Single-Nuclei RNA Sequencing Data Analysis: Cardiomyocyte-Specific Modified-mNA Targeting Cyclin D2 Turns Subpopulations of Adult Pig Cardiomyocytes, Fibroblasts, and Smooth Muscle Cells Back to Neonatal Characteristics at Day 2 After SMRT Intervention
- 1Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- 2Department of Medicine, School of Medicine, University of Minnesota, Minneapolis, MN 55455, USA
- 3Department of Medicine, Division of Cardiovascular Disease, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
Abstract
Naturally, pig hearts cannot recover from ischemic reperfusion injury; however, pig hearts receiving cardiomyocyte-specific modified-RNA (CM-SMRTs) targeting Cyclin D2 (CCND2CM-SMRTs) demonstrated significantly better cardiac function, compared to the untreated hearts receiving Green Fluorescent Protein-induced modified RNA (GFPCM-SMRTs). In this report, we generated and analyzed single-nuclei RNA sequencing (snRNAseq) data to examine the mechanism by which CCND2CM-SMRTs regulate the cardiomyocyte cell cycle and improve cardiac function in the whole heart. The snRNAseq data from CCND2CM-SMRTs-treated pig hearts (~2-month-old) were integrated with the data from age-matched GFPCM-SMRTs-treated hearts, harvested on day 2 and day 28 after treatment, as well as with naïve neonatal day 1 and 2 (with regenerative potential) and with naïve 2-month-old (without regenerative potential) data. SnRNAseq data from all cardiac cell types were analyzed using an Autoencoder pipeline. Six cardiomyocytes (CM1–CM6), four fibroblasts (FB1–FB4), six smooth muscle cells (SMC1–SMC4), five endothelial cells (EC1–EC5), four macrophages (Mph1–Mph4), and two T-cell (Tcell1 and Tcell2) clusters were defined. While CCND2 is well-known as a major cell cycle driver from G1 to S phase, the snRNAseq data did not indicate any significant changes regarding cell cycle activity among CCND2CM-SMRTs-treated pigs, compared to GFPCM-SMRTs pigs, on day 2. Rather, clusters CM1, FB1, and SMC1 were observed in neonatal pig hearts and at the injury-border zone, where CM-SMRTs were delivered, in CCND2CM-SMRT-treated hearts on day 2 after treatment; these clusters did not appear in any remote zones, which were not subjected to ischemic reperfusion and CM-SMRTs effect, or in any untreated and naïve hearts. However, on day 28, clusters of FB1, and SMC1 were no longer observed, and only CM1 were prominently seen in border zone of CCND2CM-SMRT-treated hearts. Intercellular communication analysis revealed that CM1 may impact other non-cardiomyocyte clusters early after SMRT intervention via the BMP and PDGF signaling pathways. Thus, the analysis suggested that CCND2CM-SMRTs may drive a subset of pig cardiac cells toward a neonatal state, in which pig hearts still retain regenerative capacity.
Related
- Tachy-paced cardiomyocyte-derived small extracellular vesicles impair SERCA2a-dependent Ca²⁺ handling in recipient cardiomyocytes.
- Transcriptomic analysis of human induced pluripotent stem cell cardiomyocytes and myocardial tissue reveals novel role for miR-9-5p in hypertrophic cardiomyopathy
- Two-Dimensional Size-Exclusion Chromatography-Based Isolation and Characterization of Plasma-Derived Extracellular Vesicle Subpopulations from Prostate Cancer Patients
- MiR-208b-3p is an upstream regulator of redox-associated cardiomyocyte survival
- LMOD2 attenuates Ang II-induced cardiomyocyte hypertrophy by activating the Nrf2-mediated antioxidant pathway
BibTeX
@article{nguyen2026singlenuclei,
title = {{Single-Nuclei RNA Sequencing Data Analysis: Cardiomyocyte-Specific Modified-mNA Targeting Cyclin D2 Turns Subpopulations of Adult Pig Cardiomyocytes, Fibroblasts, and Smooth Muscle Cells Back to Neonatal Characteristics at Day 2 After SMRT Intervention}},
author = {Thanh Nguyen and Kaili Hao and Daniel J. Garry and Jianyi Zhang},
journal = {Biomolecules},
year = {2026},
month = oct,
doi = {10.3390/biom16101477},
url = {https://www.mdpi.com/2218-273X/16/10/1477},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Single-Nuclei RNA Sequencing Data Analysis: Cardiomyocyte-Specific Modified-mNA Targeting Cyclin D2 Turns Subpopulations of Adult Pig Cardiomyocytes, Fibroblasts, and Smooth Muscle Cells Back to Neonatal Characteristics at Day 2 After SMRT Intervention
AU - Thanh Nguyen
AU - Kaili Hao
AU - Daniel J. Garry
AU - Jianyi Zhang
PY - 2026
DA - 2026/10/01
JO - Biomolecules
DO - 10.3390/biom16101477
UR - https://www.mdpi.com/2218-273X/16/10/1477
AB - Naturally, pig hearts cannot recover from ischemic reperfusion injury; however, pig hearts receiving cardiomyocyte-specific modified-RNA (CM-SMRTs) targeting Cyclin D2 (CCND2CM-SMRTs) demonstrated significantly better cardiac function, compared to the untreated hearts receiving Green Fluorescent Protein-induced modified RNA (GFPCM-SMRTs). In this report, we generated and analyzed single-nuclei RNA sequencing (snRNAseq) data to examine the mechanism by which CCND2CM-SMRTs regulate the cardiomyocyte cell cycle and improve cardiac function in the whole heart. The snRNAseq data from CCND2CM-SMRTs-treated pig hearts (~2-month-old) were integrated with the data from age-matched GFPCM-SMRTs-treated hearts, harvested on day 2 and day 28 after treatment, as well as with naïve neonatal day 1 and 2 (with regenerative potential) and with naïve 2-month-old (without regenerative potential) data. SnRNAseq data from all cardiac cell types were analyzed using an Autoencoder pipeline. Six cardiomyocytes (CM1–CM6), four fibroblasts (FB1–FB4), six smooth muscle cells (SMC1–SMC4), five endothelial cells (EC1–EC5), four macrophages (Mph1–Mph4), and two T-cell (Tcell1 and Tcell2) clusters were defined. While CCND2 is well-known as a major cell cycle driver from G1 to S phase, the snRNAseq data did not indicate any significant changes regarding cell cycle activity among CCND2CM-SMRTs-treated pigs, compared to GFPCM-SMRTs pigs, on day 2. Rather, clusters CM1, FB1, and SMC1 were observed in neonatal pig hearts and at the injury-border zone, where CM-SMRTs were delivered, in CCND2CM-SMRT-treated hearts on day 2 after treatment; these clusters did not appear in any remote zones, which were not subjected to ischemic reperfusion and CM-SMRTs effect, or in any untreated and naïve hearts. However, on day 28, clusters of FB1, and SMC1 were no longer observed, and only CM1 were prominently seen in border zone of CCND2CM-SMRT-treated hearts. Intercellular communication analysis revealed that CM1 may impact other non-cardiomyocyte clusters early after SMRT intervention via the BMP and PDGF signaling pathways. Thus, the analysis suggested that CCND2CM-SMRTs may drive a subset of pig cardiac cells toward a neonatal state, in which pig hearts still retain regenerative capacity.
SN - 2218-273X
ER -