According to the University of Sydney's Professor Richard Christopherson, the era of genomics and the Human Genome Project is 'old hat', with all 23,000 or so human genes sequenced.

Proteomics is where it's at and Australia is at the forefront of this science, which seeks to separate, identify and characterise cellular proteins.

Proteomics, a term coined by Australia's Professor Marc Wilkins in 1995, is the crucial next step for understanding the fundamental mechanisms of disease, particularly cancers, and how the drugs used to treat such conditions work. This is the future, Christopherson says.

"We now understand quite a lot about the mutations that cause cancer, but proteomics is really at the coal-face of working out why we have uncontrolled growth, what the underlying mechanism is that causes these human cells to grow out of control," he says.

In his own work, Christopherson is using proteomics to phenotype cancers, assaying protein markers to classify or diagnose a particular disease or affected individual, and ultimately to predict an individual's response to therapy. In other words, find protein signatures for cancer cells to improve both diagnosis and treatment.

The concept of a proteomics approach to cancer was developed with Professor Cris dos Remedios some years ago when a mutual friend was diagnosed with acute myeloid leukaemia (AML). Both agreed that what was really needed in her case, and indeed for all other leukaemia sufferers, was to know the exact repertoire of proteins expressed on the surface of the patient's leukaemia.

This information would inform both a better classification of the leukaemia and a strategy for treatment by identifying potential targets for therapeutic antibodies. The idea was subsequently implemented in Christopherson's research group about seven years ago, culminating in DotScan - a solid-phase cell-capture assay to immunophenotpye cancer cells commercialised by Sydney-based company Medsaic in 2003.

(Medsaic was spun out of the University of Sydney and has a facility at the Australian Technology Park in Eveleigh, in its time winning a BioFirst Commercialisation Award from the NSW Government. Christopherson retains a position on the scientific advisory board of the company and gives science advice when relevant, but has not been involved with the commercial activities.)

DotScan is a novel antibody microarray containing a number of monoclonal antibodies to CD antigens expressed on cell surfaces. CD or "cluster of differentiation" molecules were first identified on the surface of white blood cells or leukocytes, but we now know that CDs are expressed on all human cells in cell-specific subsets.

The assay was initially focused on diagnosing or classifying leukaemias from peripheral blood, when the predominant white blood cell type is a mononuclear leukaemia.

Technically, the assay involves centrifuging peripheral blood leukocytes from samples through Histopaque, then placing a suspension of three million mononuclear leukaemia cells or normal leukocytes onto a solid-phase carrying a microarray of up to 147 different CD antibody dots laid down in 10-nl volumes over an area of approximately 0.5 cm square.

During a 30-minute incubation, the immobilised antibodies capture live cells expressing the corresponding surface molecule or CD antigen. The end result is a dot pattern that represents the surface-expression profile or immunophenotype of the particular high-level leukaemia in the patient's blood.

Leukaemia is currently diagnosed by multiple criteria. Flow cytometry is the workhorse of the diagnosis and remains the gold standard for identifying surface molecules. In a routine haematology pathology lab, approximately15 CD antigens are screened using flow cytometry, with machine and labour costs preventing more being done.

In contrast, DotScan can screen 147 CD antigens in a single assay using about1/2000 the amount of antibody needed for flow cytometry of a patient sample. Therefore, it allows the acquisition of a lot more data at a much lower cost.

"The basic hypothesis was that a dot pattern would be sufficient to diagnose or classify the leukaemia on its own without using cytochemistry, karyotyping or even cell morphology," Christopherson says.

A recently published clinical trial from the group gives hope to this aim being realised. Blood samples from 796 leukaemia patients and normal subjects were tested using the DotScan array with the results published last year in the British Journal of Haematology.

The samples came from the MD Anderson Cancer Centre in Houston, the Department of Haematology at Cambridge University, Westmead Hospital and Symbion Health in Sydney, and the Royal Melbourne Hospital. The study took four years and identified 33 different expression profiles for different leukaemias. Christopherson says it was a complex paper involving 23 authors, "quite challenging but very satisfying to have finished".

The assay produced high levels of consistency with conventional clinical and laboratory diagnostic findings, with 93.9-97.6 per cent agreement with the established classification of these leukaemias. Christopherson says that because this was a prospective study on fresh samples, comparisons of immunophenotype with patient outcome were not possible. However, such a trial using subsequently thawed samples is underway for patients with chronic lymphocytic leukaemia (CLL).