Comprehensive transcriptome analysis of fluid shear stress altered gene expression in renal epithelial cells

Abstract

Renal epithelial cells are exposed to mechanical forces due to flow‐induced shear stress within the nephrons. Shear stress is altered in renal diseases caused by tubular dilation, obstruction, and hyperfiltration, which occur to compensate for lost nephrons. Fundamental in regulation of shear stress are primary cilia and other mechano‐sensors, and defects in cilia formation and function have profound effects on development and physiology of kidneys and other organs. We applied RNA sequencing to get a comprehensive overview of fluid‐shear regulated genes and pathways in renal epithelial cells. Functional enrichment‐analysis revealed TGF‐β, MAPK, and Wnt signaling as core signaling pathways up‐regulated by shear. Inhibitors of TGF‐β and MAPK/ERK signaling modulate a wide range of mechanosensitive genes, identifying these pathways as master regulators of shear‐induced gene expression. However, the main down‐regulated pathway, that is, JAK/STAT, is independent of TGF‐β and MAPK/ERK. Other up‐regulated cytokine pathways include FGF, HB‐EGF, PDGF, and CXC. Cellular responses to shear are modified at several levels, indicated by altered expression of genes involved in cell‐matrix, cytoskeleton, and glycocalyx remodeling, as well as glycolysis and cholesterol metabolism. Cilia ablation abolished shear induced expression of a subset of genes, but genes involved in TGF‐β, MAPK, and Wnt signaling were hardly affected, suggesting that other mechano‐sensors play a prominent role in the shear stress response of renal epithelial cells. Modulations in signaling due to variations in fluid shear stress are relevant for renal physiology and pathology, as suggested by elevated gene expression at pathological levels of shear stress compared to physiological shear.

Transcriptome comparisons of in vitro intestinal epithelia grown under static and microfluidic gut-on-chip conditions with in vivo human epithelia

“…The cell culture was performed using a protocol described previously in our studies 12,13 . A Caco-2 cell line (HTB-37), derived from a human colorectal adenocarcinoma (ATCC, Manassas, VA, USA), were grown (at passage number [29][30][31][32][33][34][35][36][37][38][39][40][41][42][43][44][45] in DMEM supplemented with 1% penicillin/streptomycin, 1% MEM non-essential amino acid and 10% FBS, further indicated as DMEM + .…”

Identification of ADPKD-Related Genes and Pathways in Cells Overexpressing PKD2

“…To our knowledge, no study has focused on the correlation between ADPKD and the ADM/IER3 genes. However, MYC/ADM/IER3 frequently appear in the lists of upregulated DEGs identified via transcriptomic analyses in various ADPKD-related studies [25,26,[49][50][51][52][53]. In addition, adrenomedullin, encoded by ADM, is a potent hypotensive peptide and has been associated with hypertension and chronic kidney disease (CKD) [54,55].…”

“…Identification of the differentially expressed gene (DEG) set (adjusted p-value ≤ 0.05 and |log 2 Fold Change| ≥ 0.26) was then performed with the DESeq2 (version 1.26.0) package [24]. In addition, a threshold counts per million (CPM) value was set to exclude hits with low expression levels (CPM < 2) [25,26]. The expression data were submitted to the Gene Expression Omnibus with the following accession number: GSE141355.…”

Perspective on the Application of Microphysiological Systems to Drug Transporter Studies

“…From a conceptual point of view, MPS models are valuable for drug transport-focused assays because they provide a system that allows correct polarization of cells with a clear basolateral to apical separation, expression of the corresponding native array of transporters, and formation of a highly tight epithelium that can selectively move molecules between compartments. Exposure to laminar flow sustains mechanosensitive responses that reshape the cellular transcriptome and upregulate expression of adhesion molecules (White and Frangos, 2007;Kunnen et al, 2018), and this stimulus has been shown to augment the expression of drug transporters in vitro (Nieskens and Wilmer, 2016).…”