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Pharmacologic profiling of transcriptional targets deciphers promoter logic

The Pharmacogenomics Journal volume 5, pages 305–323 (2005)Cite this article

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-κB 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.

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Abbreviations

CSA:

cyclosporin A

IL2:

interleukin 2

NFAT/AP1:

nuclear factor of activated T cells

PC:

principal component

PCA:

principal component analysis

PHA:

phytohemagglutinin

PI3:

phosphatidyl-inositol-3 phosphate

PMA:

phorbol myristate acetate

SOM:

self-organizing maps

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Acknowledgements

We thank Tom Misteli, Howard Young, and Pamela Schwartzberg for their critical review of this manuscript. We also thank Carl June and the members of his lab for the generous gift of αCD28 monoclonal antibodies.

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Authors and Affiliations

  1. Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, The Advanced Technology Center, Bethesda, MD, USA

    W J Freebern, C M Haggerty, I Montano, M C McNutt, I Collins, A Graham, G V R Chandramouli & K Gardner

  2. Meso Scale Discovery, Gaithersburg, MD, USA

    D H Stewart & H A Biebuyck

  3. Clinical Immunology Section, Laboratory of Immunology, Gerontology Research Center, National Institute on Aging, Baltimore, MD, USA

    D D Taub

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  1. W J Freebern
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Correspondence to K Gardner.

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Freebern, W., Haggerty, C., Montano, I. et al. Pharmacologic profiling of transcriptional targets deciphers promoter logic. Pharmacogenomics J 5, 305–323 (2005). https://doi.org/10.1038/sj.tpj.6500325

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