Researchers from the Wellcome Sanger Institute and the Children’s Medical Research Institute (CMRI) have created the ‘world’s largest’ database for predicting cancer treatment response based on cancer proteins.
The researchers created a protein map for 949 cancer cell lines across over 40 cancer types, which were tested with 650 different treatments. Advanced computational methods were then used to predict the response of cancer cells to treatment, with the results also pinpointing vulnerabilities in cancer cells that provide opportunities for developing new treatments.
The paper, published in Cancer Cell, ‘lays the foundation’ for ongoing efforts to predict the response of an individual cancer to the response of an individual cancer to drugs based on the proteins the cancer contains.
Mathew Garnett, a senior author of the study from the Wellcome Sanger Institute, said: “In addition to revealing new insights about the biology of cancer, this study is also helping to fulfil the mission of my team to generate reference datasets for widespread use in the international cancer research community.”
Thousands of different proteins, collectively referred to as the proteome, are contained in every cell in the body and are responsible for the behaviour of cancer cells and how they respond to treatment. Clinical cancer specialists have known that, for some types of cancer, measuring the quantities of a few specific proteins can help guide treatment choice, but methods for measuring the thousands of other types of proteins have not been readily available for clinical use so far.
In the study, CMRI’s ProCan team used mass spectrometry to measure thousands of different proteins in very large numbers of cancers and, using this methodology, generated a proteomic database for the 949 cancer cell lines grown by the Sanger team, who analysed the response of each cell line to up to 650 different drugs.
Cancer researchers and clinicians around the world will be able to use the cancer database as a resource.
Commenting on the study’s results, Roger Reddel, a senior author of the study and a co-founder of ProCan, said: “This study has been a collaborative team effort involving proteomics experts, software engineers, data scientists, cancer cell biologists, and oncology researchers that has resulted in important new insights into the interactions among thousands of key molecules within cancer cells, and the response of cancer cells to drug treatments.”