Children’s Medical Research Institute’s sixth annual ProCan® collaborator update was held on 1 December 2022. The hybrid in-person/online meeting included representatives of the Australian Cancer Research Foundation, members of the ProCan Consumer Advisory Panel, and cancer researchers and clinicians from around Australia and overseas.
ProCan co-Directors Prof Roger Reddel AO and Prof Phil Robinson spoke about the rapid progress the talented ProCan team has made towards the goal of providing personalised diagnosis and treatment decision-making tools for cancer clinicians, which is expected to improve survival and patient outcomes for most types of cancer affecting children and adults.
“Absolutely remarkable progress,” said Prof Curt Harris who participated in the meeting online from the US National Cancer Institute in Bethesda, Maryland. “[ProCan is] leading the whole world in these technologies and the strategies to bring them to the clinic. Progress made over the next five years will add to the importance of proteomics in improving diagnosis and prognosis—and improving patient outcomes.”
Prof Harris is a key collaborator with ProCan on an early-stage lung cancer study which is identifying new protein signatures that classify lung cancer patients according to low or high risk of relapse after surgery.
Dr Adel Aref of the ProCan Oncology team presented similar advances for pancreatic and prostate cancers with collaborators in Sydney and Zurich, respectively.
Pancreatic adenocarcinoma has a 5-year survival rate of only 11%. Dr Aref showed that ProCan has now identified a protein signature (involving 29 proteins) that can predict the outcome for pancreatic cancer patients, helping clinicians classify patients into low- and high-risk groups, and has found valuable information on the cellular pathways related to poor prognosis.
For prostate cancer, the team was able to identify independent biomarkers to predict which patients will have a recurrence of their cancer after surgical removal.
Dr Qing Zhong, who leads the Cancer Data Science team within ProCan, spoke about the pan-cancer study ProCan recently published on 949 cancer cell lines, and how the team built an artificial intelligence-powered pipeline (called DeeProM) to review thousands of proteins and find the treatments to which the cancers will be vulnerable. The ProCan team focused on the information that could be discovered only by examining proteins, not DNA or RNA.
The team is also working towards integrating the results from cancer cell lines (cancers grown in the laboratory) with the results from actual tumours.
Prof Reddel explained, “A cancer clinical trial in essence asks one question: does this one therapy effectively treat this one type of cancer? With cell lines, you can test hundreds of therapies on hundreds of cancers—you are answering many more questions.” So integrating the results from laboratory studies of cancer cell lines with clinical trial data has the potential to get answers for patients much more rapidly.
Using data from 975 cancer cell lines, Dr Zhong’s team used machine learning to diagnose the cancer type of cancer samples. They showed that adding new data increased the accuracy of the prediction, so the large amounts of data being generated by ProCan are expected to progressively increase the accuracy of the diagnosis.
Prof Rosemary Balleine, a former research leader in ProCan who established ProCan’s pathology laboratory, is now based at the Westmead Institute and continuing to collaborate with the ProCan team. Prof Balleine spoke about triple-negative breast cancer and high-grade serous ovarian cancer, both of which are difficult-to-treat, aggressive cancers with similarities in their genetic changes suggesting that immunotherapy could be a successful treatment. However, these cancers had very different responses to immunotherapy. Prof Balleine's collaborative work with ProCan has identified cancer protein signatures to help predict which breast cancer patients are likely to respond to immunotherapy. For ovarian cancer, while it was possible to identify markers to distinguish individual patients' cancers, a key step in personalised medicine, the high level of genetic changes resulting from genomic instability in the ovarian cancers appear to make it difficult to predict response to immunotherapy treatments in these patients.
Prof Eytan Ruppin also from the US National Cancer Institute congratulated the ProCan team, saying, “I think that, to summarise, Down Under has the upper hand.”
Kerry Strydom, CEO of the Australian Cancer Research Foundation, which seed funded ProCan said, “ACRF is proud to have backed this pioneering research. I am so inspired seeing outcomes and thank the entire project team for the significant progress to date.”
ProCan’s work is also made possible by funders including NSW Ministry of Health and the Office of Health and Medical Research, Cancer Institute NSW, the Australian Medical Research Futures Fund, Cancer Council NSW, National Breast Cancer Foundation, The University of Sydney and several trusts and foundations.
ProCan currently has 85 formal collaboration agreements (21 international), which cover 119 research projects that have been completed or are underway. ProCan is also part of the European Individualised Paediatric Cure (iPC) initiative and the US Cancer Moonshot (ICPC) program.