Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells

Jessie A. G. van Buggenum, Jan P. Gerlach, Sabine E. J. Tanis, Mark Hogeweg, Pascal W. T. C. Jansen, Jesse Middelwijk, Ruud van der Steen, Michiel Vermeulen, Hendrik G. Stunnenberg, Cornelis A. Albers and Klaas W. Mulder ()
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Jessie A. G. van Buggenum: Radboud University
Jan P. Gerlach: Radboud University
Sabine E. J. Tanis: Radboud University
Mark Hogeweg: Radboud University
Pascal W. T. C. Jansen: Radboud University
Jesse Middelwijk: Biolegio BV
Ruud van der Steen: Biolegio BV
Michiel Vermeulen: Radboud University
Hendrik G. Stunnenberg: Radboud University
Cornelis A. Albers: Radboud University
Klaas W. Mulder: Radboud University

Nature Communications, 2018, vol. 9, issue 1, 1-11

Abstract: Abstract Cell-based small molecule screening is an effective strategy leading to new medicines. Scientists in the pharmaceutical industry as well as in academia have made tremendous progress in developing both large-scale and smaller-scale screening assays. However, an accessible and universal technology for measuring large numbers of molecular and cellular phenotypes in many samples in parallel is not available. Here we present the immuno-detection by sequencing (ID-seq) technology that combines antibody-based protein detection and DNA-sequencing via DNA-tagged antibodies. We use ID-seq to simultaneously measure 70 (phospho-)proteins in primary human epidermal stem cells to screen the effects of ~300 kinase inhibitor probes to characterise the role of 225 kinases. The results show an association between decreased mTOR signalling and increased differentiation and uncover 13 kinases potentially regulating epidermal renewal through distinct mechanisms. Taken together, our work establishes ID-seq as a flexible solution for large-scale high-dimensional phenotyping in fixed cell populations.

Date: 2018
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DOI: 10.1038/s41467-018-04761-0

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