Abstract LB-310: hnRNPM drives cell-state specific alternative splicing during EMT through combinatorial regulation with other RNA binding proteins

Abstract

Abstract The epithelial-mesenchymal transition (EMT) is a fundamental developmental program that is abnormally activated in cancer cells, resulting in therapeutic resistance and metastasis. Dramatic changes in alternative splicing occur during EMT, however the master regulators of this critical regulatory layer are poorly understood. We previously identified the ubiquitously expressed RNA binding protein hnRNPM as a causal driver of EMT and breast cancer metastasis whereby hnRNPM drives alternative exon skipping of the cancer stem cell marker CD44 in a mesenchymal-cell-state restricted manner. However, the scope of hnRNPM-mediated regulation of the EMT post-transcriptional landscape and the mechanisms by which hnRNPM functions in a cell-state specific fashion remain uncertain. By integrating breast epithelial and mesenchymal hnRNPM-depletion RNA-sequencing datasets coupled with individual nucleotide crosslinking and immunoprecipitation of hnRNPM, we identified cell-state specific hnRNPM target RNAs undergoing alternative splicing. hnRNPM cell-state specific targets enrich for distinct gene ontology terms where epithelial targets are enriched in genes critical for the cell cycle while mesenchymal targets cluster in pathways associated with cell migration and EMT. Strikingly, we found hnRNPM regulates splicing to oppose EMT in the epithelial state but then promotes EMT in the mesenchymal state. This unexpected regulatory switch where hnRNPM maintains the cell-cycle in epithelial cells while driving cell migration and metastasis in mesenchymal cells suggests a dual role for hnRNPM in sustaining epithelial and mesenchymal-type breast cancers. Motif analysis and regulon overlap of cell-state specific hnRNPM targets identify ESRP1 and other RNA binding proteins as putative mediators of hnRNPM cell-state specific activity during EMT. Together, this study extends our functional understanding of how hnRNPM regulates the EMT post-transcriptional program and functions in different subtypes of breast cancer. Citation Format: Samuel E. Harvey, Chonghui Cheng. hnRNPM drives cell-state specific alternative splicing during EMT through combinatorial regulation with other RNA binding proteins [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr LB-310.