Towards the human proteome

As Robert Service writes in an excellent overview of the field in the September 26 issue of Science, proteomics is finally coming of age.

On the drawing board is a Human Proteome Project (HPP), a massive undertaking that will make the Human Genome Project look tame in comparison.

While there is no guarantee the project will go ahead, proteomics researchers from all over the world are in intense discussions on how to go about it. The number one issue is, of course, funding, which in today’s economic climate is going to prove a massive hurdle.

Bringing different international funding agencies together for a coordinated effort will be enormously difficult, so many research groups are attacking the issue from a national perspective.

Service reported that Genome Canada is considering a project aimed at using lentiviruses to insert tagged proteins into each of the 20,000-odd genes in the genome, and that the South Korean Government is looking at funding a pilot project to catalogue all of the proteins of chromosome 13, the second smallest chromosome, with 319 genes.

This follows a proposal by the Human Proteome Organisation (HUPO) to catalogue the smallest, chromosome 21.

For Dr Michelle Hill, who is on the organising committee of the Lorne proteomics conference, it is an exciting time for the field. “(Proteomics leaders) are proposing to characterise the whole proteome, in every tissue,” she says.

“It is going to cost a lot of money and is a huge undertaking. We’ve got several speakers coming from this program to Lorne, where it will be one of the main themes, along with metabolomics and mass imaging.”

Hill herself is facing a new challenge in proteomics – its application in a clinical setting. While the field has wide application in many areas of molecular research, clinical applications are still in their infancy.

Next year, Hill is moving from UQ’s Institute for Molecular Bioscience to the Diamantina Institute to begin a series of projects on Barrett’s oesophagus and oesophageal cancer, hoping to track down some biomarkers for potential diagnostic tests.

“(Clinical proteomics) is challenging but genes don’t tell you everything,” she says. “And a lot of things that happen in metabolism are post-translational.”

---PB--- Hands-on expertise

Hill had a very hands-on entry into the proteomics field. She did her PhD on insulin signalling, working with the noted diabetes researcher Professor David James, now director of the Diabetes & Obesity Research Program at Sydney’s Garvan Institute.

“His expertise wasn’t in proteomics so I basically had to teach myself,” Hill says. In her second year, James got in touch with Professor Richard Simpson, head of the Joint Proteomics Research Laboratory (JPSL), a joint initiative of the Ludwig Institute for Cancer Research and the Walter and Eliza Hall Institute.

Hill spent one week learning about proteomics in Simpson’s lab, and completed her PhD through collaboration with the JPSL. Hill continued her research in cell signaling with two overseas post-docs, first in Switzerland studying regulation of the protein kinase and proto-oncogene Akt, then in Ireland examining apoptosome assembly.

Upon returning from overseas, Hill joined a program headed by Professors Rob Parton and John Hancock at IMB, UQ, researching cell signalling from plasma membranes with a focus on caveolae and Ras.

With her background on protein post-translational modifications, Hill started to study ubiquitination of Ras.

“At that time there was a report that Ras was ubiquinated so I thought I’d start a little study using proteomics to work out the sites of ubiquination,” Hill says.

“That is still currently not known, so we haven’t quite got there yet. I was distracted by our success with the discovery of a caveolar coat protein.”

Caveolae are plasma membrane invaginations that are enriched in cholesterol and sphingolipids and have several functions in signal transduction.

It was known that the membrane protein caveolin was necessary for caveolae formation and function, and it was long thought to be the only one. However, by using proteomics approaches, Hill and the team discovered that by comparing cells that don’t express caveolin with ones that do, a cytosolic protein – Polymerase I and transcript release factor, or PTRF-cavin – was also necessary for caveolae formation.

“Caveolin has been implicated in a lot of cancers so when we discovered this protein, I thought I’d screen all of the available cancer cell lines to see whether there was a dysregulation of this protein and compare it to caveolin,” she says.

“The ones that came up most were breast and prostate. We looked at whether these cells formed caveolae using electron microscopy, which is Rob’s expertise, and found that this protein was needed.”

The research was published in January 2008 in Cell.

---PB--- Hormones and oesophageal cancer

Now, Hill is moving on to the Diamantina Institute to study Barrett’s oesophagus. She will still maintain links with the IMB, but her new mentor will be Professor John Prins, head of the Diamantina’s Metabolic Medicine Program.

He recently published a paper with Associate Professor David Whiteman of the Queensland Institute of Medical Research looking at different hormones involved in obesity and the incidence of Barrett’s oesophagus.

Barrett’s oesophagus is caused by persistent reflux, with stomach acid damaging the cells lining the lower oesophagus, and can lead to cancer. Prins and Whiteman have discovered that an increase in leptin in the serum increases the risk of Barrett’s oesophagus, but interestingly it is only true for males, not females.

“And leptin is secreted by fat cells and obese people have an elevated level of leptin so there is a fairly strong link,” Hill says. “And apart from the clinical proteomics I will also be looking at how leptin increases the risk of getting Barrett’s oesophagus and cancer. There is some link between the hormone there.

“What we hope to do is look at actual biopsies of patients and then work out biomarkers for diagnosis. Furthermore, we want to find biomarkers in the blood. Currently if people have Barrett’s or they complain of reflux, they have endoscopies and the endoscopist looks for lesions in their throat. That’s quite annoying for the patient and quite costly as well.

“So we hope to find biomarkers so patients just have to have a blood test and tell them whether or not it is likely to happen, and then they can go and have the more invasive test.”