Dlk1-Mediated Temporal regulation of Notch Signaling is Required for Differentiation of Alveolar Type II to Type I Cells during Lung Repair
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ABSTRACT:
PROVIDER: PRJNA511430 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8363110.fastq.gz | Fastqsanger.gz | |||
| SRR8363111.fastq.gz | Fastqsanger.gz | |||
| SRR8363112.fastq.gz | Fastqsanger.gz | |||
| SRR8363113.fastq.gz | Fastqsanger.gz | |||
| SRR8363108.fastq.gz | Fastqsanger.gz |
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Project description:Lung alveolar type I cells (AT1) and alveolar type II cells (AT2) regulate the structural integrity and function of alveoli. AT1, covering ∼95% of the surface area, are responsible for gas exchange, whereas AT2 serve multiple functions, including alveolar repair through proliferation and differentiation into AT1. However, the signaling mechanisms for alveolar repair remain unclear. Here, we demonstrate, in Pseudomonas aeruginosa-induced acute lung injury in mice, that non-canonical Notch ligand Dlk1 (delta-like 1 homolog) is essential for AT2-to-AT1 differentiation. Notch signaling was activated in AT2 at the onset of repair but later suppressed by Dlk1. Deletion of Dlk1 in AT2 induced persistent Notch activation, resulting in stalled transition to AT1 and accumulation of an intermediate cell population that expressed low levels of both AT1 and AT2 markers. Thus, Dlk1 expression leads to precisely timed inhibition of Notch signaling and activates AT2-to-AT1 differentiation, leading to alveolar repair.
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Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Lung epithelia cells were collected after 10 days of treatment by pseudomonas aeruginosa (PA), RNA-Seq and qRT-PCR were applied to analyze the high-throughput data Results: In general, the mutant type II-like cells expressed higher levels of type I cell markers and lower levels of type II cell markers
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Project description:Cancer immunotherapies have produced remarkable results in B-cell malignancies; however, optimal cell surface targets for many solid cancers remain elusive. Here, we present an integrative proteomic, transcriptomic, and epigenomic analysis of tumor specimens along with normal tissues to identify biologically relevant cell surface proteins that can serve as immunotherapeutic targets for neuroblastoma, the often fatal childhood cancer of the developing nervous system. We apply this approach to human-derived cell lines (N=9) and cell/patient-derived xenograft (N=12) models of neuroblastoma. Plasma membrane-enriched mass spectrometry identified 1,461 cell surface proteins in cell lines and 1,401 in xenograft models, respectively. Additional proteogenomic analyses revealed 71 high-confidence candidate immunotherapeutic targets and we prioritized Delta-like canonical notch ligand 1 (DLK1) for further study. High expression of DLK1 directly correlated with the presence of a super-enhancer spanning the DLK1 locus. Robust cell surface expression of DLK1 was validated by immunofluorescence, flow cytometry, and immunohistochemistry. Short hairpin RNA mediated silencing of DLK1 in neuroblastoma cells resulted in increased cellular differentiation. ADCT-701, a DLK1-targeting antibody-drug conjugate (ADC), showed potent and specific cytotoxicity in DLK1-expressing neuroblastoma xenograft models. Finally, we also found that DLK1 is highly expressed in several adult cancer types including adrenocortical carcinoma (ACC), pheochromocytoma/paraganglioma (PCPG) and small cell lung cancer (SCLC) suggesting potential clinical benefit beyond neuroblastoma. A clinical trial has been developed for evaluating ADCT-701 in neuroendocrine tumors in adults (https://www.clinicaltrials.gov/study/NCT06041516?term=adct-701&rank=1). Therefore, comprehensive characterization of cancer surfaceomes can provide biologically relevant immunotherapy targeting strategies.
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Project description:Quantification of gene expression noise on young versus aged bone marrow HSCs at single-cell resolution revealed Dlk1 increases both noise and expression levels upon aging. Dlk1, encoding a cell surface non-canonical Notch ligand, is partially expressed in the LT-HSC compartment, without generating clusters of individual subpopulations by conventional clustering analysis. We aimed to characterize the trascriptome of aged LT-HSC with positive and negative expression of Dlk1 cells. Dataset created as part of the publication: "VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells"
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Project description:While the acquisition of cellular plasticity in adult stem cells is essential for rapid restoration after tissue injury, little is known about the underlying molecular mechanisms governing this process. Here, we reveal that Notch signaling is a pivotal determinant conferring cross-compartment differentiation plasticity of airway secretory cells. Temporal Notch inhibition in secretory cells is required for alveolar differentiation upon injury, which is mediated by IL-1β-dependent modulation of Jag1/2 expression in ciliated cells. We also identify Fosl2/Fra2 as an essential transcription factor responsible for the regeneration of secretory cell-derived alveolar type 2 (sAT2) cells retaining distinct genetic/epigenetic signatures. We furthermore reveal that KDR/FLK-1+ human secretory cells display a conserved capacity to generate AT2 cells via Notch inhibition. Our results demonstrate that Notch signaling acts as a functional rheostat for fate decision of secretory cells during injury repair, proposing a new potential therapeutic target for human lung alveolar regeneration.
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Project description:While the acquisition of cellular plasticity in adult stem cells is essential for rapid restoration after tissue injury, little is known about the underlying molecular mechanisms governing this process. Here, we reveal that Notch signaling is a pivotal determinant conferring cross-compartment differentiation plasticity of airway secretory cells. Temporal Notch inhibition in secretory cells is required for alveolar differentiation upon injury, which is mediated by IL-1β-dependent modulation of Jag1/2 expression in ciliated cells. We also identify Fosl2/Fra2 as an essential transcription factor responsible for the regeneration of secretory cell-derived alveolar type 2 (sAT2) cells retaining distinct genetic/epigenetic features. We furthermore reveal that KDR/FLK-1+ human secretory cells display a conserved capacity to generate AT2 cells via Notch inhibition. Our results demonstrate that Notch signaling acts as a functional rheostat for fate decision of secretory cells during injury repair, proposing a new potential therapeutic target for human lung alveolar regeneration.
2021-09-08 | GSE153677 | GEO
Project description:Background: Mesenchyme offers microenvironment for epithelial maturation during development of the small intestine. Molecular signature of immature mesenchyme has not yet been elucidated. DLK1 is known as a Notch ligand and has been reported to be highly expressed during embryogenesis. Although it has been investigated in other branching structure organs such as lung and salivary gland, DLK1’s role in intestinal development remains unknown. Methods: Intestinal mesenchymal cells (IMCs) were collected from small intestines of embryonic day 14.5 (E14.5) and adult mice, respectively. Intestinal organoids collected from embryonic small intestines were co-cultured with IMCs. The effect of embryonic and adult IMCs on epithelial morphology and differentiation was compared using qPCR and immunocytochemistry. Organoid sustainability was compared to assess the mesenchymal effect on stemness. A global mRNA sequence analysis of differentially expressed transcripts in embryonic and adult IMCs was performed. Given DLK1 was among the morphogen genes that were differentially expressed, DLK1 expression was manipulated with recombinant protein or siRNA and its effect on organoids was investigated. The histology of DLK1 knock out mice and wild type littermates were compared with proliferation marker, Ki67 and secretory lineage staining. Results: Embryonic IMCs induced cystic change of organoids and reduced budding structure when compared with adult IMCs. Secretory lineage differentiation of epithelium was found to be reduced and secondary organoids formation was increased when co-cultured with embryonic IMCs. 23 differentially expressed morphogen genes were identified with GSEA analysis. Genes expressed in cell membranes and extracellular space were filtered and DLK1 was identified as a key mesenchymal gene for morphogenesis. Immunohistochemistry showed that DLK1 was expressed exclusively in the stroma at the top of emerging villi and co-localized with PDGFRa in E14.5 small intestine. DLK1 expression in mesenchyme decreased after birth and shifted to epithelium in adulthood. Addition of recombinant DLK1 to adult IMCs inhibited organoid differentiation, whereas siDLK1 in embryonic IMCs increased epithelial differentiation to secretory lineage cells. DLK1 knock out mice showed restricted distribution of Ki67 positive cells in the base of villi compared with wild type littermate embryos. Secretory lineage cells were increased in DLK1 knock out mice at E19.5. Conclusion: DLK1 is expressed in the mesenchyme of small intestines during embryogenesis and decreases with age. Our data suggest stromal DLK1 promotes epithelial proliferation and suppresses secretory lineage differentiation.
2021-01-14 | GSE153024 | GEO
Project description:DLK1/FA-1 (delta-like 1/fetal antigen-1) is a transmembrane protein belonging to Notch/Delta family that acts as a membrane-associated or a soluble protein to regulate regeneration of a number of adult tissues. Here, we examined the role of DLK1/FA-1 in bone biology using osteoblast-specific-Dlk1 over-expressing mice (Col1-Dlk1). Col1-Dlk1 mice displayed growth retardation and significantly reduced total body weight and bone mineral density (BMD). μCT-scanning revealed a reduced trabecular and cortical bone volume fraction. Tissue-level histomorphometric analysis demonstrated decreased bone formation rate and enhanced bone resorption in Col1-Dlk1 as compared to WT. At a cellular level, DLK1 markedly reduced the total number of bone marrow (BM)-derived CFU-F, as well as their osteogenic capacity. In a number of in vitro culture systems, DLK1 stimulated osteoclastogenesis indirectly through osteoblast-dependent increased production of pro-inflammatory bone resorbing cytokines (e.g, Il7, Tnfa and Ccl3). We found that ovariectomy (ovx)-induced bone loss was associated with increased production of DLK1 in bone marrow by activated T-cells. However, Dlk1-/- mice were protected from ovx-induced bone loss. Thus, we identified DLK1 as a novel regulator of bone mass that function to inhibit bone formation and to stimulate bone resorption. Increasing DLK1 production by T-cells under estrogen deficiency suggests its possible use as a therapeutic target for preventing postmenopausal bone loss. Calvarial osteoblasts were grown from neonatal mice overexpressing Dlk1 and their non-transgenic littermate controls. Three separate cultures from each of the two genotypes were combined and analysed by Affymetrix microarray MOE430 2.0.
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