Exploring the pattern of DNA double strand breaks in glioma cancer stem cells before and after radiation

Derby, Sarah Jane (2025) Exploring the pattern of DNA double strand breaks in glioma cancer stem cells before and after radiation. PhD thesis, University of Glasgow.

Abstract

Introduction: Glioblastoma (GBM) is an incurable brain malignancy with a median survival of 15 months. Glioma stem cells (GSCs) are a radioresistant cell subpopulation promoting recurrence with aberrant DNA damage response (DDR). Radiotherapy prolongs survival and induces DNA double strand breaks (DSBs),however the genome-wide distribution of endogenous and ionising radiation (IR) induced DSBs remain unexplored.

Aims: This will be the first study to define the DSB distribution (‘breakome’) of GSCs and their differentiated progeny before and after radiation.

Methods: Breaks ligation in-situ sequencing (BLISS) was performed in GSCs and matched differentiated progeny before and after IR exposure and correlated with RNA-seq, ATAC-seq data and public neural cell and cancer cell BLISS datasets. High DSB density locations, long genes, transcription start and termination sites (TSS & TTS) as well as euchromatin-rich regions were mapped for DSBs. Data were validated using an alternative DSB mapping technique (INDUCE-seq).

Results: Few differences in DSB distribution between GSC and differentiated progeny were observed, however DSB frequency was higher in GSCs. MALAT1 gene had the highest DSB density across all GBM lines. Long genes showed higher absolute DSBs but not higher DSB density. GSCs showed a significantly higher accumulation of DSBs at TTS compared to neural cell lines. Highly transcribed genes showed an increase in DSB density. Both BLISS and INDUCE-seq data displayed higher DSB frequency following IR in differentiated GBM R10 cells but lower DSB frequency following IR in R10 GSCs.

Conclusions: DSBs in GSCs and differentiated progeny are not random but show distinct endogenous break patterns. Additionally, DSB frequency following IR is increased in radiosensitive R10 differentiated cells but decreased in radioresistant R10 GSCs relative to unirradiated GSCs. This is likely due to changes in cellular activities including global transcriptional downregulation and improved DDR in GSCs resulting in radioresistance.

• Item Type: Thesis (PhD)
• Qualification Level: Doctoral
• Subjects: Q Science > QH Natural history > QH345 Biochemistry; Q Science > QH Natural history > QH426 Genetics
• Colleges/Schools: College of Medical Veterinary and Life Sciences > School of Cancer Sciences
• Funder's Name: Cancer Research UK (CRUK)
• Supervisor's Name: Chalmers, Professor Anthony, Carruthers, Dr. Ross and Semple, Professor Colin
• Date of Award: 2025
• Depositing User: Theses Team
• Unique ID: glathesis:2025-85342
• Copyright: Copyright of this thesis is held by the author.
• Date Deposited: 15 Jul 2025 08:56
• Last Modified: 15 Jul 2025 08:56
• URI: https://theses.gla.ac.uk/id/eprint/85342