Programming the Notch Response
Lead Research Organisation:
University of Cambridge
Department Name: Physiology Development and Neuroscience
Abstract
To build and maintain our tissues so that they are the correct shape and size it is vital that the building blocks, the cells, are able to talk to one another. They do so via specialized communication devices, one of which uses a receiver called Notch. When Notch receives a signal it then gives the cell instructions about what to do, for example whether or not to multiply. Under normal conditions there are checks and balances in the system to ensure that the cells signal correctly. However, in several types of cancers Notch signalling doesn't function properly. In many of these conditions, including T-cell acute lymphoblastic leukemia and breast cancers, there ends up being too much signal causing the cells to multiply excessively, forming tumours. Surprisingly, in some other types of cancer the converse is the case. This means that the instructions sent by Notch when it receives the signal must be different. It also makes it more difficult to use drug treatments that simply shut off the Notch signal as they could have damaging effects in some tissues.
By answering two key questions we hope to identify strategies that could be used to develop more targeted drugs so avoiding these problems. First we aim to discover what are the normal checks that prevent the Notch pathway running out-of control and how these get damaged. Second we will find out what is responsible for coding the instructions sent by Notch once it receives the signal. To do this we will use both the fruit fly and human cells and will undertake large scale analysis that allows us to read all of the instructions, in the form of the genes that are "turned on", in normal tissue and in tissues that grow too much because they have extra Notch activity. In parallel we will use strategies that enable us to find the components in cells that help Notch to pick out which genes to turn on. We use fruit flies because they have a simpler system that we can easily study in the living organism, making it more straightforward to decipher the information, yet they have over 80% of the human disease-causing genes. We then translate our discoveries from fruit-flies into the more complex human breast cells to show their relevance for disease and to identify the best routes towards uses in the clinic.
By answering two key questions we hope to identify strategies that could be used to develop more targeted drugs so avoiding these problems. First we aim to discover what are the normal checks that prevent the Notch pathway running out-of control and how these get damaged. Second we will find out what is responsible for coding the instructions sent by Notch once it receives the signal. To do this we will use both the fruit fly and human cells and will undertake large scale analysis that allows us to read all of the instructions, in the form of the genes that are "turned on", in normal tissue and in tissues that grow too much because they have extra Notch activity. In parallel we will use strategies that enable us to find the components in cells that help Notch to pick out which genes to turn on. We use fruit flies because they have a simpler system that we can easily study in the living organism, making it more straightforward to decipher the information, yet they have over 80% of the human disease-causing genes. We then translate our discoveries from fruit-flies into the more complex human breast cells to show their relevance for disease and to identify the best routes towards uses in the clinic.
Technical Summary
Notch signalling is critical for many aspects of development, from stem cell maintenance to epithelial growth control, and its dysregulation underlies many diseases, especially cancers. These conditions of pathological Notch signalling reveal that there must exist mechanisms that normally keep the Notch pathway in check, which are defective in these diseases. Furthermore, although Notch activity promotes tumourigenesis in many contexts, including T-cell acute lymphoblastic leukaemia and breast cancers, in others Notch acts to suppress tumours, making it problematic to rely on general Notch inhibitors for therapeutic intervention. It is important therefore to discover how different subsets of genes are selected for Notch regulation to account for the disparate outcomes of Notch activity.
Our goal is to use a combination of genomic, genetic and biochemical approaches in Drosophila and in human cells to discover the fundamental mechanisms that programme different Notch responses. As Notch acts directly to change gene expression, our primary focus is on the network of genes that are Notch-regulated in different contexts, including tissue hyperplasia. We have two major aims: (1) to discover the mechanisms that normally attenuate Notch signalling in different tissues and how this machinery is disrupted in disease models (2) to elucidate how genes are selected to be Notch-responsive, yielding tissue-specific differences in the outcome of Notch signalling.
Our results will uncover general principles that explain how these diverse effects of Notch activation arise in tissue development and in different types of cancers, especially breast cancers. In doing so they will identify mechanisms of attenuation and of gene selection that are indicative of particular disease outcomes, permitting better diagnosis, and suggest strategies for targeted therapies to avoid the serious side effects from more general Notch inhibitors.
Our goal is to use a combination of genomic, genetic and biochemical approaches in Drosophila and in human cells to discover the fundamental mechanisms that programme different Notch responses. As Notch acts directly to change gene expression, our primary focus is on the network of genes that are Notch-regulated in different contexts, including tissue hyperplasia. We have two major aims: (1) to discover the mechanisms that normally attenuate Notch signalling in different tissues and how this machinery is disrupted in disease models (2) to elucidate how genes are selected to be Notch-responsive, yielding tissue-specific differences in the outcome of Notch signalling.
Our results will uncover general principles that explain how these diverse effects of Notch activation arise in tissue development and in different types of cancers, especially breast cancers. In doing so they will identify mechanisms of attenuation and of gene selection that are indicative of particular disease outcomes, permitting better diagnosis, and suggest strategies for targeted therapies to avoid the serious side effects from more general Notch inhibitors.
Planned Impact
Beneficiaries:
-Industry involved in pharmaceutical research and drug development.
-Medical profession involved in treating Notch related diseases including cancers
-Business, industrial and public sector recruiting graduate level staff.
-The general public and schools, through our involvement in public engagement.
Benefits to industry will come from the scientific results and the methodologies we develop:
Notch pathway is a major target for cancer and other therapeutics. Increased knowledge about the mechanisms can lead to novel approaches for targeting the pathway and can be important in informing about unforeseen side effects. For example, our results should improve the ability to "read" better the types of targets that could be activated in a particular disease context, important because the outcomes can be very different (e.g. tumour promoting versus tumour suppressing). They could also identify novel protein:protein interactions that would be a good substrate for drug developments. Benefit is likely to be realized in the longer term and it would impact especially on enhancing quality of health.
Benefits to medicine will come from the scientific results and the insights into clinically relevant mechanisms:
A better understanding of the types and functions of Notch targets and how they are selected could be extremely valuable in diagnostic strategies because classical Notch targets (e.g., HES1) do not necessarily appear to be modulated in patient tissues. Results will also suggest new possibilities to improve on therapies targeting the Notch pathway. Currently, the main strategies use small molecule inhibitors of gamma-secretase and have serious side effects such as goblet cell metaplasia, as well as off target effects. The discovery of novel regulatory mechanisms in a subset of tissues could lead to more targeted therapies to overcome these problems.
Benefits to business, industrial and public sector recruiting graduate level staff will come from the development of relevant research sills and professional skills:
The project's diverse nature ensures that the staff will acquire a broad range of technical skills (high-end genomic and molecular biology techniques, computational approaches for working with large data sets), which will be applicable in wide range of life sciences, pharmaceutical, computational employment. Further gains come from our international collaborations, enhancing the skills training and exposure. Alongside technical skills, staff will at the same time develop generic professional skills e.g. presentational skills; writing skills; data handling, including statistics; generic computational skills; project management. Evidence of our track record in this aspect comes from subsequent employment of staff from our groups (e.g. investment banking, parliamentary advisor, publishing, venture capital advisor).
Benefits to the general public and schools, through our involvement in public engagement:
We have been involved in communicating modern scientific methodologies and approaches to the wider community. These activities will be extended to encourage scientific understanding and to extend the concepts from our research into other fields. The University of Cambridge provides excellent support for public dissemination of research through the Office of Community Affairs, including the Cambridge Science Festival, and we shall encourage the researchers to participate in these activities.
-Industry involved in pharmaceutical research and drug development.
-Medical profession involved in treating Notch related diseases including cancers
-Business, industrial and public sector recruiting graduate level staff.
-The general public and schools, through our involvement in public engagement.
Benefits to industry will come from the scientific results and the methodologies we develop:
Notch pathway is a major target for cancer and other therapeutics. Increased knowledge about the mechanisms can lead to novel approaches for targeting the pathway and can be important in informing about unforeseen side effects. For example, our results should improve the ability to "read" better the types of targets that could be activated in a particular disease context, important because the outcomes can be very different (e.g. tumour promoting versus tumour suppressing). They could also identify novel protein:protein interactions that would be a good substrate for drug developments. Benefit is likely to be realized in the longer term and it would impact especially on enhancing quality of health.
Benefits to medicine will come from the scientific results and the insights into clinically relevant mechanisms:
A better understanding of the types and functions of Notch targets and how they are selected could be extremely valuable in diagnostic strategies because classical Notch targets (e.g., HES1) do not necessarily appear to be modulated in patient tissues. Results will also suggest new possibilities to improve on therapies targeting the Notch pathway. Currently, the main strategies use small molecule inhibitors of gamma-secretase and have serious side effects such as goblet cell metaplasia, as well as off target effects. The discovery of novel regulatory mechanisms in a subset of tissues could lead to more targeted therapies to overcome these problems.
Benefits to business, industrial and public sector recruiting graduate level staff will come from the development of relevant research sills and professional skills:
The project's diverse nature ensures that the staff will acquire a broad range of technical skills (high-end genomic and molecular biology techniques, computational approaches for working with large data sets), which will be applicable in wide range of life sciences, pharmaceutical, computational employment. Further gains come from our international collaborations, enhancing the skills training and exposure. Alongside technical skills, staff will at the same time develop generic professional skills e.g. presentational skills; writing skills; data handling, including statistics; generic computational skills; project management. Evidence of our track record in this aspect comes from subsequent employment of staff from our groups (e.g. investment banking, parliamentary advisor, publishing, venture capital advisor).
Benefits to the general public and schools, through our involvement in public engagement:
We have been involved in communicating modern scientific methodologies and approaches to the wider community. These activities will be extended to encourage scientific understanding and to extend the concepts from our research into other fields. The University of Cambridge provides excellent support for public dissemination of research through the Office of Community Affairs, including the Cambridge Science Festival, and we shall encourage the researchers to participate in these activities.
People |
ORCID iD |
Sarah Bray (Principal Investigator) |
Publications
Boukhatmi H
(2020)
Notch Mediates Inter-tissue Communication to Promote Tumorigenesis.
Boukhatmi H
(2020)
Notch Mediates Inter-tissue Communication to Promote Tumorigenesis.
in Current biology : CB
Boukhatmi H
(2018)
A population of adult satellite-like cells in Drosophila is maintained through a switch in RNA-isoforms.
in eLife
Bray S
(2016)
Notch signalling in context.
Bray S
(2018)
Notch after cleavage.
Bray SJ
(2018)
Notch after cleavage.
in Current opinion in cell biology
Bray SJ
(2016)
Notch signalling in context.
in Nature reviews. Molecular cell biology
Chan SKK
(2017)
Role of co-repressor genomic landscapes in shaping the Notch response.
in PLoS genetics
Djiane A
(2014)
Notch inhibits Yorkie activity in Drosophila wing discs.
in PloS one
Djiane A
(2014)
Notch inhibits Yorkie activity in Drosophila wing discs.
Falo-Sanjuan J
(2020)
Decoding the Notch signal.
Falo-Sanjuan J
(2019)
Enhancer Priming Enables Fast and Sustained Transcriptional Responses to Notch Signaling.
in Developmental cell
Falo-Sanjuan J
(2020)
Decoding the Notch signal.
in Development, growth & differentiation
Feng S
(2020)
The SLC36 transporter Pathetic is required for neural stem cell proliferation and for brain growth under nutrition restriction.
in Neural development
Gomez-Lamarca M
(2018)
Activation of the Notch Signaling Pathway In Vivo Elicits Changes in CSL Nuclear Dynamics.
Gomez-Lamarca M
(2015)
Rme-8 depletion perturbs Notch recycling and predisposes to pathogenic signaling
in Journal of Cell Biology
Gomez-Lamarca MJ
(2018)
Activation of the Notch Signaling Pathway In Vivo Elicits Changes in CSL Nuclear Dynamics.
in Developmental cell
Housden BE
(2014)
Context-dependent enhancer selection confers alternate modes of notch regulation on argos.
in Molecular and cellular biology
Li J
(2014)
Notch signaling assays in Drosophila cultured cell lines.
in Methods in molecular biology (Clifton, N.J.)
Logeay R
(2022)
Mechanisms underlying the cooperation between loss of epithelial polarity and Notch signaling during neoplastic growth in Drosophila.
in Development (Cambridge, England)
Mihajlovic Z
(2019)
Lime is a new protein linking immunity and metabolism in Drosophila.
in Developmental biology
Pillidge Z
(2019)
SWI/SNF chromatin remodeling controls Notch-responsive enhancer accessibility.
in EMBO reports
Pézeron G
(2014)
Notch directly regulates cell morphogenesis genes, Reck , talin and trio , in adult muscle progenitors
in Journal of Cell Science
Simón R
(2014)
Drosophila p53 controls Notch expression and balances apoptosis and proliferation.
in Apoptosis : an international journal on programmed cell death
Skalska L
(2015)
Chromatin signatures at Notch-regulated enhancers reveal large-scale changes in H3K56ac upon activation.
in The EMBO journal
Slaninova V
(2016)
Notch stimulates growth by direct regulation of genes involved in the control of glycolysis and the tricarboxylic acid cycle.
in Open biology
Terriente-Félix A
(2017)
A Drosophila model of myeloproliferative neoplasm reveals a feed-forward loop in the JAK pathway mediated by p38 MAPK signalling.
in Disease models & mechanisms
Wong CC
(2014)
Inactivating CUX1 mutations promote tumorigenesis.
in Nature genetics
Yao L
(2017)
Genome-wide identification of Grainy head targets in Drosophila reveals regulatory interactions with the POU domain transcription factor Vvl.
in Development (Cambridge, England)
Zacharioudaki E
(2018)
Mi-2/NuRD complex protects stem cell progeny from mitogenic Notch signaling
Zacharioudaki E
(2019)
Mi-2/NuRD complex protects stem cell progeny from mitogenic Notch signaling.
in eLife
Zacharioudaki E
(2016)
Genes implicated in stem cell identity and temporal programme are directly targeted by Notch in neuroblast tumours.
in Development (Cambridge, England)
Zacharioudaki E
(2019)
Mi-2/NuRD complex protects stem cell progeny from mitogenic Notch signaling.
Zacharioudaki E
(2014)
Tools and methods for studying Notch signaling in Drosophila melanogaster.
in Methods (San Diego, Calif.)
Zaessinger S
(2015)
Drosophila MAGI interacts with RASSF8 to regulate E-Cadherin-based adherens junctions in the developing eye
in Development
Description | Amgen Studentship |
Amount | £3,000 (GBP) |
Organisation | Amgen Inc |
Sector | Private |
Country | United States |
Start | 06/2014 |
End | 09/2014 |
Description | Amgen summer studentship |
Amount | £3,600 (GBP) |
Organisation | Amgen Inc |
Sector | Private |
Country | United States |
Start | 05/2017 |
End | 09/2017 |
Description | BBSRC Response Mode Funding |
Amount | £381,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 06/2017 |
End | 06/2020 |
Description | Career re-entry Fellowship for Sara Morais Da Silva |
Amount | £446,000 (GBP) |
Funding ID | 107414/Z/15/Z |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 08/2015 |
End | 09/2019 |
Description | Dcotoral Traning Grant studentship |
Amount | £10,000 (GBP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 06/2015 |
End | 09/2018 |
Description | Deciphering Notch signalling dynamics in vivo |
Amount | £1,270,600 (GBP) |
Funding ID | 212207/Z/18/Z |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 06/2019 |
End | 07/2026 |
Description | EMBO Short term Fellowship |
Amount | £3,000 (GBP) |
Organisation | European Molecular Biology Organisation |
Sector | Charity/Non Profit |
Country | Germany |
Start | 08/2016 |
End | 12/2016 |
Description | RESETTING AND SCULPTING THE NOTCH RESPONSE |
Amount | £2,031,692 (GBP) |
Funding ID | MR/T014156/1 |
Organisation | Medical Research Council (MRC) |
Sector | Public |
Country | United Kingdom |
Start | 07/2020 |
End | 07/2025 |
Description | Studentship for Julia Falo SanJuan |
Amount | £37,000 (GBP) |
Funding ID | 109144/Z/15/Z |
Organisation | Wellcome Trust |
Sector | Charity/Non Profit |
Country | United Kingdom |
Start | 09/2017 |
End | 09/2020 |
Title | Cell tracker |
Description | Computer scripts for cell tracking and time-lapse movie image analysis |
Type Of Material | Technology assay or reagent |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Important method that enabled us to track cells and measure signaling levels in live stem cell cultures, underpins publication DOI:10.7554/eLife.41637 Method is just now online |
URL | http://github.com/juliafs93/CellTracker |
Title | Live imaging Notch responsive transcription |
Description | Tagging of endogenous genes with MS2 stem loops to permit live-imaging of transcription in response to Notch activation |
Type Of Material | Technology assay or reagent |
Year Produced | 2020 |
Provided To Others? | Yes |
Impact | Paper in press in Current Biology reporting inter-tissue signaling via cell processes |
Title | Notch targets in neuroblast tumours |
Description | reporter lines for Notch regulated enhnacers active in neural stem cells |
Type Of Material | Model of mechanisms or symptoms - non-mammalian in vivo |
Year Produced | 2015 |
Provided To Others? | Yes |
Impact | Contributed to Zacharioudaki et al, 2015 lines are being distributed to the community |
Title | ParB/Int locus Tag |
Description | Methof for live tagging specific gene locus in vivo |
Type Of Material | Technology assay or reagent |
Year Produced | 2018 |
Provided To Others? | Yes |
Impact | Made possible in vivo measurements of locus specific changes in live dynamics of protein binding and in epigenetic marks. Results published in Feb 2018 doi: 10.1016/j.devcel.2018.01.020. Very likely to have widespread applications |
Title | CSL binding in CNS hyperplasia |
Description | Genome-wide profile of Su(H) [CSL] binding when Notch is hyperactive in neuroblasts for 24 hours |
Type Of Material | Database/Collection of data |
Year Produced | 2015 |
Provided To Others? | Yes |
Impact | Gene Expression Omnibus (GEO) accession number GSE68614 Data on Notch regulated genes in hyperplasia available for searching by the community Underpinned the publication Zacharioudaki et al, (2016) Development.143(2):219-31 |
Title | Genomewide changes in RNA and CSL binding in tumour models |
Description | Data collection from profiling hyperproliferative tissues |
Type Of Material | Database/Collection of data |
Year Produced | 2015 |
Provided To Others? | Yes |
Impact | data is available for mining |
Description | CSL Dynamics |
Organisation | University of Cincinnati |
Country | United States |
Sector | Academic/University |
PI Contribution | Formulated the hypothesis and carrying out the in vivo experiments |
Collaborator Contribution | Providing structural advice and making biophysical measurements |
Impact | Is multidisciplinary, collaborator is a structural biologist. |
Start Year | 2014 |
Description | Cux1 and other genes associated with blood tumors |
Organisation | The Wellcome Trust Sanger Institute |
Country | United Kingdom |
Sector | Charity/Non Profit |
PI Contribution | Screening functional relevance of candidate genes |
Collaborator Contribution | identified the candidate genes, analyzed sequence data from tumour samples |
Impact | Paper in Nature Genetics Wong CC, Martincorena I, Rust AG, Rashid M, Alexadrov LB, Tiffen JC, Kober C, Lempidaki S, Green AR, Campbell PJ, Bray SJ, Papaemmanuil E, and Adams DJ (2014) Frequent inactivating Cux1 mutations in cancer drive PI3K signaling. Nature Genetics 46(1): 33-8. |
Start Year | 2012 |
Description | Locus Tag |
Organisation | Paul Sabatier University (University of Toulouse III) |
Country | France |
Sector | Academic/University |
PI Contribution | Developing locus-tag method for labelling unique gene loci in vivo |
Collaborator Contribution | Providing the basic strains and plasmids to enable the research |
Impact | Manuscripts currently under preparation will include methods paper |
Start Year | 2016 |
Description | Notch targets in neuroblasts |
Organisation | Foundation for Research and Technology Hellas (FORTH) |
Department | Institute of Molecular Biology and Biotechnology (IMBB) |
Country | Greece |
Sector | Academic/University |
PI Contribution | Provided the expertise and resources for analysis of Notch targets in neuroblasts |
Collaborator Contribution | Provided samples for the study |
Impact | EMBO Short term fellowship for Evanthia Zacharioudaki Notch targets in neuroblasts, data will be cross-referenced and integrated with other data sets we have generated. Led to Dr Zacharioudaki joining the group as a post-doc and to two substantial publicatons. These acheievements underpinned her success in winning follow on funding with an intermediate fellowship in Greece. Zacharioudaki E, Housden BE, Garinis G, Stojnic R, Delidakis C, Bray SJ (2016) Genes implicated in stem-cell identity and temporal-program are directly targeted by Notch in neuroblast tumours. Development 143 (2), pp. 219-231 Zacharioudaki E, Housden BE, Garinis G, Stojnic R, Delidakis C, Bray SJ (2016) Genes implicated in stem-cell identity and temporal-program are directly targeted by Notch in neuroblast tumours. Development 143 (2): 219-231 |
Start Year | 2010 |
Title | FRAP modelling to infer diffusion parameters |
Description | Method for analyzing and modelling data from fluroescence recovery after photobleaching. |
Type Of Technology | Software |
Year Produced | 2018 |
Impact | Software was released last month and results published online in DOI:10.1016/j.devcel.2018.01.020 |
Description | ChAOS Science roadshow EZ MGL |
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 | Contributed to an event attended by general public, especially children, aimed at engaging them with science by performing simple experimentts |
Year(s) Of Engagement Activity | 2014 |
Description | Danstem |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Invited talk at Danstem, involves scientists and practitioners |
Year(s) Of Engagement Activity | 2014 |
Description | Genes and heredity EZ MGL |
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 | Event aimed at general public to inform and engage with questions relating to genes and heredity |
Year(s) Of Engagement Activity | 2016 |
Description | Pint of Science |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Public/other audiences |
Results and Impact | Short talk for the general public on the latest science research |
Year(s) Of Engagement Activity | 2016 |
Description | School visit MJ |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | National |
Primary Audience | Schools |
Results and Impact | Talks to schoolchildren to raise awareness and to increase access |
Year(s) Of Engagement Activity | 2015 |