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The role of protein degradation in FBXO11-related intellectual disability

Periodic Reporting for period 1 - Degradation_ID (The role of protein degradation in FBXO11-related intellectual disability)

Reporting period: 2019-07-01 to 2021-06-30

Neurodevelopmental disorders (NDDs) affect 1-3% of the population and therefore represent an important health and socioeconomic problem worldwide. Genetic causes of NDDs are very heterogenous with currently variants in more than 1500 genes identified. Understanding pathomechanisms of NDDs is greatly lacking behind novel disease gene associations, thus hindering development of causative therapies. There, understanding pathomechanisms is crucial for future explorations of therapeutic development. Many disease genes can be clustered in functionally coherent modules. A promising idea is to identify functional and pathomechanistic commonalities in those modules to eventually tackle multiple genes by targeting a single central pathway, process, or molecule. One such emerging module is protein ubiquitination and protein degradation, in which only recently a growing number of genes/proteins was associated with NDDs. FBXO11 encodes an E3-ubiquitin ligase, and variants in this gene have recently been associated with a variable neurodevelopmental disorder. The first objective of this project was to characterize the molecular functions of FBXO11 in the nervous system and to investigate the role of altered degradation pathogenesis of NDDs in human neuronal cells. The second objective was to model Fbxo11 deficiency in the model organism Drosophila melanogaster to identify strategies for chemical intervention to alter phenotypes. In this project, I could show that deficiency of FBXO11 impairs programs for neuronal differentiation and dendrite formation, and that in the model organism Drosophila melanogaster some of the phenotypes resulting from Fbxo11 deficiency can be ameliorated by chemical intervention.
The action “Degradation_ID” was implemented at the initial host institution University Hospital Erlangen, Germany (UKER) for the first 18 months and due to the relocation of the supervisor, continued for the final six months at the second host institution University of Bern, Switzerland (UBERN). The first objective of the action was to study mechanisms of FBXO11 deficiency in a human cell based model. Effects of different FBXO11 variants were studied in more detail and found to affect localization and expression of FBXO11. These results were recently published in the journal Human Molecular Genetics (open access). As a tool, I successfully generated FBXO11 knockout induced pluripotent stem cells (IPSCs) and differentiated them to neural precursor cells (NPCS). Those were then further differentiated into neurons. From these cells, transcriptomic analyses were performed and used to identify deregulated gene groups and pathways. Additionally, transcriptomic analysis was performed on heads of Drosophila melanogaster with an Fbxo11 deficiency as a cross comparison and validation. Interestingly, genes deregulated were enriched for genes involved in neuronal differentiation and differentiation programs seem to be slowed in FBXO11 deficient cells. Using mass-spectrometry approaches, I could identify a key regulator of cell fate decisions and stemness factor as a potential target of FBXO11. This interaction was validated using co-immunoprecipitation experiments. This lead me to the working hypothesis that FBXO11 deficiency leads to a persistent presence of this stemness factor, which in turn lead to impaired or delayed activation of differentiation programs in neural precursor cells. Those results are currently still followed up on and will then be published in a peer-reviewed journal upon completion of experiments.
The second objective of the project was to study Fbxo11 deficiency in the model organism Drosophila melanogaster to identify phenotypes and to test potential chemical interventions to alter phenotypes. Here I could identify a defect in dendritic development using a larval sensory neuron model in Fbxo11 deficient flies. Substance tests could identify two proteasome activating substances that led to an improvement of dendritic phenotypes in Fbxo11 deficient flies. Those convincing data have already led to the expansion of this line of research to more genes associated with NDDs and involved in proteasomal degradation. Results of this study will be published together with the expanded research data in a peer reviewed journal.
The work carried out in this project has already led to a better understanding the consequences of FBXO11 missense variants in neurodevelopmental disorders. Results of this work are freely accessible to public due to open access publication. Furthermore, this work has helped to get a better understanding of FBXO11 deficiency, and altered neural differentiation programs may play an important role in the pathogenesis. Additionally, work in the fruit fly has led to the identification of certain proteasome activating substances that may be relevant for future therapeutic developments. Those results will be available to the public upon publication in the near future. This may be relevant not only for FBXO11-associated NDDs, but also for other proteasomal degradation related neurodevelopmental disorders. Together, this project addressed important questions for developmental disorders, an important health concern, and is shaping avenues of exploration for therapeutic interventions.
Image of Drosophila melanogaster larval multiple dendrite neuron