throughput screen, based on the ratiometric analysis of transcripts, to identify critical mediators of NMD. This screen revealed disruption of kinase SMG1’s phosphorylation of UPF1 as a potent disruptor of NMD. This led us to design a novel SMG1 inhibitor, KVS0001, that elevates the expression of transcripts and proteins resulting from truncating mutations in vivo and in vitro. Most importantly, KVS0001 concomitantly increased the presentation of immune-targetable HLA class I-associated peptides from NMD-downregulated proteins on the surface of cancer cells. KVS0001 provides new opportunities for studying NMD and the diseases in which NMD plays a role, including cancer and inherited diseases.

Methods
Whole transcriptome RNA-seq
LS180 or NCI-H358 cells were run in biological duplicate, treated with DMSO or 5µM LY3023414. For RNA extraction, cells were pelleted, frozen in liquid nitrogen, and stored at -80oC until RNA extraction. RNA extraction was performed using a Qiagen AllPrep DNA/RNA Mini Kit (Qiagen, Maryland, USA, Cat# 80204) per manufacturer’s instruction with cell homogenization and lysis in RLT buffer with a QIAshredder (Qiagen, Maryland, USA, Cat# 79656). RNA quality control using Agilent Tapestation 2200 (Agilent, California, USA, Cat# G2964AA) and the Agilent RNA ScreenTape (Agilent, California, USA, Cat# 5067- 5576) with Agilent RNA ScreenTape Sample Buffer and Ladder (Agilent, California, USA, Cat# 5067- 5577, Cat# 5067- 5578) per manufacturer’s instruction. Library prep using Illumina RNA library prep kit (Illumina, California, USA, Cat #RS-122-2001) and sequenced on an Illumina HiSeq 4000 150 cycle paired-end using manufacturer’s instructions. The data provided here is are the unprocessed fastq files from this run.