Non-invasive MRI Biomarkers for Oncology

Lead Research Organisation: University College London
Department Name: Computer Science

Abstract

This project develops innovative Magnetic Resonance Imaging (MRI) methods to reveal new non-invasive markers of cancer pathology. In particular the research programme develops biophysical models of tumour tissue that support non-invasive estimates of key characteristics of tissue cellular architecture including those that currently guide diagnosis, grading, and treatment assignment through classical histology. These cellular characteristics include cell size, cell shape, cell density, similar features of subcellular structures, and potentially new features that histology cannot reveal such as cell membrane permeability and cell cytoplasm viscosity. In contrast to classical histology, such an approach avoids unnecessary interventions like biopsies. Moreover, the models combine with macroscopic imaging to provide maps of histological features over the whole organ, thus evading false-positives from poor biopsy targeting. In contrast to current imaging techniques, the new model-based imaging techniques provide much greater specificity associating contrast with particular tissue changes thus providing much better information on which to assign treatment. The ultimate goal is to enable non-invasive cancer detection, staging and grading entirely through harmless imaging.

The project will leverage the advances of a method I recently devised, called VERDICT, which uses diffusion MRI to provide an early demonstration of the power of such a model-based imaging technique in estimating cancer-tissue microstructure non-invasively. This project builds on these ideas to achieve the performance levels required to allow robust detection, grading and staging for establishing non-invasive imaging as the primary cancer diagnostic method. The project exploits advances in computational methods and in MRI technology to improve sensitivity and specificity dramatically. Specifically: 1) sophisticated optimisation techniques will enhance performance and practical utility of non-invasive model-based imaging; 2) advanced MRI sequences will allow access to new and important cancer microstructural features, such as the morphology of cell nuclei, and 3) alternative contrast methods will extend the methods to other MRI modalities beyond diffusion for complementary and additional cancer malignancy information. Although the project focuses on prostate cancer, it also aims to initiate follow-on projects to explore applications to other cancers such as brain, breast and bone metastasis.

This fellowship is a significant stepping-stone for my career in fighting cancer. My aspiration is for patients to have a quick, safe and comfortable clinical cancer examination with determinate diagnosis. Towards this vision the fellowship will allow me to capitalise on my recent progress on this idea, exploiting my current expertise in diffusion MRI, and its application in cancer. It provides me the opportunity to gain experience of leading my own multidisciplinary project and research team thus establishing myself in the UK and internationally as a leader on that topic. Moreover, the fellowship will allow me to broader my skills and collaborations to the wider medical imaging arena and variety of clinical applications in cancer. This underpins my development towards an international academic leader in the fields of computational imaging and cancer research and management.

Planned Impact

In spite of significant advances in diagnosis and treatment, cancer remains a major killer. Diagnosis is often inaccurate and subsequent treatment ineffective for far too many patients. Specifically prostate cancer diagnosis still relies on traditional histology via biopsies. Each year in the UK 75000 men undergo this invasive procedure, which can have unpleasant side effects and poor sensitivity, as the biopsy may miss lesions. A recent study indicates that more than 50% of prostate biopsy analyses underestimate the severity of the disease. Simultaneously biopsy can also lead to "over-diagnosis" as it can detect small clinically insignificant lesions, by random chance, which are indolent and do not need treatment. This detection of indolent disease often leads to men undergoing unnecessary radical surgery or radiotherapy. Approximately 90% of prostate cancer patients undergo such interventions, which can cause side effects like incontinence, significantly impacting their quality of life. Additionally a negative biopsy result does not imply free of cancer and negative-biopsy patients are monitored in regular repeat exams. The on-going process increases risks of side effects and is expensive for the National Health Service. Similar statistics of risks and costs translate worldwide and are also associated with other common cancers such as breast, bowel and liver.

This project develops non-intrusive imaging methods to provide diagnostic information as powerful as current invasive techniques. Primarily this will ameliorate patient suffering from the examination and the side effects, while assisting better clinical detection, staging and diagnosis by earlier and enhanced knowledge of what is happening at the tissue level. In particular improved detection rates can reduce the number of biopsies and repeated biopsies. Fewer biopsies can also decrease the cost of treatments from avoiding side effects such as urinary retention and rectal bleeding. Avoidance of biopsies will also contribute to the sustainability of the healthcare system by drastically reducing the number of surgical procedures and histopathological evaluations. Earlier cancer diagnosis can lead to more effective and potentially less radical/harmful treatments.

The microstructure MRI methods will provide new insight into cancer biology concerning the mechanisms of tumour growth, interactions between cancer cells and healthy tissue, the role of inflammation and subtle or difficult to detect effects such as distinguishing between apoptosis and necrosis, encouraging exciting new research prospects. Further exploitation of such computational methods can lead to identification of subgroups of biological targets in the tumour that when correlated with tumour genetics could lead to the design of individualised therapies based on metabolic pathways, achieving patient stratification for precision medicine.

The development of new MRI techniques can impact the commercial and industrial sector, such as MRI manufacturers, offering opportunities that can drive future development of medical hardware; Philips Healthcare have expressed their strong support and interest in the project. Finally microstructure imaging can also inform drug development and trials, revealing the effects of treatment earlier, moving trials more quickly to the final stages and accelerating the availability of new promising cancer treatments to patients.

Publications

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Bonet-Carne E (2018) Computational Diffusion MRI

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Bourne R (2016) Limitations and Prospects for Diffusion-Weighted MRI of the Prostate. in Diagnostics (Basel, Switzerland)

 
Description I developed with my group and collaborators a new computational framework to improve performance and practical utility of the current prostate cancer microstructural imaging methods (VERDICT). The new method reduces computational cost of the current VERDICT analysis and produces stable non-invasive estimates of cancer microstructure with plausible biophysical ranges. We have also made progress in testing the original VERDICT method in other cancers such as breast tumours with encouraging preliminary results. We had significant progress developing the VERDICT model for brain tumours in a pilot clinical study with positive results. The journal paper is accepted in a clinical journal- Cancers. We also extended the VERDICT application to rectal cancer and we have the first application in patients with encouraging results. Finally we developed a robust and accurate method for validating MRI prostate cancer imaging analysis methods with histology. This technique has been adopted for a second clinical trial funded by CRUK. We have improved the current VERDICT model for prostate cancer and enhanced its sensitivity to particular histological components accounting for both diffusion and relaxation effects. The new method that is combined with robust and ultrafast AI fitting is called Relaxation-VERDICT. The method can be extended to other tumours similarly to the original model. We have also completed the first clinical VERDICT study were the key finding was that 90% of men could avoid biopsy as VERDICT can successfully identify clinically significant cancer. The method is now being tested in a multi-centre study.
Exploitation Route The new computational methods developed during this fellowship are applicable to solid tumours and can be used for large-scale clinical applications/trials. The VERDICT framework is also being tested for monitoring prostate cancer treatment.
Sectors Healthcare,Manufacturing, including Industrial Biotechology,Pharmaceuticals and Medical Biotechnology

 
Description The optimized cancer imaging methods developed in this fellowship have already started to support large clinical trials for real-time decision-making. Our flagship VERDICT method has been used for two clinical trials for prostate cancer, for imaging and analysing small cohorts of colorectal cancer patients and brain tumour patients. This year we had our first breast cancer patients too. And is also being used for monitoring treatment response.
Sector Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal

 
Description GPU Grant Program
Amount £1,381 (GBP)
Organisation NVIDIA 
Sector Private
Country Global
Start 08/2017 
End 08/2017
 
Title 3D-printed patient-specific prostate molds 
Description We developed a mold template that contains landmark features to guide MRI scanning and guides for histological slicing. Using contours from in vivo MRI scans, the mold can be designed to hold the prostate in the in vivo position and orientation following surgical removal. This allows in vivo images to be compared with those before and after fixation, as well as histological images in the same slice plane. 
Type Of Material Biological samples 
Provided To Others? No  
Impact We are using this tool to validate biomarkers from diffusion MRI using corresponding histology. The device can also be applied for validation of other MRI techniques. We are consulting with the surgical and pathological teams on the use of the device to guide histological slicing and confirm patient margins. An additional EPSRC grant has been submitted on the use of machine learning techniques to relate radiological features with histological cancer grade that would benefit from this technique. 
 
Title VERDICT in XNAT 
Description Implementation of classic VERDICT and relaxation compensated model VERDICT in XNAT to allow an automatic pipeline of method. 
Type Of Material Improvements to research infrastructure 
Year Produced 2021 
Provided To Others? No  
Impact Automatic end-to-end pipeline from input raw data (patient scan of DW-MRI) to output parametric VERDICT maps 
 
Title Dataset of histologically registered imaging for prostate as part of the VERDICT MRI validation 
Description We are creating a unique dataset of histologically registered imaging for prostate as part of the VERDICT MRI validation as a non-invasive cancer diagnostic tool. We create custom 3D-printed patient specific slicing moulds prior to surgery for Histological Validation of in-vivo and ex-vivo MRI of the human prostate. After surgery, we put the prostate into the 3D personalised mould for ex-vivo imaging to keep the in-vivo orientation. Then the prostate is cut inside the mould, which provides an accurate alignment of the MRI with histology. For each sample, we have: (1) multiparametric Magnetic Resonance Images (mpMRI), (2) in-vivo VERDICT MRI scan, (3) ex-vivo VERDICT MRI scan using the clinical scanner (3T), (4) ex-vivo high resolution MRI scan including diffusion images (9.4T) and (5) histology sections of the corresponding tissue. Additionally, we have the associated clinical data as PSA levels prior to surgery. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? No  
Impact We will be able to validate VERDICT MRI for its use in clinical practice for prostate cancer characterisation non-invasively. 
 
Description Microstructure characterization of brain tumours with VERDICT MRI in patients 
Organisation University of Sussex
Department Brighton and Sussex Medical School
Country United Kingdom 
Sector Academic/University 
PI Contribution We have processed the diffusion MRI data provided by our partner in Milan. Based on our previous experience on microstructure modeling in tumours, we have adapted the VERDICT framework (Vascular, Extracellular, and Restricted Diffusion for Cytometry in Tumors) to characterize brain tumours microstructure, particularly in terms of vascularity and cellularity. We have validated our models results with independent perfusion MRI measures and other radiological and clinical data.
Collaborator Contribution The partners have provided MRI data acquired on brain tumour patients, as well as related clinical data. They also provided the clinical and radiological expertise on brain tumours necessary to set up our models and interpret the results.
Impact We have presented a digital poster on the preliminary results of this work at the ISMRM 28th Annual Meeting & Exhibition, 8-14 August 2020, with the title "Estimation of the vascular fraction in brain tumors by VERDICT correlated with Perfusion MRI"
Start Year 2017
 
Description Microstructure characterization of brain tumours with VERDICT MRI in patients 
Organisation Vita-Salute San Raffaele University
Country Italy 
Sector Academic/University 
PI Contribution We have processed the diffusion MRI data provided by our partner in Milan. Based on our previous experience on microstructure modeling in tumours, we have adapted the VERDICT framework (Vascular, Extracellular, and Restricted Diffusion for Cytometry in Tumors) to characterize brain tumours microstructure, particularly in terms of vascularity and cellularity. We have validated our models results with independent perfusion MRI measures and other radiological and clinical data.
Collaborator Contribution The partners have provided MRI data acquired on brain tumour patients, as well as related clinical data. They also provided the clinical and radiological expertise on brain tumours necessary to set up our models and interpret the results.
Impact We have presented a digital poster on the preliminary results of this work at the ISMRM 28th Annual Meeting & Exhibition, 8-14 August 2020, with the title "Estimation of the vascular fraction in brain tumors by VERDICT correlated with Perfusion MRI"
Start Year 2017
 
Description Ultra-high resolution microimaging for validation of VERDICT MRI for prostate tissue 
Organisation University of Sydney
Country Australia 
Sector Academic/University 
PI Contribution We have contributed to the development of the acquisition protocol with our collaborator. We are now processing and analysing the data acquired, to assess how well the metrics of the VERDICT model compare to the histology.
Collaborator Contribution Our collaborator has contributed to the acquisition protocol design with us. They have also acquired and processed the prostate samples for the study and acquired the data using an ultra-high gradient (16T) MRI system.
Impact The preliminary results show potential of diffusion microimaging to validate multi-compartment models such as VERDICT and will be presented at an international conference (ISMRM, Paris, 2018).
Start Year 2016
 
Description VERDICT prostate validation with phantoms for multi-centre studies. 
Organisation University College London
Department Division of Medicine
Country United Kingdom 
Sector Academic/University 
PI Contribution We are developing a VERDICT model with no perfusion to match the data from the phantom that can be used to calibrate and test the quality of the data in different scanners. My team is developing the model and importing it in XNAT so that our collaborators can collect and analyse the data with XNAT.
Collaborator Contribution Our collaborators are performing the scanning of the phantoms and providing us preliminary data for the development of the phantom model.
Impact Not yet.
Start Year 2021
 
Description Bloomsbury festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact My PhD student and myself along with other colleagues and Phd students from CMIC and WEISS presented "all things imaging and what it is for" to school kids and the general public at the Bloomsbury Festival this year. Our stall at the Discovery Hub (Senate House, Malet Street) illustrated our various imaging technics (and what we use them for), as well as addressing those fundamental questions around how do we know where the lungs sits, what an MRI image actually looks like, is AI faster than school kids. Also, of course, an opportunity to touch on more serious questions around the applications in medical context such as cancer imaging.

Bloomsbury Festival theme this year was "Breathe" and our exhibit - "From Top to Toe - the breathing body" . Thursday and Friday were dedicated to schools, who had booked tours and brought children aged 8-12 years. We had approximately 120 students visiting us. We had excellent feedback from the enthusiastic students. During the weekend we had general audience and approximately 200 people visited during the hours of the exhibition. All children were happy to engage with the activities while we had more in depth discussions about our methods and how they aid diagnosis with parents and grandparents, but also some independent patients.
Year(s) Of Engagement Activity 2022
URL https://bloomsburyfestival.org.uk/
 
Description Early Detection Programme 6th Annual Symposium 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Talks from scientists in the field and from the ACED Clinic Cambridge team. Presented for virtual poster session, with some people showed interest on the topic by asking questions and discussion afterwards.
Year(s) Of Engagement Activity 2021
URL https://www.earlydetectioncambridge.org.uk/news-events/events/early-detection-programme-sixth-annual...
 
Description Invited talk by ACED (International Alliance fir cancer early detection) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact This ACED seminar series aimed to bring together researchers and clinicians working towards cancer early detection. As early detection is such a diverse research area the audience was as well, spanning from biology, technology through translational and population research. Approximately 50 people attended this talk, which led to discussions and interest for new collaborations.
Year(s) Of Engagement Activity 2020
 
Description Invited talk for the online International Alliance for Cancer Early Detection (ACED) seminar series 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact In this invited talk I presented the latest developments on VERDICT MRI, a technique for non-invasive tumour characterization. The talk gained a lot of interest and prompt discussions for potential new collaborations.
Year(s) Of Engagement Activity 2020
 
Description Office of the Vice-Provost (Development) Prostate Cancer Event 
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 We have demonstrated the 3D moulds from the in-vivo VERDICT MRI validation for Prostate Cancer to UCL 'fundraising events' such the Office of the Vice-Provost (Development) Prostate Cancer Event - 30th November 2017
DARO - (http://www.ucl.ac.uk/development) Raises philanthropic funds for UCL
Year(s) Of Engagement Activity 2017
URL http://www.ucl.ac.uk/development
 
Description STEM for Britain 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact The in-vivo VERDICT MRI for prostate cancer validation work has been selected (in the top 35% of entrants) to be presented in STEM for Britain on the 12th of March 2018 in the House of Commons. STEM (Science, Technology, Engineering and Maths) for Britain is an annual poster competition, for distinguished early career researchers to meet members of parliament (MPs). It is a unique opportunity to communicate our research to politicians and encourage its impact to our society.
Year(s) Of Engagement Activity 2018
URL http://www.setforbritain.org.uk/
 
Description Seminar presentation at the Developmental Imaging and Biophysics Section (DIBS) at UCL-Great Ormond Street Institute of Child Health 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Dr. Maira Tariq was invited to give a seminar at the DIBS at Great Ormond Street Institute of Child Health. The presentation was titled: "Pushing the standards for cancer characterisation with advance diffusion MRI techniques: application in prostate and rectal cancer". The talk covered the technical details of the current research being carried out as part of this award, including the work on ultra-high-field diffusion imaging of the prostate tissue, the pipeline validating MRI prostate cancer imaging analysis methods and feasibility of such imaging methods for rectal cancer characterisation. The talk simulated a great discussion with many good ideas being generated for further analysis.
Year(s) Of Engagement Activity 2018
 
Description Your Legacy: Funding the Future - London 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Patients, carers and/or patient groups
Results and Impact We have demonstrated the 3D moulds from the in-vivo VERDICT MRI validation for Prostate Cancer to this 'fundraising events' where Dr Hayley Whittaker gave a talk about her research to improve the diagnosis and treatments of prostate cancer in a way that could be easily adopted by the NHS.
Year(s) Of Engagement Activity 2017
URL https://www.eventbrite.co.uk/e/your-legacy-funding-the-future-london-tickets-37128794223