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Updated: Jun 29, 2025
Isolating, Sequencing and Analyzing Extracellular MicroRNAs from Human Mesenchymal Stem Cells
Published on: March 8, 2019
Single-Cell RNA Sequencing Reveals Repair Features of Human Umbilical Cord Mesenchymal Stromal Cells
Chanèle Cyr-Depauw1,2, David P Cook3,2, Ivana Mižik1,2
1Sinclair Centre for Regenerative Medicine and.
Insights
Mesenchymal stromal cells (MSCs) show promise for treating bronchopulmonary dysplasia (BPD). Progenitor-like UC-MSCs, identified by single-cell RNA sequencing, improved lung function in an animal model, unlike fibroblast-like cells.
Area of Science:
- Regenerative Medicine
- Neonatal Research
- Cell Biology
Background:
- Bronchopulmonary dysplasia (BPD) is a severe complication of extreme prematurity, causing impaired lung development and long-term respiratory issues.
- Current treatments for BPD are supportive, with limited options for addressing underlying lung damage.
- Umbilical cord-derived mesenchymal stromal cells (UC-MSCs) show preclinical promise for BPD, but clinical translation is hindered by a lack of criteria to define functionally distinct MSCs.
Purpose of the Study:
- To correlate single-cell transcriptomic profiles of UC-MSCs with their therapeutic potential in experimental BPD.
- To identify specific molecular markers that distinguish therapeutically effective UC-MSC subpopulations.
Main Methods:
- Single-cell RNA sequencing (scRNA-seq) was used to analyze transcriptomes of UC-MSCs and human neonatal dermal fibroblasts (HNDFs).
- The lung-protective effects of distinct UC-MSC subpopulations and HNDFs were evaluated in a rat model of hyperoxia-induced neonatal lung injury.
- Gene Ontology enrichment analysis identified distinct UC-MSC subpopulations based on transcriptomic profiles.
Main Results:
- UC-MSCs exhibited limited heterogeneity but differed transcriptomically from HNDFs, revealing progenitor-like and fibroblast-like subpopulations.
- Treatment with progenitor-like UC-MSCs significantly improved lung function, structure, and attenuated pulmonary hypertension in hyperoxia-exposed rat pups.
- scRNA-seq identified high expression of major histocompatibility complex class I as a marker of non-therapeutic UC-MSCs, associated with reduced lung retention.
Conclusions:
- Progenitor-like UC-MSCs, distinguished by their transcriptome, confer lung protection in experimental BPD, whereas fibroblast-like UC-MSCs do not.
- High expression of major histocompatibility complex class I in UC-MSCs correlates with diminished therapeutic benefit.
- scRNA-seq is a valuable tool for identifying superior MSC subsets for clinical applications in BPD and other conditions.
Abstract:
Rationale: The chronic lung disease bronchopulmonary dysplasia (BPD) is the most severe complication of extreme prematurity. BPD results in impaired lung alveolar and vascular development and long-term respiratory morbidity, for which only supportive therapies exist. Umbilical cord-derived mesenchymal stromal cells (UC-MSCs) improve lung structure and function in experimental BPD. Results of clinical trials with MSCs for many disorders do not yet match the promising preclinical studies. A lack of specific criteria to define functionally distinct MSCs persists. Objectives: To determine and correlate single-cell UC-MSC transcriptomic profiles with therapeutic potential. Methods: UC-MSCs from five term donors and human neonatal dermal fibroblasts (HNDFs; control cells of mesenchymal origin) transcriptomes were investigated using single-cell RNA sequencing (scRNA-seq) analysis. The lung-protective effect of UC-MSCs with a distinct transcriptome and control HNDFs was tested in vivo in hyperoxia-induced neonatal lung injury in rats. Measurements and Main Results: UC-MSCs showed limited transcriptomic heterogeneity but were different from HNDFs. Gene Ontology enrichment analysis revealed distinct (progenitor-like and fibroblast-like) UC-MSC subpopulations. Only treatment with progenitor-like UC-MSCs improved lung function and structure and attenuated pulmonary hypertension in hyperoxia-exposed rat pups. Moreover, scRNA-seq identified major histocompatibility complex class I as a molecular marker of nontherapeutic cells and associated with decreased lung retention. Conclusions: UC-MSCs with a progenitor-like transcriptome, but not with a fibroblast-like transcriptome, provide lung protection in experimental BPD. High expression of major histocompatibility complex class I is associated with reduced therapeutic benefit. scRNA-seq may be useful to identify subsets of MSCs with superior repair capacity for clinical application.
