Pharmacologic profiling of transcriptional targets deciphers promoter logic.
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.
Freebern
W J
WJ
Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, The Advanced Technology Center, Bethesda, MD 20892, USA.
Haggerty
C M
CM
Montano
I
I
McNutt
M C
MC
Collins
I
I
Graham
A
A
Chandramouli
G V R
GV
Stewart
D H
DH
Biebuyck
H A
HA
Taub
D D
DD
Gardner
K
K
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
D018106:CD28 Antigens; D007155:Immunologic Factors; D007376:Interleukin-2; D008934:Mitogens; D007334:Insulin-Like Growth Factor I