Detailed survey of an in vitro intestinal epithelium model by single-cell transcriptomics

Ran Ran; Javier Muñoz Briones; Smrutiti Jena; Nicole L Anderson; Matthew R Olson; Leopold N Green; Douglas K Brubaker

doi:10.1016/j.isci.2024.109383

Detailed survey of an in vitro intestinal epithelium model by single-cell transcriptomics

iScience. 2024 Mar 1;27(4):109383. doi: 10.1016/j.isci.2024.109383. eCollection 2024 Apr 19.

Authors

Ran Ran¹, Javier Muñoz Briones^{2

3}, Smrutiti Jena², Nicole L Anderson⁴, Matthew R Olson⁴, Leopold N Green², Douglas K Brubaker^{1

5}

Affiliations

¹ Center for Global Health and Diseases, Department of Pathology, Case Western Reserve University, Cleveland, OH, USA.
² Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN, USA.
³ Purdue Interdisciplinary Life Science Program, West Lafayette, IN, USA.
⁴ Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
⁵ The Blood, Heart, Lung, and Immunology Research Center, Case Western Reserve University, University Hospitals of Cleveland, Cleveland, OH, USA.

Abstract

The co-culture of two adult human colorectal cancer cell lines, Caco-2 and HT29, on Transwell is commonly used as an in vitro gut mimic, yet the translatability of insights from such a system to adult human physiological contexts is not fully characterized. Here, we used single-cell RNA sequencing on the co-culture to obtain a detailed survey of cell type heterogeneity in the system and conducted a holistic comparison with human physiology. We identified the intestinal stem cell-, transit amplifying-, enterocyte-, goblet cell-, and enteroendocrine-like cells in the system. In general, the co-culture was fetal intestine-like, with less variety of gene expression compared to the adult human gut. Transporters for major types of nutrients were found in the majority of the enterocytes-like cells in the system. TLR 4 was not expressed in the sample, indicating that the co-culture model is incapable of mimicking the innate immune aspect of the human epithelium.

Keywords: Cell biology; Expression study; Systems biology; Transcriptomics.