Deciphering the Roles of the Salvage and De Novo Pathways of Nucleotide’s Metabolism in Mitochondrial DNA Maintenance

Project Information

MITO-GARAGE

Grant agreement ID: 101065857

DOI

10.3030/101065857

Project closed

EC signature date 14 November 2022

Start date 1 July 2023

End date 30 June 2026

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 285 140,64

Coordinated by

UNIVERSIDAD DE GRANADA
Spain

Periodic Reporting for period 1 - MITO-GARAGE (Deciphering the Roles of the Salvage and De Novo Pathways of Nucleotide’s Metabolism in Mitochondrial DNA Maintenance)

Reporting period: 2023-07-01 to 2025-06-30

Summary of the context and overall objectives of the project

MITO-GARAGE is an ambitious research initiative aimed at addressing the urgent unmet medical needs posed by mitochondrial diseases, with a particular focus on primary Coenzyme Q (CoQ) deficiencies, specifically through pathogenic variants in COQ2, and mitochondrial DNA maintenance disorders (MDDS), specifically through pathogenic variants in GUK1. These rare yet devastating conditions lead to multisystemic involvement, often manifesting with severe neurological, muscular, and metabolic complications, and currently lack effective therapies.
The project builds upon a solid foundation of previous research by the two hosts groups at Columbia University (CU) in New York and the University of Granada (UGR), that has identified novel pathogenic variants and mechanistic insights into mitochondrial dysfunction. Through the integration of genetic, biochemical, and cellular approaches, such as studying patient derived fibroblasts and newly generated in vivo models, MITO-GARAGE seeks to deepen the understanding of disease pathology and to evaluate innovative therapeutic strategies.
The overall objectives of MITO-GARAGE are threefold:
1. To elucidate the molecular and cellular mechanisms underlying primary CoQ deficiencies and mtDNA maintenance disorders.
2. To develop and test novel therapeutic interventions, including small molecules and formulation improvements, aimed at restoring mitochondrial function.
3. To facilitate the path from bench to bedside through robust preclinical validation, engagement with regulatory pathways, and strategic planning for intellectual property management and potential commercialization.
The pathway to impact involves not only the generation of high-quality scientific data but also proactive dissemination to both the scientific community and broader audiences, fostering awareness and paving the way for future clinical trials. By evaluating options such as orphan drug designation, patenting, and possible spin-off creation in collaboration with technology transfer offices (e.g. Columbia Technology Ventures and UGR’s OTRI), MITO-GARAGE aims to maximize the societal and economic benefits of its findings, ultimately improving the quality of life for patients affected by mitochondrial diseases.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

During the implementation of the outgoing phase at CU, MITO-GARAGE project, a wide range of experiments were carried out to advance our understanding MDDS caused by GUK1 deficiency:
First, identified pathogenic variants in GUK1 from 4 patients of three families in Milan, Barcelona, and Washington.
To explore how these genetic changes disrupt cells, we developed laboratory models using skin cells (fibroblasts) taken directly from patients. These patient-derived cells were thoroughly studied to assess their mitochondrial health, measuring energy production enzyme activities, CoQ levels, DNA content in mitochondria (mtDNA), and markers of oxidative stress.
Functional studies elucidated how defects in GUK1 disrupted nucleotide pools (the building block of DNA) and mitochondrial replication machinery, contributing to mtDNA instability.

In parallel, we explored several potential treatments. We tested a variety of small molecules and new formulations designed to improve mitochondrial function or work around specific biochemical blockages. These therapies were systematically evaluated in patient cell models to see if they could boost mtDNA production, normalize energy metabolism, or lower oxidative stress. Encouragingly, some candidates showed the ability to rescue the mtDNA depletion in the patients fibroblasts, laying the groundwork for future studies in animal models and, eventually, early-stage clinical trials.
Taken together, the main scientific achievements of this project include the discovery of new genetic variants and disease mechanisms, the creation of well-characterized patient cell models that closely mimic the human disease, the identification of promising therapeutic candidates that can improve mitochondrial function in the lab, and the development of robust datasets and methodologies that will continue to support and inspire future research in mitochondrial medicine.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Results and potential impacts:
The Mito-Garage project has delivered significant scientific results with promising translational implications. Key outcomes include:
• Identification of novel pathogenic variants in genes such as GUK1 linked mtDNA maintenance disorders, broadening the genetic landscape of mitochondrial diseases and improving diagnostic precision.
• Elucidation of disease mechanisms, including how disruptions in nucleotide metabolism contribute to mtDNA instability, providing new molecular targets for therapeutic intervention.
• Establishment and comprehensive characterization of GUK1 mouse models, which faithfully recapitulate mitochondrial dysfunction and serve as robust platforms for mechanistic studies and drug testing.
• Discovery of promising therapeutic candidates, including small molecules and improved formulations that demonstrated the capacity to partially restore mitochondrial function in vitro. These findings create a solid basis for preclinical development.
• The estimated monthly costs for patients with mitochondrial diseases costs are higher than the overall total member population and similar to ALS and MS patients. Improved therapies will reduce costs through higher treatment efficacies and, consequently, lower palliative care costs
• The communication and dissemination activities proposed in MITO-GARAGE will create conscience about difficulties for the families that suffers MD for the general audience this increase of the visibility could lead to better opportunities and improvement of the quality life of patients and their families.
• Generation of high-quality, interoperable datasets and optimized experimental pipelines that are aligned with FAIR principles, enabling broader reuse and accelerating future mitochondrial disease research.

The MITO-GARAGE results allowed us to submit an invention report and a patent application together with the technology transfer offices at CUIMC (Columbia Technology Ventures) for our proposed treatment, with forodesine and dG, for mtDNA depletion syndrome associated to GUK1 deficiency. These results will enable us to apply for an Investigational New Drug (IND) and begin treating the patients.

Graphical Abstract GUK1