A programmable, cell-agnostic DNA nano-technology platform for CRISPR gene editing
Lead Research Organisation:
Imperial College London
Department Name: Chemistry
Abstract
CRISPR-Cas9 gene editing has warranted its developers the 2020 Nobel Prize for Chemistry, in view of the massive impact that this technology is having on biological, biotechnological and medical research.
In particular CRISPR gene editing is central to next generation cell-based therapies to treat cancer and other diseases, in which some of the patient's cells are extracted, genetically modified to fulfil specific functions, and then re-injected into the patient.
This process is however time consuming and very costly, limiting the diffusion of these potentially life-saving therapies. One of the reasons behind the prohibitive costs is the low efficiency with which one can deliver to the cells the biological machinery required to perform CRISPR gene editing, both at scale and without excessive toxicity (leading to cell death).
In this project, we will develop a novel and alternative approach to delivering CRISPR machinery to mammalian cells in vitro. Our approach will rely on specifically designed vectors, which we dub Editosomes. These are microscopic enclosures constructed from lipid membranes, similar to cell membranes, and containing large quantities of the CRISPR machinery.
For Editosomes to deliver the machinery to the target cells the two would have to fuse. We will induce fusion by decorating both Editosomes and the target cells with artificial "fusogenic" nanomachines, that by binding to each other bring the cell and Editosome membranes to within a very short distance, ultimately making them merge. The fusogenic nanostructures will be constructed from synthetic DNA molecules, which are particularly suitable for engineering nanodevices in view of the very high selectivity and programmability of the base-pairing interactions.
We envisage that Editosome technology will have a direct and profound impact on our ability to perform high-throughput, efficient, CRISPR gene editing in vivo, and thus on the accessibility and economic sustainability of the therapeutic technologies that rely on it.
Additionally, we will clarify fundamental aspects of the (bio)physics underling lipid membrane stability, fusion, and the ability of DNA nanostructures to modulate them.
In particular CRISPR gene editing is central to next generation cell-based therapies to treat cancer and other diseases, in which some of the patient's cells are extracted, genetically modified to fulfil specific functions, and then re-injected into the patient.
This process is however time consuming and very costly, limiting the diffusion of these potentially life-saving therapies. One of the reasons behind the prohibitive costs is the low efficiency with which one can deliver to the cells the biological machinery required to perform CRISPR gene editing, both at scale and without excessive toxicity (leading to cell death).
In this project, we will develop a novel and alternative approach to delivering CRISPR machinery to mammalian cells in vitro. Our approach will rely on specifically designed vectors, which we dub Editosomes. These are microscopic enclosures constructed from lipid membranes, similar to cell membranes, and containing large quantities of the CRISPR machinery.
For Editosomes to deliver the machinery to the target cells the two would have to fuse. We will induce fusion by decorating both Editosomes and the target cells with artificial "fusogenic" nanomachines, that by binding to each other bring the cell and Editosome membranes to within a very short distance, ultimately making them merge. The fusogenic nanostructures will be constructed from synthetic DNA molecules, which are particularly suitable for engineering nanodevices in view of the very high selectivity and programmability of the base-pairing interactions.
We envisage that Editosome technology will have a direct and profound impact on our ability to perform high-throughput, efficient, CRISPR gene editing in vivo, and thus on the accessibility and economic sustainability of the therapeutic technologies that rely on it.
Additionally, we will clarify fundamental aspects of the (bio)physics underling lipid membrane stability, fusion, and the ability of DNA nanostructures to modulate them.
Organisations
Publications
Malouf L
(2023)
Sculpting DNA-based synthetic cells through phase separation and phase-targeted activity
in Chem
Paez-Perez M
(2022)
Modulating membrane fusion through the design of fusogenic DNA circuits and bilayer composition.
in Soft matter
| Description | The key objective of the project was to use synthetic vesicles, made with lipid bilayers similar to those of cells, as vectors to deliver CRISPR gene editing machinery into cells. We dubbed these vesicles "editosomes". To aid this delivery, we aimed to use synthetic nanodevices made of DNA, to promote the fusion of the vesicles with cell membranes. As an intermediate step, we studied fusion of small vesicles with larger vesicles mimicking cells. We have systematically studied how the composition of these membranes and the design of the DNA nanodevices influences the efficiency of fusion and delivery as mediated by DNA nanodevices, and determined design rules that will guide future steps involving biological cells. These results are reported in a paper we published in Soft Matter (https://pubs.rsc.org/en/content/articlepdf/2022/sm/d2sm00863g). Additional findings from this project, associated to the interactions between DNA nanodevices and synthetic lipid membranes, have appeared in a recent publication in Chem (https://doi.org/10.1016/j.chempr.2023.10.004), co-authored by the PDRA funded by this project, Dr Miguel Paez Perez |
| Exploitation Route | The results on the effect of membrane composition and DNA-nanostructure design on the fusion efficiency of lipid membranes are general and will be valuable to others wanting to engineer membrane fusion pathways in the context of biomaterials, synthetic biology, biophysics and synthetic cell science. |
| Sectors | Healthcare Manufacturing including Industrial Biotechology Pharmaceuticals and Medical Biotechnology |
| Description | ESPRC Doctoral Prize Fellowship to Dr Miguel Paez-Perez |
| Amount | £70,969 (GBP) |
| Funding ID | EP/W524323 |
| Organisation | Imperial College London |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 11/2022 |
| End | 10/2023 |
| Title | DNA tendrils |
| Description | DNA nanostructures designed to favour fusion between synthetic and biological membranes, as reported in Soft Matter (DOI: 10.1039/D2SM00863G). |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | We are routinely using the DNA tendrils in our research, and are aware of other groups also using them. We are not aware of any non-academic impacts of this technology yet. |
| URL | https://pubs.rsc.org/en/content/articlehtml/2022/sm/d2sm00863g |
| Title | Raw data for "Modulating membrane fusion through the design of fusogenic DNA circuits and bilayer composition" manuscript |
| Description | Raw data associated to publication "Modulating membrane fusion through the design of fusogenic DNA circuits and bilayer composition" Soft Matter, 2022, 18, 7035 DOI: 10.1039/d2sm00863g |
| Type Of Material | Database/Collection of data |
| Year Produced | 2022 |
| Provided To Others? | Yes |
| Impact | These are the raw data in support of the publication mentioned above. The community will be able to carry out their own analysis and scrutinise the results of the paper. |
| URL | https://data.hpc.imperial.ac.uk/resolve/?doi=10867 |
| Title | Research data supporting "Sculpting DNA-based synthetic cells through phase separation and phase-targeted activity" |
| Description | Data repository for work contributing to the paper "Sculpting DNA-based synthetic cells through phase separation and phase-targeted activity". |
| Type Of Material | Database/Collection of data |
| Year Produced | 2023 |
| Provided To Others? | Yes |
| Impact | No impact is known yet given the recent publication |
| URL | https://doi.org/10.17863/CAM.101613 |
