Determining the Roles that DICER1 and Noncoding RNAs Play in Endometrial Tumorigenesis

Cancer is both a genetic and epigenetic disease. Changes in DNA methylation, histone modifications, and microRNA processing promote tumorigenesis, just as mutations in coding sequences of specific genes contribute to cancer development. In my thesis work I sought to determine the role that noncoding RNAs play in endometrial tumorigenesis. Aberrant methylation of the promoter region of the MLH1 DNA mismatch repair gene in endometrial cancer is associated with loss of MLH1 expression and a mutator phenotype in endometrial and other cancers. The molecular and cellular processes leading to aberrant methylation of the MLH1 promoter region are largely unknown. I tested the hypothesis that the EPM2AIP1 antisense transcript at the MLH1 locus could be involved in MLH1 transcriptional silencing. I characterized the MLH1/EPM2AIP1 bidirectional promoter region in endometrial cancer and normal cell lines and found an abundance of forward and reverse transcripts initiating from a large region of nucleosome-free DNA in expressing cells. The DICER1 protein, which is necessary for processing small RNAs involved in post-transcriptional silencing, is downregulated in many cancers, including endometrial cancer. I used genomic methods: RNA-Seq and MeDIP/MRE) to characterize the transcriptome and methylome of endometrial cancer cells depleted of DICER1. Using a combination of computational and wet lab methods I showed that reduced DICER1 triggers an interferon response in cancer cells because of accumulation of pre-microRNAs that activate immune sensors of viral dsRNA. The methylome of DICER1 knockdown cells revealed subtle changes in methylation, including decreased methylation at the Alu family of repetitive elements. Small RNAs processed by DICER1 may thus be involved in silencing repetitive regions. Non-coding RNA has effects on endometrial cancer cells that may contribute to tumorigenesis, such as influencing the active state of the MLH1 gene and modulating the immune response