Integration of flow studies for robust selection of mechanoresponsive genes

Abstract

Blood flow is an essential contributor to plaque growth, composition and initiation. It is sensed by endothelial cells, which react to blood flow by expressing > 1000 genes. The sheer number of genes implies that one needs genomic techniques to unravel their response in disease. Individual genomic studies have been performed but lack sufficient power to identify subtle changes in gene expression. In this study, we investigated whether a systematic meta-analysis of available microarray studies can improve their consistency. We identified 17 studies using microarrays, of which six were performed in vivo and 11 in vitro. The in vivo studies were disregarded due to the lack of the shear profile. Of the in vitro studies, a cross-platform integration of human studies (HUVECs in flow cells) showed high concordance (> 90 %). The human data set identified > 1600 genes to be shear responsive, more than any other study and in this gene set all known mechanosensitive genes and pathways were present. A detailed network analysis indicated a power distribution (e. g. the presence of hubs), without a hierarchical organisation. The average cluster coefficient was high and further analysis indicated an aggregation of 3 and 4 element motifs, indicating a high prevalence of feedback and feed forward loops, similar to prokaryotic cells. In conclusion, this initial study presented a novel method to integrate human-based mechanosensitive studies to increase its power. The robust network was large, contained all known mechanosensitive pathways and its structure revealed hubs, and a large aggregate of feedback and feed forward loops.

Zebrafish Model for Functional Screening of Flow-Responsive Genes

“…We also compared our microarray data to the list of >1600 shear-responsive genes obtained by meta-analysis of published microarray studies performed in vitro on human umbilical vein endothelial cells (Table V in the online-only Data Supplement). 39 We found that <50% of genes shown to be mechanically regulated in both data sets exhibit the same relationship with WSS. This observation further emphasizes the sensitivity of EC to physiological and mechanical stimuli that vary between in vitro and in vivo systems.…”

Large‐scale expansion of feeder‐free mouse embryonic stem cells serially passaged in stirred suspension bioreactors at low inoculation densities directly from cryopreservation

“…We have designed a protocol eliminating the need for a matrix and TGF-β) can be activated through mechanotransduction (Abuammah et al, 2018). The reaction of cells to mechanical forces, however, is complex, consisting of over 1,600 genes and 10,000 interactions with large amounts of crosstalk between signaling pathways (Frueh et al, 2013;Maimari, Pedrigi, Russo, Broda, & Krams, 2016). The identification of exact mechanisms activated within the bioreactor niche allowing ESCs to be expanded in the absence of feeder cells requires further investigation.…”

Hemodynamics in Cardiac Development&nbsp;

“…as Aurora, Intraflagellar transporters and the homodimeric Platelet derived growth factor receptor (PdgfRαα) [37]. In the cardiovascular system endothelial and endocardial cells present monocilia [38 39], particularly in areas of low shear stress [40,41].…”

“…smooth muscle and endothelial cells. ECE and Et-B are both shear stress responsive [37,68] and expression is down-regulated upon applying shear forces [69].…”

“…Both eNos and Nostrin (nitric oxide trafficker) are shear stress responsive [37]. In vitro laminar shear stress promotes NO-formation and increases the expression of Nos3 [73,74].…”