Single-cell transcriptomic mapping of intestinal epithelium that undergoes 3D morphogenesis and mechanodynamic stimulation in a gut-on-a-chip

Woojung Shin; Zhe Su; S Stephen Yi; Hyun Jung Kim

doi:10.1016/j.isci.2022.105521

Single-cell transcriptomic mapping of intestinal epithelium that undergoes 3D morphogenesis and mechanodynamic stimulation in a gut-on-a-chip

iScience. 2022 Nov 8;25(12):105521. doi: 10.1016/j.isci.2022.105521. eCollection 2022 Dec 22.

Authors

Woojung Shin^{1

2

3}, Zhe Su⁴, S Stephen Yi^{3

4

5}, Hyun Jung Kim^{3

4

6}

Affiliations

¹ Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA.
² Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
³ Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA.
⁴ Department of Oncology, Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA.
⁵ Oden Institute for Computational Engineering and Sciences (ICES), and Interdisciplinary Life Sciences Graduate Programs (ILSGP), The University of Texas at Austin, Austin, TX 78712, USA.
⁶ Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.

Abstract

The human gut-on-a-chip has demonstrated in vivo-relevant cellular fidelity and physiological functions of Caco-2 intestinal epithelium compared to its static cultures. However, transcriptomic dynamics that controls the morphogenic and mechanodynamic perturbation of Caco-2 epithelium in a microphysiological culture remain elusive. Single-cell transcriptomic analysis revealed that a gut-on-a-chip culture drives three clusters that illustrate distinct gene expressions and their spatial representation in three-dimensional (3D) epithelial layers. A pseudotemporal trajectory analysis elucidated the evolutionary transition from a homogeneous ancestral genotype in Transwell cultures into heterogeneous transcriptomes in gut-on-a-chip cultures, verified in cell cycle perturbation, cytodifferentiation, and intestinal functions in digestion, transport, and drug metabolism. Furthermore, the inversed transcriptomic signature of oncogenes and tumor-suppressor genes of Caco-2 cells confirmed that gut-on-a-chip cultures induce post-mitotic reprogramming of cancer-associated genes. Our study suggests that a physiological gut-on-a-chip culture induces the transcriptomic perturbation of Caco-2 epithelium to elicit in vivo-relevant morphogenesis and restoration of normal physiological functions.

Keywords: Biological sciences; bioengineering; biotechnology; tissue engineering; transcriptomics.

Grants and funding

R35 GM133658/GM/NIGMS NIH HHS/United States