pH-dependent mechanisms of disease caused by TBC1D24 mutations

Awardee: Dennis Brown

Institution: Massachusetts General Hospital

Grant Amount: $60,000.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

There are several lines of evidence, both from genetics and protein-protein interaction studies that there is an important physiological link between Tbc1d24 and a molecular proton pump, called V-ATPase. The major function of the V-ATPase is to pump acid (in the form of protons) into small vesicles inside the cell, such as synaptic vesicles and lysosomes. A low, acidic pH within these vesicles is required for their normal function, in particular neurotransmitter loading of synaptic vesicle in neurons or degradation of various molecules in lysosomes. In addition, proper pH gradients are required for efficient intracellular vesicle trafficking and recycling of proteins, telling them where to go inside a cell, which is extremely important at neuronal synapses. V-ATPase is not a single protein, but a protein complex, consisting of 13 core proteins, or subunits. While severe mutations in V-ATPase subunit genes causing a loss of protein function are incompatible with life, some mutations result in various diseases and syndromes, including epilepsy, hearing loss and DOORS syndrome (deafness, onychodystrophy, osteodystrophy, mental retardation and seizures). These diseases are remarkably similar to those caused by mutations in the TBC1D24 gene. We discovered recently that V-ATPase physically binds to Tbc1d24, as well as four other proteins that are structurally similar. They all contain a so-called TLDc conserved domain. We found that some mutations in the TLDc domain of one of these other proteins, called Ncoa7, disrupted its ability to bind to V-ATPase, which inhibited its acid-pumping capacity. Importantly, some of these “inhibitory” mutations correspond to the known pathogenic mutations within the Tbc1d24 protein in affected patients. Therefore, we hypothesize and aim to prove that some TBC1D24 pathogenic mutations destabilize the interaction of Tbc1d24 with V-ATPase, resulting in impaired acidification of vesicles within cells, including neuronal cells. We also plan to study where precisely the Tbc1d24/V-ATPase interaction takes place to better understand which intracellular vesicles are more severely affected by the mutations. This will facilitate the development of new treatment strategies and drugs specifically designed to target (stabilize) Tbc1d24-V-ATPase interactions. The hope is that if we can repair this interaction, it will restore the process (e. g., acidification) or pathways disrupted by at least some of pathogenic mutations in the TBC1D24 gene.

Linking SETBP1-HD EEG Biomarkers to Clinical Profiles

Awardee: Caitlin Hudac

Institution: University of South Carolina

Grant Amount: $88,740.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

A better understanding of how the brain works in SETBP1 haploinsufficiency disorder (SETBP1-HD) will be helpful to predict what treatments will be most successful. We will collect data and build biological markers (or “biomarkers”) that will capture how individuals with SETBP1-HD focus and learn about the world. Our biomarkers use electroencephalography (EEG) to record brain electricity across the head from over 100 recordings sites on a wet cap. We will collect data from an additional 25 participants with SETBP1-HD using mobile EEG data collection. Critically, this study will be the first to link these brain biomarkers to language, cognitive, and attention clinical profiles. This project will produce valid and reliable biomarkers that can be used as outcome measures to improve treatment and interventions and progress clinical trials.

Clinical trial readiness through longitudinal disease reconstruction in TBC1D24-related disorders

Awardee: Jillian McKee

Institution: University of Pennsylvania/ Children's Hospital of Philadelphia

Grant Amount: $26,962.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

The proposed research aims to understand the diverse clinical landscape and create a timeline of the likelihood of different clinical features in TBC1D24-related disorders across the lifespan. Data previously published in the literature and extracted from electronic medical records at our large academic medical center will be combined with medical records obtained from the TBC1D24 Family Foundation. Our goal is to understand the natural history and genetic basis of varying disease courses in TBC1D24-related disorders to improve clinical care. We hypothesize that we can identify previously unknown subgroups, disease trajectories, and medication responses that will allow us to predict patient outcomes more precisely, choose appropriate medical treatment strategies, and inform clinical trial design.

Congenital hyperinsulinism models for novel drug discovery

Awardee: Michael Kalwat

Institution: Indiana Biosciences Research Institute

Grant Amount: $70,200.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

Patients with congenital hyperinsulinism (HI) are in a continual battle to regulate their blood glucose levels. HI is caused by genetic mutations that lead to inappropriately high insulin levels in the blood. Insulin is normally released from beta cells within the pancreas only after meals when blood glucose is elevated. However, in HI these cells are dysfunctional and release too much insulin even when glucose levels are low. The only FDA-approved drug for HI, diazoxide, has side-effects and some patients are unresponsive. Therefore, new treatments need to be developed. To accomplish this requires the creation of new methods that allow us to test drugs on cells which mimic the human disease. In our project, we will create a human beta cell model that mimics HI and we will test new drugs to determine their ability to suppress insulin release and their mechanisms of action. Our project is broken into two Aims. In Aim 1, we will create a human β-cell line that expresses a mutant version of a gene found in HI. We will use this line alongside normal β-cells to test our new drug compounds. In Aim 2, we will collaborate with a medicinal chemist to improve the effectiveness of our top candidate compound and we will perform experiments to identify exactly which proteins are involved in our drug’s actions. We anticipate that the success of this project will propel our lab’s progress in HI research and enable us to develop improved model systems and make discoveries that will benefit HI patients.

Targeting immunosuppression in LAM

Awardee: Yan Tang

Institution: Brigham and Women's Hospital, Harvard Medical School

Grant Amount: $71,051.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

Lymphangioleiomyomatosis (LAM), pulmonary manifestation of TSC, is a destructive and often fatal lung disease of women, which can lead to lung failure and the need for lung transplantation. LAM can occur as an isolated disorder (sporadic LAM) or in association with TSC. TSC-LAM patients often have angiomyolipoma (AML), the kidney manifestation of TSC. About 60% of sporadic LAM patients also have AML. It seems that LAM and AML share same genetic mutations. We performed single cell analysis on five LAM lungs and six AML specimens and found that subsets of candidate TSC-deficient cells exhibit elevated stemness and dormancy transcriptional programs in both LAM and AML. TSC diseases also exhibit an altered immune microenvironment. We have analyzed adjacent normal kidney tissues for four of the six AML specimens and found that AML tumors are enriched with dysfunctional T cells compared to paired normal kidney. In depth analysis further revealed that stemness-dominant samples are deprived of proliferating T cells, key component in immune system to control tumor growth. In this project, we will investigate how the stemness state of TSC-deficient cells affects immune microenvironment in LAM and assess whether targeting tumor stemness can rejuvenate T cells to better control LAM development.

Rescue of defective lipid handling in Cohen syndrome

Awardee: Jens Luders

Institution: Institute for Research in Biomedicine (IRB Barcelona), Spain

Grant Amount: $83,282.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

The molecular function of VPS13B, the gene that is mutated in Cohen syndrome, is still poorly understood. Our previous work suggested that mutation of VPS13B reduces the amount of certain types of fat molecules in patient cells. Since these fat molecules are essential for the structure and function of cells and for the formation of tissues and organs during development, a reduced amount of these fat molecules may cause the clinical features observed in Cohen syndrome patients. In this project we will test which aspect of the handling of these fat molecules – uptake, transport, or storage – is defective in cells of Cohen syndrome patients. We will then try to repair the defect by introducing variants of intact VPS13B into these cells. Since VPS13B is very large, we will also test smaller versions, which are easier to work with. We will then also try to repair the loss of VPS13B in two additional models, retinal tissue grown in a culture dish that is derived from patient cells, and zebrafish embryos that lack VPS13B, which recapitulate several Cohen syndrome features including brain and eye defects. The project aims to identify VPS13B variants that can be used to provide the crucial functions of VPS13B in cells that lack VSP13B. The results may be useful for developing gene therapy in the future.

Deep Tissue and Cellular Phenotyping of APBD: A Bench to Bedside Approach

Awardee: Priya Kishnani

Institution: Duke University Medical Center

Grant Amount: $50,000.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

Adult Polyglucosan Body Disease (APBD) is an inherited metabolic disease that causes progressive neurodegeneration and reduced physical function and quality of life. There is currently no available treatment for APBD, but over the past decade, the APBD mouse model has been used to investigate potential therapeutics. However, without a full understanding of (1) the specific cells and tissues involved in APBD, and (2) how the disease pathology changes over the course of the disease, our ability to design effective treatments for APBD is limited. Utilizing a multidisciplinary approach with specialists in medical genetics and pathology, we will evaluate the extent of cellular involvement and degree of disease in human and mouse tissues. Ultimately, this work will provide precise therapeutic targets and measurable endpoints for both animal model experiments and progression to clinical trials.

Combinations of small molecule as potential therapeutic agents for APBD

Awardee: Or Kakhlon

Institution: Research Fund of the Hadassah Medical Organization

Grant Amount: $50,000.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

This proposal intends to significantly improve already very promising compounds for obtaining a cure for the adult neurodegenerative disorder Adult Polyglucosan Body Disease which inflicts paralysis, loss of sensation, and lack of urination control on its victims. These compounds will be applied in special formulations which can stabilize them and increase their tissue penetration. Using this methodology and also compound combinations we anticipate that a cure for this devastating disorder will be within reach as a syrup or a pill. APBD, or Adult Polyglucosan Body Disease, is a neurological disorder inflicting paralysis, loss of sensation, and lack of urination control on its victims. The purposes of this proposal are (1) to further improve already promising compounds for the treatment of APBD and (2) to establish new markers for the disease. The compounds will be improved by applying them in combinations and in special formulations which can stabilize them and increase their tissue penetration. The new blood markers will be: (a) neurofilaments, which are proteins derived from fragmented dead neurons and thus should decrease if treatment is successful; (b) a set of molecules in the blood, called metabolites, which can recognize the severity of the disease and how effectively it can be improved by interventions, such as the mentioned compounds.

Testing the specificity and efficacy of compounds that inhibit cAMP signaling, for the development of potential therapeutics for FD/MAS

Awardee: Fernando Fierro

Institution: University of California Davis

Grant Amount: $80,642.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

The Hoffman and Fierro laboratories would like to continue testing compounds to inhibit the excess cAMP production seen in FD/MAS. Proposed studies focus on testing the efficacy and specificity of small molecules, including some candidates identified in the laboratory of our collaborators at UCSF.

Spatial transcriptomics to elucidate the mechanism of anti-RANKL inhibition of fibrous dysplasia bone lesions

Awardee: Julia Charles

Institution: Brigham and Women's Hospital

Grant Amount: $40,321.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

Fibrous dysplasia causes fibrotic bone lesions, full of immature bone forming osteoblasts, that result in pain, deformity and fracture susceptibility. Antibody that blocks the cytokine RANKL inhibits formation of bone eroding osteoclast cells and also improves bone lesions in fibrous dysplasia, but how this works is not known. We propose to profile what both mutant and bystander wild-type cells are producing before and after RANKL is blocked to try to understand how this treatment works. This is important because blocking RANKL has side effects that limit use and understanding how it improves bone lesions could lead to developing alternative therapies.

Probing Central and Peripheral Mechanisms of Pain and Dysfunction in Fibrous Dysplasia/McCune-Albright

Awardee: Jaymin Upadhyay

Institution: Boston Children's Hospital

Grant Amount: $40,321.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

Pain remains a multifaceted and often poorly treated symptom in Fibrous Dysplasia/McCune-Albright (FD/MAS). In this project, we propose to identify and treat biopsychosocial or centralized aspects of pain in FD/MAS. We hope to expand upon what is currently understood about pain in FD/MAS and work towards providing improved treatment options to patients with FD/MAS.

Publications:

Identifying Pain Subtypes in Patients With Craniofacial Lesions of Fibrous Dysplasia/McCune-Albright Syndrome

Preclinical Validation of potential GLUT1 inducing agents for GLUT1 Deficiency Syndrome (GLUT1 DS).

Awardee: Alex MacKenzie

Institution: Children’s Hospital of Eastern Ontario, University of Ottawa

Grant Amount: $61,901.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

Glucose is an essential energy source for the growing brain; low glucose levels in the brain can result in severe delay and disruption in brain development. This is the situation in the rare genetic disorder glucose transporter 1 deficiency syndrome (GLUT1 DS). GLUT1 DS is caused by mutations in the SLC2A1 gene that makes the so called transporter protein GLUT1 which is responsible for transporting glucose from the blood into the brain. A child with GLUT1 DS has only about half the normal level of brain glucose resulting in microcephaly, the development of seizures, as well as movement, and speech disorders that get progressively worse as they age. Although in GLUT1 DS, one of the SLC2A1 genes is mutated, every person has two copies of each gene; the “turning up” of the remaining normal SLC2A1 gene to make more of the GLUT1 protein in infants and children with GLUT1 DS represents a possible treatment for this untreatable disorder. We have studied the impact of several hundred clinically approved drugs on human blood vessel cells to determine if any of them increase the expression of GLUT1; eight such drugs have been identified. The top GLUT1-inducing drugs as well as roughly an equal number of drugs with similar impact that other scientists have found and published on will be tested on a mice model that, like humans with GLUT1 DS have mutated GLUT1. We shall use a variety of approaches, including so-called PET scan, which gives read outs of actual brain glucose levels before and after drug treatment, to see which are successful in increasing glucose transport to the brain. Drugs with the capacity to increase GLUT1 levels could be used as a treatment for GLUT1 DS and will be the subject of a clinical trial.

Deep phenotyping of mouse models of UBE3A gain-of-function

Awardee: Jason Yi

Institution: Washington University School of Medicine

Grant Amount: $47,158.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

Dup15q syndrome is caused by a duplication or triplication of maternal chromosome 15q11-13 whereas individuals with paternal duplications are typically developing. There are more than 20 genes within chromosome 15q11-13, but among them, Ube3a is the only gene expressed exclusively from the maternal allele in neurons. These observations strongly suggest that excessive UBE3A protein activity is the major driver of disease phenotypes in Dup15q syndrome. This proposal will perform deep phenotypic analysis of an allelic series of mice that possess gain-of-function mutations in Ube3a of increasing severity. By doing so, our study will identify specific phenotypes in mice that are caused by excessive UBE3A protein activity. These studies will provide valuable models and information that can be leveraged to design therapeutic strategies for this disorder.

Development of a Novel Viral Vector Gene Therapy Approach to treat CACNA1A Cerebellar Disorders

Awardee: Samuel Young

Institution: University of Iowa

Grant Amount: $73,731.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

Currently, no clinically approved therapeutic strategy that treats the root cause of CACNA1A disorders exists. Due to the recent clinical successes of viral vector-mediated gene therapy, it is an attractive strategy to treat CACNA1A disorders. However, the CACNA1A cDNA sequence is 7.5 kilobases and 8.4 kilobases complete cDNA, which is too large to be used with Adeno-associated Virus (AAV), since AAV has a ~5 kb packaging capacity. Although AAV is the most widely-used gene therapy viral vector in the clinical setting, it is severely limited to treat CACNA1A disorders. Therefore, non-toxic viral vectors with large carrying capacities that are capable of long-term stable transgene expression in Purkinje cells and potentially other cerebellar cell types are needed. Development of a viral vector gene therapy approach to treat all forms of CACNA1A disorders is critical to mitigate the devastating impact on the quality of CACNA1A patient lives. This proposal represents the first steps towards establishing the feasibility of a novel gene therapy approach for CACNA1A cerebellar disorders. While our research is an early discovery stage project, the ability to generate a viable gene therapy approach will lead to a breakthrough in treating the root cause of all CACNA1A disorders.

A Multi-omics Investigation of Ring14

Awardee: Heather Mefford

Institution: St. Jude Children's Research Hospital

Grant Amount: $67,897.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

Ring14 is an understudied and life-limiting rare chromosomal disorder with symptoms including severe and drug-resistant epilepsy, slow growth, low muscle tone, intellectual disability, and other multi-system health issues. For the last 10 years, the major hurdle in studying Ring14 has been the lack of a reliable model that accurately represents what is seen in individuals with Ring14 due to the unique structure and instability of the ring chromosome. Additionally, cellular models for neurological conditions do not always mirror the true biological state of the brain. Spatial transcriptomics is a new technology that combines brain imaging, gene sequencing, and cell characterization simultaneously to provide holistic biologic insight. In this collaborative study, we will perform spatial transcriptomics in brain tissue to directly and simultaneously study how Ring14 affects the cellular structure, organization, and gene expression in the brain. We will also study methylation – a biomarker for the regulation or turning on/off of genes – in multiple Ring14 patients and compare their methylation patterns with individuals with other chromosome 14 differences (i.e., deletions) and healthy individuals without epilepsy. Previous studies and karyotypes (chromosome genetic tests) have shown that the instability of the ring chromosome causes mosaicism in the body, meaning the ring chromosome is not present in all cells. So far, no study has been able to assess the extent of mosaicism in the most disease-relevant tissue, the brain. By evaluating the content of ring14 in brain tissue and integrating methylation and transcriptomic data, we will elucidate the unique biology and mechanisms of Ring14. Our study has the potential to inform future targeted therapeutic development for this devastating life-limiting condition.

Novel Adeno-associated viral vector (AAV) mediated RNA editing treatment for KCNT1 epilepsy

Awardee: Rajvinder Karda

Institution: University College London

Grant Amount: $70,619.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

KCNT1 epilepsy is a severe childhood genetic epilepsy, which leads to life-long disability. Spelling mistakes, or mutations, in the genetic code of KCNT1 cause epilepsy of infancy with migrating focal seizures (EIMFS). EIMFS becomes apparent in the first 6 months of life, where babies present with frequent seizures, developmental delay, and movement disorders. Sadly, patients also have an increased chance of premature death. The KCNT1 gene codes for a potassium channel which changes nerve cell (neuron) excitability. Mutations associated with this form of epilepsy result in increased channel activity in brain cells, making them more excitable. Current drug treatments are unfortunately inadequate and ineffective. The process of making proteins in cells involves translating DNA (the genetic code) into RNA (the protein code) which is then made into proteins such as the KCNT1 channel. We aim to develop a novel RNA editing therapy treatment for EIMFS, altering the protein code so less protein is made. We will deliver the RNA treatment within a virus called adeno-associated virus (AAV). When the AAV enters neurons, it will reduce the amount of KCNT1 protein and normalise the channel activity. We will test this new treatment in a Kcnt1 mouse model which has an over-active KCNT1 channel and seizures very similar to those seen in patients. We will also test the treatment in neurons made from skin cells donated by patients with KCNT1 epilepsy. In the future we hope this could be developed into a treatment for patients. Although like other gene therapies it would need to be delivered to the brain, our treatment would have several advantages including being a one-off treatment unlike other RNA treatments which require repeated spinal taps or lumbar punctures. Therefore, in this proof-of-concept study we will develop and test a novel RNA editing one-off treatment to improve KCNT1-epilepsy.

SKIP-AT: a comprehensive, systematic platform approach for targeted exon skipping of ATM

Awardee: Matthis Synofzik

Institution: Hertie-Institute for Clinical Brain Research, University of Tübingen, Germany

Grant Amount: $53,240.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

We will develop and validate a systematic, comprehensive platform approach for targeted exon skipping of constitutive ATM exons. For this, we can directly leverage and extend our established, scalable platform for the development of patient-specific antisense oligonucleotides (ASOs) for ATM - with already proven efficacy from preclinical to clinical translation in our hands. Our ATM exon-skipping approach will demonstrate and validate a systematic experimental path that will allow to provide the genomic medicine field with the urgently warranted comprehensive knowledge on which exons of the ATM gene can be (ASO-)skipped - and in fact even allows to already prepare the most promising skippable exons for clinical ASO treatment development.

CSF dynamics in mucopolysaccharidosis type I

Awardee: Igor Nestrasil

Institution: University of Minnesota

Grant Amount: $60,655.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

This project aims to measure the motion of the cerebrospinal fluid (CSF) through the brain with magnetic resonance imaging (MRI) and associate these measures with disease severity in mucopolysaccharidosis type I (MPS I). The findings may determine whether CSF motion is impaired in MPS I with implications for the disease severity or the drug distribution administered to the intrathecal space (space surrounding the spinal cord) or subarachnoid space (space around the brain).

To Study the potential for Collagen Mimetic Peptides to reduce progressive damage to the Bruch's-RPE-Photoreceptor Complex in Choroideremia.

Awardee: Malia Edwards

Institution: Johns Hopkins University

Grant Amount: $64,735.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

Collagen is the most common protein in the human. It is found in all organs in either its structural form or as a major component of the extracellular matrix. The source of newly formed collagen arising during tissue growth and remodeling is the nearby cells, often mesenchymal but also epithelial. A healthy body undergoes collagen remodeling on a constant basis, but aging or gene deficiencies can cause the ability to produce replacement collagen to decrease. In certain disease states collagen-producing cells are often involved and may become damaged as well, leading to a reduction in collagen replacement which slows the tissue healing process. A therapeutic with the ability to repair damaged collagen can facilitate recovery and halt progressive damage to critical tissues and organs, like the eye, when it is subjected to such diseases. CMPs are vastly different from denatured collagen supplements, which are highly advertised nutraceutical products and which do not have the direct collagen repairative activities associated with CMPs. CMPs have been shown to be efficacious and safe in humans when applied topically as eyedrops and systemically in animals under FDA regulated toxicity studies.

Leveraging predictive models to design high-throughput assays to resolve variants of uncertain significance (VUS) in SYNGAP1

Awardee: Gemma Carvill

Institution: Northwestern University

Grant Amount: $61,222.00

Funding Period: February 1, 2024 - January 31, 2025

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Summary:

SYNGAP1-related disorder is caused by pathogenic (disease-causing) loss of function variants, and while most variants described to date are truncations, there are also at least 50 pathogenic missense variants that have been described. However, missense variants are more likely to be classified as uncertain significance i.e. of unknown impact on protein function, we call these VUS. This is because of the difficulties with predicting whether these variants impact SYNGAP1 function using current tools. Here we will use a computational approach to determine what characteristics of missense variants are more likely to impact SYNGAP1 function. We will then design and test a method/assay based on this characteristic to identify pathogenic missense variants. This method will be able to screen hundreds of missense variants at a time. We will make this data available in an accessible manner to the patient community.