Bulk RNAseq of fetal human lung fibroblasts (MRC5) and primary adult human lung mesenchyme (AHLM)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA626684 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11576978_1.fastq.gz | Fastqsanger.gz | |||
| SRR11576978_2.fastq.gz | Fastqsanger.gz | |||
| SRR11576979_1.fastq.gz | Fastqsanger.gz | |||
| SRR11576979_2.fastq.gz | Fastqsanger.gz | |||
| SRR11576980_1.fastq.gz | Fastqsanger.gz |
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Project description:The fetal human lung fibroblasts (MRC5) and primary adult human lung mesenchyme (AHLM) have different capabilities in supporting human alveolar type 2 cell transdifferentiation into basal KRT5+ cells.Therefore, we examined the transcriptome of AHLM vs. MRC5 by bulk RNAseq.
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Project description:Fibroblast Growth Factor (FGF) signaling plays an important role in lung organogenesis. Over recent decades, FGF signaling in lung development has been extensively studied in animal models. However, little is known about the expression, localization and functional roles of FGF ligands during human fetal lung development. Therefore, we aimed to determine the expression and function of several FGF ligands and receptors in human lung development. Using in situ hybridization (ISH) and RNA-sequencing, we assessed their expression and distribution in native human fetal lung. Human fetal lung explants were treated with recombinant FGF7, FGF9 or FGF10 in air-liquid interface culture. Explants were analyzed grossly, to observe differences in branching pattern, as well as at the cellular and molecular level. ISH demonstrated that FGF7 is expressed in both the epithelium and mesenchyme; FGF9 is mainly localized in the distal epithelium, whereas FGF10 demonstrated diffuse expression throughout the parenchyma with some expression in the smooth muscle cells (SMCs). FGFR2 expression was high in both proximal and distal epithelial cells as well as the SMCs. FGFR3 was expressed mostly in the epithelial cells, with lower expression in the mesenchyme, while FGFR4 was highly expressed throughout the mesenchyme and in the distal epithelium. Using recombinant FGFs, we demonstrated that FGF7 and FGF9 had similar effects on human fetal lung as on mouse; however, FGF10 caused the human explants to expand and form cysts as opposed to inducing epithelial branching as seen in the mouse. In conjunction with decreased branching, treatment with recombinant FGF7, FGF9 and FGF10 also resulted in decreased double-positive SOX2/SOX9 progenitor cells, which are exclusively present in the distal epithelial tips in early human fetal lung. Although FGF ligand localization may be somewhat comparable between developing mouse and human lungs, their functional roles may differ substantially.
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Project description:Here, we used single cell RNA-sequencing (scRNA-seq) to profile 13-week post-conception distal human fetal lung explants cultured in an air liquid interface system and treated with an LGR5 ectodomain adenovirus that inhibits R-Spondin function or control adenovirus. A third, non-infected, condition was also sequenced. We also performed scRNA-seq on distal human fetal lung tissue from an 8.4-week post-conception biological specimen. Diverse cell lineages were captured in all data sets, and include epithelium, mesenchyme, immune, neurons, and endothelium.
2022-01-01 | E-MTAB-10662 | biostudies-arrayexpress
Project description:Underdeveloped lungs are the primary cause of death in premature infants, however, little is known about stem and progenitor cell maintenance during human lung development. In this study, we have identified that FGF7, Retinoic Acid and CHIR-99021, a small molecule that inhibits GSK3 to activate Wnt signaling, support in vitro maintenance of primary human fetal lung bud tip progenitor cells in a progenitor state. Furthermore, these factors are sufficient to derive a population of human bud tip-like progenitor cells in 3D organoid structures from human pluripotent stem cells (hPSC). Functional studies showed that hPSC-derived bud tip progenitor organoids do not contain any mesenchymal cell types, maintain multilineage potential in vitro and are able to engraft into the airways of injured mice and respond to systemic factors. We performed RNA-sequencing to assess the degree of similarity in global gene expression profiles between the full human fetal lung (59-127 days gestation), isolated human fetal bud tip progenitors, organoids grown from primary fetal bud tip progenitors, and hPSC-derived bud tip organoids. Results showed that hPSC-derived organoids have molecular profiles similar to organoids generated from primary human fetal lung tissue. Gene expression differences between hPSC-derived bud tip organoids and fetal progenitor organoids may be related to the presence of contaminating mesenchymal cells in primary cultures. hPSC-derived bud tip organoids are generated from a well-defined human cell sources, offering a distinct advantage over rare primary tissue as a means to study human specific lung development, homeostasis and disease.<br>Sample Nomenclature - Description<br> -------------------------------------------------------------------------<br> Peripheral fetal lung the distal/peripheral portion of the fetal lung (i.e., distal 0.5 cm) was excised from the rest of the lung using a scalpel. This includes all components of the lung (e.g., epithelial, mesenchymal, vascular). <br>Isolated fetal bud tip the bud peripheral portion of the fetal lung was excised with a scalpel and subjected to enzymatic digestion and microdissection. The epithelium was dissected and separated from the mesenchyme, but a small amount of associated mesenchyme likely remained. <br>Fetal progenitor organoid 3D organoid structures that arose from culturing isolated fetal epithelial bud tips. <br>Foregut spheroid 3D foregut endoderm structure as described in Dye et al. (2015). Gives rise to patterned lung organoid (PLO) when grown in 3F medium. <br> Patterned lung organoid (PLO) lung organoids that were generated by differentiating hPSCs, as described throughout the manuscript. <br> Bud tip organoid organoids derived from PLOs, enriched for SOX2/SOX9 co-expressing cells, and grown/passaged in 3F medium.
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Project description:Mesenchyme-derived cells in the human airway wall including airway smooth muscle cells, fibroblasts and myofibroblasts are known to play important roles in airway remodeling. The lack of specific phenotypic markers makes it difficult to define these cell populations in primary cultures. The objectives of this study were to evaluate reported markers and to identify novel markers to define these cell types. We could not identify a specific single marker to define any of these cell populations in vitro that permitted unequivocal identification. We therefore used global gene expression profiling to identify genes that were differentially expressed in human airway mesenchymal cells. 3 samples were analysed in total - low passage human airway smooth muscle (HASM) cells (HASM-LP), high passage HASM cells (HASM-HP), MRC5 (lung fibroblasts) were used in this study for RNA extraction. MRC5 cells were used as the control cell population and were co-hybridised with HASM-LP and HASM-HP on cDNA microarrays. Spot arrays or cDNA arrays were used as a confirmatory gene expression profiling data to affymetrix arrays.
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