Analysis of Cellular Heterogeneity for high resolution understanding of cancer

Lead Research Organisation: University College London

Abstract

One of the major challenges in the treatment of cancer is the ability to predict which patients will respond to which therapy and to understand why patients stop responding. We know that cancer arises from a single cell that has undergone reprogramming so that its growth becomes deregulated. During subsequent growth, the tumour becomes increasingly heterogeneous such that the response to therapy and ability to metastasise may vary. A consequence of this this heterogeneity is that a proportion of the tumour may be sensitive to therapy while the remainder is resistant. Hence, therapy selects our resistant cells that ultimately result in relapse or progression of disease. The only way to understand tumour heterogeneity is to sample the tumour tissue by taking biopsies, but even this may be misleading since only a proportion of the tumour is surveyed and important variability may be missed. Additionally, it may be difficult, dangerous or unacceptable to patients to perform multiple biopsies at various time points throughout the patient journey. A possible solution to this is to study Circulating Tumour Cells (CTCs) as surrogates of tumour tissue. CTCs are cells that are shed into the circulation and can be isolated from the blood for further analysis. CTCs are very rare cells by comparison with blood cells and highly sophisticated technology has been developed to enrich for CTCs and isolate them. In parallel there have been technological advances in genetic sequencing such that we can now identify mutations and analyse gene expression in single cells. This means that, for the first time we can begin to understand tumour heterogeneity at the single cell level. Our proposal seeks to establish a dedicated facility with state of the art equipment to enable scientists at UCL to study CTCs and improve the outcomes for patients with cancer. Initially we will establish protocols to undertake complex single cell analysis and then develop and validate tests in patients who are undergoing treatment for cancer. We will also study these cells in order to understand how they are able to successfully spread through the blood stream to other organs and cause metastases. Metastasis is responsible for the death of 90% patients with cancer and it is critical to understand how this happens in order to develop more effective therapies.

Technical Summary

The proposed CTC Facility will provide a range of platform technologies that will enable the evaluation of tumour heterogeneity at the single cell level. The approaches can be divided into those that provide a means of i) enrichment ii) isolation and iii) molecular characterisation. CTCs represent are very rare cell population among circulating blood cells and we will employ and a range of enrichment techniques according to the demands of the analysis; broadly these will be based on selection according to antigen expression such as EpCAM using the CellSearch or CellCollector or based on size exclusion using the ISET or Parsortex approach. For isolation we will employ both FACS based approaches and the DepArray in order to isolate single cells. For molecular characterisation a spectrum of technologies are required to interrogate both genetic and non-genetic heterogeneity. These include the Illumina NextSeq 500, Fluidigm C1 microfluidics system, CyTOF and Imagestream. These will allow the study of transcription, protein expression and a dynamic assessment of phosphorylation, protein-protein interaction and cellular localisation. All these aspects of heterogeneity are critical to fully understand the nature of drug sensitivity and resistance and inform the delivery of personalised therapy.

Planned Impact

We anticipate that the research conducted in the UCL CTC Facility will establish a new strategy for the management of patients with cancer that will be informed by a more comprehensive understanding of tumour heterogeneity and evolution during treatment. CTCs will be used as a minimally invasive method of sampling the tumour throughout the patient journey. They will be subjected to genetic and epigenetic analysis that will direct therapy and will be used as pharmacodymic markers to assess the effectiveness of anti-cancer therapy. The application of this approach will enable the selection of the best therapy for each individual patient, anticipate the emergence of resistance and change treatment according to the emerging molecular characteristics of the resistant tumour. This will represent a step change in our ability to implement personalised cancer medicine and will render therapy more cost effective and reduce toxicity. The innovations achieved are expected to be of major interest to both academic and industrial partners who have already collaborated or invested in our expertise, and are likely to expand our reach and establish new partnerships. Patients and lay representatives will feed into the program through our ECMC and CRUK Centre boards and we will promote the activity of the CTC Facility though public engagement activities and more broadly through the web sites of UCL, UCLH and ULC Partners.

Publications

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Vesely C (2022) Systematic Evaluation of the Immune Environment of Small Intestinal Neuroendocrine Tumors. in Clinical cancer research : an official journal of the American Association for Cancer Research

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Rizzo FM (2018) Liquid Biopsies for Neuroendocrine Tumors: Circulating Tumor Cells, DNA, and MicroRNAs. in Endocrinology and metabolism clinics of North America

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Mandair D (2021) Prognostic Threshold for Circulating Tumor Cells in Patients With Pancreatic and Midgut Neuroendocrine Tumors in The Journal of Clinical Endocrinology & Metabolism

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Bove A (2017) Local cellular neighborhood controls proliferation in cell competition. in Molecular biology of the cell

 
Description CRUK Centre Clinical PhD Fellowship
Amount £273,972 (GBP)
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 03/2016 
End 03/2019
 
Description CRUK Development Fund: Evaluation of the expression of CXCR4 on Circulating Tumour Cells (CTCs) from Neuroendocrine Tumour (NET) patients with and without skeletal metastases
Amount £20,000 (GBP)
Organisation Cancer Research UK 
Sector Charity/Non Profit
Country United Kingdom
Start 09/2016 
End 09/2017
 
Description ENETS Clinical Fellowship
Amount € 50,000 (EUR)
Organisation European Neuroendocrine Tumor Society 
Sector Learned Society
Country Germany
Start 08/2017 
End 08/2018
 
Description Single cell analysis of circulating tumour cells in NET
Amount £43,736 (GBP)
Organisation European Neuroendocrine Tumor Society 
Sector Learned Society
Country Germany
Start 08/2017 
End 08/2018
 
Description Collaboration with Caroline Dive's lab in Manchester to analyse samples 
Organisation University of Manchester
Country United Kingdom 
Sector Academic/University 
PI Contribution We preformed assays on samples collected on clinical trials.
Collaborator Contribution They established the assays.
Impact Nothing yet
Start Year 2017
 
Description Conference Talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Conference talk on 'Circulating Tumour Cells in NETS at the British Endocrine Society annual conference.
Year(s) Of Engagement Activity 2018
 
Description Invited lecture - What can circulating tumour cells tell us about neuroendocrine tumours? 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Invited speakers to the Oxford Centre of Diabetes, Endocinology and Metabolism Centre as part of the regular external speaker seminar series
Year(s) Of Engagement Activity 2019
URL https://talks.ox.ac.uk/talks/id/6fdd7a78-6b61-4eba-8eda-7e396a16f89f/
 
Description PPI visits for the CRUK Centre 
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 Patients, carers and/or patient groups
Results and Impact Lab tours to explain the development of biomarkers for cancer.
Year(s) Of Engagement Activity 2017
 
Description Talk 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Tim Meyer - gave a talk on Liquid biopsies in NET/NEN. Hot topics in NET.
Year(s) Of Engagement Activity 2018