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Updated: Oct 22, 2025
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Published on: September 16, 2020
Multiple targets identified with genome wide profiling of small RNA and mRNA expression are linked to fracture
Matthieu Bourgery1, Erika Ekholm1, Katja Fagerlund1
1Institute of Biomedicine, University of Turku, Finland.
Abstract:
Long-bone fracture is a common injury and its healing process at the fracture site involves several overlapping phases, including inflammation, migration of mesenchymal progenitors into the fracture site, endochondral ossification, angiogenesis and finally bone remodelling. Increasing evidence shows that small noncoding RNAs are important regulators of chondrogenesis, osteogenesis and fracture healing. MicroRNAs are small single-stranded, non-coding RNA-molecules intervening in most physiological and biological processes, including fracture healing. Angiogenin-cleaved 5' tRNA halves, also called as tiRNAs (stress-induced RNAs) have been shown to repress protein translation. In order to gain further understanding on the role of small noncoding RNAs in fracture healing, genome wide expression profiles of tiRNAs, miRNAs and mRNAs were followed up to 14 days after fracture in callus tissue of an in vivo mouse model with closed tibial fracture and, compared to intact bone and articular cartilage at 2 months of age. Total tiRNA expression level in cartilage was only approximately one third of that observed in control D0 bone. In callus tissue, 11 mature 5'end tiRNAs out of 191 tiRNAs were highly expressed, and seven of them were differentially expressed during fracture healing. When comparing the control tissues, 25 miRNAs characteristic to bone and 29 miRNAs characteristic to cartilage tissue homeostasis were identified. Further, a total of 54 out of 806 miRNAs and 5420 out of 18,700 mRNAs were differentially expressed (DE) in callus tissue during fracture healing and, in comparison to control bone. They were associated to gene ontology processes related to mesenchymal tissue development and differentiation. A total of 581 miRNA-mRNA interactions were identified for these 54 DE miRNAs by literature searches in PubMed, thereby linking by Spearman correlation analysis 14 downregulated and 28 upregulated miRNAs to 164 negatively correlating and 168 positively correlating miRNA-mRNA pairs with chondrogenic and osteogenic phases of fracture healing. These data indicated that tiRNAs and miRNAs were differentially expressed in fracture callus tissue, suggesting them important physiological functions during fracture healing. Hence, the data provided by this study may contribute to future clinical applications, such as potential use as biomarkers or as tools in the development of novel therapeutic approaches for fracture healing.
Insights
Small noncoding RNAs, including microRNAs (miRNAs) and stress-induced RNAs (tiRNAs), play crucial roles in bone fracture healing. This study identified differentially expressed tiRNAs and miRNAs in fracture callus tissue, suggesting their potential as biomarkers and therapeutic targets for enhanced bone repair.
Area of Science:
- Molecular Biology
- Genetics
- Biochemistry
Background:
- Long-bone fracture healing involves complex, overlapping phases: inflammation, mesenchymal progenitor cell migration, endochondral ossification, angiogenesis, and bone remodeling.
- Small noncoding RNAs, particularly microRNAs (miRNAs), are increasingly recognized as key regulators of chondrogenesis, osteogenesis, and fracture healing.
- Angiogenin-cleaved 5' tRNA halves (tiRNAs) are stress-induced RNAs known to repress protein translation, with their role in fracture healing being less understood.
Purpose of the Study:
- To investigate the genome-wide expression profiles of tiRNAs, miRNAs, and mRNAs during the fracture healing process.
- To identify specific small noncoding RNAs and their interactions involved in the chondrogenic and osteogenic phases of fracture healing.
- To explore the potential of these small noncoding RNAs as biomarkers or therapeutic targets for fracture healing.
Main Methods:
- An in vivo mouse model of closed tibial fracture was used, with callus tissue collected up to 14 days post-fracture.
- Genome-wide expression profiling of tiRNAs, miRNAs, and mRNAs was performed and compared to intact bone and articular cartilage.
- Bioinformatic analyses, including Spearman correlation and literature searches (PubMed), were employed to identify miRNA-mRNA interactions and their association with fracture healing phases.
Main Results:
- Total tiRNA expression in cartilage was significantly lower than in control bone.
- Eleven mature 5'end tiRNAs were highly expressed in callus tissue, with seven showing differential expression during healing.
- 25 bone-specific and 29 cartilage-specific miRNAs were identified. A total of 54 differentially expressed miRNAs and 5420 differentially expressed mRNAs were found in callus tissue compared to control bone.
- 581 miRNA-mRNA interactions were identified, linking 14 downregulated and 28 upregulated miRNAs to 164 negatively and 168 positively correlating miRNA-mRNA pairs with chondrogenic and osteogenic phases.
Conclusions:
- tiRNAs and miRNAs are differentially expressed in fracture callus tissue, indicating significant roles in fracture healing.
- The identified differentially expressed miRNAs and their interactions provide insights into the molecular mechanisms regulating chondrogenesis and osteogenesis during fracture repair.
- These findings suggest that tiRNAs and miRNAs hold promise for future clinical applications, including use as biomarkers for fracture healing assessment and as targets for novel therapeutic strategies to improve bone regeneration.
