vpCells Helps Visualize Subcellular Protein Dynamics

Knowing the subcellular localizations of proteins is essential for understanding cellular biology. But observing proteins precisely within cells has been a significant technical challenge—especially in living cells, as the required fluorescent labelling had to be individually attached to each protein. However, a research group led by Stefan Kubicek at CeMM has now overcome this hurdle with a method called "vpCells, which was described in a recent Nature Cell Biology paper.

The visual proteomics cells (vpCells) approach allows for the simultaneous labeling of multiple proteins using five different fluorescent colors. This automated high-throughput technique, aided by AI-assisted image recognition, opens up new applications in various disciplines.

The key innovations of the vpCells method include comprehensive protein labeling using the CRISPR/Cas9 gene-editing tool to create a genome-wide "library" for the systematic functional exploration of human proteins, multiplexed fluorescent labeling with five complementary colors to mark two different proteins per cell along with additional colors to delineate individual cells and their nuclei, and AI-assisted image recognition that can recognize which protein is marked in which cell based solely on fluorescence microscopy images, without the need for complex DNA sequencing.

The researchers have already demonstrated the utility of vpCells in two applications. First, they generated more than 4,500 cell lines as reporters for over 1,100 proteins, and the images of the individually labeled proteins are available in a publicly accessible web database (vpcells.cemm.at). Second, they used the living reporter cells to examine the effect of more than 1,000 small-molecule substances on 61 cancer-relevant proteins, leading to the identification of a substance that inhibits protein transport from the cell nucleus, similar to a clinically approved drug for multiple myeloma.

"These results provide a first glimpse into the versatility of the vpCells method," says Kubicek. "We expect many more future applications, from fundamental cell biology to applied drug discovery."