Time-series expression profile analysis of fracture healing in young and old mice

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.

Transcriptome reveal gene regulation mechanisms of the barnacle Chthamalus challengeri for microhabitat adaption in the intertidal zone

BACKGROUND

Microhabitat environmental factors (e.g., temperature, oxygen concentration, nutrients, osmotic stress, and topography) are critical to the survival of intertidal organisms. Understanding how transcription responses are regulated in relation to intertidal microhabitat variation has important implications for studying adaptive evolution in these organisms. The barnacle Chthamalus challengeri, which survives in the intertidal zone and is subjected to periodic tidal changes, serves as an ideal species for detecting adaptive evolution in intertidal organisms.

RESULTS

In this study, we designed a series of in situ tidal conditions for C. challengeri and sequenced their transcriptome collected from various microhabitats. We aimed to detect the genetic adaptation mechanisms of barnacles responding to the microhabitat changes in the intertidal zone based on comparative transcriptomics. Our results indicated that different intertidal microhabitats significantly affected the gene expression models of C. challengeri, particularly for genes related to physiological and biochemical functions. Specifically, the expression of genes such as CYP450, HSP70, CYTB, and COX1 was significantly increased under low tide (air-exposed conditions), while genes like CNGA3, AK, and CP52 showed significantly increased expression under high tide (seawater-immersed conditions).

CONCLUSION

The results suggest that C. challengeri relies on cytochrome p450 enzymes to enhance oxidative capacity, counts on heat shock proteins and cell phagocytosis to resist microhabitat changes in response to different tidal conditions, and produces a hypoxic stress response to regulate energy metabolism and body temperature changes upon entering into seawater. This study provides genetic resources and clues for investigating the adaptation mechanisms of intertidal barnacles and identifies different gene expression models for C. challengeri responding to various microhabitats.

Proteome-Wide Mendelian Randomisation Identifies Causal Links of Plasma Proteins With Periodontitis

OBJECTIVE

Periodontitis is a complex and multifactorial disease and it is challenging to decipher its underlying causes and mechanisms. This study attempted to explore potential circulating proteins in connection to periodontitis through proteome-wide Mendelian randomisation (MR).

METHODS

We analysed 1722 circulating proteins to identify prospective drug targets for tackling periodontitis, using the genomic dataset from the FinnGen study. Two-sample MR was conducted to evaluate the bidirectional relationship between circulating proteins and periodontitis risk. A dataset from the UK Biobank was used to validate the findings. Single-cell analysis was performed to assess the cellular expression of the identified proteins within gingival tissues.

RESULTS

MR analyses found that genetically predicted circulating levels of von Willebrand factor A domain-containing 1 (von Willebrand factor A domain containing 1 [VWA1], odds ratios: 0.94, 95% CI 0.92-0.97, P = 1.28 × 10-5) were inversely associated with periodontitis. In contrast, the level of growth differentiation factor 15 (growth differentiation factor 15 [GDF15], odds ratios: 1.05, 95% CI 1.02-1.07, P = 2.12 × 10-5) might be associated with an increased risk of periodontitis. Single-cell analysis indicated that VWA1 was primarily expressed in endothelial cells of healthy gingival tissues, while the main source of GDF15 was not derived from periodontal cells.

CONCLUSIONS

The present study suggests that certain plasma proteins like VWA1 and GDF15 may be potentially indicative of the risk and susceptibility to periodontitis. These proteins could possibly be the potential therapeutic targets for treating periodontitis, and further investigation is highly warranted.

The role of EMILIN-1 in the osteo/odontogenic differentiation of dental pulp stem cells

BACKGROUND

Human dental pulp stem cells (hDPSCs) may be the best choice for self-repair and regeneration of teeth and maxillofacial bone tissue due to their homogeneous tissue origin, high proliferation and differentiation rates, and no obvious ethical restrictions. Recently, several studies have shown that extracellular matrix (ECM) proteins can effectively regulate the proliferation and differentiation fate of mesenchymal stem cells (MSCs). However, the role of elastin microfibril interface-located protein-1 (EMILIN-1), a new ECM glycoprotein, in osteo/odontogenic differentiation of hDPSCs has not been reported. The aim of this study was to explore the effect of EMILIN-1 during osteo/odontogenic differentiation of hDPSCs.

METHODS

hDPSCs were cultured in osteo/odontogenic induction medium. qPCR and Western blot analysis were performed to detect osteo/odonto-specific genes/proteins expression as well as the expression of EMILIN-1. After knockdown of Emilin-1 in hDPSCs with small interfering RNA and exogenous addition of recombinant human EMILIN-1 protein (rhEMILIN-1), Cell Counting Kit-8 assay, alkaline phosphatase staining, alizarin red S staining, qPCR and Western blot were performed to examine the effect of EMILIN-1 on proliferation and osteo/odontogenic differentiation of hDPSCs.

RESULTS

During the osteo/odontogenic induction of hDPSCs, the expression of osteo/odonto-specific genes/proteins increased, as did EMILIN-1 protein levels. More notably, knockdown of Emilin-1 decreased hDPSCs proliferation and osteo/odontogenic differentiation, whereas exogenous addition of rhEMILIN-1 increased them.

CONCLUSIONS

These findings suggested that EMILIN-1 is essential for the osteo/odontogenic differentiation of hDPSCs, which may provide new insights for teeth and bone tissue regeneration.

Application of proteomics to determine the mechanism of ozone on sweet cherries (Prunus avium L.) by time-series analysis

This research investigated the mechanism of ozone treatment on sweet cherry (Prunus avium L.) by Lable-free quantification proteomics and physiological traits. The results showed that 4557 master proteins were identified in all the samples, and 3149 proteins were common to all groups. Mfuzz analyses revealed 3149 candidate proteins. KEGG annotation and enrichment analysis showed proteins related to carbohydrate and energy metabolism, protein, amino acids, and nucleotide sugar biosynthesis and degradation, and fruit parameters were characterized and quantified. The conclusions were supported by the fact that the qRT-PCR results agreed with the proteomics results. For the first time, this study reveals the mechanism of cherry in response to ozone treatment at a proteome level.

Identifying the Potential Differentially Expressed miRNAs and mRNAs in Osteonecrosis of the Femoral Head Based on Integrated Analysis

Purpose

Osteonecrosis of the femoral head is a common disease of the hip that leads to severe pain or joint disability. We aimed to identify potential differentially expressed miRNAs and mRNAs in osteonecrosis of the femoral head.

Methods

The data of miRNA and mRNA were firstly downloaded from the database. Secondly, the regulatory network of miRNAs-mRNAs was constructed, followed by function annotation of mRNAs. Thirdly, an in vitro experiment was applied to validate the expression of miRNAs and targeted mRNAs. Finally, GSE123568 dataset was used for electronic validation and diagnostic analysis of targeted mRNAs.

Results

Several regulatory interaction pairs between miRNA and mRNAs were identified, such as hsa-miR-378c-WNT3A/DACT1/CSF1, hsa-let-7a-5p-RCAN2/IL9R, hsa-miR-28-5p-RELA, hsa-miR-3200-5p-RELN, and hsa-miR-532-5p-CLDN18/CLDN10. Interestingly, CLDN10, CLDN18, CSF1, DACT1, IL9R, RCAN2, RELN, and WNT3A had the diagnostic value for osteonecrosis of the femoral head. Wnt signaling pathway (involved WNT3A), chemokine signaling pathway (involved RELA), focal adhesion and ECM-receptor interaction (involved RELN), cell adhesion molecules (CAMs) (involved CLDN18 and CLDN10), cytokine-cytokine receptor interaction, and hematopoietic cell lineage (involved CSF1 and IL9R) were identified.

Conclusion

The identified differentially expressed miRNAs and mRNAs may be involved in the pathology of osteonecrosis of the femoral head.

COL3A1, COL6A3, and SERPINH1 Are Related to Glucocorticoid-Induced Osteoporosis Occurrence According to Integrated Bioinformatics Analysis

Background

Glucocorticoid-induced osteoporosis (GIOP) represents the most frequently seen type of secondary osteoporosis, a systemic skeleton disorder. Numerous factors are associated with GIOP occurrence, but there are no specific diagnostic and therapeutic biomarkers for GIOP so far.

Material/Methods

In this work, gene modules related to GIOP were screened through weighted gene coexpression network analysis. Moreover, protein-protein interaction (PPI) networks and gene set enrichment analysis (GSEA) were carried out for hub genes. In addition, microarray GSE30159 dataset was used as a training set to analyze gene expression within bone biopsy samples from patients with endogenous Cushing’s syndrome with GIOP and from normal controls. GSE129228 was used as the test set for investigating the hub gene involvement within GIOP.

Results

According to our results, the turquoise module showed clinical significance, and 10 genes (COL3A1, POSTN, COL6A3, COL14A1, SERPINH1, ASPN, OGN, THY1, NID2, and TNMD) were discovered to be the “real” hub genes within coexpression as well as PPI networks. GSEA showed that the interaction of extracellular matrix receptors together with the focal adhesion pathway had significant enrichment within samples with high COL3A1 and COL6A3 expression. After the results from both test and training sets were overlapped, SERPINH1 was also significantly altered between GIOP and normal control samples.

Conclusions

COL3A1, COL6A3, and SERPINH1 were identified to be the candidate biomarkers for GIOP.

Validation of reference genes for expression analysis in a murine trauma model combining traumatic brain injury and femoral fracture

Systemic and local posttraumatic responses are often monitored on mRNA expression level using quantitative real-time PCR (qRT-PCR), which requires normalisation to adjust for confounding sources of variability. Normalisation requests reference (housekeeping) genes stable throughout time and divergent experimental conditions in the tissue of interest, which are crucial for a reliable and reproducible gene expression analysis. Although previous animal studies analysed reference genes following isolated trauma, this multiple-trauma gene expression analysis provides a notable study analysing reference genes in primarily affected (i.e. bone/fracture callus and hypothalamus) and secondarily affected organs (i.e. white adipose tissue, liver, muscle and spleen), following experimental long bone fracture and traumatic brain injury. We considered tissue-specific and commonly used top-ranked reference candidates from different functional groups that were evaluated applying the established expression stability analysis tools NormFinder, GeNorm, BestKeeper and RefFinder. In conclusion, reference gene expression in primary organs is highly time point as well as tissue-specific, and therefore requires careful evaluation for qRT-PCR analysis. Furthermore, the general application of Ppia, particularly in combination with a second reference gene, is strongly recommended for the analysis of systemic effects in the case of indirect trauma affecting secondary organs through local and systemic pathophysiological responses.

The Effect of Age on Fracture Healing Time in Metacarpal Fractures

Background: Older patients are treated for fracture with increasing frequency. Although studies on animals suggest that older mice and rats heal fractures more slowly, the clinical implications remain unclear. A better understanding of differences in healing with age can help customize fracture treatment. Our purpose was to retrospectively evaluate metacarpal fractures for healing time looking specifically at age-related differences. Methods: A retrospective review of patients treated for metacarpal fractures was conducted. Patients with incomplete charts or inadequate follow-up were excluded. One hundred ninety-eight charts were analyzed. Demographic and other patient factors were documented. Fracture characteristics and treatment type were documented. Fracture healing was determined clinically. Plain radiographs and examination were used in decision making. Results: Age was not associated with fracture healing time as a continuous variable (P = .09). Patients above 75 years were not associated with increased healing time (P = .58). Fracture characteristics were related to healing time: minimally displaced and comminuted fractures healed faster than oblique fractures, spiral fractures, or transverse fractures (P = .048). Patients undergoing surgery healed faster than those without surgery (P = .046). Renal failure negatively affected fracture healing time (P = .03). Diabetes, hypothyroidism, and gender were not associated with healing time. Complications were not associated with age or other patient or fracture-related factors. Conclusions: Age does not affect clinical fracture healing time in adult. Therefore, older patients do not require disparate treatment. Other fracture-related factors and considerations such as functional demand and support systems might influence treatment decisions in fracture care.

Transcriptional profiling of intramembranous and endochondral ossification after fracture in mice

Bone fracture repair represents an important clinical challenge with nearly 1 million non-union fractures occurring annually in the U.S. Gene expression differs between non-union and healthy repair, suggesting there is a pattern of gene expression that is indicative of optimal repair. Despite this, the gene expression profile of fracture repair remains incompletely understood. In this work, we used RNA-seq of two well-established murine fracture models to describe gene expression of intramembranous and endochondral bone formation. We used top differentially expressed genes, enriched gene ontology terms and pathways, callus cellular phenotyping, and histology to describe and contrast these bone formation processes across time. Intramembranous repair, as modeled by ulnar stress fracture, and endochondral repair, as modeled by femur full fracture, exhibited vastly different transcriptional profiles throughout repair. Stress fracture healing had enriched differentially expressed genes associated with bone repair and osteoblasts, highlighting the strong osteogenic repair process of this model. Interestingly, the PI3K-Akt signaling pathway was one of only a few pathways uniquely enriched in stress fracture repair. Full fracture repair involved a higher level of inflammatory and immune cell related genes than did stress fracture repair. Full fracture repair also differed from stress fracture in a robust downregulation of ion channel genes following injury, the role of which in fracture repair is unclear. This study offers a broad description of gene expression in intramembranous and endochondral ossification across several time points throughout repair and suggests several potentially intriguing genes, pathways, and cells whose role in fracture repair requires further study.

MicroRNA‑186‑5p mediates osteoblastic differentiation and cell viability by targeting CXCL13 in non‑traumatic osteonecrosis

MicroRNAs (miRs) serve varying and important roles in the pathogenesis of non‑traumatic osteonecrosis (ON). However, the role miR‑186‑5p serves in the pathogenesis of osteonecrosis remains unknown and the clinical outcome of ON is still uncertain. The aim of the present study was to determine the expression characteristics, biological function and molecular mechanisms of miR‑186‑5p, which is associated with cancer development and progression, in osteoblastic differentiation and cell viability. The results of the present study showed that the expression levels of miR‑186‑5p were significantly higher in clinical non‑traumatic ON compared with osteoarthritis samples (P=0.0001). An inverse association was observed between miR‑186‑5p and CXCL13 expression levels. Furthermore, miR‑186‑5p inhibited phosphatidylinositol 3 kinase (PI3K)/protein kinase B (AKT) signaling, downregulated osteoblast‑specific markers and reduced the viability and differentiation of human mesenchymal stem cells from bone marrow (HMSC‑bm) through targeting CXCL13. Increasing expression of CXCL13 in HMSC‑bm cells partially restored miR‑186‑5p‑mediated inhibition. In conclusion, abrogation of PI3K/AKT signaling triggered by miR‑186‑5p/CXCL13 may contribute to ON pathogenesis. These results highlight the possible clinical value of miR‑186‑5p in treatment for non‑traumatic ON.

WARP: A Unique Extracellular Matrix Component of Cartilage, Muscle, and Endothelial Cell Basement Membranes

The von Willebrand factor A-domain-related protein (WARP) encoded by the VWA1 gene, is an orphan extracellular matrix protein that is expressed in a subset of ECM structures but whose function is poorly understood. Here, recent advances on understanding VWA1/WARP will be reviewed including analysis of VWA1 reporter and global knock-out mice, interaction studies, and recent transcriptome analyses. Anat Rec, 2019. © 2019 Wiley Periodicals, Inc.

Transcriptional Mechanisms of Secondary Fracture Healing

PURPOSE OF REVIEW

Growing evidence supports the critical role of transcriptional mechanisms in promoting the spatial and temporal progression of bone healing. In this review, we evaluate and discuss new transcriptional and post-transcriptional regulatory mechanisms of secondary bone repair, along with emerging evidence for epigenetic regulation of fracture healing.

RECENT FINDINGS

Using the candidate gene approach has identified new roles for several transcription factors in mediating the reactive, reparative, and remodeling phases of fracture repair. Further characterization of the different epigenetic controls of fracture healing and fracture-driven transcriptome changes between young and aged fracture has identified key biological pathways that may yield therapeutic targets. Furthermore, exogenously delivered microRNA to post-transcriptionally control gene expression is quickly becoming an area with great therapeutic potential. Activation of specific transcriptional networks can promote the proper progression of secondary bone healing. Targeting these key factors using small molecules or through microRNA may yield effective therapies to enhance and possibly accelerate fracture healing.