Neurogenetic insights into fragile X syndrome: The dynamic FMRP-RNA interactome and genetic modifiers of seizures Restricted; Files Only
Lee, Azalea (Spring 2025)
Abstract
Fragile X syndrome (FXS) is a genetic disorder characterized by a range of developmental, cognitive, and physical symptoms. FXS is the clinical manifestation of the functional loss of fragile X messenger ribonucleoprotein (FMRP) following silencing of the FMR1 gene due to a CGG trinucleotide repeat expansion. FMRP is an RNA-binding protein highly expressed in the brain and plays a critical role in neurodevelopment. Understanding the RNA binding targets of FMRP is crucial for elucidating the molecular pathophysiology of FXS and fragile X-associated disorders as well as developing targeted and effective therapeutic interventions. We used enhanced crosslinking immunoprecipitation followed by high-throughput sequencing (eCLIP-seq) to profile the FMRP-RNA interactome across different regions, ages, and sexes in the human brain. The findings revealed that the FMRP-RNA interactome is highly dynamic, with distinct biological processes and disease associations enriched for targets in each brain region, age group, and sex. We also performed QTL analysis and identified genetic variants that may modulate FMRP binding, underscoring the intricate interplay between genotype and FMRP-RNA interactions. Recognizing that seizures are a common comorbidity in FXS, in a separate study, we used an integrated approach combining whole genome sequencing and functional testing in Drosophila and human iPSC-derived neuronal models to identify genetic modifiers of seizures in FXS. PDE10A, PXDN, TTLL4, EIF4B, and MORF4L1 were identified as novel potential modifiers of seizures in FXS. Overall, the work presented here not only enhances the understanding of the FMRP-RNA interactome in the human brain but also provides new insights into the mechanisms underlying clinical features of FXS and establishes a foundation for developing targeted therapies.
Table of Contents
Abstract················································································································· ii
Acknowledgements··································································································· iv
List of Figures········································································································ viii
List of Tables·········································································································· xii
Chapter 1: Introduction to fragile X syndrome (FXS)························································ 1
1.1. Introduction to fragile X syndrome and pluripotent stem cell models································ 1
1.2. Two-dimensional (2D) Human iPSC-based Cellular Models of FXS································· 5
1.3. Three-dimensional (3D) hiPSC-derived models of FXS·············································· 21
Chapter 2: Investigating the spatiotemporal and sex differences of the FMRP-RNA interactome using postmortem human brain tissues·························································································································· 31
2.1 Abstract······································································································· 31
2.2 Introduction··································································································· 31
2.3 Results········································································································· 33
2.4 Discussion···································································································· 52
2.5 Figures········································································································ 58
2.6 Tables········································································································ 115
2.7 Methods····································································································· 120
2.8 Acknowledgements························································································ 123
2.9 Supplementary Methods·················································································· 124
Chapter 3: Identifying genetic modifiers of seizures in FXS using whole-genome sequencing and functional testing 141
3.1 Abstract······································································································ 141
3.2 Introduction································································································· 142
3.3 Results······································································································· 143
3.4 Discussion··································································································· 149
3.5 Figures······································································································· 153
3.6 Tables········································································································ 165
3.7 Methods····································································································· 175
3.8 Acknowledgements························································································ 182
Chapter 4: General discussion and future directions······················································· 184
4.1 Introduction································································································· 184
4.2 Consolidative discussion·················································································· 187
4.3 Future directions··························································································· 189
Chapter 5: Bibliography························································································· 192
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