Identifying the transcriptomic basis underlying individualised drug response: moving towards personalised medicine in motor neurone disease (MND) usin
Lead Research Organisation:
University of Sheffield
Department Name: Neurosciences
Abstract
Individual genetic characteristics determine how we respond to drugs, thus the need to identify the molecular mechanisms involved in treatment response. This will allow to assign the most effective drug to different groups of patients depending on their genetics. While this approach is used in asthma and cancer, no match between genetic profile and therapy has been identified for patients affected by neurodegenerative disorders.
Motor neurone disease (MND) is the most common adult onset motor disorder, characterized by progressive loss of motoneurons and death. In vitro studies pioneered by the supervisor and others have shown that astrocytes from MND patients cause wild-type motoneuron death (Re et al 2014; Meyer et al 2014).
At present, Riluzole is the only drug licensed for the treatment of MND. The mechanism(s) of action is/are unclear and it is thought that Riluzole might be active through various pathways.
Moreover, a drug screening performed in our laboratories has identified 3 potent activators of Nrf2, a transcription factor driving the expression of multiple cytoprotective genes via its interaction with the antioxidant response element (ARE) (Mead et al 2013). We have now screened increasing doses of these 3 ARE activators, as well Riluzole in a co-culture system with patient astrocytes and motoneurons. Patient astrocytes typically lead to a decrease in motoneuron survival by 50%. We found that treatment of astrocytes with these 4 compounds dampens their toxicity towards motoneurons, thus leading to an increase in motoneuron survival, depending on the donor genetic subtype.
The main aims of this study are 1) to identify modes of riluzole and ARE activators action on gene expression in astrocytes and 2) correlate the mechanism of action of specific drugs with donor genotype.
Research strategy: We will derive astrocytes from human induced neural progenitors (iNPCs) and differentiate them to astrocytes as previously described (Meyer et al 2014). We will use astrocytes from patients carrying mutations associated with MND, namely SOD1, C9orf72 and TDP43, sporadic ALS patients and controls. We will screen 3 different concentrations of Riluzole as well as 3 concentrations of each of the 3 ARE activators.
We will identify the most effective concentration of each treatment and perform RNA-sequencing before and after drug treatment.
The student will develop significant bioinformatics skills by working with the large bioinformatics group within the Institute. We will determine 1. The modes of action of each drug by comparing differentially expressed transcripts between treated and untreated samples, both patients and controls.
2. The different mechanism of action of each drug on groups of patients carrying different mutations by comparing the transcripts involved in drug response between those groups.
Identifying groups of transcripts involved in specific drug response in patients with defined genetic mutations will also help us better categorise sporadic patients, accounting for 95% of all ALS cases.
To validate our screening, we will also perform RNA-Sequencing of 10 additional sporadic samples, predict which ARE activator they should be more responsive to by looking at their transcriptomic profile and test the results in our co-culture assay.
Motor neurone disease (MND) is the most common adult onset motor disorder, characterized by progressive loss of motoneurons and death. In vitro studies pioneered by the supervisor and others have shown that astrocytes from MND patients cause wild-type motoneuron death (Re et al 2014; Meyer et al 2014).
At present, Riluzole is the only drug licensed for the treatment of MND. The mechanism(s) of action is/are unclear and it is thought that Riluzole might be active through various pathways.
Moreover, a drug screening performed in our laboratories has identified 3 potent activators of Nrf2, a transcription factor driving the expression of multiple cytoprotective genes via its interaction with the antioxidant response element (ARE) (Mead et al 2013). We have now screened increasing doses of these 3 ARE activators, as well Riluzole in a co-culture system with patient astrocytes and motoneurons. Patient astrocytes typically lead to a decrease in motoneuron survival by 50%. We found that treatment of astrocytes with these 4 compounds dampens their toxicity towards motoneurons, thus leading to an increase in motoneuron survival, depending on the donor genetic subtype.
The main aims of this study are 1) to identify modes of riluzole and ARE activators action on gene expression in astrocytes and 2) correlate the mechanism of action of specific drugs with donor genotype.
Research strategy: We will derive astrocytes from human induced neural progenitors (iNPCs) and differentiate them to astrocytes as previously described (Meyer et al 2014). We will use astrocytes from patients carrying mutations associated with MND, namely SOD1, C9orf72 and TDP43, sporadic ALS patients and controls. We will screen 3 different concentrations of Riluzole as well as 3 concentrations of each of the 3 ARE activators.
We will identify the most effective concentration of each treatment and perform RNA-sequencing before and after drug treatment.
The student will develop significant bioinformatics skills by working with the large bioinformatics group within the Institute. We will determine 1. The modes of action of each drug by comparing differentially expressed transcripts between treated and untreated samples, both patients and controls.
2. The different mechanism of action of each drug on groups of patients carrying different mutations by comparing the transcripts involved in drug response between those groups.
Identifying groups of transcripts involved in specific drug response in patients with defined genetic mutations will also help us better categorise sporadic patients, accounting for 95% of all ALS cases.
To validate our screening, we will also perform RNA-Sequencing of 10 additional sporadic samples, predict which ARE activator they should be more responsive to by looking at their transcriptomic profile and test the results in our co-culture assay.
People |
ORCID iD |
Laura Ferraiuolo (Primary Supervisor) | |
Chloe Allen (Student) |
Publications
Leah T
(2021)
A Parkinson's Disease-relevant Mitochondrial and Neuronal Morphology High-throughput Screening Assay in LUHMES Cells.
in Bio-protocol
Ciervo Y
(2021)
Adipose-derived stem cells protect motor neurons and reduce glial activation in both in vitro and in vivo models of ALS
in Molecular Therapy - Methods & Clinical Development
Allen SP
(2019)
Astrocyte adenosine deaminase loss increases motor neuron toxicity in amyotrophic lateral sclerosis.
in Brain : a journal of neurology
Allen SP
(2019)
C9orf72 expansion within astrocytes reduces metabolic flexibility in amyotrophic lateral sclerosis.
in Brain : a journal of neurology
Marchi PM
(2022)
C9ORF72-derived poly-GA DPRs undergo endocytic uptake in iAstrocytes and spread to motor neurons.
in Life science alliance
Allen CF
(2017)
Can Astrocytes Be a Target for Precision Medicine?
in Advances in experimental medicine and biology
Ferraiuolo L
(2018)
Lost in translation: microRNAs mediate pathological cross-talk between motor neurons and astrocytes.
in Brain : a journal of neurology
Varcianna A
(2019)
Micro-RNAs secreted through astrocyte-derived extracellular vesicles cause neuronal network degeneration in C9orf72 ALS.
in EBioMedicine
Iannitti T
(2018)
Translating SOD1 Gene Silencing toward the Clinic: A Highly Efficacious, Off-Target-free, and Biomarker-Supported Strategy for fALS.
in Molecular therapy. Nucleic acids
Studentship Projects
Project Reference | Relationship | Related To | Start | End | Student Name |
---|---|---|---|---|---|
MR/N013840/1 | 01/10/2016 | 30/09/2025 | |||
1812144 | Studentship | MR/N013840/1 | 01/10/2016 | 31/07/2020 | Chloe Allen |
Description | AMS horizon scanning workshop |
Geographic Reach | National |
Policy Influence Type | Participation in a guidance/advisory committee |
Description | AstraZeneca Post-doctoral programme |
Amount | £250,000 (GBP) |
Organisation | AstraZeneca |
Sector | Private |
Country | United Kingdom |
Start | 08/2018 |
End | 07/2020 |
Description | Celgene: - investigate a metabolic therapeutic target in glia in MND and PD |
Amount | £663,415 (GBP) |
Organisation | Bristol-Myers Squibb |
Department | Celgene |
Sector | Private |
Country | United States |
Start | 01/2020 |
End | 12/2022 |
Description | ITN-Horizon 2020 |
Amount | € 250,000 (EUR) |
Organisation | European Commission |
Department | Horizon 2020 |
Sector | Public |
Country | European Union (EU) |
Start | 09/2018 |
End | 08/2021 |
Description | MRC Flexible Supplement Funding |
Amount | £495 (GBP) |
Funding ID | DiMeN Flexible Funding code - X/011118-11 |
Organisation | University of Sheffield |
Sector | Academic/University |
Country | United Kingdom |
Start | 04/2018 |
End | 03/2020 |
Description | Springboard |
Amount | £100,000 (GBP) |
Organisation | Academy of Medical Sciences (AMS) |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2017 |
End | 08/2019 |
Description | Use of machine learning to identify new therapeutic targets for motor neurone disease |
Amount | £35,000 (GBP) |
Organisation | Precisionlife |
Sector | Private |
Country | United Kingdom |
Start | 01/2020 |
End | 12/2020 |
Title | human co-cultures |
Description | My group has developed an in vitro co-culture system that utilises human astrocytes and motor neurones derived from fibroblasts isolated from patients or healthy controls. |
Type Of Material | Model of mechanisms or symptoms - in vitro |
Year Produced | 2017 |
Provided To Others? | Yes |
Impact | This is a totally humanised model of disease that will considerably reduce the use of animal models |
URL | https://www.ncbi.nlm.nih.gov/pubmed/28677678 |
Title | RNA-Seq of human reprogrammed astrocytes |
Description | RNA-Seq of astrocytes reprogrammed from MND patients carrying various mutations and controls has been performed before and after drug treatment with 3 different drugs. The transcriptomic profile has highlighted biological differences between patients and controls, drug response in different genotypes and patient responders and non-responders. |
Type Of Material | Database/Collection of data |
Year Produced | 2020 |
Provided To Others? | No |
Impact | We do not have any measurable impact yet, but we expect this dataset to have important implications in understanding disease biology and drug response. In addition, and most important, we are planning to validate the drug response results in patients during a Phase II clinical trial. |
Description | BenevolentAI |
Organisation | BenevolentAI |
Country | United Kingdom |
Sector | Private |
PI Contribution | My team provides material and expertise in the field of motor neurone disease (MND) in selecting and developing new therapeutics. |
Collaborator Contribution | BenevolentAI provides expertise in chemistry and artificial intelligence |
Impact | This collaboration is multidisciplinary, involving basic biology, chemistry and bioinformatics expertise. |
Start Year | 2016 |
Description | Collaboration with Forma Therapeutics |
Organisation | FORMA Therapeutics |
Country | United States |
Sector | Private |
PI Contribution | As part of the collaboration, neurons from selected MND patients will be assessed for parameters agreed with Forma before and after drug treatment. The work will be conducted in collaboration with Dr Mortiboys |
Collaborator Contribution | Forma will provide selected compounds and expertise. |
Impact | No outputs are available yet. |
Start Year | 2018 |
Description | Using a machine learning approach to identify drug targets for ALS |
Organisation | Precisionlife |
Country | United Kingdom |
Sector | Private |
PI Contribution | When we were approached by Precisionlife we assessed their list of targets and proposed, designed and are performing in vitro assays based on patient biosamples. |
Collaborator Contribution | Precisionlife identified potential therapeutic targets based on their machine learning system and are currently providing compounds for us to screen in our in vitro assay. |
Impact | We still do not have outcomes to report |
Start Year | 2020 |
Description | ALS Research Awareness Event - Meadowhall |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | I volunteered at an event organised by the South Yorkshire Motor Neurone Disease Association in Meadowhall to raise money and awareness of the disease and care in place for people living with MND in the local area. I put on events for children, including the making of paper neurons and brain hats, and adults by showing them slides of brain cells under a microscope and talking about the research we do. The event raised roughly £200-300 for the charity and encouraged the general public to come to the open day at our department to learn more. |
Year(s) Of Engagement Activity | 2019 |
Description | Article featuring the work carried out by my laboratory in the March issue of Scitech Europa (PanEuropeanNetwork) |
Form Of Engagement Activity | A magazine, newsletter or online publication |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Media (as a channel to the public) |
Results and Impact | The PanEuropean Network aims to provide news and developments from across the entire spectrum of the European science and technology community. I was invited to submit an article about the work my lab carries out with industry and the support of EU funding. The audience of the journal is composed of EU commissioners and policy makers as well as scientists and the wider audience. |
Year(s) Of Engagement Activity | 2018 |
URL | http://edition.pagesuite-professional.co.uk/html5/reader/production/default.aspx?pubname=&edid=0e6f6... |
Description | Astrocyte tent at the Festival of the Mind |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | As part of the Public event "Festival of the Mind" in Sheffield, my group and I worked closely with an artist to produce a tent covered by 200 fluorescent astrocytes and an animation with voice-over to explain the role of astrocytes in health and disease. The event takes place every year and is visited by 50,000 people from Yorkshire and probably outside and received good national media coverage. |
Year(s) Of Engagement Activity | 2016 |
Description | SITraN Open Day |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Public/other audiences |
Results and Impact | About 50 people attended a visit of the Research Institute where I am based. We showed the public our research facility and showcased the research ongoing at SITraN, including the Parkinson's UK funded project |
Year(s) Of Engagement Activity | 2017 |
Description | School Visit |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Kids from 3 different grades attended the science workshop, which sparked their interest in neuroscience |
Year(s) Of Engagement Activity | 2016,2017,2018,2019 |
Description | School Visit to Malin Bridge Primary School & Bradfield Dungworth Primary School |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | A group of PhD students and post-doctoral researchers visited these two school on separate occasions to teach the children about the nervous system. The head PI gave the children a talk to introduce the topic and answer questions. The children were then split into small groups and would visit several different activities organised by the PhD students and post-docs e.g. making paper neurons, making brain hats, looking at samples under the microscope and simple experiments testing their reflexes. We received great feedback from the school and have been invited to teach other year groups. |
Year(s) Of Engagement Activity | 2017,2018 |
Description | Soak a Scientist |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Every summer, students at SITraN organise the 'Soak a Scientist' charity event in Endcliffe Park to commemorate the Ice Bucket Challenge which raised money for MND research. I was in charge of organising the event along with the local South Yorkshire MNDA branch to raise funds for MND research taking place in SITraN and to raise awareness of the MND charity. We raised £300 for research by selling cakes, raffle tickets and the main event in which the general public would throw ice cold buckets of water over our scientists. |
Year(s) Of Engagement Activity | 2017,2018 |
Description | Social Media Representative for the South Yorkshire Motor Neurone Disease Association |
Form Of Engagement Activity | Engagement focused website, blog or social media channel |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Patients, carers and/or patient groups |
Results and Impact | As the Social Media Representative for the South Yorkshire MNDA Branch, I am responsible for advertising upcoming charity events on the branch's Facebook and Twitter account and keeping the accounts up to date with news items which would interest folllwers of the accounts. |
Year(s) Of Engagement Activity | 2016,2017,2018,2019 |
Description | Talk at the SITraN Open Day |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Patients, carers and/or patient groups |
Results and Impact | A broad talk about mitochondrial drug screening in patient derived models of Parkinson's Disease. |
Year(s) Of Engagement Activity | 2017 |
Description | Talk at the South Yorkshire MNDA Open Meeting |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Supporters |
Results and Impact | I was invited to speak about my experience at the International MND Symposium in Perth by our local charity, the South Yorkshire MNDA which also offered £500 towards my travel for the conference. I was able to speak to attendees about the latest research on the disease presented at the conference for a lay audience. After my presentation, I received emails from the organisers that everyone enjoyed my talk and it was at the right level of understanding. |
Year(s) Of Engagement Activity | 2019 |
Description | Women Intrepreneurs |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Industry/Business |
Results and Impact | I had the opportunity to present my research activities in the field of neurodegeneration to a group of potential donors, all female business owners in the Yorkshire area. |
Year(s) Of Engagement Activity | 2019 |