Description

Spatiotemporal characterization of the human proteome

Diana Mahdessian, Devin Sullivan, Lovisa Åkesson, Mikaela Wiking, Frida Danielsson, Christian Gnann, Rutger Schutten, Mathias Uhlén, Emma Lundberg

Science for Life Laboratory, Royal Institute of Technology (KTH), Stockholm, SE-171 65, Sweden

The Cell Atlas, a subgroup of the Human Protein Atlas HPA, focuses on localizing the human proteins on a subcellular level using immunofluorescence and confocal microscopy. Using the image collection in the Cell Atlas as a starting point, my research aims to characterize variability of protein expression at a single cell level, both in terms of abundance and spatial distribution. The aim of my research project is to investigate the cell-cycle dependency of the human proteome and quantify changes both in expression levels and spatial distribution in non-perturbed asynchronous cells with single cell resolution, using affinity proteomics, microscopy and image analysis.

Cells derived from the same clonal population may display variability in protein expression patterns. This variability in protein expression is easily noted within immunofluorescence images and we denote it single cell variation (SCV). This project aims to identify the human proteins that show such a dynamic property both in terms of expression levels and spatial distribution. By re-analyzing all images in the Cell Atlas we have classified around 1,500, corresponding to 13% of all studied proteins, to display such variability. We hypothesize this variation to mainly be linked to parameters such as cell cycle position, stress and cell confluence. It is reasonable to expect a big fraction of these variations to be related to cell cycle progression, as cells are grown under asynchronous conditions. To investigate the correlation to cell cycle, the SCV classified proteins were stained in the U-2 OS FUCCI cell line. The FUCCI cells are tagged with two different fluorescent proteins fused to cell cycle regulators that allow cell cycle monitoring; Cdt1, expressed in G1 phase, and Geminin, expressed in S and G2 phases.

In this manner we could identify 600 proteins with expression variation correlated to cell cycle progression, corresponding to 44% of the tested proteins.

Sakaue-Sawano A et al, 2008