Feature: Multiplexing cancers of unknown primaries

This feature appeared in the July/August 2009 issue of Australian Life Scientist. To subscribe to the magazine, go here.

A multiplexed polymerase chain reaction (PCR) test is being developed to assist diagnosis of cancers of unknown primaries under an agreement between Victorian biotechnology company, Circadian Technologies, pathology giant, Healthscope and the Peter MacCallum Cancer Centre.

The still-experimental test, initially developed by Circadian along with Professor David Bowtell’s team at Peter Mac, will be commercialised by Healthscope in Australia, New Zealand and south-east Asia and by Circadian in the rest of the world.

Healthscope, which owns a number of private hospitals as well as the Gribbles Pathology group, will develop and clinically validate the test through its Clinical Laboratories subsidiary, part of the Gribbles group.

Under the agreement, Healthscope will pay Circadian an upfront fee, development milestones and a royalty on sales of the test. Circadian has secured worldwide rights to the test through a licensing agreement with Peter Mac through its subsidiary, Cancer Therapeutics.

The diagnostic methodology is based on gene expression analysis to determine the probable tumour type. Cancers of unknown primaries – also known as cancers of unknown origin – are metastatic cancers in which the primary site cannot be identified. They are listed as the seventh most common cancer and the fourth most common cause of cancer deaths in Australia’s cancer statistics, Bowtell said.

“Probably the reason for that is it is an aggregate of different cancers,” he said. “There is a bit of debate as to whether it is a different cancer or whether it is just a number of different cancers that are difficult to diagnose.”

Typical diagnostic work-ups include a mixture of pathologies supplemented by immunohistochemistry and genetic markers, but even these tests often fail to find the primary site.

“We had a [patient] who had a prostate cancer a long time ago and then a cancer appeared on his earlobe,” Bowtell said. “That was initially PSA [Prostate Specific Antigen] negative, but then we assayed it and found a prostate signature, and then re-did the PSA test and it was positive. So there are cases that are really unusual where you might suspect what it is and then you can use those markers.”

Bowtell said he and his team have been working on the test for a number of years, originally building a microarray database of known cancers that are typical sites for the origins of cancers of unknown primaries.

“You have your unknown cancer sample and essentially you expression profile that and run it against the database and see if it matches anything. The original test was microarray-based, but one of the practical problems is that in cases like this you are dealing with fixed material. The biopsy is taken and the pathologist can’t diagnose [the type of tumour] and at that point you have to fix the sample rather than have a fresh frozen sample. So what we’ve been doing is converting the test to a PCR test, a multiplexed PCR-based test.”

Bowtell emphasised that the test is not yet commercially available and that development and validation is still being undertaken. However, the test and others like it, have great clinical potential.

“We are getting into an era of much more science-specific treatment, and even cancers that are traditionally refractory and still are – particularly pancreatic cancer – there are still some improvements coming along in terms of treatment.

“The second thing is that we might be able to use the test to shorten the time it takes to figure out what the thing is – that terrible period of uncertainty where you don’t know what is going on.

“Thirdly, if it turns out to be something like colorectal cancer, which can have implications for the rest of the family, if there was another case of bowel cancer in the family, now there are two and that suddenly changes the dynamic in terms of family history, so there are further benefits for [this type of test].”

The work of the International Cancer Genome Consortium, of which Peter Mac is a part, will hopefully further inform this type of diagnostic methodology in the future. Bowtell and his team, well known for their work on ovarian cancer, are providing samples for the sequencing studies being conducted by Associate Professor Sean Grimmond’s expression genomics lab at the Institute for Molecular Bioscience at the University of Queensland (see the May/June 2009 issue of Australian Life Scientist).

Australia’s contribution to the consortium involves sequencing the genomes of 150 ovarian and 350 pancreatic cancers. The pancreatic work is being led by Professor Andrew Biankin from Sydney’s Garvan Institute.