Decoding fracture healing: A scoping review of mechanistic pathways derived from transcriptional analysis in murine studies

Fracture healing is a complex biological process involving orchestrated interactions among cells, growth factors, and transcriptional pathways. Despite significant advancements in understanding bone repair, non-union and delayed healing remain prevalent, especially in patients with comorbidities such as aging, diabetes, or substance use. Murine models serve as a cornerstone in fracture healing research, offering genetic manipulability, cost-effectiveness, and biological relevance to humans. This scoping review consolidates findings from studies conducted between 2010 and 2024, focusing on mechanistic pathways derived from transcriptional analysis in secondary bone healing as identified through bulk RNA sequencing of murine models. Key mechanistic pathways were categorized and analyzed across the distinct phases of fracture healing-reactive, reparative, and remodeling-highlighting their unique roles in inflammation, ECM remodeling, cell proliferation, and tissue mineralization. The most recurrent mechanistic pathways included ECM-receptor interaction, focal adhesion, and signaling mechanisms such as MAPK and TGF-beta. Variability in methodologies and limited overlap among studies underscore the need for standardized protocols in RNA sequencing analysis. Additionally, comparisons across long bone fractures, hole defects, and craniofacial bone healing revealed shared molecular mechanisms alongside unique challenges, particularly in craniofacial models. This scoping review underscores the promise of integrating systems biology approaches with transcriptomic data to elucidate the intricate regulatory networks governing fracture repair. Addressing the identified gaps in early-phase healing and harmonizing research methodologies will advance therapeutic strategies to reduce non-union rates and improve clinical outcomes.