Genetic Signatures

Genetic Signatures
(Lead Scientist: John Minna, M.D.)

Advisors and members of the ICMIC include Drs. John D. Minna (Professor of Internal Medicine; Medical Oncology and Pharmacology, Director of the Hamon Center for Therapeutic Oncology Research, and PI of an NCI P50 SPORE in Lung Cancer); Adi F. Gazdar (Professor of Pathology, Deputy Director of the Hamon Center, and PI of a NCI Early Detection Research Network, EDRN, application); and Harold “Skip” Garner (Professor of Biochemistry and Internal Medicine, founding member of the UT Southwestern Center for Biomedical Inventions, and PI of an NCI R21/R33 Innovative Technology Development grant to develop gene array techniques). They are jointly developing methods for molecular analysis of human tumors early detection, monitoring of chemoprevention, tumor prognosis, and development of new treatments. In addition to advising the overall ICMIC effort, as part of their own NCI sponsored research, they are working with the Program to develop new molecular based probes for in vivo imaging of tumors and preneoplastic lesions.

The two central issues for development of new in vivo imaging techniques in human cancer are: identifying molecular differences between tumor and normal tissues, and developing ways to non-invasively monitor tumor cell death (e.g., apoptosis) to immediately assess the efficacy of various treatments. The overarching hypothesis is that molecular abnormalities in human tumors and their predisposing preneoplastic lesions will lead to changes in gene expression profiles that will differ from normal tissues. These expression profiles can be exploited to provide in vivo imaging probes based on certain genes, whose expression is altered (either up or down regulated). A related hypothesis is that there will be a diagnostic expression profile of tumor and preneoplastic cells undergoing programmed cell death (apoptosis) after exposure to various therapies, and that this diagnostic profile can be exploited out by in vivo imaging. The plan is to develop knowledge of gene expression “fingerprints” of human tumors using microarray technology, where the expression of ~10,000 genes can be monitored simultaneously. New in vivo imaging probes based on the gene expression fingerprints will facilitate non-invasive risk assessment (e.g. how likely is it for a person to develop cancer based on the number or advanced nature of the preneoplastic lesions) and monitoring of chemoprevention therapy. With the development of a gene expression profile for programmed cell death it should be possible to develop imaging probes that assess the amount of apoptosis in a tumor (or preneoplastic lesion) before and after a course of therapy. Another use will be to correlate tumor gene expression fingerprints with a variety of clinical parameters such as survival, metastatic behavior, and response to therapy. In vivo imaging probes will be developed based on differences of the genes expressed (e.g., in tumors with high and low metastatic potential, or tumors likely to respond or be resistant to chemo- or radiotherapy), and thus, provide a variety of clinically useful information about the tumor in addition to its anatomic location.

CpG islands are frequently located in gene promoters or exons and are usually unmethylated in normal cells. Recently, aberrant methylation of CpG islands was identified as an epigenetic mechanism for the transcriptional silencing (inactivation) of tumor suppressor genes. Several genes are known to be inactivated in lung cancers by aberrant methylation. A global analysis of the methylation status of each of 98 primary human tumors estimated that an average of 600 CpG islands (range of 0 to 4,500) of the 45,000 in the genome were aberrantly methylated in the tumors, including early stage tumors. They identified patterns of CpG- island methylation that were shared within each tumor type, together with patterns and targets that displayed distinct tumour-type specificity. The expression of many of these genes was reactivated by experimental demethylation in cultured tumour cells. We have identified several genes including RARb APC and RASSF1, which are methylated in the majority of lung cancers. Panels of genes (potentially 3) will be identified that are aberrantly methylated in specific tumor types at high frequencies. We will constitute each panel so that at least one gene should be aberrantly methylated in the vast majority if not every tumor of that histological type. Panels for lung have already been identified, and those for breast cancer are nearly complete. Since aberrant methylation results in gene silencing, protein expression will be absent in such tumors. The use of labeled antibodies to the panel of markers (either individually or in cocktails) will identify the vast majority of the tumors of each type, although there may be some overlap between tumor types. Thus, the methylation of particular subsets of CpG islands may have consequences for identifying specific tumor types, for detection of metastases and, if identified, for potential novel therapeutic approaches. As these targets are identified, we will seek to generate labeled antibodies as novel imaging agents.

References:

1. Virmani, AK, Fong KM, Kodagoda D, McIntire D, Hung J, Tonk V, Minna JD, Gazdar AF. Allelotyping demonstrates common and distinct patterns of chromosomal loss in human cancer types. Genes, Chromosomes Cancer 1998, 21, 308-19.

2. Virmani, AK, Rathi A, Zöchbauer-Müller S, Sacchi N, Fukuyama Y, Bryant D, Maitra A, Heda S, Fong KM, Thunnissen F, Minna JD, Gazdar AF. Promoter methylation and silencing of the retinoic acid receptor beta gene in lung carcinomas. J. Natl. Cancer Inst. 2000., In press:.

3. Wren, JD, Eva John W. Fondon JWI, Pertsemlidis A, Cheng SY, Gallardo T, Williams RS, Shohet RV, Minna JD, Garner HR. Repeat Polymorphisms within Gene Regions: Phenotypic and Evolutionary Implications. Am. J. Hum. Genet. 2000, 67, 345-356.

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Friday, August 27, 2004

Southwestern In Vivo Cellular and Molecular Imaging Program