Evaluating somatic mosaicism In Parkinson's disease

• Main Author: Heng, Yue Jing
• Other Authors: Foo Jia Nee
• Format: Thesis-Doctor of Philosophy
• Language: English
• Published: Nanyang Technological University 2024
• Subjects: Medicine, Health and Life Sciences
• Online Access: https://hdl.handle.net/10356/174776
• Institution: Nanyang Technological University

This thesis describes efforts made in characterizing cell death mechanisms and somatic mutations at high sensitivity in post-mortem brain tissue obtained from the Multiple Sclerosis and Parkinson’s Tissue Bank at Imperial College London and the South West Dementia Brain Bank (SWDBB) at Bristol Medical School. It demonstrates the potential for utilizing next-generation sequencing (NGS) technologies combined with the latest genomic tools to identify novel somatic mutations as well as to highlight novel genes and mechanisms predisposing to Parkinson’s disease (PD). Such mutations may be incompatible with life (i.e., embryonic lethal) in germline homozygous or heterozygous states, thus limiting their observable effects to the somatic state, and may potentially be highly penetrant. High coverage whole-exome and mitochondrial DNA (mtDNA) sequencing were performed on 116 well-characterized post-mortem human brain tissues from 73 PD cases and 43 age-matched controls, to uncover genes that were recurrently mutated by somatic changes that were enriched in PD cases compared to controls. Using the MosaicForecast bioinformatics pipeline which was designed to identify somatic mutations from NGS data in the absence of paired samples, this study identified 22 genes that were recurrently mutated in >1 brain samples from between 2 to 7 PD cases. Interestingly, some of these genes were implicated in α-synuclein aggregation, one of the widely recognized hallmarks of PD, as well as in neuronal and axonal pathways. However, none of the genes identified were significantly enriched in cases compared to pathologically normal brains (p > 0.05) and none are known PD genes with germline variants previously identified by GWAS or family studies. Similarly, even though the control region of mtDNA was found to be enriched for genetic variants in PD cases compared to controls, none of the mutations identified in this region – which includes known mitochondrial transcription and replication regulatory sites – passed Bonferroni correction for multiple testing. Through neuropathology analysis of 35 tissue samples, we showed that the hypothesized spread of Lewy pathology via neural networks, best represented by PD Braak staging, strongly correlates with neuronal loss. Molecular analysis of cell death pathways confirmed that apoptosis is not the primary mechanism driving neuronal loss in PD. Instead, we uncovered co-expression of specific necroptosis and ferroptosis biomarkers, with ferroptosis being more prominent in late-stage PD than intermediate-stage PD. However, the absence of a single gene harboring somatic or germline mutations in a substantial portion of the PD brains analyzed limited our ability to establish a definitive correlation with any neuropathological observations. Therefore, no significant genotype-phenotype correlations were observed.