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CRUK Centres Network Accelerator Award

Research Resource - The Accelerator represents a unique programme, creating critical mass in areas of pivotal importance/relevance to CRUK: Molecular Pathology, Cancer Immunotherapy and Artifical Intelligence/Digital Pathology (AI/DP)

Name

Role (i.e. principal investigator, co-investigator, collaborator, project manager)

Affiliated Centre/ Institution/ Location

Description of Role in Accelerator Award

Prof Manuel Salto-Tellez

PI/Project Manager

Queen’s University Belfast (QUB)

Accelerator PI

Dr Jacqueline James

Co-investigator

QUB

Accelerator Co-lead

Prof Gareth Thomas

Co-investigator

University of Southampton

Accelerator Southampton Lead

Prof Sebastian Brandner

Co-investigator

University College London

Accelerator UCL Lead

Dr Yinyin Yuan

Co-investigator

Institute of Cancer Research

Accelerator ICR Lead

Prof Phil Sloan

Collaborator

Newcastle University

Accelerator Newcastle Lead

Dr John Le Quesne

Collaborator

University of Leicester

Accelerator Leicester Lead

How this Award fits into the existing CRUK research network and adds value

This Accelerator represents a unique programme, creating critical mass in areas of pivotal importance/relevance to CRUK: Molecular Pathology, Cancer Immunotherapy and Artificial Intelligence/Digital Pathology (AI/DP). The first 3 years have allowed centres to:

a) adopt and familiarise themselves with complex technology;

b) lead internationally in the development of new tools/software;

c) generate important scientific contributions to cancer immunotherapy and neuropathology;

d) ensure long-term sustainability for molecular pathology and DP analysis;

e) educate a new generation of pathologists

This Accelerator is linked to two Southampton-led initiatives, the CRUK Accelerator immunotherapy, and the Centre for Drug Development Biomarker Centre of Excellence, as well as the UCL–Edinburgh Accelerator (Brandner).

The contribution of the Award to the cancer research landscape

Pioneers in New Technology

QuPath is a novel, open source software for DP image analysis [https://qupath.github.io]. Developed in QUB under this Accelerator, QuPath is the first open-source software making biomarker discovery and analysis in DP powerful and accessible.  It has improved the analysis of tissue samples worldwide (more than 7,000 users globally). It holds significant advantages against other such commercially-available systems.

QuPath is used in Southampton for scoring in clinical trials. UCL is transferring multiple algorithms for biomarker quantification to QuPath. Newcastle is a regular QuPath user. Leicester’s LifeArc-funded explant group, after a detailed three-tier assessment (Visiopharm, Inform, and Qupath) has adopted the latter.

Dr Yuan’s application to spatial statistics (e.g. Moran’s I, Ripley’s K and Getis-Ord) for analysis of Tumour Ecology in complex, multiplexed images is highly original and is beginning to be adopted by the network.

Together, this development and adoption represent, arguably, the most important contribution outside large biotech industry to direct applications of DP/IA in Europe.

 

QuPath examples

Understanding the immune nature of cancer

 

Southampton has successfully extended transcriptomic analysis of intratumoral immune cells into morphological tissue analysis of immune cell phenotype and distribution using DP, identifying novel immune subsets and immune evasion mechanisms, and extended the work into prognostic biomarker studies and mouse models. 

Belfast has successfully demonstrated the clinical relevance of immunoscore-like analyses and other key precision medicine biomarkers in a DP framework and is creating the first holistic validation of wet-lab and in-silico approaches to score adaptive immunity and immune checkpoints.

UCL has, for the first time in the UK, a programme for systematic digital quantitation of oncobiomarkers and tumour microenvironment responses in neurooncology.

The network supported by the award

Network technology standardisation

The network has worked in the adoption and validation of multiplexing techniques (including Southampton’s consecutive visualization of multiple biomarkers and Newcastle’s work with the Vectra systems). Image analysis integration is happening at many levels:

a) QuPath (QUB development) is currently a system in use by most members of the network;

b) Definiens is currently validated and in use in Southampton, UCL and Belfast;

c) the approaches to tumour ecology analysis developed by ICR will be adopted by Southampton in due course.

This is leading to common practices adopted across the network.

Training

To date this CRUK Accelerator award has enabled the QUB PMC team to successfully train over 50 postgraduate taught students from Newcastle, Southampton, London and Belfast in molecular diagnostics and molecular pathology research creating the first “functional network” for future practitioners in the field.  The molecular pathology training that has been delivered is supported by innovative teaching, novel evaluation schemes and meaningful research experiences bringing together young pathologists, clinical scientists and technicians from Molecular Pathology centres across the UK.

 

 

Use the publications link below to find out more about our technology and science.