Onco Track

Methods for systematic next generation oncology biomarker development
METHODS FOR SYSTEMATIC NEXT GENERATION ONCOLOGY BIOMARKER DEVELOPMENT SUMMARY

FACTS & FIGURES

Start Date
End Date
Call
IMI1 - Call 2
Grant agreement number
115234

Type of Action: 
RIA (Research and Innovation Action)

Contributions
IMI Funding
16 757 282
EFPIA in kind
10 976 557
Other
3 346 480
Total Cost
31 080 319

Summary

Colorectal cancers are a very heterogeneous group of cancers and not all of them respond to the same drugs in the same way. By collecting tumour samples from patients and then analysing them in the laboratory, the OncoTrack project found molecular fingerprints of those tumours and then correlated them to how these tumours respond to various drugs. The project’s outputs are already helping doctors in choosing the right treatment for the right patient, and could also help in the future search for more effective drugs. As a result of the project, two spin out companies have been created and several patents filed, demonstrating tangible socio-economic benefits.

Colorectal cancer is the third most frequently occurring cancer worldwide and, at an advanced stage, one of the most common causes of death. It takes numerous forms, and not all cancers respond to the same kind of treatment. This is because tumours undergo genetic changes as they grow and spread, and these changes can vary even between patients with the same type of cancer.  To be able to predict a tumour’s response to certain drugs more accurately, IMI’s OncoTrack project set out to produce molecular fingerprints of different tumours and correlate the different fingerprints to how the tumours respond to various drugs.

By bringing together academic institutions, SMEs and pharmaceutical companies, OncoTrack scientists first collected tumour samples from over 100 colorectal cancer patients at different stages of the disease. They grew these tumours in tissue culture systems, as well as in special mouse strains, and proceeded to analyse them in the lab. In particular, the scientists looked for biomarkers, i.e. molecules that are typical of the different tumour sub-groups. Based on this analysis, they were able to produce molecular fingerprints for all of the tumours.

Next, they tested how the tumours respond to different drugs and correlated various tumour fingerprints with their response to the different clinical compounds. Among other things, they discovered two biomarkers that can predict the effectiveness of two drugs commonly used to treat this disease: Cetuximab, which inhibits the receptor for the epidermal growth factor, and the chemotherapy drug 5FU.

New 3D models of colon cancer, and other achievements

Growth of tumours took place in 3D tissue culture systems and through xenografts – tissue grafted onto mice, which creates a strain of the disease adapted to mice. Analysis covered the genetic material, RNA molecules and in some cases, the proteins of the tumours. These biological models are now considered as some of the best characterised in the field, and are already being used by pharmaceutical companies in their drug discovery and development projects.

Other important outputs generated by the project include:

  • a biorepository of patient-derived 3D cultures and patient-derived xenograft models;
  • a database which contains part of the data generated by the project, with plans to complete it in the near future.

Two spin outs and various patents

The project also resulted in two spin-out companies. One of them was created in 2014 to commercialise the technology of 3D tissue culture systems or organoids. Generated from the tumour tissue, organoids are groups of cells that grow in the culture dish, remain small, and mimic a lot of the biology of the tumour. They are potentially quite useful to pharma companies and this spin-out has been set up to commercialise this as a basis for drug testing.

The second company was set up in 2018. It spun out from a group at the University of Paris, and intends to commercialise OncoTrack’s technologies developed to improve diagnostic procedures.

One of the major goals of OncoTrack was also to find better ways to diagnose cancer, and some of the partners have refined the technologies that they have been using. Several patents have been filed as a result.

Benefits to patients

OncoTrack project outputs are already benefitting patients. For example, the analysis of tumour samples of more than 100 patients, which was done as part of this project, is now available to the doctors treating those patients. Furthermore, for drugs which are already used in the clinic, such mutation analysis is now becoming routine, helping doctors choose the right drug for the right patient.

Additionally, one of the academic partners, the Medical University in Graz, is using the 3D culture models, which were developed during the project, in an experimental setting in the clinic in order to find drugs that can potentially help patients for whom no treatment is available.

For the benefit of industry, academia and SMEs

The academic institutions in the project benefitted from access to the pharmaceutical companies’ resources, such as drugs which were tested during the project. They also got a lot more information about mechanisms of drug action then they otherwise would have. In turn, the pharmaceutical industry is benefitting from the information, materials and biological models developed during the project.

Both academia and industry partners gained a lot from collaborating and exchanging different viewpoints and perspectives. For example, academics have learned more about how the industry works, and the industry has benefited from academic expertise. The connections which have been established will last well into the future.

Finally, the SMEs in the project benefitted from increased visibility and reputation, as well as new contacts with both industry and academic partners. Participating in OncoTrack accelerated their business expansion and helped them enter into new markets.

What’s next?

The information and models created during OncoTrack are now available for future research projects. In fact, several OncoTrack partners are continuing to work together in new pan-European projects, such as the Future Health initiative. Additional new projects, funded by national or local agencies, have been initiated by some of the academic partners.  

Read the interview with project coordinators

Achievements & News

Patients are already benefiting from our project – an interview with the OncoTrack coordinators
April 2018

Colorectal cancers are a very heterogeneous group of cancers and not all of them respond to the same drugs in the same way. By collecting tumour samples from patients and then analysing them in the laboratory, the OncoTrack project found molecular fingerprints of those tumours and then correlated them to how these tumours respond to various drugs. ###The project’s outputs are already helping doctors in choosing the right treatment for the right patient, and could also help in the future search for more effective drugs. As a result of the project, two spin out companies have been created and several patents filed, demonstrating tangible socio-economic benefits. In an interview with the IMI Programme Office, project coordinator, David Henderson of Bayer, and academic coordinator Hans Lehrach of the Max Planck Institute for Molecular Genomics, explain why all this wouldn’t have been possible without the public-private collaboration brought by IMI. ‘This was an extremely complex project,’ said Henderson. ‘In order to be successful with this degree of complexity you need a lot of know-how and a lot of detailed knowledge, and you can never find all of this in one place. So the big advantage of a public-private partnership is that you can bring in the different types of detailed knowledge that are available in an industrial setting, in a biotech start-up or in an academic setting. When you bring these together, the sum becomes much greater than its individual parts.’ Read the full interview

ONCOTRACK team identifies new way of tackling colon cancer
March 2018

Scientists from IMI’s ONCOTRACK project have identified a new way of tackling colon cancer; their findings are published in the journal Cell Reports. Colon cancer is the third most common cancer and the fourth most common cause of cancer deaths worldwide. ###Research has shown that cancer stem cells, which multiply and differentiate into different cell types like normal stem cells, play a key role in driving the growth of colon cancer tumours. They are also thought to be behind relapses, when cancer returns following treatment. In this study, researchers studied the sequences of genes in cancer stem cells, and found a that cancer stem cell survival is controlled by a specific feature of the ‘Hedgehog’ signalling pathway which allows cells to respond to external signals and inhibits stem cell differentiation. Targeting the Hedgehog pathway in a similar way has delivered promising results in early-stage research on pancreatic and breast cancer cells. ‘The targeted inhibition of the Hedgehog signalling pathway, used in combination with other standard treatments to shrink tumours, may provide a new strategy for the elimination of cancer stem cells and the prevention of cancer recurrence,’ said the first author of the paper, Joseph Regan of the Charité Comprehensive Cancer Center. ‘Future research will set out to better define the downstream signalling components of the pathway and further investigate how Hedgehog signalling controls cancer stem cell survival.’

OncoTrack leads to better understanding of colon cancer, inspires a spin-out company
October 2017

Colorectal cancer is the third most frequently occurring cancer worldwide and, at an advanced stage, one of the most common causes of death. It takes numerous forms, with not all such cancers responding to the same drugs in the same way.### To improve responses of colorectal tumours to treatment and increase survival rates, IMI’s OncoTrack project collected tumour samples from 106 patients. These were grown and analysed to identify biomarkers and create molecular fingerprints for each one. Researchers then tested the response of the tumours to different drugs and correlated the molecular fingerprints and responses. This made it possible to predict whether a drug will be effective on a specific tumour. In this way, the OncoTrack researchers discovered sets of biomarkers that can predict the effectiveness of two common means of colorectal cancer treatment: Cetuximab, which stops proteins on the surface of cancer cells from causing the cells to divide and grow, and the chemotherapy drug 5FU. ###

‘The biological models of colon cancer that the consortium developed are especially well characterised and are already being used by some pharma companies for drug discovery and development projects,’ says David Henderson, who coordinates the project on behalf of Bayer AG in Germany. Growth of the tumours took place in 3D tissue culture systems and through xenografts – tissue grafted onto mice, which creates a strain of the disease adapted to mice. Use of the models developed under OncoTrack has the potential to bring about long-term benefits. One biotech company has been developing and refining a computer-based drug response prediction approach which may ultimately provide a commercial diagnostic service. ‘The xenograft models are available on a commercial basis and a new company was spun out from the project to capitalise on the technologies surrounding use of the 3D culture models in drug development,’ says Henderson.

OncoTrack identifies new biomarkers for colon cancer
March 2017

Colorectal carcinomas are a very heterogeneous group of cancers and not all of them respond equally to different drugs. Up until now, doctors have decided on which drug to use based on the tumour gene mutations. However, the mutation status alone is not specific enough.### To be able to predict a tumour’s response to certain drugs more accurately, IMI’s OncoTrack project set out to produce molecular fingerprints of different tumours and correlate the different fingerprints to how the tumours respond to various drugs. In the process, they identified two new biomarkers for colorectal cancer which could lead to more personalised and effective treatments for patients with this disease.

The study, which was recently published in the journal Nature Communications, was one of the largest public-private collaborations in this field to date. By bringing together academic institutions, SMEs and the pharmaceutical industry, OncoTrack scientists first collected tumour samples from over 100 colorectal cancer patients at different stages of the disease. They grew these tumours in tissue culture systems, as well as in special mouse strains, and proceeded to analyse them in the lab. In particular, the scientists looked for biomarkers, i.e. molecules that are typical of the different tumour sub-groups. Based on this analysis, they were able to produce molecular fingerprints for all of the tumours. Next, they tested how the tumours respond to different drugs and correlated various tumour fingerprints with their response to the different clinical compounds. Among other things, they discovered two biomarkers that can predict the effectiveness of two drugs commonly used to treat this disease: Cetuximab, which inhibits the receptor for the epidermal growth factor, and the chemotherapy drug 5FU. ‘The extensive molecular and drug sensitivity datasets generated within this study are a highly valuable resource,’ said Bodo Lange, CEO at Alacris Theranostics, one of the OncoTrack project partners. ‘Our findings provide major new insights into the molecular landscape of colorectal cancer and have the potential to guide treatment decisions.’

Smartphone microscope can sequence DNA on the spot
January 2017

An international team of scientists has developed a smartphone-based microscope that can analyse DNA sequences and spot genetic mutations in samples of bowel cancer cells and tissues. This information is vital to help doctors determine which treatments are likely to work in a patient, and the new device will make this technology more readily accessible to people in remote areas and poorer parts of the world. ###The novel device, funded in part through IMI’s bowel cancer project OncoTrack, is described in the journal Nature Communications. DNA sequencing is increasingly used in cancer treatment; if you know which mutation is driving a patient’s cancer, you can determine which treatment is most likely to beat it. However, to get this information, doctors usually have to send cell and tissue samples away to large, specialist laboratories. This new microscope, which is created by 3D printing, would allow doctors to carry out the test on the spot. When hooked up to a smartphone, it can read the DNA sequence of a tumour and flag up specific mutations. The researchers estimate that if produced in large quantities, the cost of manufacture of the microscope could be as low as USD 500 (EUR 466). For comparison, prices for standard microscopes used for sequencing start at USD 10 000 (EUR 9 300). Although the researchers focused initially on cancer, they believe the microscope could play a vital role in diagnosing infectious diseases. ‘Antibiotics are effective against bacteria. But now we are losing that weapon when bacteria become resistant,’ said Mats Nilsson of the Universities of Stockholm and Uppsala. ‘However, if we could look at the DNA level and find out if a bacterium is sensitive to a certain type of antibiotics, we could choose the right treatment from the very beginning. This is where I think this concept has its great strength.’

OncoTrack and ELIXIR team up on long-term data management
February 2016

IMI cancer project OncoTrack and life sciences data infrastructure ELIXIR are exploring how they could collaborate to ensure the provision of data storage and discovery services for data generated by the project.### OncoTrack brings together pharmaceutical companies, academics and small and medium-sized enterprises (SMEs) in a quest to develop new approaches to identifying markers for colon cancer, something which will help to improve diagnosis and treatment of the disease and may ultimately contribute to increased chances of survival. As part of this effort, the project is generating large amounts of data. ELIXIR could help OncoTrack to store and manage this data safely and securely through its European Genome-Phenome Archive (EGA). OncoTrack and ELIXIR are also exploring options for the long term management of data in TranSMART, which OncoTRACK is already using for data analysis through IMI’s eTRIKS project. Niklas Blomberg, ELIXIR Director said: ‘We are delighted to collaborate with OncoTrack, a shining example of the potential that big data has for advancing medical knowledge. This collaboration could provide a model for how translational data can be made available for long term re-use by the biomedical research community.’

OncoTrack partners found spin-off company
July 2014

Researchers working on IMI’s cancer project OncoTrack have teamed up to launch a spin-off company called Cellular Phenomics & Oncology  Berlin-Buch GmbH (CPO).### Founded by Christian Regenbrecht and Reinhold Schäfer of Charité Universitätsmedizin Berlin and Jens Hoffmann of German biotech company Experimental Pharmacology & Oncology, CPO will establish a library of patient-derived, three-dimensional cancer cell cultures that can be used in drug research and development. CPO will also work with other partners to develop the technology to identify personalised treatments for cancer patients. In the beginning, the company will focus on developing models of melanoma (skin cancer), breast cancer, lung cancer, head and neck cancers, and colorectal cancer. Christian Regenbrecht and Reinhold Schäfer are the academic leaders of OncoTrack’s cell culture work package, and the experience of creating cell cultures of human colorectal cancers under the project will be valuable when setting up the company’s workflows. All three scientists will remain with their original organisations and so will continue to work on OncoTrack. Meanwhile, CPO may well join the project in its own right. 

Participants Show participants on map

EFPIA companies
  • Astrazeneca AB, Södertälje, Sweden
  • Bayer Pharma AG, Berlin, Germany
  • Boehringer Ingelheim Internationalgmbh, Ingelheim, Germany
  • Eli Lilly and Company Limited, Basingstoke, United Kingdom
  • F. Hoffmann-La Roche AG, Basel, Switzerland
  • Janssen Pharmaceutica Nv, Beerse, Belgium
  • Merck Kommanditgesellschaft Auf Aktien, Darmstadt, Germany
  • Pfizer Limited, Sandwich, Kent , United Kingdom
Universities, research organisations, public bodies, non-profit groups
  • Charite - Universitaetsmedizin Berlin, Berlin, Germany
  • Dahlem Center For Genome Research And Medical Systems Biology GMBH, Berlin, Germany
  • Fundacio Privada Institut D'Investigacio Oncologica De Vall-Hebron, Barcelona, Spain
  • Max-Planck-Gesellschaft Zur Forderung Der Wissenschaften Ev, Munich, Germany
  • Medizinische Universitat Graz, Graz, Austria
  • Stockholms Universitet, Stockholm, Sweden
  • Technische Universitaet Dresden, Dresden, Germany
  • Universite Paris-Sud, Orsay, France
  • University College London, London, United Kingdom
  • Uppsala Universitet, Uppsala, Sweden
Small and medium-sized enterprises (SMEs)
  • Alacris Theranostics GMBH, Berlin, Germany
  • Experimentelle Pharmakologie Und Onkologie Berlin-Buch GMBH, Berlin, Germany
  • International Prevention Research Institut-Ipri Management, Lyon, France
Third parties
  • Ipri Services, Ecully, France

CONTACT

Project coordinator
David Henderson
Bayer Pharma AG
Germany
+49 30 4000 8769
david.henderson[at]bayer.com
Managing entity
Hans Lehrach
Max-Planck-Gesellschaft zur Foerderung der Wissenschaften e.V.
+49-30 8413 1220
lehrach[at]molgen.mpg.de