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

Area of Science:

• Biotechnology
• Molecular Biology
• Drug Discovery

Background:

• Cell-based screening is crucial for identifying new medicines.
• Existing screening methods lack the capacity for high-dimensional phenotyping across numerous samples.
• A universal technology for parallel measurement of molecular and cellular phenotypes is needed.

Purpose of the Study:

• To introduce and validate immuno-detection by sequencing (ID-seq) technology.
• To demonstrate ID-seq's capability for high-dimensional phenotyping in cell-based screening.
• To identify kinases involved in epidermal stem cell regulation.

Main Methods:

• Developed ID-seq by combining antibody-based protein detection with DNA sequencing using DNA-tagged antibodies.
• Applied ID-seq to simultaneously measure 70 (phospho-)proteins in primary human epidermal stem cells.
• Screened approximately 300 kinase inhibitor probes to analyze the function of 225 kinases.

Main Results:

• ID-seq successfully measured 70 protein targets in parallel.
• Identified an association between reduced mTOR signaling and increased stem cell differentiation.
• Uncovered 13 kinases potentially regulating epidermal renewal via distinct mechanisms.

Conclusions:

• ID-seq is a flexible and powerful technology for large-scale, high-dimensional phenotyping.
• This method advances cell-based screening for drug discovery and biological research.
• The study provides new insights into kinase regulation of epidermal stem cell renewal.