Combining Quantitative Proteomics and Interactomics for a Deeper Insight into Molecular Differences between Human Cell Lines

In modern biomedical research, cultivable cell lines
are an indispensable
tool, and the selection of cell lines that exhibit specific functional
profiles is often critical to success. Cellular functional pathways
have evolved through the selection of protein intra- and intermolecular
interactions collectively referred to as the interactome. In the present
work, quantitative in vivo protein cross-linking and mass spectrometry
were used to probe large-scale protein interactome differences among
three commonly employed human cell lines, namely, HEK293, MCF-7, and
HeLa cells. These data illustrated highly reproducible quantitative
interactome levels with R2 values larger
than 0.8 for all biological replicates. Proteome abundance levels
were also measured using data-independent acquisition quantitative
proteomics methods. Combining quantitative interactome and proteome
information allowed the visualization of cell type-specific interactome
changes mediated by proteome level adaptations and independently regulated
interactome changes to gain deeper insight into possible drivers of
these changes. Among the largest detected alterations in protein interactions
and conformations are changes in cytoskeletal proteins, RNA-binding
proteins, chromatin remodeling complexes, mitochondrial proteins,
and others. Overall, these data demonstrate the utility and reproducibility
of quantitative cross-linking to study system-level interactome variations.
Moreover, these results illustrate how combined quantitative interactomics
and proteomics can provide unique insight into cellular functional
landscapes.