Evidence from previous in vitro studies indicates that the enzyme folylpolyglutamate synthetase (FPGS) may be an important determinant of the antitumor activity of antifolate drugs that are substrates for this enzyme. To facilitate investigations regarding the association between FPGS content of tumor tissues and the sensitivity of tumors to antifolates, we developed a polymerase chain reaction (PCR)-based gene expression quantitation assay for measuring relative amounts of FPGS mRNA in tumor tissue specimens. From the known sequence of the human gene, FPGS-specific PCR primers were chosen that flanked a 263-base segment of the FPGS gene. The PCR carried out with these primers was linear over at least a three orders of magnitude range of starting cDNA concentration. The amount of cDNA required per assay corresponded to the quantity of RNA contained in nanogram to microgram amounts of tissue, depending on the level of gene expression. In CHO AUXB1 (FPGS) cell lines transfected with human DNA and expressing different levels of human FPGS, FPGS gene expression measured by this assay was linear with the FPGS enzyme activity in the cells. In human head and neck cell lines, which contained naturally varying levels of FPGS enzyme activity, FPGS gene expressions were also linearly proportional to FPGS enzyme content as measured both by activity in cell-free extracts and by intracellular methotrexate polyglutamate formation. Among leukemic cells from 11 acute lymphocytic leukemia and acute myelogenous leukemia patients, FPGS expression varied by over 500-fold.(ABSTRACT TRUNCATED AT 250 WORDS)