title: Pharmacologic profiling of transcriptional targets deciphers promoter logic.
abstract: The blueprint for cellular diversity and response to environmental change is encoded in the cis-acting regulatory sequences of most genes. Deciphering this 'cis-regulatory code' requires multivariate data sets that examine how these regions coordinate transcription in response to diverse environmental stimuli and therapeutic treatments. We describe a transcriptional approach that profiles the activation of multiple transcriptional targets against combinatorial arrays of therapeutic and signal transducing agents. Application of this approach demonstrates how cis-element composition and promoter context combine to influence transcription downstream of mitogen-induced signaling networks. Computational dissection of these transcriptional profiles in activated T cells uncovers a novel regulatory synergy between IGF-1 and CD28 costimulation that modulates NF-kappaB and AP1 pathways through signaling cascades sensitive to cyclosporin A and wortmannin. This approach provides a broader view of the hierarchical signal integration governing gene expression and will facilitate a practical design of combinatorial therapeutic strategies for exploiting critical control points in transcriptional regulation.
authors.affiliation: Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, The Advanced Technology Center, Bethesda, MD 20892, USA.
authors.forename: W J
authors.initials: WJ
authors.lastname: Freebern
authors.forename: C M
authors.initials: CM
authors.lastname: Haggerty
authors.forename: I
authors.initials: I
authors.lastname: Montano
authors.forename: M C
authors.initials: MC
authors.lastname: McNutt
authors.forename: I
authors.initials: I
authors.lastname: Collins
authors.forename: A
authors.initials: A
authors.lastname: Graham
authors.forename: G V R
authors.initials: GV
authors.lastname: Chandramouli
authors.forename: D H
authors.initials: DH
authors.lastname: Stewart
authors.forename: H A
authors.initials: HA
authors.lastname: Biebuyck
authors.forename: D D
authors.initials: DD
authors.lastname: Taub
authors.forename: K
authors.initials: K
authors.lastname: Gardner
mesh_terms: D000465:Algorithms; D018106:CD28 Antigens / Q000096:biosynthesis* / Q000235:genetics; D002478:Cells, Cultured; D020869:Gene Expression Profiling / Q000379:methods; D005786:Gene Expression Regulation / Q000235:genetics*; D018390:Gene Targeting / Q000379:methods; D017930:Genes, Reporter; D006801:Humans; D007155:Immunologic Factors / Q000494:pharmacology; D007334:Insulin-Like Growth Factor I / Q000096:biosynthesis / Q000235:genetics; D007376:Interleukin-2 / Q000096:biosynthesis / Q000235:genetics; D019169:Jurkat Cells; D008213:Lymphocyte Activation / Q000187:drug effects; D008934:Mitogens / Q000494:pharmacology; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis; D025341:Principal Component Analysis; D011401:Promoter Regions, Genetic / Q000187:drug effects*; D015398:Signal Transduction / Q000235:genetics; D013601:T-Lymphocytes / Q000187:drug effects / Q000378:metabolism*; D013997:Time Factors; D014158:Transcription, Genetic / Q000187:drug effects*; D014162:Transfection
chemical_list: D018106:CD28 Antigens; D007155:Immunologic Factors; D007376:Interleukin-2; D008934:Mitogens; D007334:Insulin-Like Growth Factor I