The Epigenetic Silencing of ALKBH3 and the Epitranscriptomic Regulation of DNA Repair

Abstract

The DNA damage response is crucial to maintaining the integrity of DNA and the health of a cell. Unrepaired lesions within the DNA can lead to genomic instability and potentially aid in the formation of diseases such as cancer. Some cancers possess dysfunctional DNA repair and chemotherapeutic treatments may aim to exploit this weakness that distinguishes cancer cells from normal healthy cells. ALKBH3 is a DNA repair protein involved in the repair of alkylation damage. Within The Cancer Genome Atlas we found that ALKBH3 contained a hyper-methylated promoter in 20% of breast cancers. This hyper-methylation, a form of epigenetic regulation, lead to a dramatic reduction of ALKBH3 mRNA expression and therefore a decrease in total ALKBH3 protein levels. We looked within a sample of Icelandic breast tumors and found they too possessed hyper-methylated promoters for ALKBH3. Importantly, this methylation occurs only within the tumor tissue, but not the normal tissue of the same patients. Additionally, patients who contained high levels of promoter methylation had statistically significant decreased survival. The project then explored the functional consequences of the absence of ALKBH3. We discovered that the knockdown of ALKBH3 causes a decrease in protein levels of a protein crucial in DNA double-strand break repair. We determined that this protein is regulated by ALKBH3 through a form of regulation called epitranscriptomics. Epitranscriptomics is a new field of study of how RNA fate is determined, largely through the addition and removal of methyl groups on RNA nucleotides. This project helps elucidate a potential contributing factor to cancer development as well as provide a potential target for chemotherapeutic treatment.