Cancer Genomics Summary

Project Leaders

Dr. V. Ling, Dr. M. Marra, Dr. C. Eaves

Principal Investigators

Dr. S. Jones, Dr. S. Lam, Dr. W. Lam, Dr. C. MacAulay, Dr. M. Rosin, Dr. Marianne Sadar, Dr. J. Vielkind

Cancer results from an accumulation of key mutations in expanding clones originating from tissue-specific stem cells. The recent availability of the human genome sequence, and the development of high throughput genomic technologies and methods for isolating selected cell populations from fresh, frozen and fixed tissue have introduced unprecedented opportunities for defining in precise genetic terms how human cancers develop. This information will provide the basis of more objective methods for diagnosing, classifying and staging many neoplasms. It will also revolutionize cancer treatment through the discovery of disease-specific molecular targets. Even more importantly, it should reveal changes in early lesions that can serve as molecular targets for novel prevention strategies.

The British Columbia Cancer Agency (BCCA) currently sees 12,000 new cancer patients each year and has particular clinical and research strengths in early stage oral, lung, prostate, breast, gastrointestinal/esophageal, cervical, lymphoid and myeloid malignancies. Systems for the accrual of tissue and associated clinical data have been established and a track record of nationally and internationally-funded achievement exists in genetic causes of early stage cancer as well as other basic, translational and clinical outcomes research. BCCA scientists are also recognized internationally for research in the purification, biology and genetic manipulation of stem cells. A current focus is on elucidating the molecular programs that define and control the stem cell state, normal stem cell mortality and plasticity and their relevance to cancer. Finally, the BCCA has made a major commitment to basic and applied cancer genomics research through the creation of a high throughput large scale DNA sequencing and bioinformatics facility, and state-of-the-art microdissection, FACS, transgenic and knockout mouse facilities.

This project will build on these timely scientific opportunities as well as the priorities and strengths of the BCCA to make major advances in understanding key molecular events in early stage cancers because of the enormous potential pay-off of such a focus (see "Impact" below).

Objectives

1. To obtain a complete description of genes expressed in selected stem cell populations (hematopoietic, mammary and embryonic stem cells) pre- and post-induction of proliferation and differentiation.
2. To discover new gene mutations and novel gene expression patterns that distinguish selected early stage human malignancies from the normal tissues in which they arise (oral, lung, gastrointestinal, breast, prostate, lymphoid and myeloid).
3. To identify candidate genes that contribute to the initial stages of neoplastic transformation through kinetic analyses of defined model systems (induced liver, breast and prostate tumors in rats and mice, and transformed or immortalized primary human fibroblasts, T lymphocytes, breast epithelial cells and primitive hematopoietic cells).
4. To improve SAGE, SELDI, and cDNA and BAC array technologies so that they can be applied to small samples (<105cells).
5. To create a unique and dynamic setting for the interdisciplinary training of students and fellows in cancer genomics, biology, pathology and related clinical applications.

Experimental Plan

Altered patterns of gene and protein expression and associated gene mutations that initiate neoplastic changes will be derived from comparative analyses of RNA, DNA and protein using the technologies of SAGE, cDNA microarrays, BAC arrays, exon sequencing and proteomics. Cells from well characterized clinical samples of selected early stage cancers will be isolated by microdissection or FACS. DNA, RNA and expressed protein comparisons will use parallel data sets for normal cells from tumor-containing samples and normal individuals, as well as selected normal and activated tissue-specific stem cells, and biologically well defined in vitro and in vivo models of early stage cancer development. The tumor types selected for study (within the budget available) reflect tissue availability for the analyses proposed, disease prevalence and burden, and availability of pre-existing matched data and unique collaborative opportunities. Technology development will be an ongoing activity.

Key Milestones

1. Gene expression data from 166 SAGE libraries ~ 20 different kinds of samples
2. 26,500 micro-dissections on fixed and frozen tumor samples.
3. 1140 BAC array CGH sample analyses.
4. 1000 RNA microarray analyses (primarily lymphoma, preleukemia and stem cell studies).
5. 1100 SELDI analyses.
6. Robust technology for representative SAGE library preparation from <105 cells.
7. Discovery of specific gene mutations and common gene expression pathways associated with various early stage malignancies.

Colaborations and Impact

Collaborations have been made with the National Human Genome Research Institute (NIH, USA), NCI (NIH, USA), Washington University Genome Sequencing Center (USA), the Sanger Center (UK), Drs. S. Moore and B. Benkel (Alberta), Dr. J. Rossant (Genome Ontario), Drs. J. Woodgett (Ontario Cancer Institute), Dr. R. Worton (The Stem Cell Network), and others.

Cancer kills one third of our population and is responsible for hundreds of thousands of potential years of life lost annually. Moreover, the number of new cases/year is increasing at an alarming rate (50% increase projected over the next 15 years). Major contributors to current mortality and morbidity statistics are the lack of procedures to detect many cancers at an early stage and lack of specific treatment strategies. This project will provide the information required to identify early stage cancers more readily, at reduced cost and with greater prognostic precision. It will also allow more effective, specific and non-toxic interventions to be devised. The translation of this information into medical practice and preventive procedures thus has the potential to have an enormous impact in reducing the immeasurable societal and huge financial burden (estimated as >$16 billion in 1993) that cancer now imposes. The global market potential for cancer products is similarly huge (>$15 billion in 1998 and estimated to double by 2003). Hence, we anticipate this project will spawn a number of spin-off companies focused on the development of new diagnostics and therapeutics.