According to the current paradigm, cancer originates in dysfunction at the DNA level. As such, studies into the epigenetic regulation of cancer have historically focused on the effects of DNA methylation, histone modifications, and chromatin remodeling (the last two being outcomes of DNA mutation). However, given that mutational signatures at the DNA level are insufficient to classify many subtypes of cancer, researchers have also begun exploring the role that RNA epigenetics may play in cancer progression. One potential RNA epigenetic mechanism of interest is RNA editing, or the site-specific modification of transcribed RNA by deaminases. RNA editing is known to affect splicing, amino acid coding, and microRNAs (miRNAs) and their targets. Very recently, evidence has emerged to support a direct causative role for adenosine to inosine (A-to- I) RNA editing in cancer (Chen et al., 2013). Here, I seek to determine if cytosine to uracil (C-to-U) editing, mediated by Apobec-1, can play causative roles in cancer progression. Genetic experiments had previously suggested an involvement of Apobec-1 in disease progression in the Apcmin/+ mouse model of intestinal cancer. I am therefore proposing studies to understand the mechanistic role of Apobec-1 mediated RNA editing in the context of cancer progression, in this tumor model. My preliminary data in primary mammalian cells suggest that C-to-U editing can affect translation levels of edited transcripts by modifying miRNA target sites. I hypothesize that Apobec-1-mediated RNA editing promotes a more aggressive phenotype in tumor cells by altering miRNA targeting to affect gene expression. This work will be accomplished by exploiting next generation sequencing, bioinformatics, and molecular biology techniques. Using small intestinal tissue from Apcmin/+ mice, I will: (a) catalog C-to-U edit sites throughout the transcriptome; (b) identify potential miRNA target sites affected by Apobec-1 editing, focusing on those occurring in potentially cancer-related genes; and (c) perform functional assays to evaluate the significance of the identified targets. These experiments aim to establish a direct mechanistic link between Apobec-1-mediated RNA editing and cancer. In addition, they will also provide evidence for a novel mechanism of cancer progression that could extend to all cancers, and will yield both novel diagnostic tools and chemotherapeutic targets.
Cancers can be grouped in different categories, based on overt characteristics such as DNA mutations or translocations, and finer characteristics such as DNA methylation status, or the status of the chromatin within tumor cells. The latter are termed 'epigenetic changes' because they do not change the sequence of DNA per se though they can have major impact on the life of the cancer cell, and thus in disease progression and outcome. Here I propose that RNA editing, or the site-specific alteration in the sequence of RNA, may be a new type of epigenetic alteration that is involved in driving cancer progression, and could serve as the basis for a new method to categorize tumors, thus better refining treatment options.