Dataset Information

An Integrative Transcriptome – Proteome Approach Reveals a Robust Expression Pattern of Small Intestinal Epithelial Organoids from Germ-Free and Microbiota Associated Donors

ABSTRACT: Intestinal epithelial organoids established from resected gut tissue have become a widely used research tool. However, it remains unclear how environmental cues and other sources of variation before, during and after establishment impact on organoid properties. Divergent microbiota composition in separately held mouse lines has been identified as a confounding factor in murine in vivo studies. To probe the effect of donor microbiota on organoids, we analyzed the proteomes and transcriptomes of primary organoid cultures established from colonized and germ-free mice, and further compared them to their tissue of origin and to commonly used cell lines. The long-term global impact of donor microbiota on organoid expression patterns was negligible. Instead, stochastic culture-to-culture differences accounted for a moderate variability between independently established organoids. Integration of transcriptome and proteome datasets revealed an organoid-typic expression signature comprising 14 transcripts and 10 proteins that distinguished organoids across all donors from murine epithelial cell lines and fibroblasts. This signature, which closely mimicked expression patterns in the gut epithelium, included high levels of the inflammasome scaffold protein ASC in organoids which was lacking in commonly used cell lines. Mining of the transcriptome dataset uncovered similar high expression of also other inflammasome components, including Naip1-6, Nlrc4, and Caspase-1 in all organoids compared to the reference cell lines. Taken together, these results reveal a robust global expression pattern in organoids established from colonized and germ-free animals and suggest that organoids represent a more suitable culture model than immortalized cell lines for studies of intestinal epithelial inflammasomes.

INSTRUMENT(S): TripleTOF 5600

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Intestine, Epithelial Cell, Cell Culture

SUBMITTER: Barbora Salovska

LAB HEAD: Yansheng Liu

PROVIDER: PXD016339 | Pride | 2020-03-05

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	Normalized_ProteinData_E1708151054.txt	Txt
	SampleInfo_E1708151054.txt	Txt
	yanliu_L170728_001.wiff	Wiff
	yanliu_L170728_001.wiff.scan	Wiff
	yanliu_L170728_002_SW.wiff	Wiff

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Publications

Germ-free and microbiota-associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes.

Hausmann Annika A Russo Giancarlo G Grossmann Jonas J Zünd Mirjam M Schwank Gerald G Aebersold Ruedi R Liu Yansheng Y Sellin Mikael E ME Hardt Wolf-Dietrich WD

Cellular microbiology 20200304 6

Intestinal epithelial organoids established from gut tissue have become a widely used research tool. However, it remains unclear how environmental cues, divergent microbiota composition and other sources of variation before, during and after establishment confound organoid properties, and how these properties relate to the original tissue. While environmental influences cannot be easily addressed in human organoids, mice offer a controlled assay-system. Here, we probed the effect of donor microb ...[more]

PMID: 32068945

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