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Deriving human intestinal organoids with functional tissue-resident macrophages all from pluripotent stem cells

ABSTRACT: Deriving human intestinal organoids with functional tissue-resident macrophages all from pluripotent stem cells

PROVIDER: PRJNA1072689 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27848600.fastq.gz	Fastqsanger.gz
	SRR27848601.fastq.gz	Fastqsanger.gz
	SRR27848602.fastq.gz	Fastqsanger.gz
	SRR27848603.fastq.gz	Fastqsanger.gz
	SRR27848604.fastq.gz	Fastqsanger.gz

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Deriving human intestinal organoids with functional tissue-resident macrophages all from pluripotent stem cells

Project description:Background & Aims: Organs of the gastrointestinal tract contain tissue-resident immune cells that function during tissue development, homeostasis, and disease. However, the majority of published human organoid model systems lack resident immune cells, thus limiting their potential as disease avatars. For example, human intestinal organoids (HIOs) derived from pluripotent stem cells contain epithelial and various mesenchymal cell types but lack immune cells. In this study, we aimed to develop an HIO model with functional tissue-resident macrophages. Methods: HIOs and macrophages were generated separately through the directed differentiation of human pluripotent stem cells and combined in vitro. Following two weeks of co-culture, the organoids were used for transcriptional profiling, functional analysis of macrophages, or transplanted into immunocompromised mice and matured in vivo for an additional 10–12 weeks. Results: Macrophages were incorporated into developing HIOs and persisted in the 2-week in vitro HIOs and for at least 12 week in HIOs in vivo. These macrophages expressed CD163 and had a transcriptional signature that resembled those of the human fetal intestine, indicating that they were acquiring the features of tissue-resident macrophages. HIO macrophages could phagocytose bacteria and produced inflammatory cytokines in response to proinflammatory signals such as lipopolysaccharide, which could be reversed with IL-10. Conclusions: We generated an HIO system containing functional tissue-resident macrophages for an extended period. This new organoid system can be used to investigate the molecular mechanisms involved in inflammatory bowel disease.

2025-02-26 | GSE254954 | GEO

scRNA-seq of human intestinal TRMs as well as intestinal organoids with autologous tissue-resident or blood derived immune compartment from 3 distinct donor samples

Project description:Molecular characterization of tissue-resident memory T cells cultured with or without donor-matched adult stem cell-derived intestinal organoids. Blood derived immune cells were also isolated and cultivated with autologous intestinal organoids for comparison and characterization. All conditions were derived from 3 human individuals and all samples were sequenced after 24h of in vitro culture. Data provides insights on circulating and tissue-resident immune cell populations, how these differentially interact with the epithelium and how these interactions shape both immune and epithelial cell states.

2024-06-27 | E-MTAB-14171 | biostudies-arrayexpress

Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon [scrna-seq]

Project description:Most organs have tissue resident immune cells that function during tissue development, homeostasis and disease. Human organoids, derived either from adult tissues or from pluripotent stem cells (PSCs), have been lacking these immune cells, which limits their utility to model many normal and disease processes. Here we describe that human PSC-derived colonic organoids (HCOs) co-develop a diverse population of immune cells. Comparisons to the developing human hematopoietic cells, demonstrate that HCO cultures developed hemogenic endothelium and erythromyeloid progenitors that undergo stereotypical steps in differentiation, resulting in the generation of macrophages. HCO macrophages acquired a transcriptional signature most similar to human fetal small and large intestine tissue-resident macrophages. Functional analyses demonstrate that HCO-macrophages modulate cytokine secretion in response to pro- and anti-inflammatory signals. In addition, macrophages were able to phagocytose and mount a robust response to pathogenic bacteria. In HCOs that were transplanted into mice, macrophages expanded within the colonic organoid tissue, established a close association with the colonic epithelium and were not displaced by the host bone marrow-derived macrophages. These studies support the conclusion that hemogenic endothelium in HCOs gives rise to multipotent hematopoietic progenitors and functional tissue-resident macrophages.

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Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon [bulk rna-seq]

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scRNA-seq of pluripotent stem cell derived human intestinal organoids

Project description:Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in matrigel or a non-adhesive alginate hydrogel after 28 days of in vitro growth. Additionally, we used scRNA-seq to profile HIOs derived in the presence of Neuregulin 1 (NRG1) and/or EGF after 40 days of in vitro growth.

2021-05-21 | E-MTAB-10268 | biostudies-arrayexpress

scRNA-seq of pluripotent stem cell derived human intestinal organoids grown in suspension culture

Project description:Here, we used single-cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in suspension culture after 28 days of in vitro growth. Grown in minigut media supplemented with EGF.

2022-02-04 | E-MTAB-11347 | biostudies-arrayexpress

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Project description:Here, we used single-cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell-derived human intestinal organoids (HIOs) grown in media comprised of minigut media + varying concentrations of Epiregulin (EREG) 1 ng/ml, 10 ng/ml, 100 ng/ml after 28 days of in vitro growth.

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Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon

Project description:Development of functional resident macrophages in human pluripotent stem cell-derived colonic organoids and human fetal colon

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scRNA-seq of pluripotent stem cell derived human intestinal organoids grown in an alginate matrix

Project description:Here, we used single-cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in an alginate matrix after 3, 7, and 14 days of in vitro growth. Samples were grown in minigut media supplemented with either ENR or EGF.

2022-02-01 | E-MTAB-11338 | biostudies-arrayexpress

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