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Germ-free and microbiota-associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes.
Cellular Microbiology ( IF 3.4 ) Pub Date : 2020-03-04 , DOI: 10.1111/cmi.13191
Annika Hausmann 1 , Giancarlo Russo 2 , Jonas Grossmann 2 , Mirjam Zünd 1 , Gerald Schwank 3 , Ruedi Aebersold 4 , Yansheng Liu 4, 5 , Mikael E Sellin 1, 6 , Wolf-Dietrich Hardt 1
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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 microbiota differences, previously identified as a confounding factor in murine in vivo studies, on organoids. We analysed the proteomes and transcriptomes of primary organoid cultures established from two colonised and one germ-free mouse colony of C57BL/6J genetic background, and compared them to their tissue of origin and commonly used cell lines. While an imprint of microbiota-exposure was observed on the proteome of epithelial samples, 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 and closely mimicked expression patterns in the gut epithelium. This included the inflammasome components ASC, Naip1-6, Nlrc4 and Caspase-1, which were highly expressed in all organoids compared to the reference cell line m-ICc12 or mouse embryonic fibroblasts. Taken together, these results reveal that the donor microbiota has little effect on the organoid phenotype and suggest that organoids represent a more suitable culture model than immortalised cell lines, in particular for studies of intestinal epithelial inflammasomes.

中文翻译:

无菌和微生物相关的小鼠产生具有相同且强大的转录组/蛋白质组表达表型的小肠上皮类器官。

从肠道组织建立的肠上皮类器官已成为广泛使用的研究工具。然而,目前尚不清楚建立之前、期间和之后的环境因素、不同的微生物群组成和其他变异来源如何混淆类器官的特性,以及这些特性与原始组织的关系。虽然环境影响在人类类器官中不易解决,但小鼠提供了一种受控的分析系统。在这里,我们探讨了供体微生物群差异对类器官的影响,这种差异先前被认为是小鼠体内研究中的混杂因素。我们分析了从 C57BL/6J 遗传背景的两个定植小鼠群体和一个无菌小鼠群体建立的原代类器官培养物的蛋白质组和转录组,并将它们与其来源组织和常用细胞系进行比较。虽然在上皮样本的蛋白质组上观察到微生物群暴露的印记,但供体微生物群对类器官表达模式的长期全球影响可以忽略不计。相反,随机的文化间差异导致了独立建立的类器官之间的适度变异。转录组和蛋白质组数据集的整合揭示了包含 14 个转录物和 10 个蛋白质的类器官型表达特征,可将所有供体的类器官与鼠上皮细胞系和成纤维细胞区分开来,并密切模仿肠道上皮中的表达模式。其中包括炎性体成分 ASC、Naip1-6、Nlrc4 和 Caspase-1,与参考细胞系 m-ICc12 或小鼠胚胎成纤维细胞相比,它们在所有类器官中均高度表达。综上所述,这些结果表明,供体微生物群对类器官表型几乎没有影响,并表明类器官代表了比永生化细胞系更合适的培养模型,特别是对于肠上皮炎症小体的研究。
更新日期:2020-03-04
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