Non-coding RNAs: Epigenetic regulators of bone development and homeostasis

Osteomyelitis and non-coding RNAS: A new dimension in disease understanding

Osteomyelitis, a debilitating bone infection, presents considerable clinical challenges due to its intricate etiology and limited treatment options. Despite strides in surgical and chemotherapeutic interventions, the treatment landscape for osteomyelitis remains unsatisfactory. Recent attention has focused on the role of non-coding RNAs (ncRNAs) in the pathogenesis and progression of osteomyelitis. This review consolidates current knowledge on the involvement of distinct classes of ncRNAs, including microRNAs, long ncRNAs, and circular RNAs, in the context of osteomyelitis. Emerging evidence from various studies underscores the potential of ncRNAs in orchestrating gene expression and influencing the differentiation of osteoblasts and osteoclasts, pivotal processes in bone formation. The review initiates by elucidating the regulatory functions of ncRNAs in fundamental cellular processes such as inflammation, immune response, and bone remodeling, pivotal in osteomyelitis pathology. It delves into the intricate network of interactions between ncRNAs and their target genes, illuminating how dysregulation contributes to the establishment and persistence of osteomyelitic infections. Understanding their regulatory roles may pave the way for targeted diagnostic tools and innovative therapeutic interventions, promising a paradigm shift in the clinical approach to this challenging condition. Additionally, we delve into the promising therapeutic applications of these molecules, envisioning novel diagnostic and treatment approaches to enhance the management of this challenging bone infection.

LINC01638 sustains human mesenchymal stem cell self-renewal and competency for osteogenic cell fate

The skeleton forms from multipotent human mesenchymal stem cells (hMSCs) competent to commit to specific lineages. Long noncoding RNAs (lncRNAs) have been identified as key epigenetic regulators of tissue development. However, regulation of osteogenesis by lncRNAs as mediators of commitment to the bone phenotype is largely unexplored. We focused on LINC01638, which is highly expressed in hMSCs and has been studied in cancers, but not in regulating osteogenesis. We demonstrated that LINC01638 promotes initiation of the osteoblast phenotype. Our findings reveal that LINC01638 is present at low levels during the induction of osteoblast differentiation. CRISPRi knockdown of LINC01638 in MSCs prevents osteogenesis and alkaline phosphatase expression, inhibiting osteoblast differentiation. This resulted in decreased MSC growth rate, accompanied by double-strand breaks, DNA damage, and cell senescence. Transcriptome profiling of control and LINC01638-depleted hMSCs identified > 2000 differentially expressed mRNAs related to cell cycle, cell division, spindle formation, DNA repair, and osteogenesis. Using ChIRP-qPCR, molecular mechanisms of chromatin interactions revealed the LINC01638 locus (Chr 22) includes many lncRNAs and bone-related genes. These novel findings identify the obligatory role for LINC01638 to sustain MSC pluripotency regulating osteoblast commitment and growth, as well as for physiological remodeling of bone tissue.

LINC01638 Sustains Human Mesenchymal Stem Cell Self-Renewal and Competency for Osteogenic Cell Fate

The skeleton forms from multipotent human mesenchymal stem cells (hMSCs) competent to commit to specific lineages. Long noncoding RNAs (lncRNAs) have been identified as key epigenetic regulators of tissue development. However, regulation of osteogenesis by lncRNAs as mediators of commitment to the bone phenotype is largely unexplored. We focused on LINC01638, which is highly expressed in hMSCs and has been studied in cancers, but not in regulating osteogenesis. We demonstrated that LINC01638 promotes initiation of the osteoblast phenotype. Our findings reveal that LINC01638 is present at low levels during the induction of osteoblast differentiation. CRISPRi knockdown of LINC01638 in MSCs prevents osteogenesis and alkaline phosphatase expression, inhibiting osteoblast differentiation. This resulted in decreased MSC cell growth rate, accompanied by double-strand breaks, DNA damage, and cell senescence. Transcriptome profiling of control and LINC01638-depleted hMSCs identified > 2,000 differentially expressed mRNAs related to cell cycle, cell division, spindle formation, DNA repair, and osteogenesis. Using ChIRP-qPCR, molecular mechanisms of chromatin interactions revealed the LINC01638 locus (Chr 22) includes many lncRNAs and bone-related genes. These novel findings identify the obligatory role for LINC01638 to sustain MSC pluripotency regulating osteoblast commitment and growth, as well as for physiological remodeling of bone tissue.

Integrated Analysis of Transcriptome Expression Profiles Reveals miRNA-326-NKX3.2-Regulated Porcine Chondrocyte Differentiation

The porcine body length trait is an essential factor affecting meat production and reproductive performance. It is evident that the development/lengthening of individual vertebrae is one of the main reasons for increases in body length; however, the underlying molecular mechanism remains unclear. In this study, RNA-seq analysis was used to profile the transcriptome (lncRNA, mRNA, and miRNA) of the thoracic intervertebral cartilage (TIC) at two time points (1 and 4 months) during vertebral column development in Yorkshire (Y) and Wuzhishan pigs (W). There were four groups: 1- (Y1) and 4-month-old (Y4) Yorkshire pigs and 1- (W1) and 4-month-old (W4) Wuzhishan pigs. In total, 161, 275, 86, and 126 differentially expressed (DE) lncRNAs, 1478, 2643, 404, and 750 DE genes (DEGs), and 74,51, 34, and 23 DE miRNAs (DE miRNAs) were identified in the Y4 vs. Y1, W4 vs. W1, Y4 vs. W4, and Y1 vs. W1 comparisons, respectively. Functional analysis of these DE transcripts (DETs) demonstrated that they had participated in various biological processes, such as cellular component organization or biogenesis, the developmental process, the metabolic process, bone development, and cartilage development. The crucial bone development-related candidate genes NK3 Homeobox 2 (NKX3.2), Wnt ligand secretion mediator (WLS), gremlin 1 (GREM1), fibroblast growth factor receptor 3 (FGFR3), hematopoietically expressed homeobox (HHEX), (collagen type XI alpha 1 chain (COL11A1), and Wnt Family Member 16 (WNT16)) were further identified by functional analysis. Moreover, lncRNA, miRNA, and gene interaction networks were constructed; a total of 55 lncRNAs, 6 miRNAs, and 7 genes formed lncRNA-gene, miRNA-gene, and lncRNA-miRNA-gene pairs, respectively. The aim was to demonstrate that coding and non-coding genes may co-regulate porcine spine development through interaction networks. NKX3.2 was identified as being specifically expressed in cartilage tissues, and it delayed chondrocyte differentiation. miRNA-326 regulated chondrocyte differentiation by targeting NKX3.2. The present study provides the first non-coding RNA and gene expression profiles in the porcine TIC, constructs the lncRNA-miRNA-gene interaction networks, and confirms the function of NKX3.2 in vertebral column development. These findings contribute to the understanding of the potential molecular mechanisms regulating pig vertebral column development. They expand our knowledge about the differences in body length between different pig species and provide a foundation for future studies.

Long non-coding RNA H19 regulates matrisome signature and impacts cell behavior on MSC-engineered extracellular matrices

BACKGROUND

The vast and promising class of long non-coding RNAs (lncRNAs) has been under investigation for distinct therapeutic applications. Nevertheless, their role as molecular drivers of bone regeneration remains poorly studied. The lncRNA H19 mediates osteogenic differentiation of Mesenchymal Stem/Stromal Cells (MSCs) through the control of intracellular pathways. However, the effect of H19 on the extracellular matrix (ECM) components is still largely unknown. This research study was designed to decode the H19-mediated ECM regulatory network, and to reveal how the decellularized siH19-engineered matrices influence MSC proliferation and fate. This is particularly relevant for diseases in which the ECM regulation and remodeling processes are disrupted, such as osteoporosis.

METHODS

Mass spectrometry-based quantitative proteomics analysis was used to identify ECM components, after oligonucleotides delivery to osteoporosis-derived hMSCs. Moreover, qRT-PCR, immunofluorescence and proliferation, differentiation and apoptosis assays were performed. Engineered matrices were decellularized, characterized by atomic force microscopy and repopulated with hMSC and pre-adipocytes. Clinical bone samples were characterized by histomorphometry analysis.

RESULTS

Our study provides an in-depth proteome-wide and matrisome-specific analysis of the ECM proteins controlled by the lncRNA H19. Using bone marrow-isolated MSC from patients with osteoporosis, we identified fibrillin-1 (FBN1), vitronectin (VTN) and collagen triple helix repeat containing 1 (CTHRC1), among others, as having different pattern levels following H19 silencing. Decellularized siH19-engineered matrices are less dense and have a decreased collagen content compared with control matrices. Repopulation with naïve MSCs promotes a shift towards the adipogenic lineage in detriment of the osteogenic lineage and inhibits proliferation. In pre-adipocytes, these siH19-matrices enhance lipid droplets formation. Mechanistically, H19 is targeted by miR-29c, whose expression is decreased in osteoporotic bone clinical samples. Accordingly, miR-29c impacts MSC proliferation and collagen production, but does not influence ALP staining or mineralization, revealing that H19 silencing and miR-29c mimics have complementary but not overlapping functions.

CONCLUSION

Our data suggest H19 as a therapeutic target to engineer the bone ECM and to control cell behavior.

[Regulation of long non-coding RNA in signal pathways related to osteogenic differentiation]

OBJECTIVE

To summarize the mechanism of long non-coding RNA (lncRNA) in signal pathways related to osteogenic differentiation.

METHODS

Relevant domestic and foreign researches in recent years were consulted. The characteristics and biological functions of lncRNA were introduced, and the specific mechanism of lncRNA regulating related signal pathways in osteogenic differentiation was elaborated.

RESULTS

The exertion and maintenance of normal function of bone requires the closed coordination of transcription networks and signal pathways. However, most of these signal pathways or networks are dysregulated under pathological conditions that affect bone homeostasis. lncRNA can regulate the differentiation of various bone cells by activating or inhibiting signal pathways to achieve the balance of bone homeostasis, thereby reversing the pathological state of bones and achieving the purpose of treating bone metabolic diseases.

CONCLUSION

At present, the research on the mechanism of lncRNA regulating various osteogenic differentiation pathways is still in the early stage. Its in-depth regulator mechanism, especially the cross-talk of complex signal pathways needs to be further studied. And how to apply these molecular targets to clinical treatment is also a big challenge.

Long noncoding RNA Lnc-DIF inhibits bone formation by sequestering miR-489-3p

Osteoporosis has become a high incident bone disease along with the aging of human population. Long noncoding RNAs (LncRNAs) play an important role in osteoporosis incidence. In this study, we screened out an LncRNA negatively correlated with osteoblast differentiation, which was therefore named Lnc-DIF (differentiation inhibiting factor). Functional analysis proved that Lnc-DIF inhibited bone formation. A special structure containing multiple 53 nucleotide repeats was found in the trailing end of Lnc-DIF. Our study suggested that this repeat sequence could sequester multiple miR-489-3p and inhibit bone formation through miR-489-3p/SMAD2 axis. Moreover, siRNA of Lnc-DIF would rescue bone formation in both aging and ovariectomized osteoporosis mice. This study revealed a kind of LncRNA that could function as a sponge and regulate multiple miRNAs. RNA therapy techniques that target these LncRNAs could manipulate its downstream miRNA-target pathway with significantly higher efficiency and specificity. This provided potential therapeutic insight for RNA-based therapy for osteoporosis.

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Identified LncRNA Lnc-DIF that inhibited bone formation

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Lnc-DIF sequestered multiple miR-489-3p by the repeat sequences on its trailing end

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Lnc-DIF repeat sequence inhibited bone formation via miR-489-3p/SMAD2 axis

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Lnc-DIF siRNA showed strong capability on rescuing osteoporosis

Age-associated changes in microRNAs affect the differentiation potential of human mesenchymal stem cells: Novel role of miR-29b-1-5p expression

Age-associated osteoporosis is widely accepted as involving the disruption of osteogenic stem cell populations and their functioning. Maintenance of the local bone marrow (BM) microenvironment is critical for regulating proliferation and differentiation of the multipotent BM mesenchymal stromal/stem cell (BMSC) population with age. The potential role of microRNAs (miRNAs) in modulating BMSCs and the BM microenvironment has recently gained attention. However, miRNAs expressed in rapidly isolated BMSCs that are naïve to the non-physiologic standard tissue culture conditions and reflect a more accurate in vivo profile have not yet been reported. Here we directly isolated CD271 positive (+) BMSCs within hours from human surgical BM aspirates without culturing and performed microarray analysis to identify the age-associated changes in BMSC miRNA expression. One hundred and two miRNAs showed differential expression with aging. Target prediction and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the up-regulated miRNAs targeting genes in bone development pathways were considerably enriched. Among the differentially up-regulated miRNAs the novel passenger strand miR-29b-1-5p was abundantly expressed as a mature functional miRNA with aging. This suggests a critical arm-switching mechanism regulates the expression of the miR-29b-1-5p/3p pair shifting the normally degraded arm, miR-29b-1-5p, to be the dominantly expressed miRNA of the pair in aging. The normal guide strand miR-29b-1-3p is known to act as a pro-osteogenic miRNA. On the other hand, overexpression of the passenger strand miR-29b-1-5p in culture-expanded CD271+ BMSCs significantly down-regulated the expression of stromal cell-derived factor 1 (CXCL12)/ C-X-C chemokine receptor type 4 (SDF-1(CXCL12)/CXCR4) axis and other osteogenic genes including bone morphogenetic protein-2 (BMP-2) and runt-related transcription factor 2 (RUNX2). In contrast, blocking of miR-29b-1-5p function using an antagomir inhibitor up-regulated expression of BMP-2 and RUNX2 genes. Functional assays confirmed that miR-29b-1-5p negatively regulates BMSC osteogenesis in vitro. These novel findings provide evidence of a pathogenic anti-osteogenic role for miR-29b-1-5p and other miRNAs in age-related defects in osteogenesis and bone regeneration.

Bone Phenotyping Approaches in Human, Mice and Zebrafish - Expert Overview of the EU Cost Action GEMSTONE ("GEnomics of MusculoSkeletal traits TranslatiOnal NEtwork")

A synoptic overview of scientific methods applied in bone and associated research fields across species has yet to be published. Experts from the EU Cost Action GEMSTONE ("GEnomics of MusculoSkeletal Traits translational Network") Working Group 2 present an overview of the routine techniques as well as clinical and research approaches employed to characterize bone phenotypes in humans and selected animal models (mice and zebrafish) of health and disease. The goal is consolidation of knowledge and a map for future research. This expert paper provides a comprehensive overview of state-of-the-art technologies to investigate bone properties in humans and animals - including their strengths and weaknesses. New research methodologies are outlined and future strategies are discussed to combine phenotypic with rapidly developing -omics data in order to advance musculoskeletal research and move towards "personalised medicine".

lnc94638 is a testis-specific long non-coding RNA involved in spermatozoa formation in Zeugodacus cucurbitae (Coquillett)

Long non-coding RNAs (lncRNAs) generally display tissue-specific distributions, and testis-specific lncRNAs form the highest proportion of lncRNAs in many species. Here, we presented a detailed analysis of testis-specific lncRNAs in the melon fly, Zeugodacus cucurbitae, a highly destructive insect pest of cucurbitaceous and other related crops. Most testis-specific lncRNAs were found to be long intergenic non-coding RNAs (lincRNA). The size distribution of these lncRNAs ranged between 600 and 1000 nucleotides. Testis-specific lncRNAs that harboured one isoform number and two exons were the most abundant. Compared to other male tissues, the testis had more highly expressed lncRNAs. The quantitative real-time polymerase chain reaction results of 10 randomly selected testis-specific lncRNAs showed expression patterns consistent with RNA-seq data. Further analysis of the most highly expressed testis-specific lncRNA, lnc94638, was undertaken. Fluorescent in situ hybridization assays localized lnc94638 to the apical region of the testis that contains mature spermatozoa. RNA interference-mediated knockdown of lnc94638 expression reduced spermatozoa numbers and impaired the fertility of Z. cucurbitae male. This study provides a catalogue of testis-specific lncRNAs, shows that the testis-specific lnc94638 is involved in spermatogenesis and has the potential to be used for treating male sterility.

Role of long non-coding RNA H19 in the development of osteoporosis

Background

Osteoporosis is a widespread and serious metabolic bone disease. At present, revealing the molecular mechanisms of osteoporosis and developing effective prevention and treatment methods are of great significance to health worldwide. LncRNA is a non-coding RNA peptide chain with more than 200 nucleotides. Researchers have identified many lncRNAs implicated in the development of diseases and lncRNA H19 is an example.

Results

A large amount of evidence supports the fact that long non-coding RNA (lncRNA) genes, such as H19, have multiple, far-reaching effects on various biological functions. It has been found that lncRNA H19 has a role in the regulation of different types of cells in the body including the osteoblasts, osteocytes, and osteoclasts found in bones. Therefore, it can be postulated that lncRNA H19 affects the incidence and development of osteoporosis.

Conclusion

The prospect of targeting lncRNA H19 in the treatment of osteoporosis is promising because of the effects that lncRNA H19 has on the process of osteogenic differentiation. In this review, we summarize the molecular pathways and mechanisms of lncRNA H19 in the pathogenesis of osteoporosis and summarize the research progress of targeting H19 as a treatment option. Research is emerging that explores more effective treatment possibilities for bone metabolism diseases using molecular targets.

MiR-874-3p inhibits osteogenic differentiation of human periodontal ligament fibroblasts through regulating Wnt/β-catenin pathway

Background/purpose

Previous studies have shown that miR-874 is considered to be an important regulatory factor that participated in osteoclast differentiation. The role of miR-874-3p on osteoclast differentiation of human periodontal ligament fibroblast(hPDLF), however, is still unclear. This study was aimed to delve into the related molecular mechanism of miR-874-3p on hPDLF osteoclast differentiation.

Materials and methods

The qRT-PCR assays were applied to check miR-874-3p and WNT3A expression levels during the osteoclast differentiation of hPDLF. Alkaline phosphatase (ALP) activity assays and alizarin red staining assays were applied to appraise the degree of hPDLF osteoclast differentiation. Bioinformatics method and dual-luciferase reporter assay were employed together to anticipate and certify the interaction between miR-874-3p and WNT3A. Western blot assay was applied to examine the β-catenin and WNT3A expression in transfected hPDLF.

Results

In this study, the results indicated that the expression level of miR-874-3p was gradually down-regulated while WNT3A was concomitantly increased during osteogenic differentiation of hPDLF. Overexpression or knockdown of miR-874-3p would inhibit or promote WNT3A and β-catenin protein expression as well as osteogenic differentiation of hPDLF, respectively. Further research indicated that miR-874-3p directly regulated WNT3A expression via coupling with the 3′-UTR of WNT3A. Finally, upregulation of WNT3A expression levels rescues β-catenin expression levels and osteogenic differentiation of hPDLF inhibited by miR-874-3p was explored.

Conclusion

MiR-874-3p inhibits osteogenic differentiation of hPDLF through regulating Wnt/β-catenin pathway.

Employing bioinformatics analysis to identify hub genes and microRNAs involved in colorectal cancer

The third leading cause of cancer-related deaths in the world, colorectal cancer (CRC) is a global health issue that should be addressed in both diagnostics and therapeutics to improve patient survival rate. Today, microarray data analysis is increasingly being used as a novel and effective method for classification of malignancies and making prognostic assessments. Built upon the concept of microarray data analysis and aimed at the identification of CRC-associated genes, our study has adopted an integrative analysis for the gene expression patterns of four microarray datasets in gene expression omnibus (GEO) and microRNAs (miRNAs) expression profiles. We downloaded four gene expression profiles, i.e., GSE37182, GSE25070, GSE10950, and GSE113513, miRNAs gene expression profiles and differentially expressed genes (DEGs). We used R software, the DAVID database, protein-protein interaction (PPI) networks, the Cytoscape program and receiver operating characteristic (ROC) curve for data analysis. Out of the four gene expression profiles, a total of 43 common DEGs were identified, including 10 hub genes, SLC26A3, CLCA1, GUCA2A, MS4A12, CLCA4, GUCA2B, KRT20, AQP8, MAOA, and ADH1A, and four differentially expressed miRNAs, miR-552, miR-423-5p, miR-502-3p, and miR-490-5p. The highly enriched modes of the signaling pathways among these DEGs were speculated to be involved in various processes including nitrogen metabolism, mineral absorption, pancreatic secretions, and tyrosine metabolism in Kyoto encyclopedia of genes and genomes (KEGG) database. According to our bioinformatics analysis, the DEGs identified in the present study could be considered as significant hallmarks in the molecular mechanisms of CRC development. Our findings may assist scientists with developing novel strategies not only for prediction of CRC, but also for screening and early diagnosis, and treatment of CRC patients.

NEAT1 functions as a key mediator of BMP2 to promote osteogenic differentiation of renal interstitial fibroblasts

Aim: To clarify the mechanism of NEAT1, an aberrantly upregulated lncRNA in Randall's plaques (RP) similar to biomineralization, in mediating osteogenic differentiation of human renal interstitial fibroblasts. Materials & methods: A comprehensive strategy of bioinformatic analysis and experimental verification was performed. Results: BMP2 silence abolished the osteogenic differentiation of human renal interstitial fibroblasts promoted by NEAT1. Mechanically, NEAT1 not only induced the nucleolar translocation of EGR1 binding to BMP2 promotor, but also functioned as a sponge of miR-129-5p in the cytoplasm to promote BMP2 expression. Moreover, there was a positive correlation between NEAT1 and BMP2 expression in RP instead of normal renal papilla. Conclusion: NEAT1 acted as a key mediator of BMP2 to promote human renal interstitial fibroblast osteogenic differentiation, through which NEAT1 might be involved in RP formation.

MicroRNA-365 induces apoptosis and inhibits invasion of human myeloma cells by targeting homeobox A9 (HOXA9)

The aberrant micro-RNA (miR) expression has been reported to play a vital role in proliferation and tumorigenesis and of several human cancers. MicroRNA-365 (miR-365) has been shown to exhibit tumor-suppressive or oncogenic role in several human cancers. Nonetheless, little is known about its growth regulatory role in human multiple myeloma. The present study characterized the regulatory control exercised by miR-365 in multiple myeloma. The results showed significant (P < 0.05) upregulation of miR-365 in myeloma tissues and cell lines. Overexpression of miR-365 significantly (P < 0.05) suppressed the proliferation and inhibition of miR-365 promoted the proliferation of the human myeloma cells. The tumor-suppressive effects of miR-365 were found to be the result of apoptosis in the IM-9 myeloma cells. The miR-365 overexpression also suppressed the invasion of the IM-9 myeloma cells. The homeobox gene, HOXA9 was identified as the molecular regulatory target of miR-365 in human myeloma. The overexpression of miR-365 was shown to cause suppression of HOXA9. The silencing of HOXA9 could also suppress the growth of the IM-9 myeloma cells while as the overexpression of HOXA9 could abolish the tumor-suppressive effects of miR-365. The in vivo study revealed that miR-365 inhibits the growth of the xenografted tumors. Nonetheless, the inhibition of miR-365 promotes the growth of the xenografted tumors. To sum up, the current study suggests the tumor-suppressive effects of miR-365 in human myeloma and highlights the applicability of miR-365 as vital therapeutic target against this fatal malignancy.

Role of m6A in osteoporosis, arthritis and osteosarcoma (Review)

RNA modification is a type of post-transcriptional modification that regulates important cellular pathways, such as the processing and metabolism of RNA. The most abundant form of methylation modification is RNA N6-methyladenine (m6A), which plays various post-transcriptional regulatory roles in cellular biological functions, including cell differentiation, embryonic development and disease occurrence. Bones play a pivotal role in the skeletal system as they support and protect muscles and other organs, facilitate movement and ensure haematopoiesis. The development and remodelling of bones require a delicate and accurate regulation of gene expression by epigenetic mechanisms that involve modifications of histone, DNA and RNA. The present review discusses the enzymes and proteins involved in mRNA m6A methylation modification and summarises current research progress and the mechanisms of mRNA m6A methylation in common orthopaedic diseases, including osteoporosis, arthritis and osteosarcoma.

Long Non-coding RNAs in Traumatic Brain Injury Accelerated Fracture Healing

It is commonly observed that patients with bone fracture concomitant with traumatic brain injury (TBI) had significantly increased fracture healing, but the underlying mechanisms were not fully revealed. Long non-coding RNAs (lncRNAs) are known to play complicated roles in bone homeostasis, but their role in TBI accelerated fracture was rarely reported. The present study was designed to determine the role of lncRNAs in TBI accelerated fracture via transcriptome sequencing and further bioinformatics analyses. Blood samples from three fracture-only patients, three fracture concomitant with TBI patients, and three healthy controls were harvested and were subsequently subjected to transcriptome lncRNA sequencing. Differentially expressed genes were identified, and pathway enrichment was performed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. High-dimensional data visualization by self-organizing map (SOM) machine learning was applied to further interpret the data. An xCell method was then used to predict cellular behavior in all samples based on gene expression profiles, and an lncRNA-cell interaction network was generated. A total of 874 differentially expressed genes were identified, of which about 26% were lncRNAs. Those identified lncRNAs were mainly enriched on TBI-related and damage repair-related pathways. SOM analyses revealed that those differentially expressed lncRNAs could be divided into three major module implications and were mainly enriched on transcriptional regulation and immune-related signal pathways, which promote us to further explore cellular behaviors based on differentially expressed lncRNAs. We have predicted that basophils, CD8+ T effector memory cells, B cells, and naïve B cells were significantly downregulated, while microvascular endothelial cells were predicted to be significantly upregulated in the Fr/TBI group, was the lowest and highest, respectively. ENSG00000278905, ENSG00000240980, ENSG00000255670, and ENSG00000196634 were the most differentially expressed lncRNAs related to all changes of cellular behavior. The present study has revealed for the first time that several critical lncRNAs may participate in TBI accelerated fracture potentially via regulating cellular behaviors of basophils, cytotoxic T cells, B cells, and endothelial cells.

Multi-omics integration strategies for animal epigenetic studies - A review

Genome-wide studies provide considerable insights into the genetic background of animals; however, the inheritance of several heritable factors cannot be elucidated. Epigenetics explains these heritabilities, including those of genes influenced by environmental factors. Knowledge of the mechanisms underlying epigenetics enables understanding the processes of gene regulation through interactions with the environment. Recently developed next-generation sequencing (NGS) technologies help understand the interactional changes in epigenetic mechanisms. There are large sets of NGS data available; however, the integrative data analysis approaches still have limitations with regard to reliably interpreting the epigenetic changes. This review focuses on the epigenetic mechanisms and profiling methods and multi-omics integration methods that can provide comprehensive biological insights in animal genetic studies.

The Roles of LncRNAs in Osteogenesis, Adipogenesis and Osteoporosis

BACKGROUND

Osteoporosis (OP) is the most common bone disease, which is listed by the World Health Organization (WHO) as the third major threat to life and health among the elderly. The etiology of OP is multifactorial, and its potential regulatory mechanism remains unclear. Long non-coding RNAs (LncRNAs) are the non-coding RNAs that are over 200 bases in the chain length. Increasing evidence indicates that LncRNAs are the important regulators of osteogenic and adipogenic differentiation, and the occurrence of OP is greatly related to the dysregulation of the bone marrow mesenchymal stem cells (BMSCs) differentiation lineage. Meanwhile, LncRNAs affect the occurrence and development of OP by regulating OP-related biological processes.

METHODS

In the review, we summarized and analyzed the latest findings of LncRNAs in the pathogenesis, diagnosis and related biological processes of OP. Relevant studies published in the last five years were retrieved and selected from the PubMed database using the keywords of LncRNA and OP.

RESULTS/CONCLUSION

The present study aimed to examine the underlying mechanisms and biological roles of LncRNAs in OP, as well as osteogenic and adipogenic differentiation. Our results contributed to providing new clues for the epigenetic regulation of OP, making LncRNAs the new targets for OP therapy.

Current Status of MicroRNAs that Target the Wnt Signaling Pathway in Regulation of Osteogenesis and Bone Metabolism: A Review

The directional differentiation of bone mesenchymal stem cells (BMSCs) is regulated by a variety of transcription factors and intracellular signaling pathways. In the past, it was thought that the directional differentiation of BMSCs was related to transforming growth factors, such as bone morphogenetic protein (BMP) and MAPK pathway. However, in recent years, some scholars have pointed out that the Wnt signaling pathway, which is a necessary complex network of protein interactions for biological growth and development, takes a significant role in this process and plays a major part in regulating the development of osteoblasts by exerting signal transduction into cells. Also, they have proved the Wnt protein therapeutic truly have positive effects on the viability and osteogenic capacity of bone graft. Recent studies have shown that microRNAs (miRNAs) play an important regulatory role in this process. MiRNAs such as miRNA-218, miRNA-335, miRNA-29, microRNA-30 and other miRNAs exert negative or positive effects on some crucial molecules in the Wnt/β-catenin pathway, which in turn affect bone metabolism and osteopathy. Thus, miRNAs have been suggested as therapeutic targets for some metabolic bone diseases. This article aims to provide an update on the current status of microRNAs that target the Wnt signaling pathway in the regulation of osteogenesis and bone metabolism and includes a discussion of future areas of research, which can be a theoretical basis for bone metabolism-related diseases.

A Novel Long Noncoding RNA, Lnc-OAD, Is Required for Bone Morphogenetic Protein 2- (BMP-2-) Induced Osteoblast Differentiation

Long noncoding RNAs (lncRNAs) play very important roles in cell differentiation. Our recent study has demonstrated that a novel lncRNA named lnc-OAD modulated 3T3-L1 adipocyte differentiation. In the present study, we examined the roles of lnc-OAD in bone morphogenetic protein 2- (BMP-2-) induced osteoblast differentiation. Lnc-OAD expression was increased during BMP-2-induced osteoblast differentiation in C3H10T1/2 mesenchymal stem cells and MC3T3-E1 preosteoblast cells. Knockdown of lnc-OAD expression by specific siRNA remarkably decreased early osteoblast differentiation. In addition, stable knockdown of lnc-OAD by lentivirus vector also significantly inhibited late osteoblast differentiation and matrix mineralization in vitro. Conversely, stably overexpressed lnc-OAD with lentiviral vector accelerated osteoblast differentiation. Mechanistically, knockdown of lnc-OAD reduced significantly the phosphorylation of AKT and the expression of Osterix induced by BMP-2, while overexpression of lnc-OAD enhanced the phosphorylation of AKT and the expression of Osterix. Taken together, our study suggests that lnc-OAD plays an important role in modulating BMP-2-induced osteoblast differentiation via, at least in part, regulating the AKT-Osterix signaling axis.

Long non-coding RNA DANCR modulates osteogenic differentiation by regulating the miR-1301-3p/PROX1 axis

The balance of osteoblasts and marrow adipocytes from bone marrow mesenchymal stem cells (BM-MSCs) maintains bone health. Under aging or other pathological stimuli, BM-MSCs will preferentially differentiate into marrow adipocytes and reduce osteoblasts, leading to osteoporosis. Long non-coding RNA differentiation antagonizing non-protein coding RNA (DANCR) participates in the osteogenic differentiation of human BM-MSCs, but the mechanism by which DANCR regulates the osteogenic differentiation of human BM-MSCs has not been fully explained. We observed that DANCR and prospero homeobox 1 (PROX1) were downregulated during osteogenic differentiation of human BM-MSCs, while miR-1301-3p had an opposite trend. DANCR overexpression decreased the levels of alkaline phosphatase, RUNX2, osteocalcin, Osterix in BM-MSCs after osteogenic induction, but DANCR silencing had the opposite result. Moreover, DANCR sponged miR-1301-3p to regulate PROX1 expression. miR-1301-3p overexpression reversed the suppressive role of DANCR elevation on the osteogenic differentiation of human BM-MSCs. Also, PROX1 elevation abolished the promoting role of miR-1301-3p overexpression on the osteogenic differentiation of human BM-MSCs. In conclusion, DANCR suppressed the osteogenic differentiation of human BM-MSCs through the miR-1301-3p/PROX1 axis, offering a novel mechanism by which DANCR is responsible for the osteogenic differentiation of human BM-MSCs.

Feature extraction approaches for biological sequences: a comparative study of mathematical features

As consequence of the various genomic sequencing projects, an increasing volume of biological sequence data is being produced. Although machine learning algorithms have been successfully applied to a large number of genomic sequence-related problems, the results are largely affected by the type and number of features extracted. This effect has motivated new algorithms and pipeline proposals, mainly involving feature extraction problems, in which extracting significant discriminatory information from a biological set is challenging. Considering this, our work proposes a new study of feature extraction approaches based on mathematical features (numerical mapping with Fourier, entropy and complex networks). As a case study, we analyze long non-coding RNA sequences. Moreover, we separated this work into three studies. First, we assessed our proposal with the most addressed problem in our review, e.g. lncRNA and mRNA; second, we also validate the mathematical features in different classification problems, to predict the class of lncRNA, e.g. circular RNAs sequences; third, we analyze its robustness in scenarios with imbalanced data. The experimental results demonstrated three main contributions: first, an in-depth study of several mathematical features; second, a new feature extraction pipeline; and third, its high performance and robustness for distinct RNA sequence classification. Availability:  https://github.com/Bonidia/FeatureExtraction_BiologicalSequences.

Baf45a Mediated Chromatin Remodeling Promotes Transcriptional Activation for Osteogenesis and Odontogenesis

Chromatin remodeling, specifically the tissue-specific regulation in mineralized tissues, is an understudied avenue of gene regulation. Here we show that Baf45a and Baf45d, two Baf45 homologs belong to ATPase-dependent SWI/SNF chromatin remodeling complex, preferentially expressed in osteoblasts and odontoblasts compared to Baf45b and Baf45c. Recently, biochemical studies revealed that BAF45A associates with Polybromo-associated BAF (PBAF) complex. However, the BAF45D subunit belongs to the polymorphic canonical BRG1-associated factor (cBAF) complex. Protein profiles of osteoblast and odontoblast differentiation uncovered a significant increase of BAF45A and PBAF subunits during early osteoblast and odontoblast maturation. Chromatin immunoprecipitation sequencing (ChIP-seq) during the bone marrow stromal cells (BMSCs) differentiation showed higher histone H3K9 and H3K27 acetylation modifications in the promoter of Baf45a and Baf45d and increased binding of bone and tooth specific transcription factor RUNX2. Overexpression of Baf45a in osteoblasts activates genes essential for the progression of osteoblast maturation and mineralization. Furthermore, shRNA-mediated knockdown of Baf45a in odontoblasts leads to markedly altered genes responsible for the proliferation, apoptosis, DNA repair, and modest decrease in dentinogenic marker gene expression. Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) assay in Baf45a knockout osteoblasts revealed a noticeable reduction in chromatin accessibility of osteoblast and odontoblast specific genes, along with transcription factor Atf4 and Klf4. Craniofacial mesenchyme-specific loss of Baf45a modestly reduced the mineralization of the tooth and mandibular bone. These findings indicated that BAF45A-dependent mineralized tissue-specific chromatin remodeling through PBAF-RUNX2 crosstalk results in transcriptional activation is critical for early differentiation and matrix maturation of mineralized tissues.

Diagnostic potential of peri-implant crevicular fluid microRNA-21-3p and microRNA-150-5p and extracellular vesicles in peri-implant diseases

BACKGROUND

To explore the diagnostic usefulness of extracellular vesicles (EVs), and their subpopulations (micro-vesicles and exosomes), and microRNAs (miRNA-21-3p, miRNA-150-5p, and miRNA-26a-5p) in peri-implant crevicular fluid (PICF) of subjects with healthy, peri-implant mucositis and peri-implantitis implants.

METHODS

A total of 54 patients were enrolled into healthy, peri-implant mucositis, and peri-implantitis groups. PICF samples were collected, EVs subpopulations (MVs and Exo) were isolated and characterized by nanoparticle tracking analysis and transmission electron microscopy. The expression of miRNA-21-3p, miRNA-150-5p and miRNA-26a-5p was quantified by qRT-PCR. Logistic regression models and accuracy performance tests were estimated.

RESULTS

PICF samples show the presence of EVs delimited by a bi-layered membrane, in accordance with the morphology and size (< 200 nm). The concentration of PICF-EVs, micro-vesicles and exosomes was significantly increased in peri-implantitis implants compared to healthy implants (P = 0.023, P = 0.002, P = 0.036, respectively). miRNA-21-3p and miRNA-150-5p expression were significantly downregulated in patients with peri-implantitis in comparison with peri-implant mucositis sites (P = 0.011, P = 0.020, respectively). The reduced expression of miRNA-21-3p and miRNA-150-5p was associated with peri-implantitis diagnosis (OR:0.23, CI 0.08-0.66, P = 0.007 and OR:0.07, CI 0.01-0.78, P = 0.031, respectively). The model which included the miRNA-21-3p and miRNA-150-5p expression had a sensitivity of 93.3%, a specificity of 76.5%, a positive predictive value of 77.8%, and a negative predictive value of 92.9%. The positive and negative likelihood ratios were 3.97 and 0.09, respectively. The area under the receiver operating characteristics curve for the model was 0.84.

CONCLUSIONS

An increase concentration of EVs with a downregulation expression of miRNA-21-3p and miRNA-150-5p could be related with the peri-implantitis development.

Upregulated microRNA-126 induces apoptosis of dental pulp stem cell via mediating PTEN-regulated Akt activation

INTRODUCTION

Human dental pulp stem cells (DPSCs) have potential applications in regenerative medicine. The molecular mechanisms underlying DPSCs viability and apoptosis are not completely understood. Here, we investigated the role of miR-126 in DPSCs viability and apoptosis.

MATERIAL AND METHODS

Senescent DPSCs were compared with early passage DPSCs. real-time PCR and microARRAY were performed to identify the differential expression of miR-126, and western blot was performed to detect the expression of PTEN. MTT assay was utilized to reveal the proliferative rate of both senescent and early passage DPSCs. Flow cytometry was used to examine the apoptotic rate of DPSCs. Dual-luciferase reporter assay was carried out to detect the interaction of miR-126 and PTEN.

RESULTS

Senescent DPSCs showed a high level of apoptosis. Further study showed that miR-126 is upregulated in senescent DPSCs and its overexpression in early passaged DPSCs induced apoptosis. Phosphatase and tensin homolog gene (PTEN) was identified as a target of miR-126. PTEN was downregulated in senescent DPSCs, whereas miR-126 inhibition upregulated PTEN level, and subsequently activated Akt pathway and suppressed the apoptotic phenotype of senescent DPSCs. In addition, PTEN overexpression rescued apoptosis of DPSCs at later stage.

CONCLUSION

Our results demonstrate that the miR-126-PTEN-Akt axis plays a key role in the regulation of DPSCs apoptosis and provide a candidate target to improve the functional and therapeutic potential of DPSCs.

Injectable Hydrogels as Three-Dimensional Network Reservoirs for Osteoporosis Treatment

Despite tremendous progresses made in the field of tissue engineering over the past several decades, it remains a significant challenge for the treatment of osteoporosis (OP) due to the lack of appropriate carriers to improve the bioavailability of therapeutic agents and the unavailability of artificial bone matrix with desired properties for the replacement of damaged bone regions. Encouragingly, the development of injectable hydrogels for the treatment of OP has attracted increasing attention in recent years because they can serve either as a reservoir for various therapeutic species or as a perfect filler for bone injuries with irregular shapes. However, the relationship between the complicated pathological mechanism of OP and the properties of diverse polymeric materials lacks elucidation, which clearly hampers the clinical application of injectable hydrogels for the efficient treatment of OP. To clarify this relationship, this article summarized both localized and systematic treatment of OP using an injectable hydrogel-based strategy. Specifically, the pathogenesis of OP and the limitations of current treatment approaches were first analyzed. We further focused on the use of hydrogels loaded with various therapeutic substances following a classification standard of the encapsulated cargoes for OP treatment with an emphasis on the application and precautions of each category. A concluding remark on existing challenges and future directions of this rapidly developing research area was finally made. Impact statement Effective osteoporosis (OP) treatment remains a significant challenge due substantially to the unavailability of appropriate drug carriers and artificial matrices with desired properties to promote bone repair and replace damaged regions. For this purpose, this review focused on the development of diverse injectable hydrogel systems for the delivery of various therapeutic agents, including drugs, stem cells, and nucleic acids, for effective increase in bone mass and favorable osteogenesis. The summarized important guidelines are believed to promote clinical development and translation of hydrogels for the efficient treatment of OP and OP-related bone damages toward improved life quality of millions of patients.

[The regulatory role of microRNA in osteogenic differentiation of mesenchymal stem cells and its application as a therapeutic target and diagnostic tool in orthopedic diseases]

Objective

To summarize the research progress of the regulatory role of microRNA (miRNA) in osteogenic differentiation of mesenchymal stem cells (MSCs) and its application as a therapeutic target and diagnostic tool in orthopedic diseases.

Methods

The recent literature on the regulation of MSCs osteogenic differentiation by miRNAs was extensively reviewed, and its regulatory mechanism and its application as a therapeutic target and diagnostic tool in orthopedic diseases were reviewed.

Results

miRNAs are small endogenous non-coding RNAs with a length of 20-22 nucleotides, which play an important role in the osteogenic differentiation of MSCs. Osteogenesis begins with the differentiation of MSCs into mature osteoblasts, and each stage of dynamic homeostasis of bone metabolism is associated with the regulation of different miRNAs. miRNAs are regulated from the post-transcriptional level by mRNAs cleavage, degradation, translational repression, or methylation. In addition, current studies suggest that miRNAs can be used as a new diagnostic tool and therapeutic target for orthopedic diseases.

Conclusion

Further study on the regulation mechanism of miRNAs will provide more ideas for finding new therapeutic targets and diagnostic tools for orthopedic disease.

Genome-wide analysis of long non-coding RNAs in adult tissues of the melon fly, Zeugodacus cucurbitae (Coquillett)

Background

Long non-coding RNAs (lncRNAs) are involved in many fundamental biological processes, such as transcription regulation, protein degradation, and cell differentiation. Information on lncRNA in the melon fly, Zeugodacus cucurbitae (Coquillett) is currently limited.

Results

We constructed 24 RNA-seq libraries from eight tissues (midgut, Malpighian tubules, fat body, ovary, and testis) of Z. cucurbitae adults. A total of 3124 lncRNA transcripts were identified. Among those, 1464 were lincRNAs, 1037 were intronic lncRNAs, 301 were anti-sense lncRNAs, and 322 were sense lncRNAs. The majority of lncRNAs contained two exons and one isoform. Differentially expressed lncRNAs were analyzed between tissues, and Malpighian tubules versus testis had the largest number. Some lncRNAs exhibited strong tissue specificity. Specifically expressed lncRNAs were identified and filtered in tissues of female and male Z. cucurbitae based on their expression levels. Four midgut-specific lncRNAs were validated by quantitative real-time polymerase chain reaction (RT-qPCR), and the data were consistent with RNA-seq data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses of targets of midgut-specific lncRNAs indicated an enrichment of the metabolic process.

Conclusions

This was the first systematic identification of lncRNA in the melon fly. Expressions of lncRNAs in multiple adult tissues were evaluated by quantitative transcriptomic analysis. These qualitative and quantitative analyses of lncRNAs, especially the tissue-specific lncRNAs in Z. cucurbitae, provide useful data for further functional studies.

Altered Long Noncoding RNA Expression Profile in Multiple Myeloma Patients with Bisphosphonate-Induced Osteonecrosis of the Jaw

Bisphosphonates (BPs) are inhibitors of osteoclast-mediated bone resorption used for the treatment of multiple myeloma (MM) patients with osteolytic lesions. Bisphosphonate-induced osteonecrosis of the jaw (BONJ) is an infrequent drug-caused adverse event of these agents. Long noncoding RNAs (lncRNAs) are a set of more than 200 base pairs, noncoding RNA molecules, which are critical posttranscriptional regulators of gene expression. Our study was aimed at evaluating 17 lncRNAs, whose targets were previously validated as key elements in MM, bone metabolism, and angiogenesis in MM subjects without BONJ (MM group), in MM subjects with BONJ (BONJ group), and a group of healthy controls (CTRL group). Our results demonstrated a different lncRNA profile in BONJ patients compared to MM patients and controls. Two lncRNAs (DANCR and MALAT1) were both downregulated compared to controls and MM, twelve (HOTAIR, MEG3, TP73-AS1, HOTTIP, HIF1A-AS2, MANTIS, CTD-2201E18, CTD1-2003C8, R-471B22, RP1-43E13, RP11-553L6.5, and RP1-286D6) were overexpressed in MM with BONJ, and one (H19) was upregulated compared with only MM. Two lncRNAs (JHDMD1 and MTMR9LP) had higher expression, but these differences were not statistically significant. The examined lncRNAs target several genes and metabolic pathways. An altered lncRNA signature could contribute to the onset of BONJ or have a protective action. Targeting these lncRNAs could offer a possibility for the prevention or therapy of BONJ.

The Emerging Roles of Long Noncoding RNAs in Bone Homeostasis and Their Potential Application in Bone-Related Diseases

Increasing evidence has announced the emerging roles of long noncoding RNAs (lncRNAs) in modulating bone homeostasis due to their potential regulating effects on bone-related cells' proliferation, migration, differentiation and apoptosis. Thus, lncRNAs have been considered as a promising gene tool to facilitate the bone regeneration process and then to predict and cure bone-related diseases such as osteosarcoma, osteoporosis, and osteoarthritis. In this review, we first enumerated several kinds of dysregulated lncRNAs and concisely summarized their regulating role in bone formation as well as resorption process. The related mechanisms were also discussed, respectively. Then, the positive or negative behavior of these lncRNAs in bone-related diseases was elucidated. This review provides an in-depth sight about the lncRNA's clinical values and limitations, which is conducive to explore new gene targets and further establish new therapeutic strategies for bone-related disease.

Overview of noncoding RNAs involved in the osteogenic differentiation of periodontal ligament stem cells

Periodontal diseases are infectious diseases that are characterized by progressive damage to dental support tissue. The major goal of periodontal therapy is to regenerate the periodontium destroyed by periodontal diseases. Human periodontal ligament (PDL) tissue possesses periodontal regenerative properties, and periodontal ligament stem cells (PDLSCs) with the capacity for osteogenic differentiation show strong potential in clinical application for periodontium repair and regeneration. Noncoding RNAs (ncRNAs), which include a substantial portion of poly-A tail mature RNAs, are considered “transcriptional noise.” Recent studies show that ncRNAs play a major role in PDLSC differentiation; therefore, exploring how ncRNAs participate in the osteogenic differentiation of PDLSCs may help to elucidate the underlying mechanism of the osteogenic differentiation of PDLSCs and further shed light on the potential of stem cell transplantation for periodontium regeneration. In this review paper, we discuss the history of PDLSC research and highlight the regulatory mechanism of ncRNAs in the osteogenic differentiation of PDLSCs.

LncRNA expression profiles and the negative regulation of lncRNA-NOMMUT037835.2 in osteoclastogenesis

Bone is a rigid and dynamic organ that continuously undergoes remodeling and repair. The balance between osteoblastic bone formation and osteoclastic bone resorption is essential for normal bone homeostasis. Osteoclasts are giant multinucleated cells derived from the monocyte/macrophage hematopoietic lineage and are regulated by various cytokines. Long non-coding (lnc) RNAs are known to regulate many biological processes in the skeletal system in both normal and diseased states; however, the lncRNA-mediated regulation of osteoclastogenesis has not been extensively studied. Hence, in the present study, we performed microarray analysis of lncRNAs expressed during different stages of osteoclast differentiation and fusion. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses revealed the biological functions of target genes of lncRNAs that were specifically up- or downregulated at the different stages. Microarray and bioinformatic prediction results were used to generate co-expression networks of lncRNAs-mRNAs and lncRNAs-transcription factors. Based on the analysis, we identified one lncRNA, NONMMUT037835.2, which plays an important role during osteoclastogenesis. Upregulation of lncRNA-NONMMUT037835.2 inhibited osteoclastic differentiation, whereas downregulation of lncRNA-NONMMUT037835.2 promoted osteoclast formation and fusion. Our study also indicated that lncRNA-NOMMUT037835.2 might regulated osteoclastogenesis through negatively regulating RANK expression and inhibiting NF-κB/MAPK signaling pathway. Our results lead to a better understanding of the molecular mechanisms and provided a theoretical basis for developing therapeutic agents for diseases related to dysregulation of bone homeostasis.

Osteoarthritis from evolutionary and mechanistic perspectives

Developmental osteogenesis and the pathologies associated with tissues that normally are mineralized are active areas of research. All of the basic cell types of skeletal tissue evolved in early aquatic vertebrates. Their characteristics, transcription factors, and signaling pathways have been conserved, even as they adapted to the challenge imposed by gravity in the transition to terrestrial existence. The response to excess mechanical stress (among other factors) can be expressed in the pathologic phenotype described as osteoarthritis (OA). OA is mediated by epigenetic modification of the same conserved developmental gene networks, rather than by gene mutations or new chemical signaling pathways. Thus, these responses have their evolutionary roots in morphogenesis. Epigenetic channeling and heterochrony, orchestrated primarily by microRNAs, maintain the sequence of these responses, while allowing variation in their timing that depends at least partly on the life history of the individual.

miR-224-5p protects dental pulp stem cells from apoptosis by targeting Rac1

Dental pulp stem cells (DPSCs) are reported to be enriched in stem/progenitor cells, however to the best of our knowledge they have yet to be well documented and characterized. In the present study, in order to characterize DPSCs and the effect of microRNAs (miRs/miRNAs) on DPSC properties, a miRNA array was performed between dental periodontal ligament cells (DPLCs) and DPSCs. The results revealed that miR-224-5p (miR-224) was highly expressed in the DPSCs compared with that in the DPLCs. The transfection of DPSCs with an miR-224 inhibitor impaired cell viability. In addition, miR-224 inhibition significantly promoted cell apoptosis in DPSCscompared with the NC group. In silico analysis and a dual-luciferase reporter assay demonstrated that miR-224 targets the 3′-untranslated region of the Rac family small GTPase 1 (Rac1) gene. miR-224 downregulation resulted in the increased expression of Rac1 in DPSCs compared with DPLCs. Furthermore, miR-224 inhibition caused augmented mitogen-activated protein kinase 8, caspase-3, caspase-9 and Fas ligand expression in DPSC, which may be recovered by Rac1 silencing with transfection with short hairpin RNA-Rac1. Furthermore, Annexin V-fluorescein isothiocyanate/propidium iodide flow cytometry indicated that the silencing of Rac1 restored the pro-apoptotic DPSC cell number with miR-224 transfection. Therefore, the results of the present study suggested miR-224 in DPSC serves an important function in protecting cells against apoptosis by downregulating Rac1 expression, and also identified miR-224 as a novel miRNA in regulating the features of DPSC.

LncRNA CASC11 is upregulated in postmenopausal osteoporosis and is correlated with TNF-α

Purpose

In this study, we aimed to investigate the role of lncRNA cancer susceptibility 11 (CASC11) and tumor necrosis factor (TNF-α) in postmenopausal osteoporosis (POP).

Methods and materials

POP patients and healthy controls were included in this study and levels of CASC11 and TNF-α in plasma of those participants were measured by qPCR and Western blot, respectively. ROC curve was used for diagnostic analysis. Patients were followed up for 2 years and the correlations between the levels of CASC11 and TNF-α and disease conditions were analyzed.

Results

We found that CASC11 and TNF-α were both upregulated in plasma of POP patients than in healthy controls. Plasma levels of CASC11 and TNF-α were positively correlated in both POP patients and in healthy controls. Upregulation of CASC11 and TNF-α distinguished POP patients from healthy controls. Treatment and follow-up study showed that high CASC11 levels were significantly correlated with prolonged treatment course and high recurrence rate. Plasma levels of CASC11 and TNF-α decreased after treatment. CASC11 overexpression led to upregulated TNF-α in osteoclasts.

Conclusion

CASC11 is upregulated in POP and is correlated with TNF-α.

Long Non-coding RNA HOTTIP Promotes CCL3 Expression and Induces Cartilage Degradation by Sponging miR-455-3p

Long non-coding RNAs (lncRNAs) play pivotal roles in diseases such as osteoarthritis (OA). However, knowledge of the biological roles of lncRNAs is limited in OA. We aimed to explore the biological function and molecular mechanism of HOTTIP in chondrogenesis and cartilage degradation. We used the human mesenchymal stem cell (hMSC) model of chondrogenesis, in parallel with, tissue biopsies from normal and OA cartilage to detect HOTTIP, CCL3, and miR-455-3p expression in vitro. Biological interactions between HOTTIP and miR-455-3p were determined by RNA silencing and overexpression in vitro. We evaluated the effect of HOTTIP on chondrogenesis and degeneration, and its regulation of miR-455-3p via competing endogenous RNA (ceRNA). Our in vitro ceRNA findings were further confirmed within animal models in vivo. Mechanisms of ceRNAs were determined by bioinformatic analysis, a luciferase reporter system, RNA pull-down, and RNA immunoprecipitation (RIP) assays. We found reduced miR-455-3p expression and significantly upregulated lncRNA HOTTIP and CCL3 expression in OA cartilage tissues and chondrocytes. The expression of HOTTIP and CCL3 was increased in chondrocytes treated with interleukin-1β (IL-1β) in vitro. Knockdown of HOTTIP promoted cartilage-specific gene expression and suppressed CCL3. Conversely, HOTTIP overexpression reduced cartilage-specific genes and increased CCL3. Notably, HOTTIP negatively regulated miR-455-3p and increased CCL3 levels in human primary chondrocytes. Mechanistic investigations indicated that HOTTIP functioned as ceRNA for miR-455-3p enhanced CCL3 expression. Taken together, the ceRNA regulatory network of HOTTIP/miR-455-3p/CCL3 plays a critical role in OA pathogenesis and suggests HOTTIP is a potential target in OA therapy.

Enhancement of MicroRNA-200c on Osteogenic Differentiation and Bone Regeneration by Targeting Sox2-Mediated Wnt Signaling and Klf4

MicroRNA (miR)-200c functions in antitumorigenesis and mediates inflammation and osteogenic differentiation. In this study, we discovered that miR-200c was upregulated in human bone marrow mesenchymal stromal cells (hBMSCs) during osteogenic differentiation. Inhibition of endogenous miR-200c resulted in downregulated osteogenic differentiation of hBMSCs and reduced bone volume in the maxilla and mandible of a transgenic mouse model. Overexpression of miR-200c by transfection of naked plasmid DNA (pDNA) encoding miR-200c significantly promoted the biomarkers of osteogenic differentiation in hBMSCs, including alkaline phosphatase, Runt-related transcription factor 2, osteocalcin, and mineral deposition. The pDNA encoding miR-200c also significantly enhanced bone formation and regeneration in calvarial defects of rat models. In addition, miR-200c overexpression was shown to downregulate SRY (sex determining region Y)-box 2 (Sox2) and Kruppel-like factor 4 by directly targeting 3'-untranslated regions and upregulate the activity of Wnt signaling inhibited by Sox2. These results strongly indicated that miR-200c may serve as a unique osteoinductive agent applied for bone healing and regeneration.

MICROmanagement of Runx2 Function in Skeletal Cells

Purpose of Review-

Precise and temporal expression of Runx2 and its regulatory transcriptional network is a key determinant for the intricate cellular and developmental processes in adult bone tissue formation. This review analyzes how microRNA functions to regulate this network, and how dysregulation results in bone disorders.

Recent Findings-

Similar to other biologic processes, microRNA (miRNA/miR) regulation is undeniably indispensable to bone synthesis and maintenance. There exists a miRNA-RUNX2 network where RUNX2 regulates the transcription of miRs, or is post transcriptionally regulated by a class of miRs, forming a variety of miR-RUNX2 regulatory pathways which regulate osteogenesis.

Summary-

The current review provides insights to understand transcriptional-post transcriptional regulatory network governed by Runx2 and osteogenic miRs, and is based largely from in vitro and in vivo studies. When taken together, this article discusses a new regulatory layer of bone tissue specific gene expression by RUNX2 influenced via miRNA.

Comparison of long non‑coding RNA expression profiles in human dental follicle cells and human periodontal ligament cells

The dental follicle develops into the periodontal ligament, cementum and alveolar bone. Human dental follicle cells (hDFCs) are the precursor cells of periodontal development. Long non-coding RNAs (lncRNAs) have been revealed to be crucial factors that regulate a variety of biological processes; however, whether lncRNAs serve a role in human periodontal development remains unknown. Therefore, the present study used microarrays to detect the differentially expressed lncRNAs and mRNAs between hDFCs and human periodontal ligament cells (hPDLCs). A total of 845 lncRNAs and 1,012 mRNAs were identified to be differentially expressed in hDFCs and hPDLCs (fold change >2.0 or <-2.0; P<0.05). Microarray data were validated by reverse transcription-quantitative polymerase chain reaction. Bioinformatics analyses, including gene ontology, pathway analysis and coding-non-coding gene co-expression network analysis, were performed to determine the functions of the differentially expressed lncRNAs and mRNAs. Bioinformatics analysis identified that a number of pathways may be associated with periodontal development, including the p53 and calcium signaling pathways. This analysis also revealed a number of lncRNAs, including NR_033932, T152410, ENST00000512129, ENST00000540293, uc021sxs.1 and ENST00000609146, which may serve important roles in the biological process of hDFCs. In addition, the lncRNA termed maternally expressed 3 (MEG3) was identified to be differentially expressed in hDFCs by reverse transcription-quantitative polymerase chain reaction. The knockdown of MEG3 was associated with a reduction of pluripotency makers in hDFCs. In conclusion, for the first time, to the best of our knowledge, the current study determined the different expression profiles of lncRNAs and mRNAs between hDFCs and hPDLCs. The observations made may provide a solid foundation for further research into the molecular mechanisms of lncRNAs in human periodontal development.

Extracellular vesicles from human umbilical cord blood ameliorate bone loss in senile osteoporotic mice

OBJECTIVE

Senile osteoporosis is one of the most common age-related diseases worldwide. Accumulating evidences have indicated that young blood can reverse age-related impairments. Extracellular vesicles (EVs) exert therapeutic effects in a variety of diseases by delivering bioactive molecules such as microRNAs (miRNAs). The aim of the study is to evaluate the therapeutic potential of EVs from human umbilical cord blood plasma (UCB-EVs) on senile osteoporosis and to preliminarily clarify the underlying mechanism.

METHODS

UCB-EVs were injected into the tail vein of aged (16 months old) male C57BL/6 mice. Microcomputed tomography was performed to evaluate bone mass and microarchitecture of mice. The osteogenic and osteoclastic activities were determined by quantitative real-time PCR (qRT-PCR), histological examination and western blot analysis. In vitro, qRT-PCR assay was undertaken to explore the enrichment levels of a number of miRNAs that have positive effects in reducing bone loss. The efficacy of UCB-EVs on osteoblastic differentiation of bone marrow mesenchymal stromal cells (BMSCs) and osteoclastogenesis of RAW264.7 cells were assessed by cytochemical staining. Gene and protein expression changes were detected by qRT-PCR and western blotting respectively. Meanwhile, the roles of the selected miRNA in the regulatory effects of UCB-EVs on BMSCs and RAW264.7 cells were evaluated by using specific miRNA inhibitor.

RESULTS

The intravenous injection of UCB-EVs for two months attenuated bone loss in old mice, as defined by increased trabecular and cortical bone mass, enhanced osteoblast formation and reduced osteoclast formation compared to the control mice. In vitro, UCB-EVs could promote the osteogenic differentiation of BMSCs and inhibit the osteoclastogenesis of RAW264.7 cells. Moreover, it was confirmed that miR-3960 was highly enriched in UCB-EVs and miR-3960 inhibitor reversed the stimulatory effect of UCB-EVs on osteoblastic differentiation of BMSCs.

CONCLUSION

Our findings indicate that UCB-EVs ameliorate age-related bone loss by stimulating bone formation and inhibiting bone resorption, and miR-3960 mediated the osteogenic effect of UCB-EVs on BMSCs. Thus, UCB-EVs may represent a promising agent for prevention of senile osteoporosis.

MicroRNA-224 enhances the osteoblastic differentiation of hMSCs via Rac1

Osteogenesis is the differentiation of mesenchymal stem cells (MSCs) into osteoblasts. MicroRNAs (miRNAs) are short noncoding RNAs that target specific genes to mediate translational activities. In this study, we investigated how miR-224 regulates the osteoblastic differentiation of human MSCs (hMSCs) as well as the underlying mechanism. The results revealed the upregulation of miR-224 during hMSC differentiation. In vitro experiments showed that the downregulation of miR-224 suppressed the differentiation of hMSCs into osteoblasts. However, upregulation of miR-224 was concomitant with increased expression of relevant genes and augmented activity of alkaline phosphatase. Furthermore, the results indicated that Rac1 acted as the bona fide target of miR-224 and that Rac1 depletion promoted osteogenic differentiation in miR-224-silenced hMSCs. In addition, we found that both JAK/STAT3 and Wnt/β-catenin pathways were repressed by Rac1 depletion using quantitative reverse transcription polymerase chain reaction (qRT-PCR), western blotting, and immunofluorescence. Our data indicate a novel molecular mechanism in relation to hMSCs differentiation into osteoblasts, which may facilitate bone anabolism via miR-224. SIGNIFICANCE OF THE STUDY: In this study, we mainly explored the effects of miR-224 on hMSCs differentiation into osteoblasts. We find that induced miR-224 expression in hMSCs is considered closely associated with specific osteogenesis-related genes, alkaline phosphatase activity, and matrix mineralization, indicating that miR-224 may serve as a promising biomarker for osteogenic differentiation. Our data indicate a novel molecular mechanism in relation to hMSCs differentiation into osteoblasts, which may facilitate bone anabolism via miR-224.

Deletion of Dicer blocks osteogenic differentiation via the inhibition of Wnt signalling

Micro (mi)RNAs are small, non‑coding RNAs and have been reported to have important roles in the epigenetic control of bone development. miRNAs markedly regulate osteoblast differentiation through stages of maturation as well as the activities of osteogenic signaling pathways. Dicer is an important endoribonuclease that regulates miRNA maturation. Previous studies have demonstrated that Dicer deletion decreases fetal survival and bone formation, while excision in differentiated osteoblasts increases bone mass. However, the underlying molecular mechanisms remain unclear. In the present study, whether the deletion of Dicer affects Wnt signaling, which exhibits important roles during osteogenesis, was investigated. Bone marrow stromal cells (BMSCs) were used as an osteogenic model. Dynamic changes of seven Wnt genes and downstream T‑cell factor 1 (Tcf‑1)/lymphoid enhancing binding factor were observed during the osteogenic differentiation of BMSCs, which revealed different roles at early and late differentiation stages. Following the stable knockdown of Dicer in BMSCs using lentiviral short hairpin RNA, osteogenic differentiation was blocked, and the levels of important osteogenic differentiation markers (runt related transcription factor 2 and alkaline phosphatase) were markedly inhibited. Furthermore, stage specific regulation of Wnt genes in Dicer‑deficient BMSCs was investigated in the present study. At the early differentiation stage (days 5‑7), knockdown of Dicer led to the inhibition of Wnt1, Wnt7 and Wnt10b, as well as the upregulation of Wnt4, Wnt10a and Tcf‑1. At the late stage of differentiation (days 14‑21), knockdown of Dicer significantly suppressed the expression levels of all of the included Wnt genes as well as Tcf‑1, with the exception of Wnt10a. The upregulation of Wnt10a following the deletion of Dicer was maintained throughout all stages of differentiation. In addition, differential regulation of Wnt genes and Tcf‑1 were revealed to be associated with dynamic changes in their expression levels during osteogenic differentiation. Furthermore, the four putative Wnt10a‑targeting miRNAs were investigated in the present study, and the results demonstrated that they were upregulated during osteogenic differentiation, which suggested that inhibition of Wnt10a may be an important factor associated with osteogenic differentiation. In conclusion, the present study investigated the mechanism underlying the regulation of Wnt signalling by Dicer during osteogenesis, and identified potential miRNAs targeting the components of Wnt signalling influenced by Dicer. Collectively, the present study identified the association between Dicer and Wnt signalling during bone development.

Micrornas at the Interface between Osteogenesis and Angiogenesis as Targets for Bone Regeneration

Bone formation and regeneration is a multistep complex process crucially determined by the formation of blood vessels in the growth plate region. This is preceded by the expression of growth factors, notably the vascular endothelial growth factor (VEGF), secreted by osteogenic cells, as well as the corresponding response of endothelial cells, although the exact mechanisms remain to be clarified. Thereby, coordinated coupling between osteogenesis and angiogenesis is initiated and sustained. The precise interplay of these two fundamental processes is crucial during times of rapid bone growth or fracture repair in adults. Deviations in this balance might lead to pathologic conditions such as osteoarthritis and ectopic bone formation. Besides VEGF, the recently discovered important regulatory and modifying functions of microRNAs also support this key mechanism. These comprise two principal categories of microRNAs that were identified with specific functions in bone formation (osteomiRs) and/or angiogenesis (angiomiRs). However, as hypoxia is a major driving force behind bone angiogenesis, a third group involved in this process is represented by hypoxia-inducible microRNAs (hypoxamiRs). This review was focused on the identification of microRNAs that were found to have an active role in osteogenesis as well as angiogenesis to date that were termed "CouplingmiRs (CPLGmiRs)". Outlined representatives therefore represent microRNAs that already have been associated with an active role in osteogenic-angiogenic coupling or are presumed to have its potential. Elucidation of the molecular mechanisms governing bone angiogenesis are of great relevance for improving therapeutic options in bone regeneration, tissue-engineering, and the treatment of bone-related diseases.

Circulating miR-103a-3p and miR-660-5p are associated with bone parameters in patients with controlled acromegaly

Background Biochemical control of GH/IGF-I excess in acromegaly (ACRO) is associated with persistent impairment of trabecular microstructure leading to increased risk of vertebral fractures. Circulating miRNAs modulate the activity of osteoblasts and osteoclasts, and may be potential biomarkers of osteoporosis. Aims Identify differentially expressed miRNAs in the serum of patients with controlled ACRO vs controls and correlate miRNA levels with both biochemical and structural bone parameters. Patients and methods Twenty-seven patients with controlled ACRO (11 males, 16 females; mean age, 48 ± 5 years; BMI, 28 ± 4 kg/m2) and 27 age-, gender- and BMI-matched controls were recruited. Areal BMD at lumbar spine and femur, and trabecular bone score were assessed; volumetric BMD was measured by quantitative computed tomography QCT-Pro (Mindways). Twenty miRNAs, chosen by their putative role in bone, were quantified in serum using real-time qPCR. Results In ACRO patients, miR-103a-3p and miR-191-5p were found overexpressed, whereas miR-660-5p was underexpressed (P < 0.001). miR-103a-3p levels were negatively associated with both trabecular vBMD at trochanter and serum osteoprotegerin concentrations (P < 0.05) and positively with vitamin D concentrations (P < 0.01) and total cross-sectional area of the femoral neck (P < 0.05). miR-660-5p levels were correlated with both trabecular vBMD at trochanter and OPG concentrations (P < 0.05), but were negatively associated with vitamin D levels (P < 0.05). A negative correlation between miR-103-a-3p and miR-660-5p was found in both groups (P < 0.001). Conclusions Circulating miR-103a-3p and miR-660-5p are differentially expressed in controlled ACRO patients and associated with bone structural parameters. miRNAs may be one of the mechanisms involved in the pathogenesis of bone disease and could be used as biomarkers in ACRO patients.

Methylene blue regulates inflammatory response in osteoarthritis by noncoding long chain RNA CILinc02

Long noncoding RNAs serve as novel regulatory molecules involved in various biological processes, but their role in osteoarthritis (OA) remains unknown. Therefore, we aimed to reveal the inflammatory mechanisms regulated by CILinc02 and methylene blue in human osteoarthritic cartilage and to explore the potential functions of CILinc02 and methylene blue in OA. The expression level of CILinc02 in OA cartilage tissues and primary cells was obtained using quantitative reverse transcriptase polymerase chain reaction (qRT-PCR). The cytokines, such as interleukin 1 (IL-1), IL-6, IL-17, tissue inhibitor of metalloproteinase-1 (TIMP-1) and matrix metalloproteinase (MMPs), involved in the degradation of chondrocyte in CILinc02 knockdown OA primary cells, which were treated with methylene blue that were determined by enzyme-linked immunosorbent assay, qRT-PCR and Western blot analysis. The results showed that CILinc02 was overexpressed in osteoarthritic cartilage tissues and in OA primary cells, but methylene blue can inhibit the expression of CILinc02. In addition, overexpression of CILinc02 induced the inflammation and apoptosis in primary OA cells, however, the effect of methylene blue was reversed compared to CILinc02. Meanwhile, methylene blue can regulate the expression of TIMP-1, MMP-1, and MMP-13 proteins, thereby suppressing the degradation of chondrocyte in OA. This evidence indicates that methylene blue can act as an inflammatory inhibitor by targeting CILinc02 to regulate the inflammatory response.

Regulation of osteogenesis by long noncoding RNAs: An epigenetic mechanism contributing to bone formation

Long noncoding RNAs (lncRNAs) have recently emerged as novel regulators of lineage commitment, differentiation, development, viability, and disease progression. Few studies have examined their role in osteogenesis; however, given their critical and wide-ranging roles in other tissues, lncRNAs are most likely vital regulators of osteogenesis. In this study, we extensively characterized lncRNA expression in mesenchymal cells during commitment and differentiation to the osteoblast lineage using a whole transcriptome sequencing approach (RNA-Seq). Using mouse primary mesenchymal stromal cells (mMSC), we identified 1438 annotated lncRNAs expressed during MSC differentiation, 462 of which are differentially expressed. We performed guilt-by-association analysis using lncRNA and mRNA expression profiles to identify lncRNAs influencing MSC commitment and differentiation. These findings open novel dimensions for exploring lncRNAs in regulating normal bone formation and in skeletal disorders.

microRNA Let-7b: A Novel treatment for endometriosis

Endometriosis is an oestrogen-dependent, chronic inflammatory disease that affects 10% of reproductive-aged women. Current treatment options depend on female sex steroid hormone modulation; however, all have side effects and are not useful in women who want to conceive. microRNAs treatments have provided promising results for some chronic diseases and cancers. We have previously shown the microRNA Let-7b is repressed in endometriosis and that loss of Let-7 contributes to the pathophysiology of the disease. Here, we propose using microRNA Let-7b for the treatment of endometriosis in a murine model. Endometriosis was treated using microRNA Let-7b or a scrambled control microRNA. Let-7b treatment resulted in reduced endometriosis lesion size. Decreased gene expression was noted in several genes known to promote endometriosis growth including ER-α, ER-ß, Cyp19a, KRAS 4A, KRAS 4B and IL-6. These results indicate that microRNA Let-7b has a pleiotropic role in endometriosis pathophysiology affecting oestrogen signalling, inflammation and growth factor receptors. Local treatment of endometriosis with Let-7b is a promising therapy for endometriosis that simultaneously affects multiple pathways driving endometriosis without systemic hormonal side effects.