A systems biological analysis of the ATF4-GADD34-CHOP regulatory triangle upon endoplasmic reticulum stress.

Endoplasmic reticulum (ER) stress-dependent accumulation of incorrectly folded proteins leads to activation of the unfolded protein response. The role of the unfolded protein response (UPR) is to avoid cell damage and restore the homeostatic state by autophagy; however, excessive ER stress results in apoptosis. Here we investigated the ER stress-dependent feedback loops inside one of the UPR branches by focusing on PERK-induced ATF4 and its two targets, called CHOP and GADD34. Our goal was to qualitatively describe the dynamic behavior of the system by exploring the key regulatory motifs using both molecular and theoretical biological techniques. Using the HEK293T cell line as a model system, we confirmed that the life-or-death decision is strictly regulated. We investigated the dynamic characteristics of the crucial elements of the PERK pathway at both the RNA and protein level upon tolerable and excessive levels of ER stress. Of particular note, inhibition of GADD34 or CHOP resulted in various phenotypes upon high levels of ER stress. Our computer simulations suggest the existence of two new feedback loops inside the UPR. First, GADD34 seems to have a positive effect on ATF4 activity, while CHOP inhibits it. We claim that these newly described feedback loops ensure the fine-tuning of the ATF4-dependent stress response mechanism of the cell.

Analysis of Three-Dimensional Cell Migration in Dopamine-Modified Poly(aspartic acid)-Based Hydrogels.

Several types of promising cell-based therapies for tissue regeneration have been developing worldwide. However, for successful therapeutical application of cells in this field, appropriate scaffolds are also required. Recently, the research for suitable scaffolds has been focusing on polymer hydrogels due to their similarity to the extracellular matrix. The main limitation regarding amino acid-based hydrogels is their difficult and expensive preparation, which can be avoided by using poly(aspartamide) (PASP)-based hydrogels. PASP-based materials can be chemically modified with various bioactive molecules for the final application purpose. In this study, dopamine containing PASP-based scaffolds is investigated, since dopamine influences several cell biological processes, such as adhesion, migration, proliferation, and differentiation, according to the literature. Periodontal ligament cells (PDLCs) of neuroectodermal origin and SH-SY5Y neuroblastoma cell line were used for the in vitro experiments. The chemical structure of the polymers and hydrogels was proved by 1H-NMR and FTIR spectroscopy. Scanning electron microscopical (SEM) images confirmed the suitable pore size range of the hydrogels for cell migration. Cell viability assay was carried out according to a standardized protocol using the WST-1 reagent. To visualize three-dimensional cell distribution in the hydrogel matrix, two-photon microscopy was used. According to our results, dopamine containing PASP gels can facilitate vertical cell penetration from the top of the hydrogel in the depth of around 4 cell layers (~150 µm). To quantify these observations, a detailed image analysis process was developed and firstly introduced in this paper.