• Activity and Regulation of L1 Retrotransposons in Human Genomes

      Scott, Emma Cecelia; Devine, Scott E.; 0000-0001-7854-9982 (2017)
      This dissertation investigates the activity and regulation of endogenous long interspersed element-1 (also known as LINE-1 or L1) mobile elements in normal and cancerous human genomes. L1s are autonomous retrotransposons that constitute ~17% of the human genome; the majority of these elements are no longer active due to truncations or mutations, but a small number of full-length L1 source elements remain capable of mobilizing themselves (via a "copy and paste" mechanism) and pose a huge mutagenic threat to the human genome. Traditionally, transposons were thought to be silenced outside of the germline, but recently frequent somatic activity of L1 in epithelial cancer genomes has been discovered and characterized. Somatic L1 insertions have been identified in many different types of human cancer. This dissertation addresses major unanswered questions in the field. The hypothesis of this study is that tumorigenesis can be initiated by the derepression of endogenous L1 retrotransposons in normal, noncancerous somatic cells. The chapters of this dissertation support this hypothesis by establishing that activity of a hot population-specific full-length L1 source element is capable of causing cancer and beginning to assess the expression of full-length L1 source elements in normal noncancerous tissues. Overall, this dissertation provides important contributions to the field and poses many new questions for further study.
    • Mobile Element Discovery and Activity in Human Populations and Diseases

      Gardner, Eugene James; Devine, Scott E. (2017)
      Approximately 45% of the human genome is occupied by Mobile genetic Elements (MEs). Small subsets of these are still active and belong to three different families: L1, Alu, and SVA. These active families can generate new copies known as Mobile Element Insertions (MEIs), which can be polymorphic in humans. There remain several open- ended questions as to which MEs are generating the vast majority of new MEIs, and if they are in fact active prior to, and can initiate, tumorigenesis. To investigate active MEs in these two scenarios, I designed a computational algorithm to find polymorphic MEIs in human whole genome sequencing (WGS) data: the Mobile Element Locator Tool (MELT). As part of the 1000 Genomes Project (1KGP), I used MELT to discover over 22,500 polymorphic MEIs. Using this data in combination with Neanderthal, Denisovan, and Chimp WGS, I investigated the population dynamics of ME activity in the great ape lineage. To evaluate the possibility of L1 playing a dynamic role in cancer tumorigenesis, we screened ten colorectal cancer cases for somatic L1 activity. In one of these cases, we discovered a somatic L1 insertion into the tumor suppressor gene APC, causing this particular cancer case. Follow-up studies revealed that a population-specific L1 element was responsible for the generation of this insertion, and was active in the normal soma. Overall, through the development of new computational and sequencing tools, my work demonstrates that distinct families of MEs are generating the majority of new MEIs in human genomes, that a subset of these elements are stratified by population, and that somatically active L1s can initiate cancer.