Phase One Research Projects

Necessary Funding: $2M in 2019   |  Successfully Funded: $1.5M to-date
See Path to a Cure for a detailed explanation on our phases of research. 

Project: Establishing and characterizing eight mouse model lines enabling researchers and biotechnology companies to trial therapies for FOXG1 Syndrome (FS)


Funded: year one

Dr. Lee will develop and study eight Foxg1 mouse models representing the entire gamut of FOXG1 human mutations, including a humanized mouse model. These mouse lines will be available to any scientist and biotechnology company interested in the basic biology of Foxg1 and the translational efforts to develop the cure for Foxg1 syndrome. For phenotypic analyses, Dr. Lee will characterize each mouse model using molecular, cellular, brain anatomy, and behavioral analyses. He will also test various therapies to reverse symptoms of FOXG1 mutations on these eight mouse models. OHSU has a leading gene therapy group that will partner with Dr. Lee for pre-clinical testing. 

Explanation of the 8 mouse lines:

  1. Humanized Mouse – A human FOXG1 gene is placed within a mouse model. Primate-specific (like human) sequences of FOXG1 protein are substantially different from murine Foxg1 protein (like mice). Thus, developing a humanized mouse model will contribute to FS pathophysiology and serve as a strong animal model in developing FS-treating strategy.

  2. Early Truncation Mutation – Truncation in 1~180 aa, before DNA binding domain

  3. Middle Truncation Mutation – Truncation in 181~308 aa, within or right after DNA binding domain

  4. Late Truncation Mutation – Truncation after 309 aa (potential) dominant negative

  5. Missense Mutation - Missense with complete loss of function

  6. Missense Mutation – Missense with partial loss of function

  7. FOXG1 deletion – Deletion of the entire FOXG1 gene or FOXG1 associated area

  8. FOXG1 duplication – Duplication of the entire FOXG1 gene


Project: Correcting FOXG1 loss-of-function in post-natal animals. Identification of the etiology of FOXG1 syndrome and the targets for drug discovery


Funded: year one

Dr Lee is an active contributor to the FOXG1 community. She proposes to use various FOXG1 mouse models understand the impact of loss of FOXG1 in different types of neurons (excitatory and inhibitory) as well as in oligodendrocyte precursors (another important cell type in the brain). She will then perform detailed characterization to examine the overall structure of the cerebral cortex, neuronal connections, electrophysiological activity, and behavioral outcomes in affected animals.

The investigator will also reintroduce FOXG1 at various time points, to determine whether (and when) symptoms can be reversed. Global gene expression analysis will be undertaken to identify any differences as a result of FOXG1 loss. This investigator has previously identified some functional overlap between FOXG1 and the gene FMR1, which causes Fragile X syndrome when defective. Fragile X syndrome is the most common single gene cause of autism and intellectual/developmental disabilities. Fragile X has a very active community that has pushed some drugs through to clinical trials. 


Read this incredible New York Times article on Dr. Soo-Kyung Lee and Dr. Jae Lee's journey discovering thier daughter had FOXG1 Syndrome after years of studying the FOXG1 gene.  Watch on New York Time Video.


Project: RNA Gene Therapies for FOXG1 missense mutations. Developing an integrated platform for scalable, etiopathogenic-clinical profiling of subtle FOXG1 mutations and experimental, RNA-drive rescue of their histopathogenic effects


Funded year one

Dr Mallamaci has a strong history characterizing the role of FOXG1 in brain development. The investigator aims to develop a streamlined protocol that can be used to consistently characterize the impact of various FOXG1 missense mutations. Given the investigators background, the proposed measures are focused around aspects of brain development that FOXG1 has been shown to be important for, like: self-renewal of early neural cells, differentiation into inhibitory and excitatory neurons, etc.

The investigator will also seek to determine whether bad outcomes of FOXG1 missense variants can be corrected using RNA-based gene therapy (either boosting FOXG1 expression, or silencing it).

Project: RNA gene therapy to correct FOXG1 symptoms in iPS cells. Assessing the therapeutic potential of small activating RNAs in a patient-derived cellular model of FOXG1 syndrome


Funded year one

Dr Clarke has already completed much of the groundwork for this project thanks to funding supplied the UK FOXG1 Foundation. iPS cells have been derived from FOXG1 individuals with a variety of mutation types (deletion, missense, frameshift) and differentiated into neurons. The impact on target gene expression (candidates previously identified) will be investigated, as will the electrical activity of these neurons, compared to ‘normal’.

RNAa will be used to boost expression of FOXG1 to determine whether this can correct any symptoms identified in the patient-derived neurons. The electrical analysis methodology would represent a unique feature of this proposal.

Project: FOXG1 as target for Autism. Gene targets of FOXG1 in human brain progenitors


Funded year one

Dr Vaccarino has previously demonstrated that patient-derived iPS neurons from individuals with autism spectrum disorder and macrocephaly (large head size) have higher levels of FOXG1 gene expression. She also showed that there was an imbalance in the proportion of inhibitory and excitatory neurons. Restoring FOXG1 therapy to normal using RNAi reversed these findings, suggesting that FOXG1 may be important for how autism spectrum disorders develop and progress.

The current proposal would use iPS neurons to model the effect of reduced and elevated expression of FOXG1 on global gene expression and the balance of inhibitory/excitatory neurons. Characterizing these pathways would help us understand the role of FOXG1 on important biological pathways. These target pathways could be candidates for drug therapies.

Project: CRISPR/CAS9 Mediated Gene Editing in FOXG1-mutated patient-derived cells


Funded year one

Prof. Dr. Alessandra Renieri first discovered, in 2008, the association between FOXG1 gene mutations and the severe disease in humans. In the following years she developed expertise in induced Pluripotent Stem Cells (iPSCs) characterization and differentiation in neurons from FOXG1 patients. She follows the majority of FOXG1 patients in Italy and her Medical Genetics Department is a referral center for patients in Europe.

In collaboration with Dr. Silvo Conticello, who is an expert in DNA/RNA editing, she proposes to use CRiSPR/Cas9 technology to edit FOXG1 mutations. This project will specifically cut the mutated allele and edit it using a donor DNA harbouring the normal sequence. To allow the CRiSPR/Cas9 correction system to enter the cells, a viral system (AAV = Adeno-Associated Virus) will be used as carriers.

Preliminary experiments during the ongoing first funded year demonstrate an efficient correction in patient-derived cells. Funded by Anonymous Donor

Watch this short video on how the process would work