Quantitative Single-Cell Interactome Profiling Platform (QSCIP2)

The study of the human protein interactome, i.e. all the protein complexes present in human cells, conventionally involves the use of cell populations leading to the analysis of a heterogeneous mixture of complexes, several of which not being found in the same individual cells, which has the effect of biasing the results.

The analysis of protein complexes at cellular resolution (single-cell analysis), although technically challenging, makes it possible to resolve this difficulty and to obtain results that are more representative of the biological reality.

Our new approach combines two methods used sequentially, namely

  1. the screening of a library of phages fused to naïve antibody fragments (FAB Phage Display) that bind target cells with high affinity, allowing to unbiasedly (blindly) discover new cell surface epitopes; and,

  2. quantitative mass spectrometry at single-cell resolution (single-cell proteomics) on sorted cell populations expressing each new epitope individually.

The combined results allow high-resolution mapping of the interactome of individual cells. Importantly, a subtraction step during screening by phage display makes it possible to enrich the epitopes of one cell type compared to another (differential screening). Proteomics results on a large number of individual cells are then transposed on an interaction map built from previous public datasets, allowing changes in whole protein complexes, not merely individual subunits, to be assessed.