ProCan at the five-year mark

On 13 October, CMRI held its annual ProCan® Collaborators’ Update with 125 attendees, including researchers, funders, and members of ProCan’s consumer advisory panel. Collaborating cancer researchers from across Australia as well as the USA, Canada, and Europe joined the videoconference hosted by co-founder Professor Phil Robinson for a presentation and discussion of ProCan’s research achievements in the five years since the facility’s launch in September 2016.

ProCan co-founder, Professor Roger Reddel outlined the ambitious aim of the program: “to develop proteomic technology that can be combined with other data to provide a report to cancer clinicians that will aid treatment decisions within 48 hours of receiving a cancer tissue sample.”

An essential step toward this goal has been the establishment of a high-performing multidisciplinary team of more than 30 staff in the diverse fields of oncology, histopathology, proteomics, software engineering, data science, ethics, contract management, and project management.

A key change over the past year has been the strengthening of project management capability to streamline the large number of projects that are being undertaken simultaneously with leading cancer researchers in Australia and other countries. In addition, the team now has four medical oncologists who work with collaborating scientists to define research questions that are of high clinical value and assemble cohorts of cancer samples that are suitable for addressing those questions using proteomics.

A major focus of the program to date has been the development of efficient and reliable sample processing, and operationalisation of a suite of high-tech equipment and – recently – a new software pipeline to handle the vast amounts of cancer molecular data.

For the past three years, ProCan has been achieving its target of 20,000 mass spectrometry runs per year, with six instruments operating around the clock, and a total of 75,500 runs completed over five years – producing the largest known cancer dataset of this kind.

“We have developed a robust Quality Control Pipeline that is suitable for high-throughput clinical application – producing consistent data across multiple instruments over five years of continuous operation,” said proteomicist, Natasha Lucas.

“The team has developed a proteomic workflow that is clinically relevant,” said Professor Reddel. “We can generate reliable data from amounts of cancer material that are equivalent in size to small biopsy samples, and have the ability to generate proteomic data from a routinely processed cancer tissue sample in under 9 hours – in a process that is scalable and suitable for automation.”

“Having developed suitable technology, we are now well underway in building the first-ever large pan-cancer database of proteomic and clinical outcome data using a single proteomic platform,” said Professor Reddel.

Medical oncologist, Dr Jenny (Jia) Liu, described results from one type of cancer obtained in a collaboration with cancer researchers in Brisbane. “We examined cancer samples from 124 patients with HPV-positive head and neck cancer and tested whether proteomics could be used to distinguish cancers that would relapse from those that wouldn’t.

“ProCan has identified a set of proteins as ‘biomarkers’ that classify these cancers into three categories: high, medium and low risk of relapse. While the data need to be validated in a different cohort of patients, it could mean in future that patients with cancers diagnosed as low-risk could be spared aggressive treatment while a more tailored treatment plan could be used from the start for those in the medium- and high-risk categories.”

Similarly, ProCan is studying a range of cancers including lung cancer, breast cancer, bone cancers and other sarcomas, bowel cancer, cancer of the skin (including melanoma), brain cancer, liver cancer, ovarian cancer, kidney cancer, endometrial cancer, and many types of childhood cancer. With dozens of cancer projects already in the pipeline, the ProCan team is looking to collaborate with many dozens of additional cancer research groups over the next few years.

ProCan was seed-funded by the inaugural $10 million grant from the Australian Cancer Research Foundation and is also generously supported by the Australian Government’s Medical Research Future Fund, NSW Ministry of Health, Cancer Institute NSW, Cancer Council NSW, National Health and Medical Research Council, University of Sydney, National Breast Cancer Foundation, and others.

This article originally appeared on the Children’s Medical Research Institute website. ACRF has backed $12m of brilliant research at the Children’s Medical Research Institute.