Fluid shear stress-modulated chromatin accessibility reveals the mechano-dependency of endothelial SMAD1/5-mediated gene transcription

A cost-effective vessel-on-a-chip for high shear stress applications in vascular biology

The vascular endothelium is constantly subjected to hemodynamic forces, including tangential shear stress, which are crucial for maintaining vascular homeostasis. Pathological shear stress levels, such as those observed in pulmonary arterial hypertension (PAH) or atherosclerosis, disrupt this balance, driving vascular remodeling and endothelial dysfunction. Current microfluidic platforms for studying these conditions are limited by high costs, excessive reagent requirements, and non-physiological channel geometries. Here we introduce a novel microfluidic chip system, a Nylon Vessel-on-a-Chip (NVoC) which represents a cost-effective and straightforward fabrication platform that eliminates the need for specialized equipment and enables a physiologically relevant round channel geometry. The NVoC was fabricated using Polydimethylsiloxane (PDMS) and nylon threads, with surface activation achieved through polydopamine and collagen-I coating, enabling robust endothelial cell (EC) attachment and long-term culture. Immortalized endothelial colony-forming cells (iECFCs) and human umbilical vein EC (HUVECs) were used to optimize and validate the platform, demonstrating its compatibility with high shear stress conditions (up to 90 dyne/cm2) and various molecular biology techniques, including RT-qPCR, Western blotting, and immunofluorescent staining. With fabrication costs six times lower than commercial alternatives and overall experimental costs reduced threefold, the NVoC offers the ability to expose endothelial cells to physiological and pathological shear stress levels in a reproducible, accessible, and scalable manner. Its versatility and affordability make it a valuable tool for investigating shear stress-related mechanisms in microvascular diseases, particularly PAH, with potential applications in drug discovery and translational research.

The Link Between TGF-β Signaling and Chromatin Dynamics Takes an Unexpected Path

The TGF-β/BMP signaling superfamily plays critical roles in regulating a wide range of physiological and pathological processes. A recent study on Tgfbr1 function during mouse embryonic development found that, in the absence of this gene, the primordium of the external genitalia changes its fate, forming an additional set of hindlimbs and resulting in the so-called "six-legged" mice. Analysis of these embryos demonstrated that Tgfbr1 induces global remodeling of chromatin accessibility, establishing distinct regulatory elements that other morphogenetic factors use to drive either hindlimb or genital development. While global changes in chromatin structure have been previously associated with TGF-β signaling, the alterations seen in six-legged embryos differ significantly from previously described mechanisms. In this review, I discuss these distinctions and underscore the importance of studying biological processes within their natural tissue context, where essential tissue interactions are preserved.

Rare but specific: 5-bp composite motifs define SMAD binding in BMP signaling

BACKGROUND

Receptor-activated SMADs trimerize with SMAD4 to regulate context-dependent target gene expression. However, the presence of a single SMAD1/5/8 binding motif in cis-regulatory elements alone does not trigger transcription in native contexts. We hypothesize that binding to composite motifs in which at least two SMAD binding sites are in close proximity would be enough to induce transcription as this scenario allows the simultaneous interaction of at least two SMAD proteins, thereby increasing specificity and affinity.

RESULTS

Using more than 65 distinct firefly luciferase constructs, we delineated the minimal requirements for BMP-induced gene activation. We propose a model in which two SMAD-MH1 domains bind a SMAD-composite motif in a back-to-back fashion with a 5-bp distance between the SMAD-motifs on opposing DNA strands. However screening of SMAD1-bound regions across a variety of cell types highlights that these composite motifs are extremely uncommon, explaining below 1% of SMAD1 binding events.

CONCLUSIONS

Deviations from these minimal requirements prevent transcription and underline the need for co-transcription factors to achieve gene activation.

Protocol for chromatin accessibility profiling of human endothelial cells cultured under fluid shear stress using ATAC-seq

Chromatin accessibility influences gene regulation and can be quantified using assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq). Recapitulating in vivo fluid shear stress (FSS) mechano-regimes in vitro allows the study of atheroprone and atheroprotective mechanisms. In this protocol, we show how to culture and harvest endothelial cells from microfluidic channels for the preparation of ATAC-seq, highlighting optional growth factor stimulation and different FSS rates. This extends the application of ATAC-seq to the analysis of in vitro mechanically stimulated cells. For complete details on the use and execution of this protocol, please refer to Jatzlau et al.1.