The Impact of Mechanical Cues on the Metabolomic and Transcriptomic Profiles of Human Dermal Fibroblasts Cultured in Ultrashort Self-Assembling Peptide 3D Scaffolds

Abstract

Cells' interactions with their microenvironment influence their morphological features and regulate crucial cellular functions including proliferation, differentiation, metabolism, and gene expression. Most biological data available are based on in vitro two-dimensional (2D) cellular models, which fail to recapitulate the three-dimensional (3D) in vivo systems. This can be attributed to the lack of cell−matrix interaction and the limitless access to nutrients and oxygen, in contrast to in vivo systems. Despite the emergence of a plethora of 3D matrices to address this challenge, there are few reports offering a proper characterization of these matrices or studying how the cell−matrix interaction influences cellular metabolism in correlation with gene expression. In this study, two tetrameric ultrashort self-assembling peptide sequences, FFIK and FIIK, were used to create in vitro 3D models using well-described human dermal fibroblast cells. The peptide sequences are derived from naturally occurring amino acids that are capable of self-assembling into stable hydrogels without UV or chemical cross-linking. Our results showed that 2D cultured fibroblasts exhibited distinct metabolic and transcriptomic profiles compared to 3D cultured cells. The observed changes in the metabolomic and transcriptomic profiles were closely interconnected and influenced several important metabolic pathways including the TCA cycle, glycolysis, MAPK signaling cascades, and hemostasis. Data provided here may lead to clearer insights into the influence of the surrounding microenvironment on human dermal fibroblast metabolic patterns and molecular mechanisms, underscoring the importance of utilizing efficient 3D in vitro models to study such complex mechanisms.

Selectively Positioned Catechol Moiety Supports Ultrashort Self-Assembling Peptide Hydrogel Adhesion for Coral Restoration

“…Thus, we conducted NMR, Raman spectroscopy measurements, and MD simulations to explain this behavior. By using 15 N 1 H HSQC, we assigned the N protons to these peptide sequences: IIZK, DoIIZK, IIZDoK, IIZKDo. By using 13 C 1 H HSQC, we assigned the C protons of the dopa ring in DoIIZK, IIZDoK, and IIZKDo (Table S7 in the Supporting Information).…”

“…Afterward, by performing 15 N NOESY, we were able to identify the true space interactions occurring between the peptide monomers (see Figure 5a, as well as Figure S13 in the Supporting Information). In particular, we observed a true space vicinity between the NH and the CH of the peptide chains.…”

“…60 Each spectrum was measured using the hsqcetf3gpsi pulse program from the Bruker pulse library by collecting 512 t 1 increments and 64 scans with a 5 s recycle delay time. The spectra were recorded under the same conditions and instrumental parameters with a reduced spectra width of 15 N 44 pm centered on 118 ppm. Bruker Topspin 3.5pl7 software was used for both data collection and for spectral processing.…”

“…Soft-solid hydrogels made from rationally designed ultrashort self-assembling peptides (USPs) are synthetic in nature and are characterized by high water retention, low immunogenicity, high biocompatibility, tunable biomolecular and biophysical properties, and antibacterial properties. − Moreover, in our previous work, we validated their potential for wound healing, skin grafting, neuronal growth, osteogenesis, and three-dimensional (3D) bioprinting. − …”

“…By performing AFM force spectroscopy in a liquid environment, we demonstrate how the absolute position of dopa in the sequence influences the adhesive properties of the peptide hydrogels on silicon surfaces. Aided by 15 N NMR, 2D NOESY, Raman spectroscopy, and MD simulation, we discovered important effects of the cation-π interaction occurring between dopa and lysine of facing peptides. We find that dopa-modified peptide hydrogels behave differently in various solutions.…”