Cancer Genetics Program

The goal of the Cancer Genetics Program is to apply discoveries about cancer genetics to treatments.

Members of the Cancer Genetics Program are:

Michael McClelland: Salmonella, Prostate Cancer
John Welsh: Promoters, Rare and Short Lived mRNA

Cancer Genetics intersects with many other programs at SKCC. Among the heaviest users among the faculty are John Welsh and Michael McClelland, who collaborate on a number of intersecting projects in prostate cancer research.

One major project, is a "Director's Challenge" grant from the National Cancer Institute (NCI), which is studying gene expression in tumors recovered from prostatectomies to develop a molecular phenotype for prostate cancer. Investigators are using a number of genomics tools to achieve this objective. One of the major tools being used is microarray technology in which portions of thousands of individual genes are arrayed on a solid substrate. Then cDNA from RNA samples are fluorescently labeled, hybridized to the complementary gene on the array, and the amount of each transcript is measured.

Prostate cancer studies at SKCC do not occur solely in the world of laboratory science but seek to understand the disease. Genomics is essential to a complete understanding of this disease. About 70% of 70 year-old men have some form of prostate cancer, although only a small proportion progress to life-threatening disease. Nevertheless, among cancers, prostate cancer is the third leading cause of death in men. Therapies for prostate cancer, such as prostatectomy, have their own risks, complications, and impact on quality of life. Thus, an important goal of prostate cancer research is to identify features that characterize the common less malignant forms of the disease that do not need the aggressive therapies appropriate for the more malignant form that will be life threatening. Then, many men may be spared treatment they do not need while others receive appropriately aggressive therapies.

Prostatectomy specimens are retrieved from patients who volunteer to provide their complete medical history and future course of disease. These features are tracked by SKCC personnel and entered in a database. Over 600 patients are going into the analysis. PSA values, the extent of disease (stage), the nature of the cancer cells (grade), drug use, family history of prostate cancer and all the facts of recurrence of disease are recorded and compared with the molecular events. It is likely that aggressive cancers utilize different genes and that the detection of these in newly diagnosed patients will provide critical information. Bioinformatics at SKCC and with our collaborators on the "Directors Challenge" project will also be used to make these identifications.

Another NCI funded project is measuring gene expression in prostate tumors that have been cultured outside humans and then transferred to mice where the properties of the tumors can be studied in an experimental model. Dr. Glinsky is studying the effect of selection of cancer cells in blood on the expression profiles in cancers. This method may reveal some of the genes critical to the metastasis of cancer, a lethal event in which cancer spreads to other sites in the body. Finally, there is a mouse model in which mice get prostate cancer at a high frequency. The progression of this model of prostate cancer is being monitored by arrays. These projects have yielded a number of excellent gene candidates that will now be investigated to determine whether changes in their expression correlate with the outcome of prostate cancer. If this proves to be the case, these genes may be of use for determining therapeutic strategies for individual patients. Such genes will also be of interest because they may reveal something about the mechanism of the disease, and thereby supply potential targets for new therapeutics.

Dr. Mercola's lab is using oligonucleotides that are complementary to particular mRNAs to target and destroy these RNAs. Some of the genes up-regulated in prostate cancer may proved to be good targets for such an "antisense oligonucleotide" therapeutic strategy. For example, one pathway implicated in the progression of prostate carcinoma is regulated by an enzyme termed Jun Kinase-2. Mice bearing prostate tumors treated with complementary oligonucleotides that eliminate this enzyme exhibit tumor regression. Thus, the genes regulated by Jun Kinase-2 may be crucial for understanding important aspects of prostate cancer and these can now be studied by preparing RNA from treated and untreated prostate cells and applying it to arrays.

A novel use of array technology stems from the analysis of the transcription factor Egr-1, which is implicated as an important agent in the progression of cancer. Transcription factors directly bind to genes and this binding determines when the gene is used or not. The genes activated by this factor are being captured from the in vivo setting by a new "in vivo crossing linking" approach. The identity of these genes is being determined by the preparation of a new kind of array in the Genomics Core. These arrays are largely composed of just the part of genes that interact with transcription factors. Prototype arrays have been produced and are being tested. This program interacts with the Mercola lab and with our colleagues in the neighboring institute, The Burnham Institute.

Michael McClelland and John Welsh are working on a number of technical improvements in arrays. These methods include the use of reduced complexity probes to increase signal to noise ratios and thus detect rare transcripts. This general strategy is also being applied to promoter arrays to detect changes in methylation.

Another area of active genomics research at SKCC is the study of Salmonella. This is one of the most common causes of severe gastroenteritis and causes large numbers of deaths, particularly in children and the elderly. It is also used as a delivery agent for vaccines and for cancer therapuetics. The latter because Salmonella has a natural propensity to concentrate in solid tumors. SKCC has been involved in a collaboration that has sequenced the S. typhimurium genome, the most common cause of Salmonellosis (http://genome.wustl.edu/gsc/Projects/S.typhimurium/ Array analysis and bioinformatic methods are being used to understand which genes are responsible for the pathogenic mechanism and host-range of Salmonella. A potential application of this information may be in the construction of smaller arrays of s elected sequences that may be useful for diagnosis by medical laboratories in hospitals, food preparation facilities, public health laboratories and elsewhere. In collaboration with Joseph Lustgarten, the McClelland lab is pursuing the use of Salmonella flagella as targeting agents of potential anticancer immunogens to dendritic cells.

Data storage and data analysis are the main rate limiting steps in Genomics. For example, one project alone, the "Director's Challenge" program has already utilized over 150 microarrays. As described by one participant, "it is like learning to drink from a fire hose". Data tracking, data analysis, and presentation present monumental challenges. The recruitment of Dr. Gu and the development an SKCC "supercomputer" is major advance in this task. Moreover, SKCC will be part of a growing national effort to share methods and results. To properly utilize the wealth of information "out there", state of the art computing and bioinformatics will be essential. Importantly, ZJ Gu recently joined SKCC and has been given funds to further strengthen Genomics and to build up bioinformatics software and to hire bioinformaticists. Dr. Gu will be recruiting specialists to make SKCC computing stay abreast of the "fire hose" of Genomics results.

Dr. ZJ Gu is also an expert in "Single Nucleotide Polymorphisms" of "SNPs", and he has used array-based methods to use this genetic typing method to characterize differences among humans in the pathways involved in drug utilization and metabolism. Such tests will ultimately allow drugs to be tailored to the genetic make-up of each individual patient. Dr. Gu's lab is now focusing on developing advanced SNP genotyping and SNPs-based linkage analysis for gene discovery. SNPs can also be used to study the genetic components of cancer susceptibility and to follow some kinds of chromosomal changes.

Cancer Genetics at SKCC is supported by a Genomics core facility with state of the art equipment. This equipment includes an Affymetrix hybridization and data analysis suite. This system uses commercially available arrays that can be cross-referenced to data from other labs using the same tools. The Institute also has a separate microarrayer for custom slides, and a fluorescent confocal slide reader that allow the Institute to manufacture it's own custom arrays. This ability is enhanced by advanced BioMek FX robot, which can handle thousands of samples and rearrange and manipulate them at will. This robot is also useful for any other large-scale method, such as drug screening. The real-time PCR machine allows the accurate quantitation of 384 genes simultaneously from very small amounts of starting nucleic acids. The facility is partly supported by a facilities grant from NIH on which Michael McClelland is PI for the genomics component and a grant to Dan Mercola supporting the real-time PCR machine.