1. Computational and Systems Biology

Virtual patient ‘surrogates’ can personalise cancer treatments

Mathematical models used as patient surrogates could help clinicians select the best cancer treatment before going to the patient’s bedside.
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Scientists have developed mathematical models that act as patient ‘surrogates’ for evaluating potential prostate cancer treatments.

The research, published today in eLife, could ultimately help clinicians choose the most effective drug combination before they start to treat a patient, potentially improving their response and avoiding drug resistance.

Researchers used an approach called Boolean modelling, which is already used to describe dynamics of complex cell signalling processes. But existing models have been generic and have not accounted for the differences between individual patients’ diseases or how they respond to treatment.

“The dream has always been to use more and more complex models and data until we can have digital twins, or virtual humans or surrogates – a simulation that helps select the proper clinical treatment for a given patient with high degrees of specificity or sensitivity,” explains Arnau Montagud, who was a researcher at Institut Curie, Paris, France, at the time the study was carried out, and is now at the Barcelona Supercomputing Center (BSC), Spain. “We wanted to know if our method of tailoring Boolean models of cell signalling was accurate enough to discriminate between different patients, and whether the models could be used as testbeds to rank personalised drug treatments.”

To begin, the team used data from The Cancer Genome Atlas (TCGA) and other databases to create a network of all relevant pathways involved in prostate cell signalling. Then they converted this into a generic Boolean model where all the nodes in the network can be assigned one of two values – 0 (inactivated or absent) or 1 (activated or present). Data from 488 prostate cancer patients from TCGA were used to create 488 patient-specific Boolean models. For example, where a patient’s tumour had a mutation in a specific gene, this meant the node in the network was inactivated, and assigned a value of 0.

Having built these models, the team looked in each patient model for genes that, when inhibited, would block growth or encourage death of cancer cells. They narrowed these genes down to a list of targets of existing drugs, and ran simulations to predict what would happen if the drugs were combined. This allowed them to compare the effects of individual drugs on each patient, and to propose certain drugs that would work for specific patients or for groups of patients. Inactivation of some of the genes had a greater effect in some patients compared with others, highlighting opportunities for personalised drug treatments. The simulations also spotted patterns linked to the grade of patients’ tumours as measured by the Gleason score, suggesting it might be possible to tailor drug treatments to prostate cancer patients according to their score in the future.

Testing whether these treatment predictions hold true in patients would require a clinical trial, so the team instead built eight different personalised prostate cancer cell line models from publicly available data. As with the patient models, they looked for commonly occurring mutations in the cell lines that influenced cancer cell growth or death. This resulted in the identification of 17 proteins that could be targeted with drugs.

Next, to investigate if drugs targeting these proteins would have the anticipated effects, they mimicked the effect of different drug dosages in the model by switching off each node from 100% active to 0% active and looking at the effects on growth, death and spread of the cancer cells. When they carried out the same experiment in real cell lines, it confirmed that blocking the identified nodes in the model had differential effects on cell growth and survival. Moreover, the model could predict synergistic effects of treatments that work against different nodes in the network, which could help to identify promising drug combinations for future investigation.

“Our personalised models suggest single and combined drug treatments for individual prostate cancer patients,” concludes Laurence Calzone, a researcher at Institut Curie, and a co-senior author of the study alongside Julio Saez-Rodriguez, from Heidelberg University, Germany. “These advances are incremental steps towards having digital twins that will help clinicians before they go to the patient's bedside, allowing them to capture patient individualities and test and rank different drug treatments.”

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This research was granted European funding by the H2020 projects PrECISE, INFORE and the HPC/Exascale Centre of Excellence in Personalised Medicine (PerMedCoE).

To read more about author Arnau Montagud, visit https://www.bsc.es/montagud-arnau.

And for more information about Heidelberg University, see https://www.uni-heidelberg.de/en.

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    eLife
    e.packer@elifesciences.org
    +441223855373

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About eLife

eLife is a non-profit organisation created by funders and led by researchers. Our mission is to accelerate discovery by operating a platform for research communication that encourages and recognises the most responsible behaviours. We review selected preprints in all areas of biology and medicine, including Computational and Systems Biology, while exploring creative new ways to improve how research is assessed and published. eLife receives financial support and strategic guidance from the Howard Hughes Medical Institute, the Knut and Alice Wallenberg Foundation, the Max Planck Society and Wellcome. Learn more at https://elifesciences.org/about.

To read the latest Computational and Systems Biology research published in eLife, visit https://elifesciences.org/subjects/computational-systems-biology.

About BSC

BSC is the leading supercomputing centre in Spain. It specialises in high-performance computing. It has a dual role: providing infrastructure and a supercomputing service for Spanish and European scientists, and generating knowledge and technology to be transferred to society.

BSC has a staff of about 700 workers, most of whom are scientists who use supercomputers to conduct research in Computer Science, Life Sciences, Earth Sciences, and Engineering. The BSC is at the service of the international scientific community through the European research infrastructure PRACE (Partnership for Advanced Computing in Europe) and manages the Spanish Supercomputing Network (RES).

BSC is a public consortium owned by the Spanish Government Ministry of Science and Innovation (60%), the Catalan Government Department of Research and Universities (30%) and the Polytechnic University of Catalonia (10%). For more information, visit ​​https://www.bsc.es.

About PerMedCoE

PerMedCoE is the HPC/Exascale Centre of Excellence for Personalised Medicine in Europe and aims to provide an efficient and sustainable entry point to the HPC/Exascale-upgraded methodology to translate omics information into actionable models of cellular functions of medical relevance. Coordinated by the Barcelona Supercomputing Center (BSC), this CoE has been awarded €5 million in funding from the European Commission and will run from October 1, 2020, to September 30, 2023. A range of 12 world-class academic and industry partners from across Europe are participating in the CoE: BSC, CSC – IT Center for Science, University of Luxembourg, Institut Curie, University Hospital Heidelberg, Atos Spain, KTH Royal Institute of Technology, European Molecular Biology Laboratory, Centre for Genomic Regulation, Max Delbrück Center for Molecular Medicine, University of Ljubljana and ELEM Biotech.

About Institut Curie

Institut Curie, France’s leading cancer centre, combines an internationally renowned research centre with a cutting-edge hospital group that treats all types of cancer, including the rarest. Founded in 1909 by Marie Curie, Institut Curie employs 3,700 researchers, physicians and health professionals across three sites (Paris, Saint-Cloud and Orsay), working on its three missions: treatment, research and teaching. A private foundation with public utility status, Institut Curie is authorised to receive donations and legacies, and thanks to the support of its donors, is able to make discoveries more quickly, improving treatments and quality of life for patients. For more information, visit https://science.institut-curie.org, or contact Elsa Champion, Press Officer, at elsa.champion@curie.fr or +330764430928.