Gene expression profiling of human hepatocytes grown on differing substrate stiffness
To study the effects of different substrate stiffness on human hepatocytes using RNA sequencing (RNA-Seq) technology. The stiffness was corresponding to physiology and pathology stiffness of liver tissues.
With the aid of RNA-Seq technology, our study characterizes the transcriptome of hepatocytes cultured on soft, moderate, stiff and plastic substrates. Compared to soft substrate, our RNA-Seq results revealed 1131 genes that were up-regulated and 2534 that were down-regulated on moderate substrate, 1370 genes that were up-regulated and 2677 down-regulated genes on stiff substrate. Functional enrichment analysis indicated that differentially expressed genes were associated with the regulation of actin cytoskeleton, focal adhesion, tight junction, adherens junction as well as antigen processing and presentation. RNA-Seq results were further verified by a quantitative real-time reverse transcriptase polymerase chain reaction.
Our study provides a comprehensive picture of the gene expression landscape in hepatocytes grown on different substrate stiffness, offering insights into the role of substrate stiffness in hepatic pathology.
KeywordsDifferentially expressed gene Hepatocyte RNA-sequencing Substrate stiffness
This work was supported by National Natural Science Foundation of China (31270990, 11532004) and Innovation and Attracting Talents Program for College and University (“111” Project) (B06023).
Supplementary Table 1—Primer sequence of selected genes designed for qRT-PCR.
Supplementary Table 2—Quality examination of sequence data.
Supplementary Fig. 1—GO functional classification on DEGs in soft, moderate and stiff substrates.
Supplementary Fig. 2—Statistical representation of DEG pathway enrichment in soft vs moderate, soft vs stiff and soft vs plastic groups.
Supplementary Fig. 3—Statistics of pathway enrichment of DEGs expressed in soft, moderate and stiff groups.
Compliance with ethical standards
Conflicts of interest
The authors declare that they have no conflict of interest.
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