Chromatin structuring factor HMGA2 controls subtelomere stability and cancer chemosensitivity

• Main Author: Syed Moiz Ahmed
• Other Authors: Peter Droge
• Format: Thesis-Doctor of Philosophy
• Language: English
• Published: Nanyang Technological University 2020
• Subjects: Science::Biological sciences::Molecular biology
• Online Access: https://hdl.handle.net/10356/137770
• Institution: Nanyang Technological University

The maintenance of eukaryotic genomes in a complete and undamaged state is critical for any tightly regulated DNA process such as replication and transcription to function efficiently. With DNA damage response and repair systems predominantly slow, cells must be equipped with factors that work at the root of the problem, tackling genome-wide challenges that are thrown at them, for example, during chemotherapy. The oncofetal architectural factor HMGA2, by utilizing its three DNA binding domains has been shown to bind stalled replication forks and prevent their collapse into genotoxic DNA strand breaks in fast replicating cancer cells, hESCs as well as in other heterologous yeast and bacterial cell systems. However, the exact mechanism behind its fork protection function remained elusive. A recent report found HMGA2 to bind supercoiled DNA, one of the many transient structures generated at stalled replication forks, with high affinity. In addition, studies in yeast found HMGA2 to prevent the formation of a potentially topologically driven, pathological fork structure, thereby preventing fork collapse and hinting at a possible mechanism of fork protection. To dwell deeper into HMGA2’s proposed chaperone function, I utilized four different cancer cell line model systems and induced replication/topological stress by targeting DNA polymerase or topoisomerases. I identified that the expression levels of HMGA2 are critical in determining sensitivity to SN38, a clinically active TOP1 inhibitor and found that cancer cells that express high levels of HMGA2 are resistant to SN38 whereas, surprisingly, low to moderate HMGA2 expression sensitized the cells to drug induced DNA damage. I show that this differential chemosensitivity to SN38 correlated with HMGA2-mediated TOP1-DNA cleavage complexes (TOP1cc) formation, highlighting HMGA2 can either interfere with drug binding to TOP1 generating low levels of the toxic TOP1cc or increase SN38-TOP1-DNA interactions, leading to higher TOP1cc levels. Further analysis also revealed that specific subtelomeric regions (30-100 kb) are extremely sensitive to the topological stress induced by DNA synthesis or TOP1 inhibitors. Furthermore, I corroborated our ex vivo observations in an in vivo setting, using patient-derived tumor xenografts in mice and found HMGA2 expression to determine the effectiveness of a clinically relevant TOP1 poison. Next, I showed here for the first time that HMGA2 expression confers resistance against both a TOP2 poison (etoposide) and catalytic inhibitor (merbarone), that cause DNA damage by stabilizing the intermediate TOP2-DNA cleavage complexes (TOP2cc) and by inducing topological stress, respectively. I attribute this wide-spread protection across various cell lines tested in this study to the constrainment of sc DNA and/or catalytic activation of TOP2A mediated by HMGA2, which, remarkably, could provide a mechanistic explanation for the recent observation of poor clinical outcomes in bone-marrow derived mononuclear cells of acute myeloid leukemia patients that express HMGA2. Taken together, our study reveals a fascinating aspect of HMGA2 dependent fork protection mechanism that counteracts replication induced DNA topological stress and marks a potential clinical impact that could aid chemotherapy related decision making, in particular for leukemic and colorectal cancer patients.