Development and validation of an AI/ML platform for the discovery of splice-switching oligonucleotide targets

This study demonstrates the value that artificial intelligence/machine learning (AI/ML) provides for the identification of novel and verifiable splice-switching oligonucleotide (SSO) targets in-silico. SSOs are antisense compounds that act directly on pre-mRNA to modulate alternative splicing (AS). To leverage the potential of AS research for therapeutic development, we created SpliceLearn, an AI/ML algorithm for the identification of modulatory SSO binding sites on pre-mRNA. SpliceLearn also predicts the identity of specific splicing factors whose binding to pre-mRNA is blocked by SSOs, adding considerable transparency to AI/ML-driven drug discovery and informing biological insights useful in further validation steps. Here we predicted NEDD4L exon 13 (NEDD4Le13) as a novel target in triple negative breast cancer (TNBC) and computationally designed an SSO to modulate NEDD4Le13. Targeting NEDD4Le13 with this SSO decreased the proliferative and migratory behavior of TNBC cells via downregulation of the TGF{beta} pathway. Overall, this study illustrates the ability of AI/ML to extract actionable insights from RNA-seq data. SpliceLearn is part of the SpliceCore(R) platform, an AI/ML predictive ensemble for AS-based drug target discovery.