Establishment of the Cambridge Single Cell Analysis Clinical Core Facility [SCACCF]

Lead Research Organisation: University of Cambridge
Department Name: Clinical School

Abstract

Recent technology developments have revolutionised our ability to characterize, quantify and isolate single cells. Examination of diseases at single cell resolution, both at diagnosis and after treatment, will transform the practice of molecular medicine by improving the quality of patient diagnosis, refining treatment options, monitoring of response to treatment, and detecting the emergence of resistance to treatment. Cambridge scientists have been at the forefront of basic research in single cell expression profiling and the analysis of circulating tumour DNA, as well as setting up local Biotech companies that develop novel single cell technologies. Here we propose to use MRC Infrastructure funding to create a new shared core facility for single cell analysis (the Cambridge Single Cell Analysis Clinical Core Facility [SCACCF]), which will serve all major molecular medicine programmes in Cambridge: cancer, neurosciences, immunity and inflammation, infectious diseases, stem cell and regenerative medicine, metabolic medicine and experimental therapeutics. SCACCF will be well placed to act as a hub for the UK and will work closely with our outstanding strategic partners in the Cambridge area (Babraham Institute, Wellcome Trust Sanger Institute, the European Bioinformatics Institute, the MRC Laboratory for Molecular Biology, major pharma & biotech), to bring their different capabilities to bear on clinical research challenges.

Technical Summary

Recent technology developments have revolutionised our ability to characterize, quantify and isolate single cells. Examination of disease genotype/phenotype at single cell resolution, both at baseline and after therapeutic intervention, will transform the practice of molecular medicine in all its facets: diagnosis, therapeutic stratification, monitoring of response to treatment, and emergence of resistance. Cambridge scientists have been at the forefront of basic research in single cell expression profiling [Nat Methods 6:377-382, 2009; Cell Stem Cell 6:468-478, 2010] and the analysis of circulating tumour DNA [Nature 497:108-112, 2013; N Eng J Med 368: 1199-1209, 2013], as well as setting up local Biotech companies that develop novel single cell technologies [e.g. Sphere Fluidics]. Here we propose to use MRC Infrastructure funding to create a new shared core facility for single cell analysis that will serve all major molecular medicine programmes in Cambridge: cancer, neurosciences, immunity and inflammation, infectious diseases, stem cell and regenerative medicine, metabolic medicine and experimental therapeutics. The new Cambridge Single Cell Analysis Clinical Core Facility [SCACCF] will be well placed to act as a hub for the UK and will work closely with other centres of excellence. We are closely collocated with outstanding strategic partners (Babraham Institute, Wellcome Trust Sanger Institute, the European Bioinformatics Institute, the MRC Laboratory for Molecular Biology, major pharma & biotech; see attached letters of support). This initiative will be catalytic in bringing their different capabilities to bear on clinical research challenges.

Planned Impact

It is now widely recognised that single cell technology will transform molecular medicine. We interpret this current initiative as recognition by the MRC that substantial investment into state of the art equipment is now required to capitalise on the huge potential offered by single cell technology, especially for translational patient-centric research. We therefore propose to use MRC infrastructure funding under the Clinical Research Capabilities & Technologies initiative to create a new core facility in the Cambridge University Clinical School. This new Single Cell Analysis Clinical Core Facility [SCACCF] will be embedded in the Hospital to deliver new technologies at the clinical 'front end' of molecular medicine.

We have taken the following steps to maximise the potential impact of this investment:
1) Leveraged over £4,000,000 of existing funds within the school to ensure sustained running of this new facility, closely embedded with other core facilities such as cancer diagnostics and immune phenotyping. Much of this leverage is for staff costs, which cannot be applied for in this MRC call, but will be absolutely essential to run a successful core facility.
2) Engaged widely with all major molecular medicine programmes in Cambridge. Right from the outset therefore we have taken steps to maximise the chances that newly deployed single cell technology will have a wide impact to enhance clinical research across the entire clinical school
3) Secured support from research institutes and pharmaceutical/biotech industries in the Cambridge area (Babraham Institute, Wellcome Trust Sanger Institute, the European Bioinformatics Institute, the MRC Laboratory for Molecular Biology, Astra Zeneca, Sphere Fluidics; see attached letters of support). The new clinical core facility will be catalytic in bringing their different capabilities to bear on clinical research challenges, and therefore ensure sustained 'pull-through' of new technology into clinical care.
4) Establishd a network of scientists with world-leading expertise in both technical and bioinformatic aspects of single cell genomics, which will establish the new single cell clinical core facility here in Cambridge as a potential hub for the UK. We will endeavour to work closely with other centres of excellence, and this spirit of openness is evidenced already by our close interactions with all other applicants to this MRC initiative who are requesting installation of CyTOF technology.

To maximise the chances of single cell technology uptake, we will:
1) Establish a website explaining the potential uses of all the new technology we propose to install
2) Hold a number of seminars across Cambridge advertising the capabilities of the new facility
3) Establish a strong training programme, based on the template provide by the existing FACS phenotyping hub
4) Establish quarterly meetings with the EBI/Sanger single cell genomics core to keep us aware of the latest technology developments, and also offer our facility as a route towards early clinical translation
5) Establish a network of all single cell technology researchers in the Cambridge area (from the University, research institutes and industry), and hold an annual workshop similarto last year's Fluidigm European Single Cell Genomics workshop, which was held in Cambridge
6) Engage with the other centres across the UK that may be funded through this initiative, to share latest protocols and also explore possible shared training activities.
7) Engage with other funders to enhance the capabilities beyond what is requested here.

Finally, engagement with the wider public forms an important part of our overall strategy. We will therefore shortlist the new Single Cell Core Facility for any public engagement opportunities, such as open days, disease-specific patient events in the hospital or events associated with the Science Week here in Cambridge.

Publications

10 25 50

publication icon
Ali HR (2015) PD-L1 protein expression in breast cancer is rare, enriched in basal-like tumours and associated with infiltrating lymphocytes. in Annals of oncology : official journal of the European Society for Medical Oncology

publication icon
Basilico S (2017) Dysregulation of haematopoietic stem cell regulatory programs in acute myeloid leukaemia. in Journal of molecular medicine (Berlin, Germany)

publication icon
Beddowes E (2017) Predicting treatment resistance and relapse through circulating DNA. in Breast (Edinburgh, Scotland)

 
Description Applying single cell genomics technology to CAR-T-cell therapy
Amount £100,000 (GBP)
Organisation Autolus Limited 
Sector Private
Country United Kingdom
Start 12/2016 
End 12/2017
 
Description BBSRC Research Grant
Amount £534,778 (GBP)
Funding ID BB/P002293/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 09/2019
 
Description BIRAX
Amount £197,871 (GBP)
Organisation British Council 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2018 
End 02/2021
 
Description CRUK Programme Grant
Amount £1,489,605 (GBP)
Funding ID C1163/A21762 
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 02/2017 
End 01/2022
 
Description Collaborative Research Grant
Amount £26,000 (GBP)
Organisation Wiener-Anspach Foundation 
Sector Learned Society
Country Belgium
Start 10/2018 
End 12/2020
 
Description Confidence in Concept Award
Amount £71,077 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 12/2017 
End 08/2018
 
Description ERC Starting Grant
Amount € 1,500,000 (EUR)
Organisation European Research Council (ERC) 
Sector Public
Country European Union (EU)
Start 04/2017 
End 03/2022
 
Description GSK Varsity Research Project Grant
Amount £104,000 (GBP)
Organisation GlaxoSmithKline (GSK) 
Sector Private
Country Global
Start 04/2016 
End 12/2017
 
Description Intramural Institute
Amount £3,300,000 (GBP)
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 07/2017 
End 06/2022
 
Description Multiple Sclerosis Society Project Grants
Amount £297,145 (GBP)
Organisation Multiple Sclerosis Society 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2016 
End 03/2019
 
Description Open Innovation Programme
Amount £72,526 (GBP)
Organisation AstraZeneca 
Sector Private
Country United Kingdom
Start 01/2019 
End 07/2020
 
Description Quantitative Analysis of Clonality in Haematopoiesis - Concepts, methods and potential
Amount £9,073 (GBP)
Funding ID BB/R021465/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2018 
End 10/2018
 
Description Research Grant - Human Cell Atlas
Amount £518,800 (GBP)
Funding ID MR/S036113/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 12/2018 
End 04/2021
 
Description Senior Investigator Award
Amount £2,028,031 (GBP)
Funding ID 206328/Z/17/Z 
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 02/2018 
End 01/2023
 
Description Skills Development Fellowship
Amount £365,508 (GBP)
Funding ID MR/P014178/1 
Organisation Medical Research Council (MRC) 
Sector Academic/University
Country United Kingdom
Start 08/2017 
End 07/2020
 
Description Wellcome Trust Centre
Amount £9,800,000 (GBP)
Organisation Wellcome Trust 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2017 
End 06/2022
 
Title Pipeline for the analysis of single cell qPCR data 
Description Using the single cell facility funded by this grant, a pipeline was developed for the analysis of single cell qPCR data that uses the mathematics behind bursty expression to develop more accurate and robust algorithms for analyzing the origin of heterogeneity in experimental samples, specifically an algorithm for clustering cells by their bursting behavior (Simulated Annealing for Bursty Expression Clustering, SABEC) and a statistical tool for comparing the kinetic parameters of bursty expression across populations of cells (Estimation of Parameter changes in Kinetics, EPiK). 
Type Of Material Improvements to research infrastructure 
Year Produced 2016 
Provided To Others? Yes  
Impact Using the pipeline, detailed information about gene regulatory mechanisms can be obtained simply from high throughput single cell gene expression data. As the availability of single cell genomic approaches rise, in part through the growth of facilities such as the one funded by this grant, it is likely to be widely adopted. 
 
Title Single Cell Network Synthesis 
Description The Single Cell Network Synthesis toolkit (SCNS) is a general-purpose computational tool for the reconstruction and analysis of executable models from single-cell gene expression data. Through a graphical user interface, SCNS takes single-cell qPCR or RNA-sequencing data taken across a time course, and searches for logical rules that drive transitions from early cell states towards late cell states. Because the resulting reconstructed models are executable, they can be used to make predictions about the effect of specific gene perturbations on the generation of specific lineages. 
Type Of Material Model of mechanisms or symptoms - human 
Year Produced 2018 
Provided To Others? Yes  
Impact The tool has been made available for free public use on multiple websites. 
 
Title BTR 
Description Using the single cell data produced by the facility funded by this grant, BTR, an algorithm for training asynchronous Boolean models with single-cell expression data using a novel Boolean state space scoring function, was developed. 
Type Of Material Computer model/algorithm 
Year Produced 2016 
Provided To Others? Yes  
Impact BTR is capable of refining existing Boolean models and reconstructing new Boolean models by improving the match between model prediction and expression data. It can be used to improve published Boolean models in order to generate new biological insights as demonstrated in Lim et al. BMC Bioinformatics 2016. 
 
Title Diffusion map of haematopoietic stem and progenitor cell differentiation 
Description The single cell facility established by this grant was used to sequence more than 1600 single haematopoietic stem and progenitor cells allowing the production of a diffusion map as published in Nestorowa et al. Blood 2016. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact The online diffusion map is the first of its kind for single haematopoietic stem and progenitor cell transcriptome data. Researchers can use it to visualise haematopoietic stem cell-to-progenitor transitions, highlight putative lineage branching points and identify lineage-specific transcriptional programs, which will have a strong impact on their future research. 
URL http://blood.stemcells.cam.ac.uk/single_cell_atlas.html
 
Description A protein-transcriptome atlas of haematopoiesis across the human life span 
Organisation Newcastle University
Department Institute of Cellular Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution Using Cite-Seq technology to generate combined protein and transcriptome profiles for haematopoietic progenitor and mature cells across the human lifespan
Collaborator Contribution Providing human samples and performing Cite-Seq analysis
Impact The collaboration began in December 2018 and will run to April 2021. Our primary output, combined protein and transcriptome profiles for haematopoietic progenitor and mature cells across the human lifespan which will feed into the Human Cell Atlas, will be produced incrementally through the duration of the collaboration. Data will be made freely available through the Human Cell Atlas portal and the DNA sequencing databases maintained by EBI and NCBI. We also aim to publish report of our research which will demonstrate the application of Cite-Seq technology.
Start Year 2018
 
Description A protein-transcriptome atlas of haematopoiesis across the human life span 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Using Cite-Seq technology to generate combined protein and transcriptome profiles for haematopoietic progenitor and mature cells across the human lifespan
Collaborator Contribution Providing human samples and performing Cite-Seq analysis
Impact The collaboration began in December 2018 and will run to April 2021. Our primary output, combined protein and transcriptome profiles for haematopoietic progenitor and mature cells across the human lifespan which will feed into the Human Cell Atlas, will be produced incrementally through the duration of the collaboration. Data will be made freely available through the Human Cell Atlas portal and the DNA sequencing databases maintained by EBI and NCBI. We also aim to publish report of our research which will demonstrate the application of Cite-Seq technology.
Start Year 2018
 
Description Capturing the Early Stages of Acute Myeloid Leukaemia to Evaluate New Therapeutics 
Organisation AstraZeneca
Country United Kingdom 
Sector Private 
PI Contribution scRNA-Seq analysis of drug treatment on mixed lineage leukaemia
Collaborator Contribution In vivo validation
Impact The collaboration began in January 2019 and will run until July 2020. Full output will not be available until late in the collaboration when we should be able to identify molecules (or combinations of molecules) that are specifically effective against leukaemic and/or pre-leukaemic cells.
Start Year 2019
 
Description Single cell collaboration with EBI 
Organisation EMBL European Bioinformatics Institute (EMBL - EBI)
Country United Kingdom 
Sector Academic/University 
PI Contribution Single cell experimentation.
Collaborator Contribution Joint supervision and design of the study; data analysis.
Impact The collaboration has produced the first transcriptome-wide in vivo view of early mesoderm formation during mammalian gastrulation as published in Scialdone et al. Nature 2016.
Start Year 2015
 
Description CRUK Cambridge Institute Annual International Symposium: Tumors at Cellular Resolution 
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 Two day scientific symposium bringing together international leaders considering key questions in applying single cell approaches to unanswered questions in cancer
Year(s) Of Engagement Activity 2016
URL http://www.cruk.cam.ac.uk/symposium/home