Gene expression analysis reveals a strong signature of an interferon induced pathway in childhood lymphoblastic leukemia as well as in breast and ovarian cancer

Abstract

On the basis of epidemiological studies, infection was suggested to play a role in the etiology of human cancer. While for some cancers such a role was indeed demonstrated, there is no direct biological support for the role of viral pathogens in the pathogenesis of childhood leukemia. Using a novel bioinformatic tool, that alternates between clustering and standard statistical methods of analysis, we performed a "double blind" search of published gene expression data of subjects with different childhood ALL subtypes, looking for unanticipated partitions of patients, induced by unexpected groups of genes with correlated expression. We discovered a group of about thirty genes, related to the interferon response pathway, whose expression levels divide the ALL samples into two subgroups; high in 50, low in 285 patients. Leukemic subclasses prevalent in early childhood (the age most susceptible to infection) are over-represented in the high expression subgroup. Similar partitions, induced by the same genes, were found also in breast and ovarian cancer but not in lung cancer, prostate cancer and lymphoma. About 40% of breast cancer samples expressed the "interferon- related" signature. It is of interested that several studies demonstrated MMTV-like sequences in about 40% of breast cancer samples. Our discovery of an unanticipated strong signature of an interferon induced pathway provides molecular support for a role for either inflammation or viral infection in the pathogenesis of childhood leukemia as well as breast and ovarian cancer.