CANCER-ID

Cancer treatment and monitoring through identification of circulating tumour cells and tumour related nucleic acids in blood

Summary

The CANCER-ID project advanced the science that will lead to more widespread use of liquid biopsy in clinical trials of cancer drugs, and in the clinical treatment of patients with cancer. Liquid biopsy is a method of capturing cancer cells and cancer-derived cellular material (DNA, RNA, proteins) from cancerous tumours via blood samples, as opposed to via invasive tissue biopsies. Focusing on specific types of breast and lung cancer, the project studied and compared the different tools that can be used to isolate and examine three specific tumour biomarkers (CTC, ctDNA, miRNA). They developed guidelines that can help make decisions about which technology should be used in which case, and a set of protocols that describe the standardised ways they should be used, including how samples should be handled.

Their protocols were tested in a series of studies across multiple sites, and the knowledge from these studies has contributed significantly to efforts to increase the use of liquid biopsy in prognosis, patient selection, and monitoring for drug efficacy and resistance. CANCER-ID also produced protocols for using liquid biopsy to select patients who may benefit from immune checkpoint inhibition, a type of immunotherapy, and these are among the findings that are now included in EU-level technology standards guidelines. The project partners met with advisors from the European and American regulatory bodies to get advice on standardised assays, and this and other relationships fostered during the course of the project are being sustained via the European Liquid Biopsy Society (ELBS). The ELBS consortium continues the exchanges between the network of experts, technology makers and patients that started during CANCER-ID (in Europe and beyond) and continues to push the science forward, making Europe a hub of international liquid biopsy research.   

Background

Cancer is the second biggest cause of death in Europe, after cardiovascular disease. One of the many challenges in treating cancer is the difficulty in monitoring how a tumour responds to treatment, and detecting mutations that can lead to drug resistance. Tissue biopsies, where a piece of tumour is physically excised from the body of the patient, are currently used to diagnose and monitor the disease, but they can’t be performed too often because they are invasive, costly, and often risky for the patient.

Tumours shed cells and fragments of DNA into the bloodstream and these ‘biomarkers’ can potentially be used to monitor how the tumour is evolving in real time. This is especially useful when classic biopsy is not possible either because the cancer is in its early stages and there’s not a lot of tumour, or when taking a biopsy is too risky because the tumour is in a tricky place, such as the lung or certain parts of the brain. There have been technical advances that allow certain biomarkers to be detected and isolated from the blood, but many challenges remain: looking for them is often like looking for a needle in a haystack. Complicating things even further is the fact that even small changes in the way a blood sample is handled can affect the results. CANCER-ID examined the existing technologies for enriching, isolating and analysing three blood-based biomarkers, benchmarked the technologies, and then developed and validated protocols for how they should be used in any laboratory in a standardised way.

Technologies and protocols

There are three types of biomarkers that were central to the project. These were circulating tumour cells (CTCs), circulating-free tumour DNA (ctDNA) and circulating micro-RNAs (miRNAs). Before CANCER-ID, there was not only a lack of accepted, standard definitions and rules for the use of different technologies that extract and analyse the biomarkers; even some basic definitions were lacking, for example what constitutes a circulating tumour cell (CTC). This has severely hindered the use of liquid biopsy in drug development and patient treatment. Beyond producing protocols for the use of different analytical technologies, methods and sample-handling practices, CANCER-ID tested and confirmed the feasibility of carrying out multicentric studies under standardised conditions. They also put together detailed proposals on ways that labs can decide which technology to use for a given type of question, and other guidance to help those who wish to implement the technologies.

These protocols are important because they offer a way for diverse clinical and academic laboratories to make sure they are carrying out their analysis in a standardised way, essentially creating more confidence in – and giving more meaning to – the results. The project also studied the value of liquid biopsy technologies in the selection of patients who may benefit from immune checkpoint inhibition (ICI) treatment. The protocols were and continue to be further tested for fitness in the set-up of clinical studies at different sites across Europe.

Studies and findings

CANCER-ID researchers published over 50 papers in scientific journals, covering standards for reproducible cell lines that enrich, isolate and analyse circulating tumour cells, an algorithm that can automate the analysis of CTC images, and the harmonised protocols for sample handling, benchmarking liquid biopsy technologies, and using the technologies in the lab. Other papers assessed the use of standard materials for ctDNA technology benchmarking, established and implemented clinical-ready protocols for ctDNA analysis, and confirmed that ctDNA levels and mutant variant allele frequency are predictive markers for the efficacy of ICI treatment.

Ultimately the findings of CANCER-ID revealed that the protocols need to be adapted to different clinical settings – there is no ‘one size fits all’ solution. A clear-cut definition of pre-analytical variables is vital for liquid biopsy studies, and this conclusion is now impacting the choice of assays and the way studies are planned.

Legacy - the European Liquid Biopsy Society

The results of the studies ultimately had an impact on several best practice documents issued by the European Committee for Standardization (CEN) Technical Committee. The CEN standardisation documents now reflect not only protocols, but also CANCER-ID’s confirmation that changes in the count of CTCs is a predictive biomarker for ICI treatment success in patients with a type of cancer called non-small-cell lung carcinoma. CANCER-ID also advanced the regulatory approval of liquid biopsy technologies by working with regulators like the European Medicines Agency (EMA) and the Food and Drug Administration (FDA) in the US to gather their perspectives, along with patient advocates.

An important task for the exploitation of the results is the maintenance of the liquid biopsy stakeholder network that was set up as part of the consortium. The European Liquid Biopsy Society (ELBS) consortium carries on the exchange with regulatory bodies, patient advocates and technology providers, and continues to benchmark emerging liquid biopsy technologies. The aim is to support European technology providers to shorten development timelines, and to provide access to interested clinical research groups.

Beyond the ELBS, plus the knowledge, guidelines, standards and training generated through CANCER-ID, the project’s lasting legacy is closer interaction between the currently more than 60 academia and industry partners in the consortium, their equivalent networks outside Europe, and all the other stakeholders who have an interest in making liquid biopsy standard clinical practice, thus cementing Europe as a leading hub for this field of research.

Achievements & News

CANCER-ID hunts for cancer clues in blood samples

Today, many cancer patients have to undergo biopsy surgery to provide doctors with the cell samples they need to diagnose the disease, determine the treatment needed, and then monitor how well a treatment is working. ###Needless to say, doctors cannot carry out biopsies too often because they are invasive, costly, and risky to the patient. Yet cancer is a dynamic disease and patients would benefit immensely from more regular analyses of their condition.

Cancerous tumours shed cells and fragments of DNA into the bloodstream, and IMI’s CANCER-ID project has developed and validated a range of methods and protocols to detect these ‘circulating tumour cells’ (CTCs) and DNA and analyse them – a so-called ‘liquid biopsy’.

According to project coordinator Dr Thomas Schlange of Bayer, the results revealed that the protocols need to be adapted to different clinical settings – there is no ‘one size fits all’ solution. ‘CANCER-ID helped a lot to raise awareness of the necessity to clearly define the intended context of use for each and every liquid biopsy assay in order to be able to deliver meaningful results,’ he says.

CANCER-ID officially ended in December 2019, but its legacy will be carried forward by the newly-created European Liquid Biopsy Society (ELBS), which brings together many project partners and already has strong ties with the global liquid biopsy research community.

‘The story of standardising and benchmarking liquid biopsy assays is far from over,’ notes Dr Schlange. ‘New technologies are being developed and will require the same analytical rigour that has been applied in CANCER-ID to prove their clinical validity and consequent utility.’

Read more

Developing liquid biopsy tests to diagnose cancer

Liquid biopsies can help to diagnose cancer in its early stages, and assist clinicians in monitoring the impact of treatment at any point. While offering great potential, a lack of standardised assays – or tests – have hampered research and slowed clinical adoption. The CANCER-ID project brought together 38 partners from 13 European countries, as well as groups from the US and a company in Singapore, to develop and validate standardised operating procedures for liquid biopsies.###

'Liquid biopsies pose a very difficult analytical challenge because we are looking for very rare events,' says CANCER-ID academic coordinator Klaus Pantel of the University Medical Center Hamburg-Eppendorf. Tumour cells can be difficult to detect in the human bloodstream, with sometimes less than one tumour cell to every million white blood cells. The CANCER-ID team focused on four specific work streams covering all aspects of liquid biopsy testing for cancer. Specifically, these included developing the criteria for evaluating circulating tumour cells; defining the methods for analysis of nucleic acids; developing clinic-ready protocols for liquid biopsy testing; and creating protocols for the management and storage of data. Together, they provide a comprehensive framework for using liquid biopsies. Informed by both public and private partners, the protocols are designed to provide best-practice guidelines and will be made freely available via open-source platforms, providing a standardised basis for research and, in the future, clinical practice.

CANCER-ID method marks step towards liquid biopsies for cancer patients

Scientists from the CANCER-ID project have developed a streamlined procedure for studying certain alterations in cancer cells found circulating in the blood stream. The method could prove useful in helping clinicians to better identify which treatments will work in which patients, and to monitor disease progression. ###Cancerous tumours regularly shed individual cells into the blood stream. If captured through a blood test, these ‘circulating tumour cells’ (CTCs) have the potential to provide a lot of information about the state of the tumour. This is particularly important for cancers that cannot be biopsied without major surgery, for example. This study focused on the analysis of copy number alterations (CNAs) in the tumour cells; CNAs are mutations where multiple copies of a gene are found in the genome. Different CNA profiles have been linked to increased response or resistance to different types of drugs. However, current techniques to analyse CNAs are complex and not easy to apply in the clinic. In PLoS ONE, the CANCER-ID team describes a robust yet simple, one-step method to detect the number of CNAs in single cells. According to lead author Nicolò Manaresi of Menarini Silicon Biosystems, the new technique, dubbed Ampli1, provides comparable or superior performance at lower cost than current methods. ‘Our streamlined workflow will further decrease the cost of copy number analysis in the future and pave the way to a simpler blood test to study cancer heterogeneity in liquid biopsy,’ he said.

Read the Menarini Silicon Biosystems press release

CANCER-ID finds clues to cancer drug effectiveness in blood

Changes in the genes of cancer cells found in the blood could help to identify patients for whom a standard drug is most likely to be effective, according to a new study by scientists from IMI’s CANCER-ID project. The findings, published in the journal Cancer Research, could ultimately result in tests that would allow doctors to distinguish between patients who should keep taking the drug and patients who would benefit from trying alternative treatments.### The scientists focused on a form of non-small cell lung cancer (NSCLC) that is driven by mutations in a gene called ALK. There is a drug, crizotinib, that targets ALK. However, while crizotinib helps some patients to keep the cancer in check for years, in others its effects last for just a few months. The challenge for doctors is to identify which patients are unlikely to respond well to treatment, so that they can be offered a different treatment. It is not practical to subject NSCLC patients to regular biopsies to track the progress of their disease. However, some cancer cells break off from the tumour and enter the blood stream. These circulating tumour cells (CTCs) can be identified and analysed via a simple blood test. In this latest study, scientists took blood samples from ALK-NSCLC patients both before and two months after starting crizotinib treatment. They then analysed the CTCs found in the blood samples for both ALK rearrangements and multiple copies of the ALK gene. This revealed that patients who showed a decrease in the number of CTCs with multiple copies of the ALK gene after two months on crizotinib had an average progression free survival (i.e. their condition did not worsen) of 14 months. In comparison, patients where the number of CTCs with multiple copies of the ALK gene stayed the same or increased had an average progression free survival of just six months. ‘In this study, we showed that analysis of ALK copy number in CTCs before starting crizotinib treatment and after two months of crizotinib treatment may provide a biomarker for predicting the effectiveness of the therapeutic,’ said the lead author of the paper, Françoise Farace of INSERM in France. ‘This is important because there is currently no means of distinguishing those patients likely to gain long-term benefit from crizotinib from those who are not and who should consider trying some of the newer ALK-targeted therapeutics that have been more recently developed.’ Larger studies are now needed to validate the findings, and the technology used to study the CTCs is not yet ready for large-scale application. Nevertheless, Dr Farace points out: "The results reflect the potential of liquid biopsies to monitor treatment response in real time and tailor treatments at the individual patient level."

Could a blood test offer clues to cancer gene activity?

Scientists from IMI’s CANCER-ID project have obtained unprecedented levels of information on genetic activity in cancerous tumours by analysing fragments of tumour DNA taken from blood samples. The study, published in Nature Genetics, adds to our understanding of the genetics of cancer and will aid in the development of new treatments.### Ultimately, it should help to improve cancer diagnosis and treatment. Cancerous tumours regularly shed fragments of genetic material like DNA into the blood, and there is a lot of research into the best ways of capturing and analysing this material. Until now, the most advanced techniques allowed researchers to identify which mutations were present in the tumour DNA. Now, CANCER-ID researchers from the Medical University of Graz have succeeded in going a step further and identifying whether the genes are actually active or not. According to the researchers, knowing which genes are active in tumours will aid in the identification of potential drug targets and could also improve the clinical management of patients with cancer. Looking to the future, the team hopes to use their new technique to determine whether gene activity remains stable in tumours or whether it varies in response to external factors such as treatments.

IMI welcomes a new project: CANCER-ID
CANCER-ID, a new IMI project to validate blood-based biomarkers for cancer, has just got started. Blood-based biomarkers such as circulating tumour cells, circulating free tumour DNA (cfDNA) and microRNAs (miRNAs) are potential indicators for the tumour burden of patients living with cancer. Derivation of these markers from blood may offer an invaluable tool for cancer therapy: ###blood-based tests are instrumental when biopsies of the tumour are not accessible, and they may allow a close follow-up of disease markers offering a means to monitor the efficacy of treatment and potentially improve the choice of treatment options. CANCER-ID brings together 33 partners from 13 countries -  experts from academic and clinical research, innovative SMEs, diagnostics companies and the pharmaceutical industry - aiming at the establishment of standard protocols for and clinical validation of blood-based biomarkers. The total budget of CANCER-ID is EUR 14.5 million. Find out more on the project website
(April 2015)

Participants

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EFPIA companies
  • Bayer Aktiengesellschaft, Leverkusen, Germany
  • Boehringer Ingelheim Internationalgmbh, Ingelheim, Germany
  • Eli Lilly And Company LTD, Basingstoke, United Kingdom
  • Institut De Recherches Servier, Suresnes, France
  • Menarini Silicon Biosystems S.A, Bologna, Italy
  • Orion Oyj, Espoo, Finland
Universities, research organisations, public bodies, non-profit groups
  • Academisch Ziekenhuis Groningen, Groningen, Netherlands
  • Charite - Universitaetsmedizin Berlin, Berlin, Germany
  • Deutsches Krebsforschungszentrum Heidelberg, Heidelberg, Germany
  • Ethniko Kai Kapodistriako Panepistimio Athinon, Athens, Greece
  • European Organisation For Research And Treatment Of Cancer Aisbl, Brussels, Belgium
  • Heinrich-Heine-Universitaet Duesseldorf, Düsseldorf, Germany
  • Helsingin Ja Uudenmaan Sairaanhoitopiirin Kuntayhtymä, Helsinki, Finland
  • Institut Curie, Paris, France
  • Institut Gustave Roussy, Villejuif, France
  • Istituto Oncologico Veneto, Padova, Italy
  • Max-Planck-Gesellschaft Zur Forderung Der Wissenschaften Ev, Munich, Germany
  • Medizinische Universitat Graz, Graz, Austria
  • Oslo Universitetssykehus Hf, Oslo, Norway
  • The University Of Manchester, Manchester, United Kingdom
  • Universita Degli Studi Di Torino, Turin, Italy
  • Universitaetsklinikum Hamburg-Eppendorf, Hamburg, Germany
  • Universite De Montpellier, Montpellier, France
  • Universiteit Twente, Enschede, Netherlands
  • University of Cambridge, Cambridge, United Kingdom
Small and medium-sized enterprises (SMEs)
  • Agena Bioscience GmbH, Hamburg, Germany
  • Alacris Theranostics GMBH, Berlin, Germany
  • Arttic, Paris, France
  • Gilupi GMBH, Potsdam, Germany
  • Tataa Biocenter AB, Göteborg, Sweden
  • VyCAP BV, Deventer, Netherlands
Non EFPIA companies
  • ANGLE Europe Ltd, Guildford, United Kingdom
  • Agilent Technologies Sales & Services GmbH & Co. KG, Waldbronn, Germany
  • Clearbridge Biomedics Pte Ltd, Singapore, Singapore
  • LIFE TECHNOLOGIES GmbH, Darmstadt, Germany
  • Luxembourg Institute Of Health, Luxembourg, Luxembourg
  • Qiagen GMBH, Hilden, Germany
  • Seracare Life Sciences Inc, Delaware, United States
  • Siemens Healthcare Diagnostics Products GMBH, Marburg, Germany
  • Terumo Bct Europe Nv, Lakewood, United States

Participants
NameIHI funding in €
Academisch Ziekenhuis Groningen319 298
Alacris Theranostics GMBH240 000
Arttic213 211
Charite - Universitaetsmedizin Berlin80 000
Deutsches Krebsforschungszentrum Heidelberg80 000
Ethniko Kai Kapodistriako Panepistimio Athinon239 970
European Organisation For Research And Treatment Of Cancer Aisbl140 000
Gabo:Mi Gesellschaft Fur Ablauforganisation:Milliarium mbH & Co. KG (left the project)116 787
Gilupi GMBH169 948
Heinrich-Heine-Universitaet Duesseldorf319 298
Institut Curie79 500
Institut Gustave Roussy319 581
Istituto Oncologico Veneto319 298
Leukocare AG (left the project)73 846
Luxembourg Institute Of Health238 410
Max-Planck-Gesellschaft Zur Forderung Der Wissenschaften Ev240 000
Medizinische Universitat Graz300 000
Oslo Universitetssykehus Hf80 000
Tataa Biocenter AB169 500
The University Of Manchester420 000
Universita Degli Studi Di Torino80 000
Universitaetsklinikum Hamburg-Eppendorf981 575
Universite De Montpellier239 778
Universiteit Twente750 000
University of Cambridge240 000
VyCAP BV170 000
Total Cost6 620 000