Research
Proteome-scale Binary Interactomics in Human Cells*

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Because proteins are the main mediators of most cellular processes they are also prime therapeutic targets. Identifying physical links among proteins and between drugs and their protein targets is essential in order to understand the mechanisms through which both proteins themselves and the molecules they are targeted with act. Thus, there is a strong need for sensitive methods that enable mapping out these biomolecular interactions. Here we present a robust and sensitive approach to screen proteome-scale collections of proteins for binding to proteins or small molecules using the well validated MAPPIT (Mammalian Protein-Protein Interaction Trap) and MASPIT (Mammalian Small Molecule-Protein Interaction Trap) assays. Using high-density reverse transfected cell microarrays, a close to proteome-wide collection of human ORF clones can be screened for interactors at high throughput. The versatility of the platform is demonstrated through several examples. With MAPPIT, we screened a 15k ORF library for binding partners of RNF41, an E3 ubiquitin protein ligase implicated in receptor sorting, identifying known and novel interacting proteins. The potential related to the fact that MAPPIT operates in living human cells is illustrated in a screen where the protein collection is scanned for interactions with the glucocorticoid receptor (GR) in its unliganded versus dexamethasone-induced activated state. Several proteins were identified the interaction of which is modulated upon ligand binding to the GR, including a number of previously reported GR interactors. Finally, the screening technology also enables detecting small molecule target proteins, which in many drug discovery programs represents an important hurdle. We show the efficiency of MASPIT-based target profiling through screening with tamoxifen, a first-line breast cancer drug, and reversine, an investigational drug with interesting dedifferentiation and antitumor activity. In both cases, cell microarray screens yielded known and new potential drug targets highlighting the utility of the technology beyond fundamental biology.

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Author contributions: S.L., J.V., D.M., L.D., I.P., S.G., L.M., K.D., C.L., and J.T. designed research; S.L., J.V., D.M., L.D., I.P., S.G., D. Defever, N.V., and A.D. performed research; V.D., V.V., I.L., D. De Clercq, S.V., L.M., D.H., and M.V. contributed new reagents or analytic tools; S.L., J.V., D.M., L.D., I.P., S.G., V.D., V.V., S.E., K.D., C.L., and J.T. analyzed data; S.L., J.V., D.M., L.D., V.D., I.L., and J.T. wrote the paper.

Financial interests: J.T. is scientific cofounder of and has financial interests in Orionis Biosciences, which practices technologies described in this publication. S.L. is an employee of Orionis Biosciences.

*

This work was supported by grants from the Belgian government (Interuniversity Attraction Poles Project P6/36), the Fund for Scientific Research - Flanders (FWO-V Project G.0864.10) and the NIH (U01 HG001715). J.T. is the recipient of an ERC Advanced Grant (# 340941).

This article contains supplemental material.

1

The abbreviations used are:

    PPI

    protein-protein interaction

    GRE

    GR response element

    MAPPIT

    mammalian protein-protein interaction trap

    MASPIT

    mammalian small molecule-protein interaction trap

    MTX

    methotrexate

    ORF

    open reading frame

    SAR

    structure-activity relationship

    TMP

    trimethoprim.

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Current address: Orionis Biosciences, Ghent, Belgium.

a

Sorbonne Universités, UPMC, INSERM, Centre de Recherche Saint-Antoine, Paris, France.

b

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts.