Single-Cell RNA Sequencing to Guide Autologous Preterm Cord Mesenchymal Stromal Cell-Therapy

Chanèle Cyr-Depauw; Ivana Mižik; David P Cook; Flore Lesage; Arul Vadivel; Laurent Renesme; Yupu Deng; Shumei Zhong; Pauline Bardin; Liqun Xu; Marius A Möbius; Jenny Marzahn; Daniel Freund; Duncan J Stewart; Barbara C Vanderhyden; Mario Rüdiger; Bernard Thébaud

doi:10.1164/rccm.202403-0569OC

Single-Cell RNA Sequencing to Guide Autologous Preterm Cord Mesenchymal Stromal Cell-Therapy

Am J Respir Crit Care Med. 2024 Nov 25. doi: 10.1164/rccm.202403-0569OC. Online ahead of print.

Authors

Chanèle Cyr-Depauw^{1

2}, Ivana Mižik^{1

3

4

5}, David P Cook^{2

6}, Flore Lesage¹, Arul Vadivel⁷, Laurent Renesme^{8

2}, Yupu Deng⁹, Shumei Zhong^{8

2}, Pauline Bardin¹⁰, Liqun Xu⁸, Marius A Möbius¹¹, Jenny Marzahn¹², Daniel Freund¹³, Duncan J Stewart^{8

2}, Barbara C Vanderhyden^{6

14}, Mario Rüdiger^{15

13}, Bernard Thébaud^{8

2

16

17}

Affiliations

¹ Ottawa Hospital Research Institute, Sinclair Centre for Regenerative Medicine, Ottawa, Ontario, Canada.
² University of Ottawa, Cellular and Molecular Medicine, Ottawa, Ontario, Canada.
³ University of Ottawa, Cellular and Molecular Medicine, Faculty of Medicine, Ottawa, Ontario, Canada.
⁴ University Hospital Heidelberg, Department of Translational Pulmonology and Translational Lung Research Center Heidelberg, Heidelberg, Baden-Württemberg, Germany.
⁵ German Center for Lung Research, Department of Translational Pulmonology and Translational Lung Research Center Heidelberg, Giessen, Hessen, Germany.
⁶ Ottawa Hospital Research Institute, Cancer Therapeutics Program, Ottawa, Ontario, Canada.
⁷ Sinclair Centre for Regenerative Medicine, The Ottawa Hospital Research Institute (OHRI), Ottawa, Ontario, Canada.
⁸ Ottawa Hospital Research Institute, Regenerative Medicine, Ottawa, Ontario, Canada.
⁹ Ottawa Health Research Institute, Ottawa, Ontario, Canada.
¹⁰ Ottawa Hospital Research Institute, Sinclair Centre for Regenerative Medicine, 501 Smyth road, Ottawa, Ontario, Canada.
¹¹ Universitätsklinikum Carl Gustav Carus, Neonatalogy and Pediatric Critical Care Medicine, Dresden, Sachsen, Germany.
¹² Technische Universität Dresden, Dresden, Sachsen, Germany.
¹³ DFG Research Center and Cluster of Excellence for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Dresden, Saxony, Germany.
¹⁴ University of Ottawa, Obstetrics and Gynecology, Ottawa, Ontario, Canada.
¹⁵ Medical Faculty and University Hospital Carl Gustav Carus, Technische Universität Dresden, Neonatology and Pediatric Critical Care Medicine, Dresden, Saxony, Germany.
¹⁶ Children's Hospital of Eastern Ontario, Department of Pediatrics, Division of Neonatology, Ottawa, Ontario, Canada.
¹⁷ Children's Hospital of Eastern Ontario Research Institute, Molecular Biomedicine Program, Ottawa, Ontario, Canada; bthebaud@toh.ca.

PMID: 39586004
DOI: 10.1164/rccm.202403-0569OC

Abstract

Rationale: The chronic lung disease bronchopulmonary dysplasia (BPD) remains the most common complication of extreme prematurity (<28 weeks of gestation). Umbilical cord-derived mesenchymal stromal cells (UC-MSCs) represent an opportunity for autologous cell-therapy, as UC-MSCs have been shown to improve lung function and structure in experimental BPD. However, characterization and repair capacity of UC-MSCs derived from donors with pregnancy-related complications associated with prematurity remain unexplored.

Objectives: To characterize UC-MSCs' transcriptome and determine if pregnancy-related complications (preeclampsia and chorioamnionitis) alter their therapeutic potential.

Methods: Single-cell RNA sequencing (scRNA-seq) was used to compare the transcriptome of UC-MSCs derived from five term donors, 16 preterm donors, and human neonatal dermal fibroblasts (HNDFs, control cells of mesenchymal origin), and correlated with their therapeutic potential in experimental BPD. Using publicly available neonatal lung single-nuclei RNA sequencing data, we also determined putative communication networks between UC-MSCs and resident lung cell populations.

Measurements and main results: Most UC-MSCs displayed a similar transcriptome despite of their pregnancy-related conditions and mitigated hyperoxia-induced lung injury in newborn rats. Conversely, HNDFs, one term and two preeclampsia preterm UC-MSC donors exhibited a distinct transcriptome enriched in genes related to fibroblast function and senescence and were devoid of therapeutic benefit in hyperoxia-induced BPD. Conversely, therapeutic UC-MSCs displayed a unique transcriptome active in cell proliferation and distinct cell-cell interactions with neonatal lung cell populations, including NEGR and NRNX pathways.

Conclusion: Term and preterm UC-MSCs are lung protective in experimental BPD. scRNA-seq allows to identify donors with a distinct UC-MSC transcriptome characteristic of reduced therapeutic potential.

Keywords: MSCs; bronchopulmonary dysplasia; hyperoxia; lung; scRNA-seq.