Elucidating the Genetic Landscape of the Frontotemporal Dementias using Next-Generation Sequencing and In-Silico Analyses

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URI: http://hdl.handle.net/10900/125414
Dokumentart: Dissertation
Date: 2022-03-17
Language: English
Faculty: 4 Medizinische Fakultät
Department: Medizin
Advisor: Heutink, Peter (Prof. Dr.)
Day of Oral Examination: 2021-12-17
DDC Classifikation: 500 - Natural sciences and mathematics
License: Publishing license including print on demand
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Frontotemporal Dementia and Amyotrophic Lateral Sclerosis comprise a spectrum of heterogenous disorders that lie on the "FTD/ALS" spectrum, characterized by similar pathology and genetics but highly variable clinical symptoms that can im- pact behaviour, cognition or/and motor skills. These diseases have a late age at onset, rapid progression and debilitating symptoms that have devastated tens of thousands of families over the last few decades. To-date, treatment includes only symptom management. Rapid advances in genomic technologies over the last decade have enabled scientists to investigate the complexities that underlie disease progression and identify some at-risk populations, but much of the genetic variability is still undiscovered. In this dissertation, we apply an in-depth and systematic approach to study the genetic landscape of FTD/ALS in protein coding genes as well as in non-coding genetic el- ements called long non-coding RNAs (lncRNAs). In chapters 2 and 3, we apply a step-wise genetic screen of FTD/ALS patients to study the frequencies of both pathogenic and potentially pathogenic mutations in known neurodegenerative disease (NDD) genes. We discover an overlap of path- ways previously thought to be associated with other NDDs such as Alzheimer’s Dis- ease and type B Kufs disease. As a result of our findings, we propose the inclusion of two genes, CTSF and SERPINA1, in future genetic screens for FTD/ALS. Through rare-variant association tests, we also find an excessive burden of rare, damaging variants in human autophagy associated genes in FTD/ALS cases versus controls. In chapters 4 and 5, we perform a two-phase study to investigate the role of lncR- NAs in NDDs and healthy ageing. In phase 1, we perform antisense oligonucleotide based knockdowns in highly expressed lncRNAs in the brain. Additionally, we test these lncRNAs for evidence of cis-regulation of proximal genes. In phase 2, we de- sign a genomewide CRISPRi experiment, including a novel sgRNA library targeting ∼4000 lncRNAs and 360 negative controls. This, to the best of our knowledge, is the first sgRNA library targeting a genomewide set of lncRNAs expressed in neu- ronal cell lines. Finally, we perform a series of in-silico analyses using both in-house and public data to gather functional evidence of lncRNAs inageing, cognitive im- pairment, antisense regulation of NDD genes, eQTL associatedgene regulation as well as those that were differentially expressed in FTD cases versus controls. As a result, we curate a list of 119 lncRNAs with evidence of function in human NDDs and healthy ageing. This is one of the first ever large-scale studies investigating the role of lncRNAs in neurodegeneration.

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