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

Contributions
IMI Funding
16 757 282
EFPIA in kind
10 976 557
Other
3 346 480
Total Cost31 080 319

Summary

The OncoTrack project will focus on its goal of identifying biological markers that will help our understanding of the variable composition of tumors and the relationship between biological heterogeneity and tumor variation in response to treatment. In particular, biomarkers for cancer of the colon will be analysed through the development and application of research techniques with unprecedented high sensitivity levels.

The research will allow the identification and qualification of biomarkers predictive of patient response as well as those useful for monitoring of therapeutic efficacy. The OncoTrack consortium will use an approach based on the “Virtual Patient” computer modelling system and state-of-art “omics” technologies and systems biology approaches to develop new generation biomarkers and diagnostics that can be used to implement personalized medicine.

The aim is to validate available and predicted biomarkers in large studies which will ultimately produce useable data in a suitable format for point-of-care diagnostic tools.

Oncotrack is coordinated by Bayer Healthcare Pharmaceuticals and Hoffmann La-Roche AG and the managing entity of IMI JU funding is the Max-Planck Society for the Advancement of Science, Germany.

In total there are 18 multidisciplinary partners -11 academic and SMEs and 7 from EFPIA spread across 6 European countries.

Achievements & News

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
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.’
 - Read the OncoTrack press release
 - Read the project factsheet
(March 2017)

Smartphone microscope can sequence DNA on the spot
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.’
 - Read the press releases of Stockholm University and the University of California
(January 2017)

OncoTrack and ELIXIR team up on long-term data management
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
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. 
(July 2014)

Participants Show participants on map

EFPIA companies
  • AstraZeneca AB, Södertälje, Sweden
  • Bayer AG, Berlin, Germany
  • Boehringer Ingelheim International GmbH, Ingelheim, Germany
  • Eli Lilly and Company Ltd, Basingstoke, United Kingdom
  • F. Hoffmann-La Roche Ltd, Basel, Switzerland
  • Janssen Pharmaceutica NV, Beerse, Belgium
  • Merck KGaA, Darmstadt, Germany
  • Pfizer Limited, Sandwich, Kent , United Kingdom
Universities, research organisations, public bodies, non-profit groups
  • Charité – Universitätsmedizin Berlin, Berlin, Germany
  • Dahlem Centre for Genome Research and Medical Systems Biology, Berlin, Germany
  • Fundacio Privada Institut D’Investigacio Oncologica De Vall-Hebron, Barcelona, Spain
  • Max-Planck-Gesellschaft zur Foerderung der Wissenschaften e.V., Munich, Germany
  • Medical University of Graz, Graz, Austria
  • Stockholms Universitet, Stockholm, Sweden
  • Technische Universitat Dresden, Dresden, Germany
  • University College London, London, United Kingdom
  • Université Paris-Sud, Orsay, France
  • Uppsala universitet, Uppsala, Sweden
Small and medium-sized enterprises (SMEs)
  • Alacris Theranostics GmbH, Berlin, Germany
  • Experimental Pharmacology and Oncology Berlin-Buch GmbH, Berlin, Germany
  • International Prevention Research Institute SAS, Lyon, France
Third parties
  • Ipri Services, Ecully, France

CONTACT

Project coordinator
David Henderson
Bayer Pharma AG
+49 160 97244447
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