Differential structural alterations and expression of immunoglobulin (Ig), T cell receptor (TCR), and various growth effecting genes are studied in malignant tumors and their derivative cell types. Studies are carried out to diagnose, classify, and stage lymphoid malignancies via a) Southern and Northern blot analysis and b) RNA-RNA tissue in situ hybridization. A. DNA and RNA is extracted from the tumors of patients with acute lymphoblastic leukemia (ALL) of infancy, pre B ALL, T cell ALL, mycosis fungoides, and Sezary syndrome. The structural reconfigurations of DNA around the Ig and TCR loci resulting from the normal functional activation of these loci in these cells provide unique """"""""fingerprints"""""""" for identifying clonal populations in the samples and following these populations during the course of treatment. We have shown by these analyses that the above listed lymphoid malignancies each manifest generally distinguishing genotypic patterns reflecting target cell maturation which to a certain extent recapitulates the age incidence of the development of these tumors. These studies are now being extended in an exhaustive analysis of 90 patients with B cell precurser ALL. Correlations between genetype and clinical presentation and cause are being established. In addition, we are establishing criteria for the definitive genotypic diagnosis of particular tumors. B. RNA-RNA tissue in situ hybridization. The expression of individual cells within tissue sections from lymph node biopsies and peripheral blood from patients with lymphoid malignancies have been analyzed with immunoglobulin, T cell receptors, and oncogene probes. This technique refines the analysis of such tissue to the point where the unique gene expression of one cell in hundreds of thousands can be identified. Furthermore we have developed a technique of direct RNA sequencing the allows us to utilize tumor specific gene expression as a tumor specific marker providing a potentially powerful and sensitive means of cancer diagnosis and staging.
