Proteomic approaches to study osteoclast biology

LncRNAs modulating tooth development and alveolar resorption: Systematic review

Tooth development is an intricate process that encompasses cellular activities, molecular signaling pathways, and gene expression patterns. Disruptions in any of the processes can lead to structural anomalies, impairments in function, and increased vulnerability to oral disorders. Alveolar resorption, which refers to the pathological loss of alveolar bone around teeth, poses a substantial clinical problem in periodontal disorders such as periodontitis. Long non-coding RNAs (LncRNAs) have been implicated in the regulation of these physiological and pathological processes, and they exert their impact on gene expression through both transcriptional and post-transcriptional mechanisms. However, they also interact with certain microRNAs (mi-RNAs), thereby modulating the expression of downstream genes that are involved in tooth development. An exemplar is lncRNA ZFAS1, which has been demonstrated to regulate gene expression and impact these physiological and pathological processes. As a result, lncRNAs contribute to these processes by interacting with chromatin regulators, RNA enhancers, mi-RNAs, and their modulating signaling pathways involved in tooth development and alveolar resorption. Taken together, this review explores and gives a systematic account of the recent research findings that enhance our understanding of the molecular mechanisms that drive these processes and their potential consequences for the remodeling of teeth and bones in the oral cavity.

Bone Trans-omics: Integrating Omics to Unveil Mechanistic Molecular Networks Regulating Bone Biology and Disease

PURPOSE OF REVIEW

Recent advancements in "omics" technologies and bioinformatics have afforded researchers new tools to study bone biology in an unbiased and holistic way. The purpose of this review is to highlight recent studies integrating multi-omics data gathered from multiple molecular layers (i.e.; trans-omics) to reveal new molecular mechanisms that regulate bone biology and underpin skeletal diseases.

RECENT FINDINGS

Bone biologists have traditionally relied on single-omics technologies (genomics, transcriptomics, proteomics, and metabolomics) to profile measureable differences (both qualitative and quantitative) of individual molecular layers for biological discovery and to investigate mechanisms of disease. Recently, literature has grown on the implementation of integrative multi-omics to study bone biology, which combines computational and informatics support to connect multiple layers of data derived from individual "omic" platforms. This emerging discipline termed "trans-omics" has enabled bone biologists to identify and construct detailed molecular networks, unveiling new pathways and unexpected interactions that have advanced our mechanistic understanding of bone biology and disease. While the era of trans-omics is poised to revolutionize our capacity to answer more complex and diverse questions pertinent to bone pathobiology, it also brings new challenges that are inherent when trying to connect "Big Data" sets. A concerted effort between bone biologists and interdisciplinary scientists will undoubtedly be needed to extract physiologically and clinically meaningful data from bone trans-omics in order to advance its implementation in the field.

Perspective of the GEMSTONE Consortium on Current and Future Approaches to Functional Validation for Skeletal Genetic Disease Using Cellular, Molecular and Animal-Modeling Techniques

The availability of large human datasets for genome-wide association studies (GWAS) and the advancement of sequencing technologies have boosted the identification of genetic variants in complex and rare diseases in the skeletal field. Yet, interpreting results from human association studies remains a challenge. To bridge the gap between genetic association and causality, a systematic functional investigation is necessary. Multiple unknowns exist for putative causal genes, including cellular localization of the molecular function. Intermediate traits ("endophenotypes"), e.g. molecular quantitative trait loci (molQTLs), are needed to identify mechanisms of underlying associations. Furthermore, index variants often reside in non-coding regions of the genome, therefore challenging for interpretation. Knowledge of non-coding variance (e.g. ncRNAs), repetitive sequences, and regulatory interactions between enhancers and their target genes is central for understanding causal genes in skeletal conditions. Animal models with deep skeletal phenotyping and cell culture models have already facilitated fine mapping of some association signals, elucidated gene mechanisms, and revealed disease-relevant biology. However, to accelerate research towards bridging the current gap between association and causality in skeletal diseases, alternative in vivo platforms need to be used and developed in parallel with the current -omics and traditional in vivo resources. Therefore, we argue that as a field we need to establish resource-sharing standards to collectively address complex research questions. These standards will promote data integration from various -omics technologies and functional dissection of human complex traits. In this mission statement, we review the current available resources and as a group propose a consensus to facilitate resource sharing using existing and future resources. Such coordination efforts will maximize the acquisition of knowledge from different approaches and thus reduce redundancy and duplication of resources. These measures will help to understand the pathogenesis of osteoporosis and other skeletal diseases towards defining new and more efficient therapeutic targets.

External cervical resorption-a review of pathogenesis and potential predisposing factors

External cervical resorption (ECR) refers to a pathological state in which resorption tissues penetrate into the dentin at the cervical aspect of the root. Despite being latent in its initial phase, ECR could cause severe damage to mineralized dental tissue and even involve the pulp if not given timely diagnosis and treatment. Nevertheless, the etiology of ECR is still poorly understood, which adds to the difficulty in early diagnosis. ECR has received growing attention in recent years due to the increasing number of clinical cases. Several potential predisposing factors have been recognized in cross-sectional studies as well as case reports. In the meantime, studies on histopathology and pathogenesis have shed light on possible mechanisms of ECR. This review aims to summarize the latest findings in the pathogenesis and potential predisposing factors of ECR, so as to provide pragmatic reference for clinical practice.

Morphological and genomic shifts in mole-rat 'queens' increase fecundity but reduce skeletal integrity

In some mammals and many social insects, highly cooperative societies are characterized by reproductive division of labor, in which breeders and nonbreeders become behaviorally and morphologically distinct. While differences in behavior and growth between breeders and nonbreeders have been extensively described, little is known of their molecular underpinnings. Here, we investigate the consequences of breeding for skeletal morphology and gene regulation in highly cooperative Damaraland mole-rats. By experimentally assigning breeding 'queen' status versus nonbreeder status to age-matched littermates, we confirm that queens experience vertebral growth that likely confers advantages to fecundity. However, they also upregulate bone resorption pathways and show reductions in femoral mass, which predicts increased vulnerability to fracture. Together, our results show that, as in eusocial insects, reproductive division of labor in mole-rats leads to gene regulatory rewiring and extensive morphological plasticity. However, in mole-rats, concentrated reproduction is also accompanied by costs to bone strength.

A Review of External Cervical Resorption

External cervical resorption (ECR) is a relatively uncommon yet aggressive form of dental hard tissue destruction. It is initiated at the cervical aspect of the root surface and extends apicocoronally and circumferentially inside the dentin. Despite the large number of case reports and clinical studies that have investigated ECR, its etiology remains unclear. Recent advancements in clinical assessment measures, such as the use of cone-beam computed tomographic imaging, have provided additional insights into the nature of this lesion. This has facilitated the continued development and improvement of treatment methods for this condition. In this article, we provide an overview of the latest research pertaining to the etiology, histopathology, predisposing factors, diagnosis, classification, and treatment of ECR. Furthermore, we provide a summary of the different classification schemes for ECR and highlight the relevant therapeutic principles.

Radiation alters osteoclastogenesis by regulating the cytoskeleton and lytic enzymes in RAW 264.7 cells and mouse bone marrow-derived macrophages

PURPOSE

The aim of the present study was to investigate the duality of irradiation effect on osteoclastogenesis, particularly on the cytoskeleton and expression of lytic enzymes in osteoclast precursors. Therefore, the present study may serve as a useful reference for the prevention and treatment of radiation-induced bone loss in the clinic.

MATERIALS AND METHODS

Two typical osteoclast precursors, murine RAW 264.7 macrophage cells and mouse bone marrow-derived macrophages (BMMs), were exposed to radiation in the order of 0.25-8 Gy, and the effects on cell viability, TRAP activity and bone resorption were subsequently investigated. Furthermore, changes in the cytoskeleton, cell apoptosis, and expression of lytic enzymes in osteoclasts were examined to elucidate the molecular mechanism of the duality of irradiation on osteoclastogenesis.

RESULTS

Morphological changes and impaired viability were observed in RAW 264.7 cells and BMMs treated with 1-8 Gy irradiation with or without RANKL. However, the cell fusion tendency of osteoclasts was enhanced after 2 Gy irradiation, and an increased number of fused giant osteoclasts and enhanced F-actin ring formation were observed. Consistently, the bone resorption activity and the enzyme expression of TRAP, cathepsin K, matrix metalloproteinase 9, activator protein 1, and Caspase 9 were increased following irradiation with 2 Gy. Furthermore, intracellular ROS production and apoptosis of osteoclast precursors were increased.

CONCLUSIONS

Irradiation with 2 Gy inhibited the viability of osteoclast precursors, but increased osteoclastogenesis by enhancing cell fusion and increasing the secretion of lytic enzymes, which may be an important mechanism of radiation-induced bone loss.

Primary myeloid cell proteomics and transcriptomics: importance of β-tubulin isotypes for osteoclast function

Among hematopoietic cells, osteoclasts (OCs) and immature dendritic cells (DCs) are closely related myeloid cells with distinct functions: OCs participate skeleton maintenance while DCs sample the environment for foreign antigens. Such specificities rely on profound modifications of gene and protein expression during OC and DC differentiation. We provide global proteomic and transcriptomic analyses of primary mouse OCs and DCs, based on original stable isotope labeling with amino acids in cell culture (SILAC) and RNAseq data. We established specific signatures for OCs and DCs, including genes and proteins of unknown functions. In particular, we showed that OCs and DCs have the same α- and β-tubulin isotype repertoire but that OCs express much more of the β tubulin isotype Tubb6 (also known as TBB6). In both mouse and human OCs, we demonstrate that elevated expression of Tubb6 in OCs is necessary for correct podosomes organization and thus for the structure of the sealing zone, which sustains the bone resorption apparatus. Hence, lowering Tubb6 expression hinders OC resorption activity. Overall, we highlight here potential new regulators of OC and DC biology, and illustrate the functional importance of the tubulin isotype repertoire in the biology of differentiated cells.

PDK1 is important lipid kinase for RANKL-induced osteoclast formation and function via the regulation of the Akt-GSK3β-NFATc1 signaling cascade

Perturbations in the balanced process of osteoblast-mediated bone formation and osteoclast-mediated bone resorption leading to excessive osteoclast formation and/or activity is the cause of many pathological bone conditions such as osteoporosis. The osteoclast is the only cell in the body capable of resorbing and degrading the mineralized bone matrix. Osteoclast formation from monocytic precursors is governed by the actions of two key cytokines macrophage-colony-stimulating factor and receptor activator of nuclear factor-κB ligand (RANKL). Binding of RANKL binding to receptor RANK initiates a series of downstream signaling responses leading to monocytic cell differentiation and fusion, and subsequent mature osteoclast bone resorption and survival. The phosphoinositide-3-kinase (PI3K)-protein kinase B (Akt) signaling cascade is one such pathway activated in response to RANKL. The 3-phosphoinositide-dependent protein kinase 1 (PDK1), is considered the master upstream lipid kinase of the PI3K-Akt cascade. PDK1 functions to phosphorylate and partially activate Akt, triggering the activation of downstream effectors. However, the role of PDK1 in osteoclasts has yet to be clearly defined. In this study, we specifically deleted the PDK1 gene in osteoclasts using the cathepsin-K promoter driven Cre-LoxP system. We found that the specific genetic ablation of PDK1 in osteoclasts leads to an osteoclast-poor osteopetrotic phenotype in mice. In vitro cellular assays further confirmed the impairment of osteoclast formation in response to RANKL by PDK1-deficient bone marrow macrophage (BMM) precursor cells. PDK1-deficient BMMs exhibited reduced ability to reorganize actin cytoskeleton to form a podosomal actin belt as a result of diminished capacity to fuse into giant multinucleated osteoclasts. Notably, biochemical analyses showed that PDK1 deficiency attenuated the phosphorylation of Akt and downstream effector GSK3β, and reduced induction of NFATc1. GSK3β is a reported negative regulator of NFATc1. GSK3β activity is inhibited by Akt-dependent phosphorylation. Thus, our data provide clear genetic and mechanistic insights into the important role for PDK1 in osteoclasts.

[Research progress on the pathogenesis of inflammatory external root resorption]

Inflammatory external root resorption (IERR) refers to the pathological process of dissolving the hard tissue on the outer surface of the tooth root by the body's own immune system under the stimulation of various physical and chemical factors such as infection, stress, trauma and orthodontic treatment. Severe IERR can lead to endodontic and periodontal diseases, and even the loss of teeth. Therefore, understanding the etiology and the pathogenic mechanism of IERR are of importance in its prevention and treatment. This article will review the etiology and the regulation mechanisms of IERR.

Influence of anti-allergic drugs used systemically on the process of root resorption during delayed tooth replantation: A study in rats

BACKGROUND/AIM

Anti-allergic drugs can inhibit the hard tissue resorption process, and due to similarities between root resorption and bone mechanisms, it can be inferred that these drugs may also control root resorption. The aim of this study was to analyze the effects of anti-allergic drugs used systemically on the process of root resorption following delayed tooth replantation.

MATERIALS AND METHODS

Thirty-two maxillary right incisors of rats were extracted and subsequently replanted. Rats were divided into four groups according to the anti-allergic drug administered: the rats in groups DEX, Q, and MO were treated systemically with dexamethasone phosphate, quercetin, and montelukast, respectively, and no systemic medication was administered to rats in group C. After 60 days, the animals were euthanized, and the specimens were processed for histomorphometric and immunohistochemical analyses. Statistical significance was set at P < .05.

RESULTS

There were no significant differences between the groups in terms of inflammatory resorption, replacement resorption, or presence of tartrate-resistant acid phosphatase. In terms of events occurring in the periodontal ligament space, there was a difference between groups Q and MO due to the presence of dental ankylosis and inflammatory connective tissue (P < .05). A difference in inflammatory cells was also observed through CD45 immunolabeling between the DEX and Q groups when compared to the C group (P < .05).

CONCLUSION

The systemic administration of anti-allergic drugs did not have an effect on the process of root resorption following delayed tooth replantation.

Regulator of G protein signaling 12 enhances osteoclastogenesis by suppressing Nrf2-dependent antioxidant proteins to promote the generation of reactive oxygen species

Regulators of G-protein Signaling are a conserved family of proteins required in various biological processes including cell differentiation. We previously demonstrated that Rgs12 is essential for osteoclast differentiation and its deletion in vivo protected mice against pathological bone loss. To characterize its mechanism in osteoclastogenesis, we selectively deleted Rgs12 in C57BL/6J mice targeting osteoclast precursors using LyzM-driven Cre mice or overexpressed Rgs12 in RAW264.7 cells. Rgs12 deletion in vivo led to an osteopetrotic phenotype evidenced by increased trabecular bone, decreased osteoclast number and activity but no change in osteoblast number and bone formation. Rgs12 overexpression increased osteoclast number and size, and bone resorption activity. Proteomics analysis of Rgs12-depleted osteoclasts identified an upregulation of antioxidant enzymes under the transcriptional regulation of Nrf2, the master regulator of oxidative stress. We confirmed an increase of Nrf2 activity and impaired reactive oxygen species production in Rgs12-deficient cells. Conversely, Rgs12 overexpression suppressed Nrf2 through a mechanism dependent on the 26S proteasome, and promoted RANKL-induced phosphorylation of ERK1/2 and NFκB, which was abrogated by antioxidant treatment. Our study therefore identified a novel role of Rgs12 in regulating Nrf2, thereby controlling cellular redox state and osteoclast differentiation.

Proteomic studies of bone and skeletal health outcomes

Proteins are an essential part of essentially all biological processes, and there is enormous variation in protein forms and concentrations that is not reflected in DNA or RNA. Recently there have been rapid advances in the ability to measure protein sequence, modification and concentration, particularly with methods based in mass spectrometry. Global measures of proteins in tissues or in the circulation provide a broad assessment of the proteome that can be extremely useful for discovery, and targeted proteomic measures can yield specific and sensitive assessments of specific peptides and proteins. While most proteomic measures are directed at the detection of consensus peptide sequences, mass spectrometry based proteomic methods also allow a detailed examination of the peptide sequence differences that result from genetic variants and that may have important effects on protein function. In evaluating proteomic data, a number of analytical considerations are important, including an understanding of missing data, the challenge of multiple testing and replication, and the use of rapidly evolving methods in systems biology. While proteomics has not yet had a major impact in skeletal research, interesting recent research has used these approaches in the study of bone cell biology and the discovery of biomarkers of skeletal disorders. Proteomics can be expected to have an increasing influence in the study of bone biology and pathophysiology.

Comparative Characterization of Osteoclasts Derived From Murine Bone Marrow Macrophages and RAW 264.7 Cells Using Quantitative Proteomics

Osteoclasts are bone-resorbing cells differentiated from macrophage/monocyte precursors in response to macrophage colony-stimulating factor (M-CSF) and receptor activator of NF-κB ligand (RANKL). In vitro models are principally based on primary bone marrow macrophages (BMMs), but RAW 264.7 cells are frequently used because they are widely available, easy to culture, and more amenable to genetic manipulation than primary cells. Increasing evidence, however, has shown that the vastly different origins of these two cell types may have important effects on cell behavior. In particular, M-CSF is a prerequisite for the differentiation of BMMs, by promoting survival and proliferation and priming the cells for RANKL induction. RAW 264.7 cells readily form osteoclasts in the presence of RANKL, but M-CSF is not required. Based on these key differences, we sought to understand their functional implications and how it might affect osteoclast differentiation and related signaling pathways. Using a robust and high-throughput proteomics strategy, we quantified the global protein changes in osteoclasts derived from BMMs and RAW 264.7 cells at 1, 3, and 5 days of differentiation. Data are available via ProteomeXchange with the identifier PXD009610. Correlation analysis of the proteomes demonstrated low concordance between the two cell types (R² ≈ 0.13). Bioinformatics analysis indicate that RANKL-dependent signaling was intact in RAW 264.7 cells, but biological processes known to be dependent on M-CSF were significantly different, including cell cycle control, cytoskeletal organization, and apoptosis. RAW 264.7 cells exhibited constitutive activation of Erk and Akt that was dependent on the activity of Abelson tyrosine kinase, and the timing of Erk and Akt activation was significantly different between BMMs and RAW 264.7 cells. Our findings provide the first evidence for major discrepancies between BMMs and RAW 264.7 cells, indicating that careful consideration is needed when using the RAW 264.7 cell line for studying M-CSF-dependent signaling and functions. © 2018 American Society for Bone and Mineral Research. © 2018 The Authors. JBMR Plus published by Wiley Periodicals, Inc. on behalf of American Society for Bone and Mineral Research.

"Ruffled border" formation on a CaP-free substrate: A first step towards osteoclast-recruiting bone-grafts materials able to re-establish bone turn-over

Osteoclasts are large multinucleated giant cells that actively resorb bone during the physiological bone turnover (BTO), which is the continuous cycle of bone resorption (by osteoclasts) followed by new bone formation (by osteoblasts). Osteoclasts secrete chemotactic signals to recruit cells for regeneration of vasculature and bone. We hypothesize that a biomaterial that attracts osteoclasts and re-establishes BTO will induce a better healing response than currently used bone graft materials. While the majority of bone regeneration efforts have focused on maximizing bone deposition, the novelty in this approach is the focus on stimulating osteoclastic resorption as the starter for BTO and its concurrent new vascularized bone formation. A biodegradable tyrosine-derived polycarbonate, E1001(1k), was chosen as the polymer base due to its ability to support bone regeneration in vivo. The polymer was functionalized with a RGD peptide or collagen I, or blended with β-tricalcium phosphate. Osteoclast attachment and early stages of active resorption were observed on all substrates. The transparency of E1001(1k) in combination with high resolution confocal imaging enabled visualization of morphological features of osteoclast activation such as the formation of the "actin ring" and the "ruffled border", which previously required destructive forms of imaging such as transmission electron microscopy. The significance of these results is twofold: (1) E1001(1k) is suitable for osteoclast attachment and supports osteoclast maturation, making it a base polymer that can be further modified to optimize stimulation of BTO and (2) the transparency of this polymer makes it a suitable analytical tool for studying osteoclast behavior.

Regulation of Osteoclast Growth and Fusion by mTOR/raptor and mTOR/rictor/Akt

Osteoclasts are giant bone cells formed by fusion from monocytes and uniquely capable of a complete destruction of mineralized tissues. Previously, we have demonstrated that in energy-rich environment not only osteoclast fusion index (the number of nuclei each osteoclast contains), but also cytoplasm volume per single nucleus was increased. The goal of this study was to investigate the regulation of metabolic sensor mTOR during osteoclast differentiation in energy-rich environment simulated by addition of pyruvate. We have found that in the presence of pyruvate, the proportion of mTOR associated with raptor increased, while mTOR-rictor-mediated Akt phosphorylation decreased. Inhibition of mTOR with rapamycin (10 nM) significantly interfered with all aspects of osteoclastogenesis. However, rapamycin at 1 nM, which preferentially targets mTOR-raptor complex, was only effective in control cultures, while in the presence of pyruvate osteoclast fusion index was successfully increased. Inhibition of Akt drastically reduced osteoclast fusion, however in energy-rich environment, osteoclasts of comparable size were formed through increased cytoplasm growth. These data suggest that mTOR-rictor mediated Akt signaling regulates osteoclast fusion, while mTOR-raptor regulation of protein translation contributes to fusion-independent cytoplasm growth. We demonstrate that depending on the bioenergetics microenvironment osteoclastogenesis can adjust to occur through preferential multinucleation or through cell growth, implying that attaining large cell size is part of the osteoclast differentiation program.

Cellular and Molecular Pathways Leading to External Root Resorption

External apical root resorption during orthodontic treatment implicates specific molecular pathways that orchestrate nonphysiologic cellular activation. To date, a substantial number of in vitro and in vivo molecular, genomic, and proteomic studies have supplied data that provide new insights into root resorption. Recent mechanisms and developments reviewed here include the role of the cellular component-specifically, the balance of CD68⁺, iNOS⁺ M1- and CD68⁺, CD163⁺ M2-like macrophages associated with root resorption and root surface repair processes linked to the expression of the M1-associated proinflammatory cytokine tumor necrosis factor, inducible nitric oxide synthase, the M1 activator interferon γ, the M2 activator interleukin 4, and M2-associated anti-inflammatory interleukin 10 and arginase I. Insights into the role of mesenchymal dental pulp cells in attenuating dentin resorption in homeostasis are also reviewed. Data on recently deciphered molecular pathways are reviewed at the level of (1) clastic cell adhesion in the external apical root resorption process and the specific role of α/β integrins, osteopontin, and related extracellular matrix proteins; (2) clastic cell fusion and activation by the RANKL/RANK/OPG and ATP-P2RX7-IL1 pathways; and (3) regulatory mechanisms of root resorption repair by cementum at the proteomic and transcriptomic levels.