The role of RNA in the response to cellular stress
Lead Research Organisation:
University of Cambridge
Department Name: UNLISTED
Abstract
Recently, a new gene delivery system has been developed, to specifically provide diseased cells with a particular protein to correct cell function. This method using messenger RNA molecules as a delivery vehicle. By changing the RNA molecules different proteins can be encoded on these RNA molecules and different human disease can be treated. However, our lack of understanding of these molecules has resulted in safety issue, which need to be resolved before they can be used to treat a large range of human diseases. Our laboratory has been investigating how RNAs are regulated and we have discovered that two particular RNA binding proteins associate with translationally repressed mRNAs. Using methods developed in our laboratory we can now identify RNA repression mechanisms operating in different tissues and thus tailor these RNA molecules for specific delivery to different tissue types, reducing toxic side effects. We will determine the applicability of this approach to identify the repertoire of repressive mechanisms operating within a cell, in order to engineer therapeutic-mRNAs for restricted on-target expression in particular tissues/cell types and disease states. This will facilitate the development of the next generation of mRNA-based therapeutics which will be specifically designed to minimise potential off-target adverse effects.
Technical Summary
Modulation of gene expression via the delivery of nucleotide-based therapeutics has great potential for the treatment of a large range of human diseases. Major challenges still exist in the development of these next generation drugs due to limitations in our knowledge of RNA biology and delivery methodologies. In recent years, most attention with regard to gene-based therapies has focused on DNA and viral systems; however, their use is limited due to low efficacy, genetic transfer risk and poor control over dosage. More recently, the incorporation of modified nucleotides has meant that in vitro transcribed mRNA molecules have been successfully used for the delivery of genetic information without risk of genomic integration. These mRNAs are produced using modified nucleotides that mimic endogenous mRNA molecules and thus avoid activating the innate immune response. The relatively short half-life of RNA compared to DNA also allows precise control over final protein dosage.
In terms of the safety of these synthetic molecules, there are major challenges that need to be addressed before the full potential of mRNA-based therapeutics can be realised. These issues mainly revolve around our current lack of understanding of how these RNA molecules are controlled. Our laboratory has been investigating how mRNAs are regulated and we have discovered that two RNA DEAD-box helicases associate with translationally repressed mRNAs. The association of mRNAs with these DEAD-box proteins has allowed us to identify multiple repressive mechanisms imposed by the major cellular mRNA silencing apparatus - the Ccr4-NOT complex. Until now, identification of mRNAs controlled by the variety of mechanisms that the Ccr4-NOT complex plays a role in would have been extremely labour-intensive, requiring a number of different techniques and would not have given sufficient resolution for mRNAs with low cellular abundance. In contrast, our methodology is a relatively straightforward approach, which allows for simultaneous identification of mRNAs repressed by the Ccr4-NOT1 complex in a given cell type or tissue. These repressive characteristics can be used to build a signature of the regulatory mechanisms operating within a particular cell type. We will determine the applicability of this approach to identify the repertoire of repressive mechanisms operating within a cell, in order to engineer therapeutic mRNAs for restricted on-target expression in particular tissues/cell types and disease states. This will facilitate the development of the next generation of mRNA-based therapeutics which will be specifically designed to minimise potential off-target adverse effects.
In terms of the safety of these synthetic molecules, there are major challenges that need to be addressed before the full potential of mRNA-based therapeutics can be realised. These issues mainly revolve around our current lack of understanding of how these RNA molecules are controlled. Our laboratory has been investigating how mRNAs are regulated and we have discovered that two RNA DEAD-box helicases associate with translationally repressed mRNAs. The association of mRNAs with these DEAD-box proteins has allowed us to identify multiple repressive mechanisms imposed by the major cellular mRNA silencing apparatus - the Ccr4-NOT complex. Until now, identification of mRNAs controlled by the variety of mechanisms that the Ccr4-NOT complex plays a role in would have been extremely labour-intensive, requiring a number of different techniques and would not have given sufficient resolution for mRNAs with low cellular abundance. In contrast, our methodology is a relatively straightforward approach, which allows for simultaneous identification of mRNAs repressed by the Ccr4-NOT1 complex in a given cell type or tissue. These repressive characteristics can be used to build a signature of the regulatory mechanisms operating within a particular cell type. We will determine the applicability of this approach to identify the repertoire of repressive mechanisms operating within a cell, in order to engineer therapeutic mRNAs for restricted on-target expression in particular tissues/cell types and disease states. This will facilitate the development of the next generation of mRNA-based therapeutics which will be specifically designed to minimise potential off-target adverse effects.
People |
ORCID iD |
Martin Bushell (Principal Investigator) |
Publications
Arnould C
(2023)
Chromatin compartmentalization regulates the response to DNA damage.
in Nature
Bader AS
(2023)
iMUT-seq: high-resolution DSB-induced mutation profiling reveals prevalent homologous-recombination dependent mutagenesis.
in Nature communications
Bader AS
(2022)
DDX17 is required for efficient DSB repair at DNA:RNA hybrid deficient loci.
in Nucleic acids research
Bader AS
(2020)
DNA:RNA hybrids form at DNA double-strand breaks in transcriptionally active loci.
in Cell death & disease
Bader AS
(2020)
The roles of RNA in DNA double-strand break repair.
in British journal of cancer
Godfrey JD
(2018)
MiR-142-3p is downregulated in aggressive p53 mutant mouse models of pancreatic ductal adenocarcinoma by hypermethylation of its locus.
in Cell death & disease
Grosso S
(2021)
The pathogenesis of mesothelioma is driven by a dysregulated translatome.
in Nature communications
Lu WT
(2018)
Drosha drives the formation of DNA:RNA hybrids around DNA break sites to facilitate DNA repair.
in Nature communications
Marini A
(2018)
TAp73 contributes to the oxidative stress response by regulating protein synthesis.
in Proceedings of the National Academy of Sciences of the United States of America
Related Projects
Project Reference | Relationship | Related To | Start | End | Award Value |
---|---|---|---|---|---|
MC_UU_00025/1 | 31/03/2018 | 30/07/2020 | £1,680,000 | ||
MC_UU_00025/2 | Transfer | MC_UU_00025/1 | 31/03/2018 | 29/09/2020 | £3,488,000 |
MC_UU_00025/3 | Transfer | MC_UU_00025/2 | 31/03/2018 | 30/03/2027 | £3,703,000 |
MC_UU_00025/4 | Transfer | MC_UU_00025/3 | 31/03/2018 | 31/03/2024 | £3,108,000 |
MC_UU_00025/5 | Transfer | MC_UU_00025/4 | 31/03/2018 | 31/03/2024 | £2,200,000 |
MC_UU_00025/6 | Transfer | MC_UU_00025/5 | 31/03/2018 | 30/05/2019 | £76,000 |
MC_UU_00025/7 | Transfer | MC_UU_00025/6 | 31/03/2018 | 31/03/2024 | £2,547,000 |
MC_UU_00025/8 | Transfer | MC_UU_00025/7 | 30/09/2019 | 31/03/2024 | £2,438,000 |
MC_UU_00025/9 | Transfer | MC_UU_00025/8 | 31/08/2019 | 31/03/2024 | £1,721,000 |
Description | CRT translational control allience |
Amount | £23,000,000 (GBP) |
Organisation | Cancer Research Technology (CRT) |
Sector | Private |
Country | United Kingdom |
Start | 05/2018 |
End | 06/2021 |
Description | BMS collaboration using tool compounds to target eIF2B |
Organisation | Bristol-Myers Squibb |
Country | United States |
Sector | Private |
PI Contribution | We have initiated a collocation with BMS to evaluate targeting eIF2B activity in the tour environment |
Collaborator Contribution | Providing tool compounds and funding. |
Impact | Funding from BMS (£218,000) |
Start Year | 2021 |
Description | CTR Collaboration |
Organisation | Cancer Research Technology (CRT) |
Country | United Kingdom |
Sector | Private |
PI Contribution | Our Lab is actively engaged with CRT within a new alliance to target translational control. |
Collaborator Contribution | Drug discovery efforts |
Impact | This has just begun and no outputs so far |
Start Year | 2017 |
Description | Cancer Research Technology mRNA Translation |
Organisation | Cancer Research Technology (CRT) |
Country | United Kingdom |
Sector | Private |
PI Contribution | This is a drug discovery pipeline around translational control. I am a led PI within this consortium directly contributing to multiple projects. |
Collaborator Contribution | CRT are conducting the drug discovery activities within this alliance. |
Impact | I outputs currently that I can comment upon. |
Start Year | 2017 |
Description | Bart's RNA and cancer meeting June 2023 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited speaker. I give a talk about our research and people were very positive and said it had changed the way they were thinking about translational control |
Year(s) Of Engagement Activity | 2023 |
Description | Belfast talk |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | I give a talk about our research and people were very positive and said it had changed the way they were thinking about translational control |
Year(s) Of Engagement Activity | 2023 |
Description | Feb congress Tours France |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I give a talk about our research and people were very positive and said it had changed the way they were thinking about translational control |
Year(s) Of Engagement Activity | 2023 |
URL | https://2023.febscongress.org/program |
Description | Geneve |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | Invited speaker at Univ of Geneva |
Year(s) Of Engagement Activity | 2022 |
Description | Invited Speaker Sussex Univ |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Invited speaker at Sussex University. Gave a talk on translation control and changed the way people think about this level of gene expression control |
Year(s) Of Engagement Activity | 2019 |
Description | Invited Speaker Wurburg |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited speaker in Wurzburg Germany. I gave a talk to science in the area and got great feedback and changed the way they think about translational control |
Year(s) Of Engagement Activity | 2020 |
Description | Invited speaker CSHL |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited speaker at CSHL translational control meeting |
Year(s) Of Engagement Activity | 2022 |
Description | Invited speaker Dundee |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Professional Practitioners |
Results and Impact | Invited speaker at the University of Dundee. Gave a talk on translational control and changed the way they think about this level of gene expression control. |
Year(s) Of Engagement Activity | 2019 |
Description | Invited speaker Galway |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited speaker Galway Ireland. Gave a talk on translational control and changed the way they think about this level of gene regulation. |
Year(s) Of Engagement Activity | 2019 |
Description | Invited speaker european society of toxicologist |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | To talk to the European Society of toxicologist. |
Year(s) Of Engagement Activity | 2021 |
Description | Organiser for Beatson International Science Meeting |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Postgraduate students |
Results and Impact | I was one of the organisers for this meeting which brought in people from all over the world to talk about their recent results. One of the sessions was focused on translational control which I run and talked in. |
Year(s) Of Engagement Activity | 2019 |
Description | Royal pathology Society invited speaker |
Form Of Engagement Activity | A formal working group, expert panel or dialogue |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Professional Practitioners |
Results and Impact | Presentation was to the Royal Society of pathologist. To update them in emerging technologies round RNA based therapeutic and prognostic approaches. |
Year(s) Of Engagement Activity | 2022 |
Description | Translation UK 2020 organiser |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | This is a major meeting for the whole field and occurs yearly. I was an organiser for this meeting. Importantly this year we had a large number of people from industry activity developing drugs to target this field and they sponsored this meeting and chaired a session. Got great feed back about this meeting and how good it was. This was organiser by the biochem doc. |
Year(s) Of Engagement Activity | 2019 |
Description | Translation UK Keynote address Cambridge July 2023 |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | I was asked to give the keynote address at the translation UK. I give a talk about our research and people were very positive and said it had changed the way they were thinking about translational control |
Year(s) Of Engagement Activity | 2023 |
Description | UCSF talk |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited speaker UCSF |
Year(s) Of Engagement Activity | 2022 |