How to measure >70 (phospho-) protein levels via sequencing DNA-tagged antibodies

Jessie van Buggenum and Klaas Mulder, theme Cancer development and immune defense, show in Nature Communications how immuno-detection by sequencing (ID-seq) uses antibodies tagged with DNA barcodes and high-throughput sequencing to detect up to 70 phospho-proteins in skin stem cell.

Publication in Nature Communications: link.

Jessie van Buggenum (photo).
Klaas Mulder.

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 they present the immuno-detection by sequencing (ID-seq) technology that combines antibody-based protein detection and DNA-sequencing via DNA-tagged antibodies. They 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, their work establishes ID-seq as a flexible solution for large-scale high-dimensional phenotyping in fixed cell populations.