LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells

Abstract

LIN28 is an evolutionarily conserved RNA-binding protein with critical functions in developmental timing and cancer. However molecular mechanisms underlying LIN28's oncogenic properties are yet to be described. RIP-Seq analysis revealed significant LIN28 binding within 843 mRNAs in breast cancer cells. Many of the LIN28 bound mRNAs are implicated in the regulation of RNA and cell metabolism. We identify heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), a protein with multiple roles in mRNA metabolism, as a LIN28 interacting partner. Subsequently, we use a custom computational method to identify differentially spliced gene isoforms in LIN28 and hnRNP A1 siRNA-treated cells. Results reveal these proteins regulate alternative splicing and steady state mRNA expression of genes implicated in aspects of breast cancer biology. Notably, cells lacking LIN28 undergo significant isoform switching of the ENAH gene, resulting in a decrease in the expression of ENAH exon 11a isoform. Expression of ENAH isoform 11a has been shown to be elevated in breast cancers that express HER2. Intriguingly, analysis of publicly available TCGA array data reveals LIN28 expression is significantly different in HER2 compared to other breast cancer subtypes. Collectively, our data suggests that LIN28 may regulate splicing and gene expression programs that drive breast cancer subtype phenotypes.