Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses

Toufighi, Kiana, 1980-; Yang, Jae-Seong; Luis, Nuno Miguel, 1982-; Aznar Benitah, Salvador; Lehner, Ben, 1978-; Serrano Pubull, Luis, 1982-; Kiel, Christina

doi:http://dx.doi.org/10.1371/journal.pcbi.1004256

Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses

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Toufighi K, Yang JS, Luis NM, Aznar Benitah S, Lehner B, Serrano L et al. Dissecting the calcium-induced differentiation of human primary keratinocytes stem cells by integrative and structural network analyses. PLoS computational biology. 2015;11(5):e1004256. DOI: 10.1371/journal.pcbi.1004256

Abstract

The molecular details underlying the time-dependent assembly of protein complexes in cellular networks, such as those that occur during differentiation, are largely unexplored. Focusing on the calcium-induced differentiation of primary human keratinocytes as a model system for a major cellular reorganization process, we look at the expression of genes whose products are involved in manually-annotated protein complexes. Clustering analyses revealed only moderate co-expression of functionally related proteins during differentiation. However, when we looked at protein complexes, we found that the majority (55%) are composed of non-dynamic and dynamic gene products ('di-chromatic'), 19% are non-dynamic, and 26% only dynamic. Considering three-dimensional protein structures to predict steric interactions, we found that proteins encoded by dynamic genes frequently interact with a common non-dynamic protein in a mutually exclusive fashion. This suggests that during differentiation, complex assemblies may also change through variation in the abundance of proteins that compete for binding to common proteins as found in some cases for paralogous proteins. Considering the example of the TNF-α/NFκB signaling complex, we suggest that the same core complex can guide signals into diverse context-specific outputs by addition of time specific expressed subunits, while keeping other cellular functions constant. Thus, our analysis provides evidence that complex assembly with stable core components and competition could contribute to cell differentiation.