Vol. 56, Issue 2, 359-369, August 1999

Selective Killing of Cancer Cells Based on Loss of Heterozygosity and Normal Variation in the Human Genome: A New Paradigm for Anticancer Drug Therapy

James P. Basilion, Andrea R. Schievella, Erica Burns, Patrice Rioux, Jeffrey C. Olson, Brett P. Monia, Kristina M. Lemonidis, Vincent P. Stanton, Jr., and David E. Housman

Variagenics Inc., Cambridge, Massachusetts (J.P.B., A.R.S., E.B., P.R., J.C.O., V.P.S.); Department of Molecular Pharmacology, Isis Pharmaceuticals, Carlsbad, California (B.P.M., K.M.L.); and Department of Biology and Center for Cancer Research, Massachusetts Institute of Technology, Cambridge Massachusetts (D.E.H.)

Most drugs for cancer therapy are targeted to relative differences in the biological characteristics of cancer cells and normal cells. The therapeutic index of such drugs is theoretically limited by the magnitude of such differences, and most anticancer drugs have considerable toxicity to normal cells. Here we describe a new approach for developing anticancer drugs. This approach, termed variagenic targeting, exploits the absolute difference in the genotype of normal cells and cancer cells arising from normal gene sequence variation in essential genes and loss of heterozygosity (LOH) occurring during oncogenesis. The technology involves identifying genes that are: 1) essential for cell survival; 2) are expressed as multiple alleles in the normal population because of the presence of one or more nucleotide polymorphisms; and 3) are frequently subject to LOH in several common cancers. An allele-specific drug inhibiting the essential gene remaining in cancer cells would be lethal to the malignant cell and would have minimal toxicity to the normal heterozygous cell that retains the drug-insensitive allele. With antisense oligonucleotides designed to target two alternative alleles of replication protein A, 70-kDa subunit (RPA70) we demonstrate in vitro selective killing of cancer cells that contain only the sensitive allele of the target gene without killing cells expressing the alternative RPA70 allele. Additionally, we identify several other candidate genes for variagenic targeting. This technology represents a new approach for the discovery of agents with high therapeutics indices for treating cancer and other proliferative disorders.