Click Chemistry for Future Gene Therapies to Benefit Citizens, Researchers and Industry

Project Information

ClickGene

Grant agreement ID: 642023

DOI

10.3030/642023

Project closed

EC signature date 5 December 2014

Start date 1 January 2015

End date 31 December 2018

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 3 556 990,44

EU contribution

€ 3 556 990,44

Coordinated by

DUBLIN CITY UNIVERSITY
Ireland

Periodic Reporting for period 2 - ClickGene (Click Chemistry for Future Gene Therapies to Benefit Citizens, Researchers and Industry)

Reporting period: 2017-01-01 to 2018-12-31

Summary of the context and overall objectives of the project

Gene therapy is expected to play a key role in next-generation medicine by correcting the underlying genetic causes of disease, thereby facilitating a personalised approach to medicine. As this technology can address a wide range of medical conditions, along with finding substantive application within plant genetics, extensive growth in this sector of the biopharmaceutical and agricultural industry are widely predicted. Thus, to enhance the human understanding and application of gene therapy, highly qualified experts of this field are urgently required. ClickGene addressed this need by providing cross-disciplinary training to 14 early-stage researchers (ESRs) in an exciting academia-industry collaboration focused on the development of next-generation gene silencing therapeutics and epigenetic DNA probes.

The main goal of the European Training Network (ETN) ClickGene was to develop new materials and methodologies for site-selective genetic engineering by training researchers within an innovative, multi-disciplinary and entrepreneurial environment so that they can meet the challenges facing future scientific leaders in Europe’s industry. Over the four project years, our multidisciplinary consortium provides world-class training to the ESRs in the areas of synthetic click chemistry, nanotechnology, liposomal drug delivery and nucleic acid (DNA and RNA) chemistry. We generated scientific excellence and technological innovation in the areas of gene silencing and epigenetic base detection by generating 1) unique gene silencing tools that interact with DNA in a fundamentally different way compared with current start-of-art-technology on the market, 2) new liposomal and nanoparticle drug delivery agents, and 3) novel fluorogenic probes for epigenetic base detection in high-throughput PCR assays.

These objectives are important for society as this network has trained the next generation of leading scientists in critical research fields that are required to maintain and enhance EU competitiveness in the areas of gene editing technology, nanotechnology, and nucleic acid chemistry. As such, this network has enhanced biopharmaceutical, biodiagnostic, and agricultural EU societal sectors. Secondly, the scientific and technological advantages for developing new tools for gene editing, epigenetic base detection, and nanoparticle drug delivery are all important for mankind and strive toward improving healthcare and the availability of cutting-edge biomedical diagnostics for European citizens and beyond.

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

The ClickGene project began in January 2015 and recruited 14 ESRs across 9 beneficiary host organisations. Our main research focus was within gene silencing and epigenetic base detection and these activates, so far, resulted in the publication of almost 40 peer reviewed scientific publications, many of which have appeared in premier journals. ClickGene researchers contributed scientific talks and poster presentations at numerous scientific conferences throughout Europe. For example, our network interfaced with COST Action CM1201 ‘Biomimetic Radical Chemistry’ and together we have held two joint research meetings (Dublin, July 2015 and Grenoble, April 2016) that allowed ClickGene ESRs to present their research to the wider European scientific community. We also hosted a major international conference—the 17th Symposium on Chemistry of Nucleic Acid Components (SCNAC) in Česky Krumlov, Czech Republic. In 2018, ClickGene ESRs and PIs organised a high-caliber scientific workshop on nucleic acids research in the University of Oxford that combined industry-focused tours of both Oxford Nanopore Technologies and ATDBio Ltd. Aside from publishing a large number of research papers in top-tier journals, we have also developed new IP in the area of nucleic acid click chemistry and applied this to launch a new commercial product for enhanced cell proliferation, called the EdU detect Pro kit. Throughout the project, we actively disseminated our research activates via a dedicated website (www.clickgene.eu) and by Twitter (@ClickGene_H2020). Our research teams also promoted nucleic acid chemistry through a range of workshops and information sessions for high school students and teachers and we have written content for an open access e-book on nucleic acids (https://www.atdbio.com/nucleic-acids-book). All 14 of our ESRs have either submitted or are writing their PhD thesis.

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)

The scientific and technological progress we achieved in this network can be summarised in three main ways:

1. Developing unique gene silencing tools. We have made significant inroads in this field and demonstrated that small molecule DNA oxidants, alone, can be applied for protein engineering, as potential chemotherapeutic agents, and as recognition elements that bind DNA sequence specifically. We then applied this technology to the development of target-specific gene knockout agents using nucleic acid click chemistry. This effort involved large-scale interdisciplinary collaboration between many of our academic beneficiaries at DCU, Oxford, Munich, and IOCB and industry partners ATDBio and baseclick. We are about to publish several exciting studies showing how this can be achieved and, as such, we believe the ClickGene network has reached a major landmark in the design and development of new gene silencing tools with an alternative mechanism to state-of-art gene editing technologies such as CRISPR/Cas9.
2. Liposomal and nanoparticle drug delivery agents. ESRs have engineered exciting new nanoparticle drug delivery agents that respond to external stimuli (e.g. heat and pH). Nano-carrier sizes can be further controlled to allow delivery of specific cargo and we have applied this for the controlled release of anticancer drug molecules developed in this network. Liposomal transfection agents were also investigated, and, in collaboration with our industrial beneficiary LipiNutaGen Srl, the design of specific liposomal carriers that can selectively target human cancer cells was successfully demonstrated.
3. Probes for epigenetic base detection. Our ESRs developed gene targeting probes to localize epigenetic marks at specific sequences. The probe strands were constructed using click chemistry. In a first step, new DNA probes were generated by the Carell group in combination with quantitative PCR to detect single epigenetic fdC (formyl-deoxycytidine) bases at defined positions in the genome. At baseclick, new click chemistry technology was developed and applied to launch a new commercial product for enhanced cell proliferation called the EdU detect Pro kit. ATDBio, in collaboration with the University of Oxford, then successfully developed high-throughput and large-scale production of clickable fluorogenic probes that were applied to triplex-forming oligonucleotides (TFOs). This technology can now be applied to mainstream probe development. Another successful application of new probe technology was demonstrated by the IOCB group when they demonstrated regulation/triggering of cleavage of DNA sequences by restriction enzymes through bioorthogonal transformations in the major-groove.

In sum, the ClickGene ETN was completed at the end of 2018. The results of our research results have exceeded initial expectations and our training programme has made a significant contribution to the ESRs's career development for a prosperous future.

ClickGene group picture during the 4th Network Meeting in Oxford, UK

ClickGene ESRs

Performance of the Baseclick's EdU DetectPro kit (right image) for cell proliferation detection