Genomic DNA provides clues to new advances in cancer diagnostics

Researchers at the University of Illinois at Chicago have identified a method of assessing the malignant potential of cells based on the sensitivity of cellular DNA to enzyme digestion.

The article by Andrew J. Maniotis et al., "Chromatin sensitivity to Alu I restriction enzyme decreases with malignancy and is regulated by the extracellular matrix and cytoskeleton," appears in the April 2005 issue of The American Journal of Pathology and is accompanied by a commentary.

Using an enzyme (Alu I) that cuts DNA at a common sequence in the human genome, Dr. Maniotis's group classified cells based on sensitivity or resistance to DNA digestion. Non-malignant cells were sensitive to DNA digestion by Alu I while highly malignant cells were resistant. These results suggest that a cell's DNA, or chromatin, is protected during malignancy. This effect was confirmed using three pairs of cell types (normal melanocytes and melanoma cells, normal breast epithelium and breast carcinoma cells, and normal fibroblasts and fibrosarcoma cells) and diagnostic biopsy samples.

Will these methods help clinicians in diagnosing cancer? Because the investigators utilized several practical methods in their study, potential exists for future diagnostic applications. The cell smear assay, which is similar to methods commonly used in diagnostics laboratories (such as Pap smears), could be applied to such a purpose. The authors also used flow cytometry to characterize melanomas of varying invasiveness. Further study will be required to determine the specificity and sensitivity of these methods before they are used in the clinical setting.

Physicians and researchers alike know that how a cancer cell interacts with its microenvironment is important for cancer progression. Such interactions must be aberrant for abnormal cell growth and metastasis to occur. Indeed, Dr. Maniotis and his colleagues found that the extracellular matrix (ECM), or the microenvironment surrounding the cell, influenced whether the cell's chromatin was sensitive or resistant to Alu I. The group also implicated the cell's cytoskeleton, the internal scaffolding that gives the cell its shape, in this process. Changes to the ECM and cytoskeleton are critical to migration of a cancer cell from one site in the body to another.

The researchers could alter the Alu I sensitivity of a cell's chromatin by exposing the cell to a single extracellular matrix molecule or by disrupting any of three cytoskeletal systems, which link the outside of the cell to the genome. Using this information, Dr. Maniotis's group developed a new kind of extracellular matrix chip (patent pending) that is being used to study drug-resistance mechanisms to develop new protocols and methods to treat cancer.

Ultimately, the cellular changes that occur during cancer formation affect how the cell interacts with its microenvironment (ECM) and direct changes to the cytoskeleton and finally to the chromatin. Such changes can now be measured directly at the chromatin level. These findings may provide the basis for the design of a new generation of cancer therapeutic agents.