Abstract LB250: Dynamics of transcript alternations and differential splicing in the evolution of acquired MAPKi resistance in melanoma
Authors: Mukherjee Sumit , Singh Arashdeep , Joo Hyunjeong , Patiyal Sumeet , Kim Hyungsoo , Pal Lipika R. , Wang Kun , Day Chi-Ping , Ronai Ze’ev A. , Ruppin Eytan , Hannenhalli Sridhar 
Published: April 2024

The primary therapy for melanoma with a BRAF mutation involves Mitogen-Activated Protein Kinase inhibitors (MAPKi), targeting the dysregulated MAPK signaling pathway. Despite the initial response, many patients often develop acquired resistance. Resistance to MAPKi could be linked to various altered signaling pathways, including reactivation of the MAPK pathway, activation of alternative survival pathways like PI3K/PTEN/AKT, engagement of receptor tyrosine kinases (RTKs) such as PDGFRβ and EGFR, and developmental pathways. While numerous omics studies have aimed to understand the mechanism of acquired resistance, how these pathways are altered remains elusive. To gain further insights into the acquired MAPKi resistance in melanoma, we explored the role of RNA splicing events in this context by analyzing publicly available datasets of pre- and post-MAPKi treated melanoma from patients and in vitro studies using cell lines. We investigated the differential transcript usage (DTU) to detect the specific splice variants that are altered during the development of resistance. We find that the genes involving DTU are enriched in various pathways related to MAPKi resistance, such as the MAPKi signaling pathway, PI3K/AKT pathway, signaling by RTKs, etc. Furthermore, the DTU-centered analysis provides better insights into MAPKi resistance mechanisms compared to standard differential gene expression analysis. Next, we analyzed the developmental splicing signatures during MAPKi resistance development, revealing developmental reprogramming as a key factor in MAPKi resistance. Further, we identified the top 10 transcription factors as potential upstream regulators of the perturbed transcripts, among which five have been previously reported to be involved in various stages of embryonic development. This finding suggests a link between the reactivation of developmental pathways and MAPKi resistance development. Further, by analyzing MAPKi-treated melanoma cell-line models at different time points, such as no-treatment, on-treatment, and at the resistant stage, we observed significant alterations in transcript isoforms during the development of resistance. These changes involve lipid metabolic reprogramming and PI3K/Akt/mTOR signaling, providing further insights into the mechanisms of MAPKi resistance. Our study also uncovers a global shift in transcript profiles towards shorter 3’ and 5’ UTRs in response to MAPKi treatment, suggesting the existence of a master regulatory mechanism influencing global splicing changes during therapy resistance. In summary, our study deciphered the post-transcriptional mechanism coordinating the signaling changes, underscoring the complexity of MAPKi resistance in melanoma, as revealed by the joint analysis of both transcript alterations and splicing events.

Citation Format: Sumit Mukherjee, Arashdeep Singh, Hyunjeong Joo, Sumeet Patiyal, Hyungsoo Kim, Lipika R. Pal, Kun Wang, Chi-Ping Day, Ze’ev A. Ronai, Eytan Ruppin, Sridhar Hannenhalli. Dynamics of transcript alternations and differential splicing in the evolution of acquired MAPKi resistance in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB250.