Logical networks inferred from highly specific discovery of transcriptionally regulated genes predict protein states in cultured gliomas Hassan M. Fathallah-Shaykh * Department of Neurological Sciences, Section of Neuro-Oncology, Rush University Medical Center, 1725 West Harrison Street, Chicago, IL 60612, USA Received 26 August 2005 Available online 12 September 2005 Abstract Cultured glioma cells are motile and invasive. The phenotype of tumor cell motility is likely created by a complex system of molecular interactions because it requires the orchestration of molecular and physical events that modify the cytoskeleton, cell membrane, extra- cellular matrix, and signaling. Recent reports have described an algorithm for microarray data analysis that generates highly specific genome-scale discovery; these methods identify states of differential gene expression that are true to a high degree of certainty. Here, highly specific discovery of transcriptionally regulated genes combined with logical networks inferred from the functions of known genes predicts states of protein activation, which are validated in cultured glioma cells by independent laboratories. Highly specific discovery of transcriptionally regulated genes facilitates functional genomics of complex molecular systems. Ó 2005 Elsevier Inc. All rights reserved. Keywords: Glioma; Microarrays; Expression discovery; Motility; Molecular systems; Systems biology The phenotype of motility is not only critically relevant to the understanding and therapeutics of cancer but is also important in several pathological processes including vas- cular disease, osteoporosis, rheumatoid arthritis, and men- tal retardation. Tumor cell migration and invasion involves highly coordinated steps of dissociation of existing cellular adhesions, remodeling the actin cytoskeleton to project lamellipodium extensions, formation of new adhesions, and tail detachment along with proteolytic processing and secretion of extracellular matrix proteins along the tra- jectory [1]. Malignant gliomas are characterized by diffuse invasion of distant brain tissue; in addition, clinical and experimental data demonstrate that the phenotype of motility is generated by a complex combination of multiple molecular processes [2]. Cultured glioma cells retain the phenotype of invasive- ness/motility [3–5]. Here, highly specific genome-scale dis- covery is applied to analyze the expression datasets of 19,200 cDNAs in cultured glioma cells as compared to nor- mal brain RNA, which appears to best represent genetic expression in normal adult glial cells. Embryonal human glial cultures are not readily available and genetic expres- sion differs between embryonal and mature cells. Further- more, the discovered genes are expected to be relevant to motility because unlike glioma cells, the various cell types of normal adult brain do not exhibit the motility phenotype. The molecular mechanisms that create the phenotype of motility in cultured glioma cells may not be extrapolated to glioma cells in vivo; specifically, Camphausen et al. [6] study the expression profiles of 7680 human cDNA clones, gene expression profiles of human glioma cell lines. Using clustering algorithms, the authors find different molecular signatures in cells grown in vitro as compared to subcuta- neous or as intracerebral xenografts. Similarly, Tatenhorst et al. [7] used oligonucleotide microarrays to study the expression patterns of 8832 genes in rat C6 glioblastoma 0006-291X/$ - see front matter Ó 2005 Elsevier Inc. All rights reserved. doi:10.1016/j.bbrc.2005.08.254 * Fax: +1 312 563 3562. E-mail address: hfathall@rush.edu. www.elsevier.com/locate/ybbrc Biochemical and Biophysical Research Communications 336 (2005) 1278–1284 BBRC