Analysis of Cellular Heterogeneity for high resolution understanding of cancer
Lead Research Organisation:
University College London
Department Name: Cancer Biology
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
Meyer T
(2022)
Circulating tumour cells and tumour biomarkers in functional midgut neuroendocrine tumours
in Journal of Neuroendocrinology
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
Childs A
(2021)
Whole-genome sequencing of single circulating tumor cells from neuroendocrine neoplasms.
in Endocrine-related cancer
Turati VA
(2021)
Chemotherapy induces canalization of cell state in childhood B-cell precursor acute lymphoblastic leukemia.
in Nature cancer
Mandair D
(2021)
Prognostic Threshold for Circulating Tumor Cells in Patients With Pancreatic and Midgut Neuroendocrine Tumors
in The Journal of Clinical Endocrinology & Metabolism
Litchfield K
(2021)
Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition.
in Cell
Au L
(2021)
Determinants of anti-PD-1 response and resistance in clear cell renal cell carcinoma.
in Cancer cell
Ghorani E
(2020)
The T cell differentiation landscape is shaped by tumour mutations in lung cancer.
in Nature cancer
Chen W
(2019)
Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome.
in Communications biology
Joshi K
(2019)
Spatial heterogeneity of the T cell receptor repertoire reflects the mutational landscape in lung cancer.
in Nature medicine
Biswas D
(2019)
A clonal expression biomarker associates with lung cancer mortality.
in Nature medicine
Rizzo FM
(2019)
Circulating tumour cells and their association with bone metastases in patients with neuroendocrine tumours.
in British journal of cancer
Agerbæk MØ
(2018)
The VAR2CSA malaria protein efficiently retrieves circulating tumor cells in an EpCAM-independent manner.
in Nature communications
Lima AF
(2018)
Osmotic modulation of chromatin impacts on efficiency and kinetics of cell fate modulation.
in Scientific reports
Peltzer N
(2018)
LUBAC is essential for embryogenesis by preventing cell death and enabling haematopoiesis.
in Nature
Lima AF
(2018)
Author Correction: Osmotic modulation of chromatin impacts on efficiency and kinetics of cell fate modulation.
in Scientific reports
Rizzo FM
(2018)
Liquid Biopsies for Neuroendocrine Tumors: Circulating Tumor Cells, DNA, and MicroRNAs.
in Endocrinology and metabolism clinics of North America
Diot A
(2018)
Validating the RedMIT/GFP-LC3 Mouse Model by Studying Mitophagy in Autosomal Dominant Optic Atrophy Due to the OPA1Q285STOP Mutation.
in Frontiers in cell and developmental biology
Teschendorff AE
(2017)
Single-cell entropy for accurate estimation of differentiation potency from a cell's transcriptome.
in Nature communications
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(2017)
Prolonged intracellular accumulation of light-inducible nanoparticles in leukemia cells allows their remote activation
in Nature Communications
Yuan G
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in Genome Biology
Liu TH
(2017)
Expression of the fetal hematopoiesis regulator FEV indicates leukemias of prenatal origin.
in Leukemia
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(2017)
Local cellular neighborhood controls proliferation in cell competition.
in Molecular biology of the cell
Guibentif C
(2017)
Single-Cell Analysis Identifies Distinct Stages of Human Endothelial-to-Hematopoietic Transition.
in Cell reports
Migueles RP
(2017)
Transcriptional regulation of Hhex in hematopoiesis and hematopoietic stem cell ontogeny.
in Developmental biology
Billing M
(2016)
A network including TGFß/Smad4, Gata2, and p57 regulates proliferation of mouse hematopoietic progenitor cells.
in Experimental hematology
Stunnenberg HG
(2016)
The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery.
in Cell
Anguita E
(2016)
A somatic mutation of GFI1B identified in leukemia alters cell fate via a SPI1 (PU.1) centered genetic regulatory network.
in Developmental biology
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(2016)
Expression of somatostatin receptors 2 and 5 in circulating tumour cells from patients with neuroendocrine tumours.
in British journal of cancer
Ebinger S
(2016)
Characterization of Rare, Dormant, and Therapy-Resistant Cells in Acute Lymphoblastic Leukemia.
in Cancer cell
Nimmo RA
(2015)
Primed and ready: understanding lineage commitment through single cell analysis.
in Trends in cell biology
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Single-Cell Network Analysis Identifies DDIT3 as a Nodal Lineage Regulator in Hematopoiesis.
in Cell reports
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(2015)
The histone demethylase Jarid1b is required for hematopoietic stem cell self-renewal in mice.
in Blood
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 |