Periodic Reporting for period 2 - StarT (European Training Network to Diagnose, Understand and Treat Stargardt Disease, a Frequent Inherited Blinding Disorder)
Okres sprawozdawczy: 2020-10-01 do 2023-03-31
• What is the problem/issue being addressed?
StarT has created an interdisciplinary and intersectoral European training network focusing on different aspects of autosomal recessive Stargardt disease (STGD1), a frequent inherited blinding disorder that affects an estimated 925,000 persons worldwide. STGD1 is due to ABCA4 mutations, however up to 35% of STGD1 cases carries one or no ABCA4 coding mutation. New unconventional classes of ABCA4 mutations were discovered by us, the significance of which largely remained elusive. In order to understand the mechanisms triggered by these missing ABCA4 mutations and to design new therapies for STGD1 cases, challenging research questions have been addressed by the integration of unique skills from the StarT network.
• What are the overall objectives?
StarT research aimed to uncover the regulation of ABCA4, the disease gene for STGD1 and its missing heritability, in order to develop novel treatments. StarT training aimed to give young researchers unparalleled training opportunities in outstanding vision research groups with unique expertise in omics technologies, bioinformatics, stem cell biology, animal models of disease, and therapeutics, providing each ESR with the necessary competences in state-of-the-art academic and industrial research.
• Why is it important for society?
StarT has performed cutting edge research using innovative and interdisciplinary approaches: (functional) genomics and transcriptomics, bioinformatics, CRISPR/Cas9 genome editing, generation of stem cell and animal disease models and design of new treatments. The training objectives have been met through academic and industrial training-by-research via individual research projects, secondments, and network-wide training sessions.
StarT has created an interdisciplinary and intersectoral European training network focusing on different aspects of autosomal recessive Stargardt disease (STGD1), a frequent inherited blinding disorder that affects an estimated 925,000 persons worldwide. STGD1 is due to ABCA4 mutations, however up to 35% of STGD1 cases carries one or no ABCA4 coding mutation. New unconventional classes of ABCA4 mutations were discovered by us, the significance of which largely remained elusive. In order to understand the mechanisms triggered by these missing ABCA4 mutations and to design new therapies for STGD1 cases, challenging research questions have been addressed by the integration of unique skills from the StarT network.
• What are the overall objectives?
StarT research aimed to uncover the regulation of ABCA4, the disease gene for STGD1 and its missing heritability, in order to develop novel treatments. StarT training aimed to give young researchers unparalleled training opportunities in outstanding vision research groups with unique expertise in omics technologies, bioinformatics, stem cell biology, animal models of disease, and therapeutics, providing each ESR with the necessary competences in state-of-the-art academic and industrial research.
• Why is it important for society?
StarT has performed cutting edge research using innovative and interdisciplinary approaches: (functional) genomics and transcriptomics, bioinformatics, CRISPR/Cas9 genome editing, generation of stem cell and animal disease models and design of new treatments. The training objectives have been met through academic and industrial training-by-research via individual research projects, secondments, and network-wide training sessions.
First, we defined the ABCA4 transcriptional unit and of gene regulatory networks controlling ABCA4. Moreover, we generated a cis-regulatory map in human adult retina and in model organisms combining chromatin interaction mapping such as HiChIP and UMI-4C, and other epigenomic signatures such as ATAC-seq and ChIP-seq, and bulk and single-cell transcriptomics. Furthermore, we functionally assessed cis-regulatory elements (CREs) of ABCA4 using in vitro studies in human retinal cells and in vivo enhancer assays in aquatic animal models. Overall, this research has contributed to the annotation of the non-coding genome in retina that may be a target for mutations in many other IRD.
Second, we aimed to identify and characterize missing heritability in the ABCA4 gene in STGD1. Despite genomic advances, 20-35% of STGD1 cases remained genetically unexplained, rendering ABCA4 an excellent model gene to identify and functionally assess missing heritability. Novel therapies are being developed for STGD1 cases that have an unequivocal genetic diagnosis. Here, we identified structural and sequence variants of the ABCA4 locus in monoallelic STGD1 cases. We performed in vitro analyses of ABCA4 splice defects and we identified ABCA4 RNA defects in retinal stem cells of monoallelic STGD1 cases. Lastly, we performed functional studies of ABCA4 cis-regulatory variants such as 5’UTR variants.
Third, we developed innovative therapeutic strategies that could overcome limitations of currently used lentiviral-based delivery of ABCA4 and develop new concepts to treat ABCA4-related retinal disease. These included antisense oligonucleotide (AON)-based splice modulation, dual AAV-based delivery of ABCA4 cDNA in a pig model, CRISPR/Cas9-based genome editing of deep intronic variants, mitochondrial gene therapy to modulate energy metabolism in the degenerating retina, and pharmacological modulation of ABCA4 protein folding to restore protein expression and function. The preclinical efficacy of these approaches was assessed in state-of-the-art cellular models, such as patient-derived iPSCs and iPSC-derived photoreceptor precursor cells and retinal organoids, as well as animal model systems, including mouse and pig.
The training network was designed to train 14 ESRs to become excellent interdisciplinary research scientists with in-depth knowledge on innovation in academic, industrial and non-profit organisations. Network-wide training was provided in the form of seven Complementary Skills (CS) courses and four Research Training (RT) workshops. Due to the COVID-19 pandemic, some events were moved online or postponed to enable in person meetings.
The StarT network aimed to disseminate its research results to the scientific community via publication in peer reviewed scientific journals and presentations at national and international meetings.
StarT organised an ‘Excellence in Science Communication’ course as part of the network training schedule and additional training on how to communicate research to the broad public. A StarT website was created and maintained, with publications and outreach activities. ESRs performed personal outreach activities: they wrote layman’s contributions about their research for the general public, and prepared infographics and videos on their research topics.
Second, we aimed to identify and characterize missing heritability in the ABCA4 gene in STGD1. Despite genomic advances, 20-35% of STGD1 cases remained genetically unexplained, rendering ABCA4 an excellent model gene to identify and functionally assess missing heritability. Novel therapies are being developed for STGD1 cases that have an unequivocal genetic diagnosis. Here, we identified structural and sequence variants of the ABCA4 locus in monoallelic STGD1 cases. We performed in vitro analyses of ABCA4 splice defects and we identified ABCA4 RNA defects in retinal stem cells of monoallelic STGD1 cases. Lastly, we performed functional studies of ABCA4 cis-regulatory variants such as 5’UTR variants.
Third, we developed innovative therapeutic strategies that could overcome limitations of currently used lentiviral-based delivery of ABCA4 and develop new concepts to treat ABCA4-related retinal disease. These included antisense oligonucleotide (AON)-based splice modulation, dual AAV-based delivery of ABCA4 cDNA in a pig model, CRISPR/Cas9-based genome editing of deep intronic variants, mitochondrial gene therapy to modulate energy metabolism in the degenerating retina, and pharmacological modulation of ABCA4 protein folding to restore protein expression and function. The preclinical efficacy of these approaches was assessed in state-of-the-art cellular models, such as patient-derived iPSCs and iPSC-derived photoreceptor precursor cells and retinal organoids, as well as animal model systems, including mouse and pig.
The training network was designed to train 14 ESRs to become excellent interdisciplinary research scientists with in-depth knowledge on innovation in academic, industrial and non-profit organisations. Network-wide training was provided in the form of seven Complementary Skills (CS) courses and four Research Training (RT) workshops. Due to the COVID-19 pandemic, some events were moved online or postponed to enable in person meetings.
The StarT network aimed to disseminate its research results to the scientific community via publication in peer reviewed scientific journals and presentations at national and international meetings.
StarT organised an ‘Excellence in Science Communication’ course as part of the network training schedule and additional training on how to communicate research to the broad public. A StarT website was created and maintained, with publications and outreach activities. ESRs performed personal outreach activities: they wrote layman’s contributions about their research for the general public, and prepared infographics and videos on their research topics.
• Expected scientific, economic and technological impacts:
The demand for tailored treatments is increasing, as is the case for STGD1, a frequent inherited blinding disorder that affects an estimated 925,000 persons worldwide. It is expected that the StarT project will lead to a better understanding of the underpinnings of STGD1, to advanced diagnostic protocols and ultimately to improved treatment outcomes. The StarT ESRs have developed a broad range of technical skills preparing them to lead future science developments in this area, while the experience of working within a trans-European network including industrial partners will position them perfectly to lead the coming revolution in vision research and therapy.
• Expected societal impact(s) – health impact:
StarT improved complex genetic testing in unsolved STGD1 cases and develop new preclinical models and therapeutics for STGD1. Our framework will be transferred to clinical stakeholders beyond our consortium through the patient organizations involved such as Retina International and Fighting Blindness Ireland, and through the European Retinal Disease Consortium (ERDC) and the European Network for Rare Eye Diseases (ERN-EYE).
• Expected societal impact(s) – Impact on the European level:
StarT will foster existing collaborations between the various academic and private sector teams, develop new long-term partnerships and create a lasting structured training program aligned between the network partners across Europe. Network-level training, as well as CS training, became an integral part of each ESR’s doctoral training. This provided high-level training in specific technologies and also trained ESRs to communicate across disciplines and sectors. The integrated nature of StarT, the frequent meetings, training schools/workshops, exchanges and secondments and the resultant joint publications fostered an EU-wide cooperative spirit to continue long after the end of project. StarT will be a source of inspiration for structuring European intersectoral doctoral training and research collaborations.
The demand for tailored treatments is increasing, as is the case for STGD1, a frequent inherited blinding disorder that affects an estimated 925,000 persons worldwide. It is expected that the StarT project will lead to a better understanding of the underpinnings of STGD1, to advanced diagnostic protocols and ultimately to improved treatment outcomes. The StarT ESRs have developed a broad range of technical skills preparing them to lead future science developments in this area, while the experience of working within a trans-European network including industrial partners will position them perfectly to lead the coming revolution in vision research and therapy.
• Expected societal impact(s) – health impact:
StarT improved complex genetic testing in unsolved STGD1 cases and develop new preclinical models and therapeutics for STGD1. Our framework will be transferred to clinical stakeholders beyond our consortium through the patient organizations involved such as Retina International and Fighting Blindness Ireland, and through the European Retinal Disease Consortium (ERDC) and the European Network for Rare Eye Diseases (ERN-EYE).
• Expected societal impact(s) – Impact on the European level:
StarT will foster existing collaborations between the various academic and private sector teams, develop new long-term partnerships and create a lasting structured training program aligned between the network partners across Europe. Network-level training, as well as CS training, became an integral part of each ESR’s doctoral training. This provided high-level training in specific technologies and also trained ESRs to communicate across disciplines and sectors. The integrated nature of StarT, the frequent meetings, training schools/workshops, exchanges and secondments and the resultant joint publications fostered an EU-wide cooperative spirit to continue long after the end of project. StarT will be a source of inspiration for structuring European intersectoral doctoral training and research collaborations.