Periodic Reporting for period 2 - NATURE-ETN (Nucleic Acids for Future Gene Editing, Immunotherapy and Epigenetic Sequence Modification)
Periodo di rendicontazione: 2022-04-01 al 2024-09-30
The NATURE-ETN project forged a new integrated network between 10 industry-academia partners and trained 15 early-stage researchers (ESRs) using cutting-edge resources at leading research facilities, universities, and biopharmaceutical enterprises throughout the EU. The research programme involved world-leading chemists in combination with high-tech/biotech companies (baseclick) and small and medium-sized enterprises (SMEs) (NIBRT and ATDBio). NATURE-ETN executed three main objectives:
1. We provided training excellence and expertise to 15 ESRs in cutting-edge research areas of nucleic acid chemistry, bioinorganic chemistry, biological chemistry, gene editing, X-ray crystallography, cancer immunotherapy, epigenetic base manipulation and DNA sequencing. ESRs within NATURE-ETN undertook two, independent, secondment periods to industry and cross-disciplinary academia. Though this bespoke programme, we fostered collaborative relationships, creativity, and confidence to enhance the training experience, productivity, scientific excellence, and cooperation of all 15 fellows.
2. Our ESRs developed a deep skillset in scientific and transferable skills and in the translation of basic research into high-functioning commercial nucleic acid therapies in breakthrough research areas of gene therapy and epigenetic base manipulation.
3. Research within NATURE-ETN focused on:
a. New types of gene editing technologies that differ from the current state-of-art;
b. New approaches to probing the prebiotic origins of life and in the development of cell-based cancer immunotherapy by employing therapeutic oligonucleotides, and;
c. Novel sequencing, imaging, and profiling technologies for epigenetic base detection and manipulation.
NATURE-ETN’s ESRs were trained to address some of the most important scientific questions while also engaging with societal needs. We anticipate the newly trained NATURE-ETN ESRs will evolve to become the next-generation of pioneering scientific leaders in Europe, where they can grow our commercial need for disruptive technologies in 21st-century medicine.
1. We provided training excellence and expertise to 15 ESRs in cutting-edge research areas of nucleic acid chemistry, bioinorganic chemistry, biological chemistry, gene editing, X-ray crystallography, cancer immunotherapy, epigenetic base manipulation and DNA sequencing. ESRs within NATURE-ETN undertook two, independent, secondment periods to industry and cross-disciplinary academia. Though this bespoke programme, we fostered collaborative relationships, creativity, and confidence to enhance the training experience, productivity, scientific excellence, and cooperation of all 15 fellows.
2. Our ESRs developed a deep skillset in scientific and transferable skills and in the translation of basic research into high-functioning commercial nucleic acid therapies in breakthrough research areas of gene therapy and epigenetic base manipulation.
3. Research within NATURE-ETN focused on:
a. New types of gene editing technologies that differ from the current state-of-art;
b. New approaches to probing the prebiotic origins of life and in the development of cell-based cancer immunotherapy by employing therapeutic oligonucleotides, and;
c. Novel sequencing, imaging, and profiling technologies for epigenetic base detection and manipulation.
NATURE-ETN’s ESRs were trained to address some of the most important scientific questions while also engaging with societal needs. We anticipate the newly trained NATURE-ETN ESRs will evolve to become the next-generation of pioneering scientific leaders in Europe, where they can grow our commercial need for disruptive technologies in 21st-century medicine.
The NATURE-ETN project started in April 2020 and recruited 15 ESRs across 10 beneficiary host organisations. The project officially ended in September 2024. All ESRs acquired training in state-of-art research facilities and their research efforts focused on developing new gene-editing technologies, designing therapeutic oligonucleotides that modulate immune-responses required for treating cancer, exploring prebiotic chemistry to probe the origin of life, and the development of new DNA sequencing reagents for epigenetic base detection. The research connected with therapeutic oligonucleotides branched out to take advantage of i.) emerging prebiotic model systems; and ii.) the urgent need to develop new antiviral Covid-19 treatments. The scientific results achieved within the project were disseminated in the form of peer-reviewed scientific publications including papers in Nature, Organometallics, Journal of Biological Inorganic Chemistry, Nature Communications, Nucleic Acids Research, Molecules, Chemical Science, and Angewandte Chemie. Significantly, a number of new research publications are set to emerge into the future, beyond the end date of the project. NATURE-ETN ESRs attended, and presented, their work at 36 scientific conferences throughout Europe, as well as online scientific meetings. In total, seven (7) training events were delivered throughout the project (online, Munich, Dublin, Oxford, Reading, and Paris) which included high-quality scientific lectures, experimental techniques, workshops on Scientific Writing & Publishing by Nature Publishing Group, soft skills workshops, and several industry-focused workshops. Additionally, a total of 17 secondments were undertaken to industry and cross-disciplinary academia.
NATURE-ETN’s beyond state-of-the-art scientific and technological progress focused on:
1. Developing new methods for artificial gene editing. Firstly, we made significant contributions to this field by developing new DNA-binding and -damaging metallodrugs. The project then attempted to produce advanced nucleic acid-metallodrug hybrids with sequence-specific gene targeting properties. Here, artificial gene-editing systems were developed using triplex-forming oligonucleotides conjugated to metallodrugs using click chemistry methods. A number of new metallodrugs that can be light and chemically activated were produced (cf. Gasser et al., RSC Chem. Biol., 2022, 3; Kellett et al., RSC Med. Chem., 2024, 15, Kellett et al., Angew. Chemie, 2023, e202305759). Another aim was to crystallise and structurally characterise new metal complexes that can bind in the major groove of DNA. Here, expertise from the Cardin group: i.) Cardin et al., Angew. Chemie, 2024, e202318863; ii.) Cardin et al., Chem. Sci., 2024, 15) was used to identify the structures of new DNA damaging agents. Several of the metallodrugs were then modified and attached to gene targeting groups, such as triplex-forming oligonucleotides, and examined for their sequence-specific interactions with cancer causing genes.
2. Synthesis and delivery of nucleic acid therapeutics that promote cell-based cancer immunotherapy. NATURE-ESRs engaged in the development of geranylated nucleosides to anchor RNA to nanoparticles for transfection. Moreover, one ESR focused on establishing prebiotically plausible scenarios of an RNA–peptide world and this work was published in Nature (Carell et al., Nature, 2022, 605). Another of NATURE’s ESR investigated the stabilisation effects of a specific nucleobase called m6A in RNA constructs, including guide-RNA in combination with dCas13-fused methyltransferases. Further research was dedicated to the design of antisense oligonucleotides containing artificial cleaving agents which have Cas13-like behaviour, but without the protein component. The outcome from this research strategy could have a major future impact on cancer therapy since the work aims to both simultaneously reduce immunogenicity and enhance mRNA expression.
3. Generation of new reagents for high-sensitivity epigenetic base detection. Reading the epigenetic status of DNA bases encoded in the human genome gives us vital information related to gene expression (Carell et al., Nature Communications, 2021, 12; Carell, Kellett et al. Angew. Chemie, 2023, e202215704). NATURE-ETN ESRs focused on sequencing the epigenome and addressed current limitations in sequencing technologies. ESRs attempted to develop breakthrough materials for epigenetic base oxidation for use in next-generation sequencing (NGS). Progress was made on establishing analytical methods for quantification of cAzadC and metabolites prepared using isotopically labelled compounds for metabolic assays. The successful development of this analytical protocol may now enable rapid and parallel monitoring of dC and metabolites thereby revolutionising epigenetic monitoring and diagnostics. In parallel, new Fe(IV)-oxo complexes were investigated as potential new agents capable of oxidising 5mC and 5hmC to 5fC. In this area of research, baseclick GmbH, a NATURE-ETN industrial beneficiary, aimed to exploit other important avenues for probe development. One strategy identified a click chemistry-based method for the generation and amplification of full-length cDNA libraries from total RNA for next-generation sequencing.
1. Developing new methods for artificial gene editing. Firstly, we made significant contributions to this field by developing new DNA-binding and -damaging metallodrugs. The project then attempted to produce advanced nucleic acid-metallodrug hybrids with sequence-specific gene targeting properties. Here, artificial gene-editing systems were developed using triplex-forming oligonucleotides conjugated to metallodrugs using click chemistry methods. A number of new metallodrugs that can be light and chemically activated were produced (cf. Gasser et al., RSC Chem. Biol., 2022, 3; Kellett et al., RSC Med. Chem., 2024, 15, Kellett et al., Angew. Chemie, 2023, e202305759). Another aim was to crystallise and structurally characterise new metal complexes that can bind in the major groove of DNA. Here, expertise from the Cardin group: i.) Cardin et al., Angew. Chemie, 2024, e202318863; ii.) Cardin et al., Chem. Sci., 2024, 15) was used to identify the structures of new DNA damaging agents. Several of the metallodrugs were then modified and attached to gene targeting groups, such as triplex-forming oligonucleotides, and examined for their sequence-specific interactions with cancer causing genes.
2. Synthesis and delivery of nucleic acid therapeutics that promote cell-based cancer immunotherapy. NATURE-ESRs engaged in the development of geranylated nucleosides to anchor RNA to nanoparticles for transfection. Moreover, one ESR focused on establishing prebiotically plausible scenarios of an RNA–peptide world and this work was published in Nature (Carell et al., Nature, 2022, 605). Another of NATURE’s ESR investigated the stabilisation effects of a specific nucleobase called m6A in RNA constructs, including guide-RNA in combination with dCas13-fused methyltransferases. Further research was dedicated to the design of antisense oligonucleotides containing artificial cleaving agents which have Cas13-like behaviour, but without the protein component. The outcome from this research strategy could have a major future impact on cancer therapy since the work aims to both simultaneously reduce immunogenicity and enhance mRNA expression.
3. Generation of new reagents for high-sensitivity epigenetic base detection. Reading the epigenetic status of DNA bases encoded in the human genome gives us vital information related to gene expression (Carell et al., Nature Communications, 2021, 12; Carell, Kellett et al. Angew. Chemie, 2023, e202215704). NATURE-ETN ESRs focused on sequencing the epigenome and addressed current limitations in sequencing technologies. ESRs attempted to develop breakthrough materials for epigenetic base oxidation for use in next-generation sequencing (NGS). Progress was made on establishing analytical methods for quantification of cAzadC and metabolites prepared using isotopically labelled compounds for metabolic assays. The successful development of this analytical protocol may now enable rapid and parallel monitoring of dC and metabolites thereby revolutionising epigenetic monitoring and diagnostics. In parallel, new Fe(IV)-oxo complexes were investigated as potential new agents capable of oxidising 5mC and 5hmC to 5fC. In this area of research, baseclick GmbH, a NATURE-ETN industrial beneficiary, aimed to exploit other important avenues for probe development. One strategy identified a click chemistry-based method for the generation and amplification of full-length cDNA libraries from total RNA for next-generation sequencing.