New Ideas, Funding Infused into Search for Blood Markers of Cancer

By Jeffrey Norris Clinicians dream of being able to diagnose cancer reliably with a simple lab test. Cancerous cells make some proteins abnormally. Some of these proteins are secreted or shed, and make their way into body fluids. The quest to identify proteins in blood or urine that signal the presence of cancer has long been a focus of research. There is one well-known test used clinically. The prostate-specific antigen (PSA) protein test is used to identify men likely to have prostate cancer, but an invasive clinical workup is required to confirm or rule out cancer. Now new strategies to identify reliable cancer markers, however, are being pursued by a team - led by Susan Fisher, a Lawrence Berkeley National Laboratory (LBNL) biologist and UCSF professor - thanks to a new $1 million per year grant from the National Cancer Institute. Mass Spectrometry May Be Key The new grant funds research to probe molecules in biological samples with a technique called mass spectrometry. People who do not follow sports doping scandals or see a fictional version of "mass spec" being used by forensic scientists on television's CSI may not have heard of it. Users most often are academic researchers who rarely catch the public eye. Fisher, director of the UCSF Biomolecular Resource Center, will lead the newly funded project with co-principal investigators Joe W. Gray, associate laboratory director for life and environmental sciences at the LBNL, and Bradford W. Gibson, director of chemistry at the Buck Institute for Age Research. Gray and Gibson also are UCSF faculty members.

Susan Fisher

In addition, the team includes researchers from California Pacific Medical Center in San Francisco, M.D. Anderson Cancer Center in Houston and University of British Columbia in Vancouver. The researchers were able to acquire needed research instruments, thanks to a start-up grant from the Sandler Family Supporting Foundation. The initial focus of the collaborators will be on identifying markers of breast cancer in a mouse model of the disease. The mice, unlike humans, are inbred, lessening the inter-individual variability that can complicate the establishment of standard laboratory protocols for analyzing samples prepared from blood. Promising lab tests then will be applied to human samples. Decorated Christmas Trees Proteins are made from strings of amino acids according to directions encoded by the DNA in genes, but these proteins subsequently undergo important modifications. "When it is first translated from the genetic code, a protein is like a bare Christmas tree," Fisher says. "For any given protein encoded by the same genetic code, one protein molecule looks just like another. But the addition of small molecules through post-translational modification is like adding ornaments to the Christmas tree branches. Differences in protein molecules may begin to emerge that are not apparent through analysis of the DNA in the gene." Certain proteins in cancer cells may exhibit different patterns of post-translational modifications, compared with their counterparts in normal cells, and the modified proteins may contribute to the survival, growth and spread of cancerous cells. Mass spectrometry is a powerful technique for identifying proteins that carry these modifications. Exon Arrays The Fisher lab at UCSF will focus on searching for the addition of new sugars to proteins that could be an early sign of breast cancer. They are also searching for protein fragments that could be used for the same purpose. The Gibson lab will primarily investigate the addition of phosphate groups to proteins and the subtraction of such groups from proteins, and will search for molecular evidence of oxidative damage to proteins.

Samples are sprayed as small droplets into the mass spectrometer.

Gray is investigating the role of "splice variants" in cancer. Each gene consists of several coding regions, called exons. Exons are spliced together to encode the amino acid strands from which proteins are constructed. These amino acid pieces are sometimes spliced together in an unusual fashion. A handful of these unusual protein splice variants already have been identified as possibly playing a functional role in cancer. To find splice variants, the researchers first measure the levels of every exon in every gene. To make the measurements, they use tens of thousands of microscopic lab tests arranged in columns on what resembles a glass microscope slide - a microarray chip. Aided by sophisticated bioinformatics analysis, the researchers can use these exon microarray study results to predict which proteins may appear as splice variants in a serum sample. A preparation likely to contain splice variant proteins can be derived from the serum, and then run through a mass spectrometer. The results can be further analyzed to nail suspected culprits - a CSI drama on a molecular scale. (This story first appeared in the Winter 2007 issue of the UCSF Comprehensive Cancer Center Report.) Photos/Elisabeth Fall Related Links: UCSF Comprehensive Cancer Center UCSF Biomolecular Resource Center Fisher Lab Gibson Lab
Buck Institute for Age Research Gray Lab
Ernest Orlando Lawrence Berkeley National Laboratory Fueled By Major Grant, Scientists to Identify Protein Markers for Cancer
UCSF News Release, September 27, 2006