Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling

Abstract Organoids culture provides unique opportunities to study human diseases and to complement animal models. Several organs and tissues can be in vitro cultured in 3D structures resembling in vivo tissue organization. Organoids culture contains most of the cell types of the original tissue and...

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Autores principales:	Jing Lu, Anna Krepelova, Seyed Mohammad Mahdi Rasa, Francesco Annunziata, Olena Husak, Lisa Adam, Suneetha Nunna, Francesco Neri
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/922f51cd44344c1fa5a78e768fd26719
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spelling	oai:doaj.org-article:922f51cd44344c1fa5a78e768fd267192021-12-02T18:51:41ZCharacterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling10.1038/s41598-021-96321-82045-2322https://doaj.org/article/922f51cd44344c1fa5a78e768fd267192021-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-96321-8https://doaj.org/toc/2045-2322Abstract Organoids culture provides unique opportunities to study human diseases and to complement animal models. Several organs and tissues can be in vitro cultured in 3D structures resembling in vivo tissue organization. Organoids culture contains most of the cell types of the original tissue and are maintained by growth factors mimicking the in vivo state. However, the system is yet not fully understood, and specific in vivo features especially those driven by cell-extrinsic factors may be lost in culture. Here we show a comprehensive transcriptome-wide characterization of mouse gut organoids derived from different intestinal compartments and from mice of different gender and age. RNA-seq analysis showed that the in vitro culture strongly influences the global transcriptome of the intestinal epithelial cells (~ 60% of the total variance). Several compartment-, age- and gender-related transcriptome features are lost after culturing indicating that they are driven by niche or systemic factors. However, certain intrinsic transcriptional programs, for example, some compartment-related features and a minority of gender- and aging- related features are maintained in vitro which suggested possibilities for these features to be studied in this system. Moreover, our study provides knowledge about the cell-extrinsic or cell-intrinsic origin of intestinal epithelial transcriptional programs. We anticipated that our characterization of this in vitro system is an important reference for scientists and clinicians using intestinal organoids as a research model.Jing LuAnna KrepelovaSeyed Mohammad Mahdi RasaFrancesco AnnunziataOlena HusakLisa AdamSuneetha NunnaFrancesco NeriNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Jing Lu Anna Krepelova Seyed Mohammad Mahdi Rasa Francesco Annunziata Olena Husak Lisa Adam Suneetha Nunna Francesco Neri Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling
description	Abstract Organoids culture provides unique opportunities to study human diseases and to complement animal models. Several organs and tissues can be in vitro cultured in 3D structures resembling in vivo tissue organization. Organoids culture contains most of the cell types of the original tissue and are maintained by growth factors mimicking the in vivo state. However, the system is yet not fully understood, and specific in vivo features especially those driven by cell-extrinsic factors may be lost in culture. Here we show a comprehensive transcriptome-wide characterization of mouse gut organoids derived from different intestinal compartments and from mice of different gender and age. RNA-seq analysis showed that the in vitro culture strongly influences the global transcriptome of the intestinal epithelial cells (~ 60% of the total variance). Several compartment-, age- and gender-related transcriptome features are lost after culturing indicating that they are driven by niche or systemic factors. However, certain intrinsic transcriptional programs, for example, some compartment-related features and a minority of gender- and aging- related features are maintained in vitro which suggested possibilities for these features to be studied in this system. Moreover, our study provides knowledge about the cell-extrinsic or cell-intrinsic origin of intestinal epithelial transcriptional programs. We anticipated that our characterization of this in vitro system is an important reference for scientists and clinicians using intestinal organoids as a research model.
format	article
author	Jing Lu Anna Krepelova Seyed Mohammad Mahdi Rasa Francesco Annunziata Olena Husak Lisa Adam Suneetha Nunna Francesco Neri
author_facet	Jing Lu Anna Krepelova Seyed Mohammad Mahdi Rasa Francesco Annunziata Olena Husak Lisa Adam Suneetha Nunna Francesco Neri
author_sort	Jing Lu
title	Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling
title_short	Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling
title_full	Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling
title_fullStr	Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling
title_full_unstemmed	Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling
title_sort	characterization of an in vitro 3d intestinal organoid model by using massive rnaseq-based transcriptome profiling
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/922f51cd44344c1fa5a78e768fd26719
work_keys_str_mv	AT jinglu characterizationofaninvitro3dintestinalorganoidmodelbyusingmassivernaseqbasedtranscriptomeprofiling AT annakrepelova characterizationofaninvitro3dintestinalorganoidmodelbyusingmassivernaseqbasedtranscriptomeprofiling AT seyedmohammadmahdirasa characterizationofaninvitro3dintestinalorganoidmodelbyusingmassivernaseqbasedtranscriptomeprofiling AT francescoannunziata characterizationofaninvitro3dintestinalorganoidmodelbyusingmassivernaseqbasedtranscriptomeprofiling AT olenahusak characterizationofaninvitro3dintestinalorganoidmodelbyusingmassivernaseqbasedtranscriptomeprofiling AT lisaadam characterizationofaninvitro3dintestinalorganoidmodelbyusingmassivernaseqbasedtranscriptomeprofiling AT suneethanunna characterizationofaninvitro3dintestinalorganoidmodelbyusingmassivernaseqbasedtranscriptomeprofiling AT francesconeri characterizationofaninvitro3dintestinalorganoidmodelbyusingmassivernaseqbasedtranscriptomeprofiling
_version_	1718377396972814336

Characterization of an in vitro 3D intestinal organoid model by using massive RNAseq-based transcriptome profiling

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