Quantitative Dynamics of Proteome, Acetylome, and Succinylome during Stem-Cell Differentiation into Hepatocyte-like Cells

Stem-cell
differentiation is a complex biological process controlled
by a series of functional protein clusters and signaling transductions,
especially metabolism-related pathways. Although previous studies
have quantified the proteome and phosphoproteome for stem-cell differentiation,
the investigation of acylation-mediated regulation is still absent.
In this study, we quantitatively profiled the proteome, acetylome,
and succinylome in pluripotent human embryonic stem cells (hESCs)
and differentiated hepatocyte-like cells (HLCs). In total, 3843 proteins,
185 acetylation sites in 103 proteins, and 602 succinylation sites
in 391 proteins were quantified. The quantitative proteome showed
that in differentiated HLCs the TGF-β, JAK-STAT, and RAS signaling
pathways were activated, whereas ECM-related processes such as sulfates
and leucine degradation were depressed. Interestingly, it was observed
that the acetylation and succinylation were more intensive in hESCs,
whereas protein processing in endoplasmic reticulum and the carbon
metabolic pathways were especially highly succinylated. Because the
metabolism patterns in pluripotent hESCs and the differentiated HLCs
were different, we proposed that the dynamic acylations, especially
succinylation, might regulate the Warburg-like effect and TCA cycle
during differentiation. Taken together, we systematically profiled
the protein and acylation levels of regulation in pluripotent hESCs
and differentiated HLCs, and the results indicated the important roles
of acylation in pluripotency maintenance and differentiation.