Combined physical and genetic map finds cancer's 'ignition key'

The research model can be used to study other cancers of the epithelium -- the tissue that lines the surfaces and cavities of the body's organs. Epithelial cancers, or carcinomas, make up 80 percent of all cancers.

The researchers report that silenced forerunner genes involved in early development of bladder cancer also are silenced to varying degrees in lung, breast, blood and common pediatric malignancies.

Map leads way to six chromosomal regions

The 29-page paper, which covers multi-step genetic screening, validation studies of initial findings, studies of gene expression, gene sequencing and a regulatory process known as methylation, functional studies of candidate genes and epidemiological analysis, takes up half of Laboratory Investigation’s space for original research in its July issue.

“We’ve basically cleared out the issue for this paper,” said the journal’s editor, James M. Crawford, M.D., Ph.D., professor and chair of the University of Florida College of Medicine Department of Pathology, Immunology and Laboratory Medicine. Devoting that much space to a single paper is highly unusual, but Crawford is convinced it’s worthwhile. “A person should be able to read this paper and know this entire, important story,” Crawford said.

The paper documents three waves of genetic hits, mainly involving genetic deletions, that drive cells from normal to precancerous states. The first wave leads to widespread expansion of urothelial cells that harbor genetic changes but otherwise appear normal under microscopic analysis.

The second wave provides a growth advantage to cells that now have recognizable outward features of dysplasia – precancerous cellular abnormalities. The third wave fully transforms the cell’s appearance and features the onset of severe dysplasia or carcinoma in situ, noninvasive cancer still limited to its tissue of origin, in this case the urothelium. Carcinoma in situ and dysplasia advance to invasive cancer.

The team mapped the tissue of five cancerous bladders. Next, they employed 787 DNA markers to identify chromosomal regions that display genetic deletions. By superimposing the low-resolution map of genetic variation over the geographic map of the organ’s tissue, they identified regions associated with both first-wave and second-wave cells.

Additional analysis narrowed the chromosomal regions to portions of six chromosomes. These six sites were confirmed by testing multiple markers of genetic loss in those chromosomal regions in the urine and blood of 32 bladder cancer patients and 31 disease-free patients with a history of bladder cancer. Genetic losses from at least one of the six regions were found in 98 percent of patients. In 82 percent of the cases, two to five chromosomal regions were involved.

Silenced forerunners stifle a tumor-suppressor

The team chose the 13q14 region on chromosome 13, which they knew harbored the tumor-suppressor RB1, for high-resolution genetic analysis to identify candidate genes affecting RB1 by using single-nucleotide polymorphisms (SNPs) as markers. SNPs are points in the genome that vary by a single DNA chemical building block or nucleotide.

They examined 92 SNPs mapping to a region around the RB1 gene in 84 paired samples of bladder tumors and blood DNA. This high-resolution genetic analysis pointed to the same section of the chromosome that whole organ histologic and genetic mapping had identified with expansion of abnormal cells.