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RNA-Binding Protein Signature in Proliferative Cardiomyocytes: A Cross-Species Meta-Analysis from Mouse, Pig, and
Thanh Nguyen1, Kaili Hao1, Yuji Nakada1
1Department of Biomedical Engineering, School of Medicine and School of Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
Insights
Understanding RNA-binding proteins (RBPs) is key to heart repair. This study found specific RBPs are crucial for cardiomyocyte proliferation in mammals, offering new avenues for cardiovascular research and regenerative medicine.
Area of Science:
- Cardiovascular Sciences
- Molecular Biology
- Regenerative Medicine
Background:
- Mammalian cardiomyocyte cell-cycle withdrawal after birth limits heart repair following myocardial injury.
- Neonatal mammals can regenerate myocardium after injury due to cardiomyocyte proliferation.
- RNA-binding proteins (RBPs) regulate the translation of cell-cycle machinery mRNA, impacting proliferation.
Purpose of the Study:
- To investigate the relationship between RNA-binding protein (RBP) expression and cardiomyocyte proliferation.
- To identify conserved RBPs associated with cardiomyocyte proliferation across species.
Main Methods:
- Meta-analysis of single-nuclei RNA sequencing (snRNA-seq) data from regenerating mouse and pig hearts using an Autoencoder.
- Bulk RNA sequencing (RNA-seq) analysis of human-induced pluripotent stem cell-derived (hiPSC) cardiomyocyte (hiPSC-CM) cell lines at different proliferation stages.
- Cross-species comparison of RBP expression in proliferating cardiomyocytes.
Main Results:
- Twenty-one RBPs were consistently upregulated, and six were downregulated in proliferating cardiomyocytes across mouse, pig, and hiPSC-CM models.
- Immunofluorescence validated increased protein levels of DHX9, PTBP3, HNRNPUL1, and DDX6 in proliferating pig cardiomyocytes.
- A strong association between RBP expression and cardiomyocyte proliferation was demonstrated across species.
Conclusions:
- Specific RNA-binding proteins play a conserved role in regulating cardiomyocyte proliferation.
- These findings highlight RBPs as potential targets for promoting heart regeneration.
- The study provides a foundation for developing novel therapeutic strategies for cardiovascular diseases.
Abstract:
In mammals, because cardiomyocytes withdraw from cell-cycle activities shortly after birth, the heart cannot repair the damage caused by a myocardial injury; thus, understanding how cardiomyocytes proliferate is among the most important topics in cardiovascular sciences. In newborn neonatal mammals, when a left ventricular injury is applied in hearts earlier than postnatal day 7, the cardiomyocytes actively proliferate and regenerate lost myocardium in the following weeks. The regulators promoting cardiomyocyte proliferation were discovered by analyzing transcriptomic data generated from models. Most of these regulators support the mRNA production of cell-cycle machinery, yet the mRNA requires translation into functional proteins under the regulation of RNA-binding proteins (RBPs). In this work, we performed a meta-analysis to study the relationship between RBP expression and cardiomyocyte proliferation. To identify RBPs associated with mouse and pig cardiomyocyte proliferation, the single-nuclei RNA sequencing (snRNA-seq) data from regenerating mouse and pig hearts were reanalyzed via an Autoencoder focusing on RBP expression. We also generated and analyzed new bulk RNA-seq from two human-induced pluripotent stem cell-derived (hiPSC) cardiomyocyte (hiPSC-CM) cell lines; the first cell line was harvested sixteen days after differentiation, when the cells still actively proliferated, and the second cell line was harvested one hundred and forty days after differentiation, when the cells ceased cell cycle activity. Then, the RBP associated with mouse, pig, and hiPSC-CM were compared across species. Twenty-one RBPs were found to be consistently upregulated, and six RBPs were downregulated in proliferating mouse, pig, and hiPSC-derived cardiomyocytes. Among upregulated RBPs across species, an immunofluorescence-based imaging analysis validated the significant increase in the proteins of DHX9, PTBP3, HNRNPUL1, and DDX6 in pig hearts with proliferating CMs. This meta-analysis in all species demonstrated a strong relationship between RBP expression and cardiomyocyte proliferation.
