Nanopore sequencing reveals U2AF1 S34F-associated full-length isoforms

U2AF1 S34F is one of the most recurrent splicing factor mutations in lung adenocarcinoma (ADC) and has been shown to cause transcriptome-wide pre-mRNA splicing alterations. While U2AF1 S34F-associated splicing alterations have been described, the function of altered mRNA isoform changes remains largely unexplored. To better understand the impact U2AF1 S34F has on isoform fate and function, we conducted high-throughput long-read cDNA sequencing from isogenic human bronchial epithelial cells with and without U2AF1 S34F mutation. We found that nearly 75% (49,366) of our long-read constructed multiexon isoforms do not overlap GENCODE or short-read assembled isoforms. We found 198 transcript isoforms with significant expression and usage changes caused by U2AF1 S34F mutation, including a novel lncRNA. Isoforms from immune-related genes were largely downregulated in mutant cells, none of which were found to have splicing changes. Finally, isoforms likely targeted by nonsense-mediated decay were preferentially downregulated in U2AF1 S34F cells, suggesting that the impact of observed isoform changes may alter the translational output of affected genes. Altogether, long-read sequencing provided additional insights into transcriptome alterations and downstream functional consequences associated with U2AF1 S34F mutation.