Epigenetic Regulation of Autophagy in Bone Metabolism.

Introduction

The skeletal system, characterized by its dense and robust tissues, serves as a cornerstone in supporting bodily functions, safeguarding vital organs, facilitating hematopoiesis, and storing essential minerals. 1–3 Maintaining bone homeostasis is paramount for ensuring the normal functionality of the skeleton, encompassing critical aspects such as bone density, structural integrity, and regenerative processes. 4

Autophagy sequesters cellular waste, damaged proteins, and organelles within autophagosomes, subsequently subject to degradation and recycling. 5 The outcome of autophagy in bone metabolism depends on various factors, including autophagy regulation, cell type, environmental cues, and physiological context. 6

While traditionally perceived as a cytoplasmic process, 7 autophagy is subject to transcriptional and epigenetic regulation within the nucleus. 8–10 However, the precise impact of epigenetic regulation, encompassing DNA methylation, histone modifications, and non-coding RNA (ncRNA) expression, on cellular fate remains incompletely elucidated. 8 The interplay between autophagy and epigenetic modifications adds a layer of complexity to bone cell regulation.

This article explores the intricate interplay between these two regulatory paradigms, shedding light on the epigenetic control of autophagy within the realm of bone metabolism. This exploration enhances our comprehension of bone metabolism-related disorders and pondered the future and challenges of epigenetic regulation of autophagy in bone metabolism.

Overview of Epigenetic Modifications

Epigenetics broadly pertains to inheritable modifications in phenotype that do not involve modifications in DNA sequences. 11 , 12 While the genotype remains unchanged, hereditary alterations occur in the phenotype. Among the most well-established epigenetic mechanisms are DNA methylation, post-translational modifications of histones, and ncRNAs. 13–15 These mechanisms serve as key regulators of gene expression, functioning either through the modulation of chromatin structure and gene transcription or, in the case of ncRNAs, through post-transcriptional control of protein translation. 16 , 17 Epigenetics plays a regulatory role in various biological processes, including the specific expression of genes in different tissues, the inactivation of chromosomes, genomic imprinting, and the differentiation of cells. 18 , 19 With the advancement of research techniques, epigenetic abnormalities have been implicated in causing malignancies, metabolic disorders, somatic diseases, and autoimmune diseases. 20 Epigenetics highlights the intricate interplay between genetic and environmental factors and plays a crucial role in regulating bone metabolism, 21 particularly in the differentiation of bone cells, providing insights into the study of bone metabolic disorders and their treatment directions.

DNA Methylation

DNA methylation stands as one of the most extensively studied and common epigenetic modifications in mammals. 22 This entails methylating the 5′ carbon of cytosine, leading to the formation of 5-methylcytosine (5-mC). 23 , 24 Cytosine methylation predominantly occurs within specific dinucleotide sequences known as CpG sites. Importantly, these CpG sites are not randomly distributed across the genome but are concentrated in regions called CpG islands, often situated at the 5′ ends of genes. High methylation levels in CpG islands are commonly associated with gene silencing, while low methylation levels are linked to gene activation. 25 , 26

The enzymes responsible for transferring methyl groups from S -adenosylmethionine (SAM) to DNA include DNA methyltransferase 1 (DNMT1), DNMT3a, DNMT3b, and DNMT3L. 27 Demethylation of DNA can occur either passively following DNA replication, leading to reduced maintenance methylation, or actively. 28 The precise molecular mechanisms underlying active demethylation are not yet fully understood. For instance, in the context of bone biology, Interferon Regulatory Factor 8 (IRF8) transcription factor inhibits osteoclast formation. 29 Experimental evidence has revealed that DNMT3a plays a significant role in inhibiting the activity of IRF8 by increasing methylation at distal regulatory elements associated with the IRF8 gene. Elevated levels of SAM can enhance this methylation, ultimately promoting osteoclast differentiation and bone resorption. 30 Deleting DNMT3a in osteoclasts (OC) or using the inhibitor TF-3 in mice protects against bone loss after ovarian removal. 31 Moreover, in multiple myeloma patients, alterations in bone resorption have been associated with elevated IRF8 methylation, induced by myeloma cells’ release of thymidine phosphorylase (TP), leading to decreased IRF8 expression and enhanced bone resorption. 32

The transcription factors runt-related transcription factor 2 (Runx2) and Osterix (OSX) play critical roles in regulating osteoblast (OB) differentiation and bone matrix synthesis. Runx2 activates the promoter of OSX, indicating Runx2’s position as an upstream transcription factor in osteogenesis. 33 During mesenchymal stem cell differentiation into osteoblasts, there is a reduction in the methylation level of Runx2, underscoring the significant regulatory function of Runx2 methylation during osteoblast differentiation. 29 Additionally, epigenetic regulation of OSX is vital for guiding mesenchymal stem cells (MSCs) into osteoblast differentiation. 34

The Ten-Eleven-Translocation (TET) family of enzymes are recognized for their ability to remove methyl groups from DNA, converting 5-mC into 5-hydroxymethylcytosine (5-hmC). Demethylation mediated by TET enzymes enhances chromatin accessibility for target genes controlled by Runx2, facilitating transcriptional regulation. TET proteins engage with Runx2 via their catalytic domain, influencing cytosine methylation patterns around the Runx2 binding region. 35 Disruptions in the promoter methylation of key bone-related genes, such as bone morphogenetic protein 2 (BMP2), may lead to irregularities in bone formation. 29

Post-Translational Histone Modifications

Inside the eukaryotic nucleus, a segment of double-stranded DNA spanning 147 base pairs coils around eight histone proteins, which include two copies of H2A, H2B, H3, and H4, creating nucleosomes. These nucleosomes are linked by DNA segments and organize into structured chromatin formations called chromatin, which subsequently compact into chromosomes. 36–38 The N-terminal amino acid tails of H3 and H4 undergo post-translational modifications that profoundly affect both chromatin structure and DNA-associated activities. 39 Research has unveiled that euchromatin, representing a relaxed and actively transcribed DNA state, is marked by elevated levels of acetylation and trimethylation at H3K4, H3K36, and H3K79. In contrast, reduced acetylation levels and heightened methylation at H3K9, H3K27, and H4K20 indicate a more condensed, transcriptionally inactive heterochromatin structure. 23 , 40 Histone modification is the most intricate mode of regulation among the three epigenetic modifications. 41 Currently, the most extensively studied histone modifications in bone metabolism are histone acetylation and histone methylation.

Histone Acetylation

Histone acetylation involves the addition of acetyl groups to histones and is governed by histone acetyltransferases (HATs). Conversely, histone deacetylases (HDACs) regulate the removal of these acetyl groups, leading to histone deacetylation. 42 This balance between HATs and HDACs maintains a delicate equilibrium.

Histone acetyltransferases facilitate the attachment of acetyl-CoA molecules onto histones, promoting a relaxed nucleosome structure. 43 This structural change activates the transcriptional machinery, enhancing gene expression. In cases where HAT activity is hindered or inhibited, the repair of damaged DNA may be compromised, potentially resulting in cellular apoptosis or programmed cell death. This underscores the crucial role of HATs in DNA repair and cell survival. 44 Unlike HATs, HDACs remove acetyl groups from histones, causing histones to tightly bind to negatively charged DNA. This leads to dense chromatin compaction and the inhibition of gene transcription. 45

Histone acetyltransferases are classified into distinct subfamilies based on their catalytic domains structural and functional similarities, represented as HAT domains. These subfamilies include p300/CBP, HAT1, MYST, PCAF/Gcn5, and Rtt109. 46 Conversely, HDACs are categorized into 4 classical classes according to their sequence similarities: Class I, Class II, Class III, and Class IV. 47 The Class I, II, and IV HDACs contain a conventional deacetylase domain, while Class III HDACs feature a NAD + -dependent catalytic domain ( Table 1 ). 48

The transcriptional activity of the Runx2 gene is modulated by the acetyltransferase P300 and nicotinamide phosphoribosyltransferase (Nampt). P300 enhances osteogenic differentiation in MSCs through H3K14 acetylation, while Nampt does so in MC3T3-E1 cells via H3K9 acetylation. 49 , 50 Other acetyltransferases, GCN5 and PCAF, which acetylate histone H3K9, are known to enhance osteogenic differentiation and bone formation by acetylating H3K9 loci in the promoters of Wnt and BMP genes. However, their levels have been found to decline significantly in mice with ovariectomy-induced osteoporosis (OVX). 51 , 52 In contrast to acetyltransferases, 2 HDACs, HDAC1 and Sirtuin1 (SIRT1), play roles in osteogenesis. HDAC1 promotes MSC osteogenesis through the deacetylation of Forkhead box O3a (FoxO3a), while SIRT1 inhibits osteogenic differentiation in Bone Marrow Stromal Cells (BMSCs) by deacetylating JAGGED1 (JAG1). 53 , 54

In terms of bone health, numerous studies indicate that HDACs, particularly SIRT, play a significant role in bone development. They influence processes such as bone formation, repair, and regeneration. 55 SIRT1, a representative of Class III HDACs, activation induces autophagy during cellular stress, directly deacetylating autophagy-related proteins (ATG5, ATG7, LC-3) to initiate autophagy. 56 , 57 SIRT1 also deacetylates FoxO3, a transcription factor for autophagy-related genes. 58 SIRT1 plays a pivotal role in driving MSC differentiation toward osteoblasts. 59 , 60

Histone Methylation

Histone methylation mainly happens at lysine (K) and arginine (R) residues found at histones’ N-terminal regions. In contrast to acetylation, methylation events at these sites contribute to both transcriptional activation and inhibition. For instance, trimethylation of H3K4, H3K36, and H3K79 is associated with gene activation, while trimethylation of H3K27, H3K9, and H4K20 is linked to gene repression. 71 , 72

Histone methylation is dynamically regulated by methyltransferases and demethylases. 73 , 74 Methylation enzymes such as Suppressor of Variegation 3-9 Homolog 1 (SUV39H1), G9a, and Enhancer of Zeste Homolog 2 (EZH2) add methyl groups, while demethylation enzymes such as Lysine-specific demethylase 1 (LSD1) and JmjC domain (JMJD)-containing proteins remove methyl groups.

Methyltransferases and demethylases play pivotal roles in regulating gene expression in osteoblasts and osteoclasts, thereby influencing the functioning of related genes. ( Table 2 ) For instance, SUV39H1/2 methyltransferases predominantly regulate the abundance of trimethylated H3K9. Knockdown of SUV39H1 leads to a reduction in H3K9me3 levels, enhancing DNA repair capabilities and delaying cellular senescence in progeroid cells. 75

Excessive EZH2 activity leads to elevated H3K27me3 levels, causing a shift in the lineage commitment of BMMSCs toward adipocytes during osteoporosis. 76 Further investigations reveal significant enrichment of both EZH2 and H3K27me3 in the promoters of Wnt1, Wnt6, and Wnt10a within BMMSCs of mice subjected to ovariectomy. 77 , 78 Notably, EZH2 reduces the enrichment of H3K27me3 on these promoters, consequently suppressing the expression of Wnt genes. Overexpressing EZH2 results in heightened H3K27me3 levels at the transcription start sites (TSS) of Runx2 and Bglap, pivotal factors initiating osteogenesis.

The histone methyltransferase SET-domain-containing 2 (SETD2) catalyzes the modification of H3K36 trimethylation. It facilitates the binding of trimethylated histones to promoters associated with lipopolysaccharide-binding protein (LBP), thus influencing the specification of adipogenic and osteogenic pathways. Disrupting SETD2 through knockout shifts the fate of mesenchymal stem cells toward adipocyte formation, impairing their potential to differentiate into osteoblasts. In mice lacking Setd2 specifically in osteoprogenitor cells, there is a notable decrease in trabecular volume and bone formation rate, accompanied by an excessive accumulation of marrow fat. 79

JMJD3 functions as a demethylase targeting H3K27. JMJD3 plays a regulatory role in influencing the expression of genes related to bone health, such as nuclear factor of activated T-cells cytoplasmic 1 (NFATC1), 80 Runx2, OSX, osteopontin, bone sialoprotein (BSP), and osteocalcin (OCN). 79 , 81 In vitro experiments reveal that inhibiting LSD1 through knockdown using shRNA or pharmacological inhibitors suppresses osteoblast function and differentiation. When LSD1 activity is inhibited in vivo, it leads to a reduction in both osteoblast count and activity, consequently resulting in osteopenia. Selective elimination of LSD1 from mesenchymal cells also results in osteopenia and disturbs the structure of the growth plate. 82

Non-Coding RNAs

Non-coding RNAs constitute a significant portion of the human genome, with approximately 2% consisting of protein-coding genes. The majority of the genome is made up of non-protein-coding RNAs, 91 , 92 involving long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and small non-coding RNAs (sncRNAs). Within the category of sncRNAs, there are further subdivisions, such as microRNAs (miRNAs), piwi-interacting RNAs (piRNAs), small-interfering RNAs (siRNAs), and more. These ncRNAs play crucial roles in gene expression, cell differentiation, development, and various diseases, making them a prominent area of study in modern biology. 93

Long Non-Coding RNAs

Long Non-Coding RNAs (LncRNAs) are ncRNAs that consist of more than 200 nucleotides in length. They have emerged as non-canonical regulators participating directly in various pathophysiological processes, including autophagy. 94

As research advances, increasing evidence suggests that lncRNAs, as key regulators of gene expression, play pivotal roles in the proliferation, differentiation, apoptosis, and activity of osteoblasts and osteoclasts ( Table 3 ). Disruptions in their expression patterns have been linked to numerous diseases, such as aging, cancer, metabolic disorders, and osteoporosis (OP).

Several lncRNAs have been identified as positive regulators of osteoblastogenesis, including PGC1β-OT1, 95 OGRU, 96 AK0, 97 LINC02349, 98 KCNQ10T1, 99 MALAT1, 100 Rhno1, 101 MCF2L-AS1, 102 H19, 103 GAS5, 104 and more. These lncRNAs promote osteogenic differentiation by various mechanisms, such as acting as sponges for miRNAs or regulating key osteogenic factors. On the other hand, some lncRNAs negatively regulate osteogenic differentiation, including HOTAIR, 105 ODIR1, 106 SNHG1, 107 UCA1, 108 and more. These lncRNAs inhibit osteogenesis by suppressing specific signaling pathways or inhibiting the expression of osteogenic marker genes.

Long non-coding RNAs also play dual roles in osteoclastogenesis. For example, MIRG has been shown to have a positive regulatory role, 109 while NEAT1 110 , Bmncr, 110 NRON, 111 and others inhibit osteoclast formation by various mechanisms. Overall, lncRNAs represent a diverse class of regulatory molecules with complex roles in the regulation of osteoblasts and osteoclasts, influencing bone health and associated diseases.

MicroRNAs

MicroRNAs (miRNAs) are short, ncRNA molecules typically composed of 19 to 25 nucleotides in length. They are highly conserved across species and play a crucial role in post-transcriptional gene regulation. 120 MicroRNAs do not code for proteins themselves but instead regulate gene expression by binding to complementary sequences within the target mRNA, leading to the degradation of the target mRNA or translational repression. 121 The intricate interplay between miRNAs and their target mRNAs is influenced by various factors, including the strength of their interaction, target mRNA abundance, and intracellular localization of both miRNA and mRNA. 122

In the context of osteogenesis and bone cell differentiation, miRNAs have several key roles: regulation of bone formation, diverse functions and mechanisms, targeting multiple genes and potential therapeutic targets ( Table 4 ).

Overall, miRNAs are essential regulators of osteogenesis and bone cell differentiation, contributing to the maintenance of bone tissue and the equilibrium between bone formation and resorption. Understanding the roles and regulatory networks of miRNAs in bone biology is crucial for advancing our knowledge of bone-related diseases and potential therapeutic interventions.

Autophagy in Bone Metabolism

In mammals, three specific types of autophagy have been recognized: macroautophagy, microautophagy, and chaperone-mediated autophagy. Of these, macroautophagy is the most prevalent and is intricately intertwined with cellular physiology, biological functions, and the development of diseases within the context of bone. 134 In this review, we will primarily focus on macroautophagy when referring to autophagy.

Autophagy typically progresses through four key stages: the creation of autophagosome precursors, followed by the formation of autophagosomes, then the development of autolysosomes, and finally, the degradation phase. During the degradation phase, sizable cellular molecules are disintegrated into amino acids, lipids, nucleotides, and energy, facilitating both the cell's metabolic necessities and the rejuvenation of specific organelles. 135

Currently, there are more than 40 ATG genes known to regulate autophagy. 136 Each gene plays distinct roles at specific stages. ULK1, a key protein, forms the ULK1 complex (ULK1-ATG13-FIP200-ATG101) initiating autophagy. During starvation, mTOR inhibition and AMPK activation prompt ULK1 phosphorylation, initiating autophagy. Beclin1, similar to yeast ATG6, interacts with proteins to form the PI3K complex, crucial for autophagy initiation. ATG14 and UVRAG play roles in autophagosome elongation and autophagosome-lysosome fusion, respectively. Proteins such as ATG12, ATG5, and LC-3 control autophagosome formation. LC3-II, a key autophagy marker, encapsulates materials for degradation. Finally, the autophagosome fuses with lysosomes to form autolysosomes, where degradation provides cells with energy against stress. 137

Importance of Autophagy in Bone Homeostasis and Remodeling

Bone homeostasis refers to the delicate balance maintained within the skeletal system through a dynamic interplay between bone-forming cells (osteoblasts), bone-resorbing cells (osteoclasts), and bone matrix. 138 This intricate equilibrium is crucial for preserving the overall health, strength, and functionality of bones ( Figure 1 ).

Bone remodeling involves three cell types: MSCs differentiate into osteoblasts (OB) on the bone surface, secreting bone matrix. This matrix, with OB, transforms into osteocytes, forming a vital mechanosensory network in bones, essential for signaling; simultaneously, multinucleated osteoclasts (OC) derived from hematopoietic stem cells constantly break down and absorb the neighboring bone matrix. 138 , 139 Generally, the balance between bone formation and resorption is continually coordinated. In this manner, the quality, structure, and function of bone tissue can be influenced by internal or external stimuli. Autophagy helps OB, OC, and chondrocytes cope with stress and nutrient deficiencies, promoting survival in harsh hypoxic and hypertonic conditions. Autophagy can also enable the long-term terminal differentiation of osteocytes. The process of autophagy encompasses not only the osteoclastic resorption process but also the acquisition of energy sources during osteoblast differentiation. 140 Altered autophagy can disrupt bone cell balance, potentially causing various diseases.

Role of Autophagy in Mesenchymal Stem Cells, Osteoblasts, Chondrocytes, Osteoclasts, and Osteoclasts

Autophagy in BMSCs

As a rare and diverse subset of stromal cells, BMSCs exhibit the capacity for both self-renewal and differentiation. These cells are capable of undergoing differentiation into various lineages, not limited solely to mesenchymal lineages such as osteocytes, chondrocytes, and adipocytes, 141 , 142 autophagy is vital in controlling the roles, differentiation, and survival of BMSCs. Modulating autophagic activity in these stem cells could have implications for enhancing bone regeneration, treating bone-related diseases, and addressing age-related bone health issues.

Autophagy-regulated redox state participates in determining the fate of BMSC differentiation. It has been reported that elevated ROS levels in BMSCs can promote adipogenesis while inhibiting osteogenic differentiation. When excessive ROS is generated within cells, the autophagic mechanism is activated to reduce ROS levels, thereby restoring osteogenic differentiation of BMSCs. 143 Additionally, research has demonstrated that administering the neuropeptide substance P (SP) to rats enhances BMSC autophagic activity through the AMPK and mammalian target of rapamycin (mTOR) pathways, concurrently reducing ROS production and facilitating osteogenic differentiation. 144 Rapamycin (RAPA), a well-known inhibitor of the mTOR, triggers autophagy by binding to mTOR and activating the mTOR signaling pathway. Research has indicated that RAPA enhances autophagy and influences the osteogenic differentiation of MSCs. 145

Autophagy in Osteoblast

Osteoblasts are central to the processes of bone growth, repair, and remodeling. They synthesize collagen proteins and other bone matrix molecules, providing structural support to the skeleton. Osteoblasts also release bone formation-related proteins, hormones, and cytokines, such as alkaline phosphatase, osteocalcin, and others, which play significant roles in regulating bone metabolism and maintaining bone homeostasis. 146

Autophagic proteins such as Beclin1, ATG5, and ATG7 play an essential role in facilitating the mineralization of osteoblast cell lines. Osteoblast autophagy deficiency can reduce its mineralization ability, leading to a low bone mass phenotype. 147 Insufficient or deficient autophagy in osteoblasts leads to an increase in oxidative stress, which in turn elevates the production of TNFSF11. This further enhances the differentiation of osteoclasts, ultimately resulting in a phenotype resembling osteoporosis. 148 Transcription factors FoxO and ATF4 have been extensively studied in the regulation of autophagy during the differentiation and function of osteoblasts. FoxO binds to the promoter regions of autophagy genes, increasing autophagic activity. This activation may promote the differentiation of MSCs into osteoblasts and inhibit fat generation. 149 Additionally, under endoplasmic reticulum (ER) stress and amino acid deficiency conditions, ATF4 can promote autophagosome formation and autophagic flux by regulating the expression of autophagy initiation-related genes, contributing to the maintenance of osteoblast homeostasis. 150

Autophagy in Osteoclasts

Osteoclasts primarily engage in bone resorption in the body and play a role in bone homeostasis. When their activity is excessively high, it can lead to osteoporosis, while conversely, decreased activity can result in increased bone formation. 151 The microenvironment where osteoclasts are distributed, such as the sealing zone and the interior of bone trabeculae, is characterized by low oxygen levels, which support the survival and maturation of osteoclasts. 152 Under low oxygen conditions, the expression of Hypoxia-inducible factor 1 alpha (HIF-1α) and its downstream signaling molecule BNIP3 increases, leading to elevated levels of autophagy-related proteins such as ATG5, ATG12, and Beclin1. Consequently, LC-3 is recruited to autophagosomes, enhancing the expression of bone resorption factors such as RANKL, matrix metalloproteinase K (MMP), tissue protease K, NFATc1. This, in turn, leads to increased osteoclast formation. 153 , 154 Research has provided evidence that the targeted removal of ATG7 in osteoclast precursors in mice resulted in the improvement of bone loss and the excessive activation of osteoclasts triggered by glucocorticoids or ovariectomy. 155

During the adhesion and migration of osteoclast precursor cells, chemotactic factors CXCL12 and S1P play roles in this process. Specifically, S1P binds to its receptor S1PR on the membrane of osteoclast precursor cells, participating in the migration process. 156 S1P also modulates autophagy through mTOR, serving as a link between autophagy and the accumulation of osteoclasts. 157 RANKL and RANK (receptor activator of NF-κB) play essential roles in osteoclast differentiation and maturation. RANKL induces autophagy activation through pathways such as MAPK and NF-κB during this process. 158

Autophagy in Osteocytes

Osteocytes establish an extensive interconnected network throughout the entire skeleton. They do this through multiple branching processes that resemble dendrites, allowing them to connect with other types of bone cells such as osteoblasts, bone lining cells, and stromal cells. 159 This network spans from the innermost bone regions to the blood vessel linings. 160 Osteocytes play multifaceted roles: they regulate mineral metabolism and the remodeling of the perilacunar matrix, while also serving as mechanosensory cells. 161

Osteocytes play a central role in regulating bone remodeling in response to mechanical loading. 162 Autophagy is a vital mechanism that ensures the survival of osteocytes and enhances their capacity for mechanotransduction in the context of bone remodeling. Recent investigations have unveiled autophagy’s responsiveness to mechanical cues in osteocytes. Mechanistically induced autophagy contributes to the preservation of adenosine triphosphate (ATP) and fosters osteocyte survival. Furthermore, given the unique features of terminal differentiation, the prolonged lifespan of bone cells, and their oxygen and nutrient-deprived environment, autophagy becomes a key player in the regular physiological processes of these cells. 140 , 163 Unsurprisingly, osteocytes exhibit a notable baseline level of autophagy both in laboratory settings and within living organisms. Selectively deleting the autophagy-related gene ATG7 in osteocytes inhibits autophagy, causing decreased bone formation and reduced bone mass in young adult mice, resembling the effects of aging on the skeletal system. 164 Dysregulated autophagy in osteocytes, as seen in Ephrin B2 deficiency or triggered by substances such as pinocembrin, can affect bone health and apoptotic processes. 165 , 166 Beyond its role as a degradative mechanism, recent evidence has spotlighted the involvement of autophagy in protein secretion, referred to as secretory autophagy, bridging intracellular autophagy with the extracellular microenvironment. 167 This phenomenon may offer insights into understanding the impacts of osteocyte autophagy triggered by physical forces exerted on osteoblasts and osteoclasts. 168

Autophagy in Chondrocytes

MSCs in the bone marrow differentiate into osteoprogenitor cells, which further differentiate into chondrocytes that form the cartilage primordia. 169 , 170 Conversely, they develop into endochondral bone, determining the rate and length of longitudinal bone growth. Most skeletal growth is achieved through the ossification of cartilage in the epiphyseal growth plate of bones. Due to the low regenerative capacity of chondrocytes and limited vascularity within the growth plate, chondrocytes are prone to hypoxia and nutrient deficiency. 171 It has been demonstrated that inflammatory mediators including reactive oxygen species (ROS), IL-1β, nitric oxide (NO), Fas, and tumor necrosis factor-alpha (TNF-α) are strongly associated with chondrocyte apoptosis. 172

Autophagy, a cellular degradation mechanism responsible for maintaining cellular energy metabolism homeostasis, possesses the ability to restore impaired chondrocyte functionality. 173 When cellular ATP levels decrease, AMPK activates and triggers autophagy, restoring nutrients and ATP, thus maintaining cellular energy balance. Autophagy also impacts protein and lipid metabolism in chondrocytes through the mTOR pathway. 174

It has been demonstrated that chondrocyte degeneration and apoptosis are considered primary factors in the development of osteoarthritis (OA). 175 Consequently, numerous experiments have been designed to enhance chondrocyte autophagy as a means to alleviate OA. For instance, Interventions such as vitamin D and tofacitinib exhibit potential in protecting against OA by promoting autophagy and preventing chondrocyte degeneration. 176 , 177 Proteins such as PGRN and G protein-coupled receptor family C group 5 member B (GPRC5B) play roles in maintaining chondrocyte health through their involvement in autophagy. 178 , 179 Moderate mechanical strain can promote the restoration of metabolic homeostasis by inhibiting inflammation and excessive autophagy.

Epigenetic Regulation of Autophagy in Bone Metabolism

Epigenetic modifications, alterations in gene expression without DNA sequence changes, 11 intersect significantly with autophagy, a process vital for cellular stress response and recycling. This intricate relationship profoundly influences bone metabolism and homeostasis.

Epigenetic Modifications and Autophagy

DNA methylation, a heritable epigenetic modification, impacts autophagy regulation in diverse cancers and stem cells. 173 Hypermethylation of LC-3A 174 and Beclin1 175 inhibits autophagy, promoting tumorigenesis. Conversely, demethylation enhances autophagy, showing therapeutic potential in cancer treatments. 176 , 178 , 179 Additionally, in conditions like osteoporosis and osteoarthritis, abnormal DNA methylation affects autophagy, highlighting its role in bone health. 180

Histone modifications such as methylation and acetylation regulate autophagy-related genes. G9a-mediated histone methylation inhibits autophagy, while its dissociation activates this process, crucial in non-alcoholic fatty liver disease. 181 Enzymes such as JMJD3 182 , 183 and SIRT 184 , 185 family members modulate histone demethylation and deacetylation, respectively, impacting autophagy regulation in cellular processes.

Non-coding RNAs, including miRNAs and lncRNAs, regulate autophagy at different stages in various diseases. 186 MiRNAs influence autophagy-related genes, affecting cancer cell survival and response to treatments. 187–190 Long non-coding RNAs, such as H19 191 , 192 and GAS5, 193 , 194 exhibit both positive and negative regulatory effects on autophagy, impacting bone-related disorders such as osteoarthritis.

Epigenetic Regulation of Autophagy in Bone Metabolism-Related Diseases

Epigenetic mechanisms are crucial in regulating autophagy processes, influencing its transcriptional and post-translational regulation. 195 , 196 These epigenetic mechanisms can be further influenced by external stimuli, alterations in phenotypic states, or pathological environmental conditions. 197 Epigenetic modifications and autophagy interact in bone metabolism, regulating gene expression, cellular clearance, and stress responses, crucial for maintaining bone tissue homeostasis and function. The convergence of genetic and environmental factors, causing disruption in the epigenetic regulation of autophagy, has the potential to detrimentally affect bone metabolism, thereby contributing to the onset and advancement of bone-related disorders ( Figure 2 ).

Osteoporosis

Osteoporosis is a degenerative bone disorder marked by reduced bone mineral density (BMD), degraded bone microstructure, increased bone fragility, and a higher susceptibility to fractures. 198 , 199 Fundamentally, it arises from an imbalance where bone resorption surpasses bone formation, resulting in a loss of bone tissue. 200 As the population ages, the rates of osteoporosis-related fragility fractures, disability, and mortality are increasing year by year. 201

Numerous studies have confirmed that autophagy increases osteoclast formation under in vitro oxidative stress, low oxygen conditions, and microgravity conditions, leading to an imbalance where bone resorption surpasses bone formation, ultimately triggering osteoporosis ( Figure 3 ). 202 , 203 Several studies have demonstrated that miRNAs play a role in regulating bone resorption and bone formation in the process of osteoporosis formation by mediating autophagy-related factors ( Figure 2 ). Research on RAW 264.7 cells under low oxygen conditions revealed that miR-20a directly targets the 3'UTR of ATG16L1, suppressing autophagy by reducing the levels of autophagy-related proteins LC-3 and ATG16L1, which is favorable for osteoclast differentiation. Furthermore, during osteoclast differentiation induced by hypoxia, HIF-1α can regulate miR-20a, and the HIF-1α-miR20a-ATG16L1 axis plays a significant role. 204 MiR-99 may play a role in fine-tuning and integrating the mTOR signaling pathway to promote optimal osteoclast differentiation. 205 , 206 Histone demethylases KDM4B and KDM6B play a crucial role in osteogenic commitment of MSCs by removing H3K9me3 and H3K27me3 marks. 207 Upregulation of USP7 enhances osteogenic differentiation in human adipose-derived stem cells (hASCs) to suppress osteogenesis progression. 208 USP7 promotes the expression of KDM6B by enhancing its stability. 90 Elevated levels of miR-15b in osteoporosis inhibit the USP7/KDM6B axis, thereby suppressing osteoblast differentiation and autophagy, exacerbating osteoporosis. 209 DOT1L, as a histone methyltransferase, can methylate H3k79. Experiments by Gao et al. confirmed that inhibiting DOT1L in vitro increased autophagosome assembly proteins (ATG3 and ATG8-like Gabarapl2) and autophagy receptors (Sqstm1), activated autophagy, increased pre-osteoclast migration, and increased bone density. Absorption increases and osteoporosis occurs. 210 A research report suggests that age-related upregulation of HDAC9 accelerates bone loss in mice by promoting damaged-induced autophagy. 211 However, administering an HDAC9 inhibitor to elderly mice can restore mesenchymal osteoblastic function and recover bone mass. 212

Osteoarthritis

Osteoarthritis is a degenerative condition characterized by cartilage degeneration, subchondral bone remodeling, and synovial inflammation. The development of OA is typically associated with factors such as joint stress, genetic predisposition, obesity, aging, and metabolic or hormonal changes. 213 Additionally, inflammatory mediators such as interleukin (IL)-1, IL-6, and TNF are excessively produced in chondrocytes and matrix cells. 214 Excessive accumulation of ROS resulting from oxidative stress leads to cartilage degradation. 215

In the early stages of human OA, the level of autophagy increases, contributing to the maintenance of chondrocyte homeostasis. 216 However, in late-stage OA, when chondrocytes endure prolonged stress, autophagy weakens, leading to further deterioration of cartilage ( Figure 3 ). 217

Disruption of normal age-related epigenetic patterns could contribute to age-related conditions such as OA. 218 Aberrant gene activation in osteoarthritis may be associated with epigenetic derepression that leads to inflammation and catabolic metabolic phenotypes in chondrocytes. Proinflammatory cytokines decrease methylation at crucial CpG sites in the IL-1β promoter, resulting in prolonged induction of this cytokine. 219 Stimulation of human chondrocytes with IL-1β leads to decreased methylation at CpG sites in the IL-8 promoter and notably triggers this chemokine in chondrocytes affected by OA. 220 In the study investigating the relationship between autophagy in rat articular chondrocytes and the PI3K/AKT/mTOR signaling pathway in OA, it was found that inflammation can inhibit the proliferation of rat chondrocytes, disrupt the cell cycle, and reduce the rate of autophagy. 221 Furthermore, DNA demethylation is linked to the upregulation of essential cartilage-degrading proteases such as MMP-3, MMP-9, MMP-13, and ADAMTS-4, as well as iNOS. 222 Multiple epigenetic modifications have been found to cooperate in regulating gene expression within the context of osteoarthritic lesions. For example, reduced SOX9 expression in hip OA is likely due to a combination of factors, including elevated DNA methylation, heightened gene-inactivating histone marks (H3K9 and H3K27) methylation, and decreased histone acetylation at the SOX9 promoter. Furthermore, miRNA-145 has also been confirmed to inhibit the expression of SOX9 . 223

Multiple experiments have also confirmed that miRNAs play a significant role in regulating autophagy in the development of OA ( Figure 2 ). MiR-20 is a member of the miR-17-92 cluster located on the chromosome. 224 In OA, the expression of miR-20 is increased. It can target ATG10 through the PI3K/AKT/mTOR signaling pathway, leading to its reduction, thereby inhibiting chondrocyte proliferation and autophagy. 225 In the cartilage tissue of OA, miR-375 is found to be overexpressed. It can target the ATG2B–3′ UTR and inhibit its expression in chondrocytes, suppressing autophagy and promoting endoplasmic reticulum stress (ERs), thereby exacerbating cartilage damage. 226 The experiment indicated that in chondrocytes treated with IL-1β, miR-27a expression is upregulated. It targets the 3′-UTR of the PI3K gene, leading to its downregulation. Through the PI3K-AKT-mTOR pathway, miR-27a activates autophagy and inhibits the proliferation of chondrocytes treated with IL-1β, providing a protective effect against OA. 227 In addition, multiple experiments have confirmed that miR-155, 228 miR-34a, 229 and miR-449a 230 inhibit chondrocyte autophagy, aggravate chondrocyte apoptosis and cause osteoarthritis.

Osteosarcoma

Osteosarcoma is a malignant tumor that originates from mesenchymal tissue, typically found at the metaphysis of long bones such as the femur, tibia, and humerus. Although it primarily affects children and adolescents, it can also occur in adults. 231 The standard treatment for osteosarcoma involves a combination of preoperative and postoperative chemotherapy along with surgical tumor removal, which may even necessitate amputation in severe cases. 66 Despite aggressive treatment, the prognosis for osteosarcoma remains relatively poor, with a 5-year survival rate of 60%-70% post-surgery. Metastasis, particularly to the lungs, significantly contributes to this unfavorable prognosis, with roughly 20% of patients experiencing metastasis and a subsequent 5-year survival rate of only 30%. 232

Autophagy plays a dual role at different stages of osteosarcoma ( Figure 3 ). In one study, miR-22 was shown to reduce the expression of Beclin1, LC-3, MTDH, and ATG5 mRNA by targeting MTDH, thereby inhibiting autophagy and suppressing osteosarcoma cell proliferation. 233 Conversely, inhibiting autophagy was found to promote osteosarcoma cell proliferation in another experiment. In this case, miR-19 was upregulated in osteosarcoma cells, targeting SPRED2 and reducing its expression, which suppressed autophagy, ultimately promoting the proliferation and malignant transformation of osteosarcoma cells. 234

Epigenetic regulation plays a significant role in autophagy within the context of osteosarcoma ( Figure 2 ). Trichostatin A (TSA), a histone deacetylase inhibitor (HDACi), induces autophagy in osteosarcoma cells by suppressing the AKT-mTOR signaling pathway and activating FoxO1, thereby enhancing the survival of osteosarcoma cells. However, inhibiting autophagy significantly enhances TSA-induced cell death in osteosarcoma. 235 Additionally, miR-145-3p, which is downregulated in human osteosarcoma cell lines, targets the 3′-UTR region of HDAC4, increasing HDAC4 levels. This, in turn, promotes apoptosis and autophagy in osteosarcoma cells. 236 Another study involving osteosarcoma cells showed that LHX2 overexpression upregulated mTOR expression, which negatively regulated autophagy through the activation of the mTOR pathway, contributing to the progression of osteosarcoma. MiR-129-5p directly targeted LHX2 3′-UTR to downregulate LHX2, making the miR-129-5p/LHX2/mTOR axis a potential target for osteosarcoma treatment. 237 Additionally, DANCR is a lncRNA that acts as a ceRNA by sequestering miR-335-5p and miR-1927 in osteosarcoma, promoting ROCK1-mediated proliferation and metastasis. 238 Another study on osteosarcoma reveals that miR-193b directly targets the 3′-UTR of FEN1, negatively regulating the expression of FEN1, increasing the expression of Beclin 1 and the LC3-II/I ratio, activating autophagy, and inducing cell apoptosis. 239

Rheumatoid Arthritis

Rheumatoid Arthritis (RA) is a chronic autoimmune inflammatory disorder marked by synovial hyperplasia, persistent inflammation, cartilage degradation, and bone erosion. 240–242 This condition leads to joint deformities and is characterized by swelling and pain. As RA progresses, it can also affect organs and systems outside the joints, such as the heart. 243 The treatment of RA typically involves a comprehensive approach, including medication, physical therapy, and lifestyle management, aimed at alleviating symptoms, controlling inflammation, and maintaining the patient’s quality of life. 244 Early diagnosis and treatment are essential for managing the condition and preventing joint damage. 245

Epigenetic mechanisms, such as DNA demethylation and hypomethylation, play significant roles in altering DNA methylation patterns during B cell to plasma cell differentiation and in RA. These alterations impact disease progression and the expression of key genes. 246 , 247 Histone modifications are also involved in RA, with histone H3 in the promoter region of the IL-6 gene being highly acetylated in fibroblast-like synoviocytes (FLS) from RA patients, leading to increased IL-6 expression and disease progression. Inhibitors of HAT, such as curcumin, can reduce IL-6 secretion. 248

Autophagy in RA has a dual role, exerting both positive and negative effects, depending on specific cellular and molecular regulatory mechanisms. 249 , 250 Autophagy plays a crucial role in osteoclast differentiation and maturation under hypoxic conditions, leading to increased bone resorption and accelerated progression of RA. 251 Additionally, conditions such as nutrient deficiency and endoplasmic reticulum stress promote autophagy, which acts as a self-protective mechanism, allowing RA cells to evade apoptosis and prolong their lifespan. 252

Research by Li et al. demonstrated that the lncRNA MEG3 is upregulated in synovial tissues of RA patients. MEG3 targets miR-141, and their expression is negatively correlated. By inhibiting the AKT/mTOR pathway and activating autophagy, MEG3 suppresses inflammation, promotes chondrocyte proliferation, and inhibits RA progression. 253 In experiments by Zhou et al. using a CIA rat model, it was confirmed that treatment with WJR (Wenhua Juanbi Recipe) may inhibit autophagy by affecting the PI3K/AKT/mTOR pathway mediated by miRNA-146a. This inhibition of autophagy leads to the suppression of cell apoptosis and FLS proliferation. 254 Moreover, in a study by Yang et al., it was found that ZFAS1 (lncRNA ZNFX1 antisense RNA) plays a regulatory role in FLS-RA through the miR-2682-5p/ADAMTS9 axis. Knockdown of ZFAS1 significantly inhibits FLS-RA cell proliferation, inflammatory response, autophagy, and promotes cell apoptosis ( Figure 2 ). 255

Future Directions and Challenges

Currently, the group of epigenetic drugs includes 256 , 257 DNMTis (such as decitabine used in the treatment of AML and high-risk myelodysplastic syndromes, 258 and 5-azacitidine used in high-risk myelodysplastic syndromes 259 ), HDAC inhibitors (like TSA mentioned earlier, activating autophagy in osteosarcoma 235 ), HAT inhibitors (curcumin can reduce IL-6 secretion in RA 248 ), histone methyltransferase inhibitors (BIX01294 inhibits G9a in multiple myeloma 260 ), and various miRNA-based molecular targeted therapy drugs. Despite their role in disease treatment, these epigenetic drugs lack specificity in target therapy and often exhibit toxicity. Future research directions in the epigenetic regulation of autophagy for bone metabolism-related diseases aim to minimize these drugs’ side effects and identify specific epigenetic modifications involved in autophagy for bone metabolism-related diseases.

The currently well-researched histone modifications in bone metabolism-related diseases include histone methylation and acetylation. Other histone modifications, such as histone phosphorylation, 261 ADP-ribosylation, 262 ubiquitination, 263 SUMOylation, 264 glutamylation, 265 glycosylation, 266 hydroxylation, 267 and isomerization, 268 are also covalent modifications that potentially regulate gene expression by altering chromatin structural states and functions, or affecting the affinity between transcription factors and gene promoters. Despite extensive research in fields such as tumorigenesis, energy metabolism, and cellular aging, limited reporting exists on their role in bone metabolism-related diseases. Future comprehensive investigations into the regulation of these histone modifications in autophagy concerning bone metabolism-related diseases might unveil new targets for preventing and treating these conditions and guide the development of novel epigenetic drugs.

Research on miRNA regulation of autophagy in bone metabolism-related diseases is burgeoning and provides potential targets for treating these conditions. A crucial aspect in precise treatment for bone-related diseases involves transferring target miRNAs or anti-miRNAs to target cells without being degraded by endogenous RNA or causing off-target effects. Presently, experimental delivery systems include aptamers, single-stranded DNA or RNA, 269 , 270 8-repeat aspartic acid sequences (D-Asp8), 271 and bacteriophage MS2 virus-like particles (MS2 VLPs). 272 Future advancements should emphasize developing delivery systems that enhance miRNA stability and cellular uptake efficiency. MiRNAs, capable of mimicking or inhibiting the expression of target genes, have the potential to regulate bone biology processes such as bone formation, resorption, and regeneration by activating or inhibiting autophagy.

Conclusion

In this paper, we delved into the critical roles of genetic regulation and autophagy in bone metabolism and highlighted key insights relevant to bone health. Through the culmination of our research, we draw the following conclusions:

Firstly, genetic regulation and autophagy play pivotal roles in bone metabolism. Genetic regulation, by modulating gene expression, determines the differentiation, proliferation, and function of bone cells. Autophagy, on the other hand, is a self-regulating cellular process indispensable for clearing aged or damaged cells, maintaining intracellular homeostasis, and facilitating bone tissue repair. These two mechanisms intricately intertwine and cooperate to uphold bone health.

Secondly, research indicates that abnormalities in genetic regulation and autophagy are closely associated with the onset and progression of various bone metabolic disorders and bone-related diseases. Not only do genetic mutations lead to the hereditary transmission of certain bone diseases, but environmental factors, lifestyles, and aging impact the functionality of autophagy, thereby exerting adverse effects on bone health. Consequently, understanding the roles and dysregulation of these regulatory mechanisms is paramount for preventing, diagnosing, and treating bone disorders.

Lastly, we emphasize the significance of further research in propelling advancements in the field of bone health. By delving deeper into the molecular mechanisms of epigenetic regulation and autophagy, we can identify novel therapeutic targets and develop more effective treatment strategies. Simultaneously, with the aid of precision medicine and personalized treatment approaches, we can better cater to the diverse needs of individual patients, elevating the management of bone diseases.

In conclusion, this paper underscores the importance of genetic regulation and autophagy in maintaining bone health and their close connections with bone metabolic disorders and related diseases. We encourage future research to continue delving into these domains, with the aim of providing innovative solutions for preventing and treating bone disorders, ultimately enhancing the quality of life and health of patients. Through collaboration and exploration of new frontiers, we can collectively drive progress in the field of bone health, paving the way for new possibilities in future medical and clinical practices.

Acknowledgement

We express our gratitude to Jiang Pei, Director of the Translational Pharmacy Laboratory at Jining First People’s Hospital, for providing valuable guidance and support throughout this study. The graphical abstract was created using BioRender.

Author Contributions

Y.Z. wrote and edited the manuscript. Q.W. conceived the manuscript. H.X., Y.G., and S.W. revised and edited the manuscrip. F.L. and L.G. designed and provide the graphic image. W.P. and P.J. provided significant assistance. All authors have read and approved the final manuscript. All authors edited and approved the final manuscript.

Funding

The study was supported by the National Natural Science Foundation of China [81602846; 82272253] and the Natural Science Foundation of Shandong Province [ZR2021MH145, ZR2020MH375], the Traditional Chinese Medicine Science and Technology Development Plan of Shandong Province [M-2022066],China International Medical Foundation [No. Z-2018-35-2002].

Conflict of Interest

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Data Availability

The data involved in this review article are available from the corresponding author on reasonable request.

References

1. Stieglitz J , Beheim BA , Trumble BC , Madimenos FC , Kaplan H , Gurven M . Low mineral density of a weight-bearing bone among adult women in a high fertility population . American J Phys Anthropol . 2015 ; 156 ( 4 ): 637 – 648 . 10.1002/ajpa.22681 PMC4368479 25488367

2. Desai S , Jayasuriya CT . Implementation of endogenous and exogenous mesenchymal progenitor cells for skeletal tissue regeneration and repair . Bioeng . 2020 ; 7 ( 3 ): 86 . 10.3390/bioengineering7030086 PMC7552784 32759659

3. Sheehy EJ , Kelly DJ , O'Brien FJ . Biomaterial-based endochondral bone regeneration: a shift from traditional tissue engineering paradigms to developmentally inspired strategies . Materials Today Bio . 2019 ; 3 : 100009 . 10.1016/j.mtbio.2019.100009 PMC7061547 32159148

4. Omata Y , Okada H , Uebe S et al. Interspecies single-cell RNA-seq analysis reveals the novel trajectory of osteoclast differentiation and therapeutic targets . JBMR Plus . 2022 ; 6 ( 7 ): e10631 . 35866155 10.1002/jbm4.10631 PMC9289986

5. Valdor R , Macian F . Autophagy and the regulation of the immune response . Pharmacol Res . 2012 ; 66 ( 6 ): 475 – 483 . 23063674 10.1016/j.phrs.2012.10.003 PMC3508673

6. Conciatori F , Bazzichetto C , Falcone I et al. Role of mTOR signaling in tumor microenvironment: an overview . Int J Mol Sci . 2018 ; 19 ( 8 ): 2453 . 30126252 10.3390/ijms19082453 PMC6121402

7. Gomes LR , Menck CFM , Leandro GS . Autophagy roles in the modulation of DNA repair pathways . Int J Mol Sci . 2017 ; 18 ( 11 ): 2351 . 29112132 10.3390/ijms18112351 PMC5713320

8. Ghavami S , Zamani M , Ahmadi M et al. Epigenetic regulation of autophagy in gastrointestinal cancers . Biochimica et Biophysica Acta (BBA)—Molecular Basis of Disease . 2022 ; 1868 ( 11 ): 166512 . 35931405 10.1016/j.bbadis.2022.166512

9. Yu YS , Shin HR , Kim D et al. Pontin arginine methylation by CARM1 is crucial for epigenetic regulation of autophagy . Nat Commun . 2020 ; 11 ( 1 ): 6297 . 33293536 10.1038/s41467-020-20080-9 PMC7722926

10. Yu YS , Kim H , Kim KI , Baek SH . Epigenetic regulation of autophagy by histone-modifying enzymes under nutrient stress . Cell Death Differ . 2023 ; 30 ( 6 ): 1430 – 1436 . 36997734 10.1038/s41418-023-01154-9 PMC10244364

11. Liu MM , Chan CC , Tuo J . Epigenetics in ocular diseases . CG . 2013 ; 14 ( 3 ): 166 – 172 . 10.2174/1389202911314030002 PMC3664466 24179439

12. Castro-Muñoz LJ , Ulloa EV , Sahlgren C et al. Modulating epigenetic modifications for cancer therapy (Review) . Oncol Rep . 2023 ; 49 ( 3 ):doi: 10.3892/or.2023.8496 . PMC9942256 36799181

13. Loughlin J . Genetic contribution to osteoarthritis development: current state of evidence . Curr Opin Rheumatol . 2015 ; 27 ( 3 ): 284 – 288 . 25775188 10.1097/BOR.0000000000000171 PMC4423655

14. Jeffries MA . Epigenetic editing: how cutting-edge targeted epigenetic modification might provide novel avenues for autoimmune disease therapy . Clin Immunol . 2018 ; 196 : 49 – 58 . 29421443 10.1016/j.clim.2018.02.001 PMC6078821

15. Núñez-Carro C , Blanco-Blanco M , Villagrán-Andrade KM , Blanco FJ , de Andrés MC . Epigenetics as a Therapeutic Target in Osteoarthritis . Pharmaceuticals . 2023 ; 16 ( 2 ): 156 . 37259307 10.3390/ph16020156 PMC9964205

16. Reddy MA , Park JT , Natarajan R . Epigenetic modifications and diabetic nephropathy . Kidney Res Clinical Practice . 2012 ; 31 ( 3 ): 139 – 150 . 10.1016/j.krcp.2012.07.004 PMC4716094 26894019

17. Furey TS , Sethupathy P , Sheikh SZ . Redefining the IBDs using genome-scale molecular phenotyping . Nat Rev Gastroenterol Hepatol . 2019 ; 16 ( 5 ): 296 – 311 . 30787446 10.1038/s41575-019-0118-x PMC8311467

18. Olsson AH , Volkov P , Bacos K et al. Genome-wide associations between genetic and epigenetic variation influence mRNA expression and insulin secretion in human pancreatic islets . PLoS Genet . 2014 ; 10 ( 11 ): e1004735 . 25375650 10.1371/journal.pgen.1004735 PMC4222689

19. de Melo FHM , Oliveira JS , Sartorelli VOB , Montor WR . Cancer chemoprevention: classic and epigenetic mechanisms inhibiting tumorigenesis. what have we learned so far? . Front Oncol . 2018 ; 8 : 644 . 30627525 10.3389/fonc.2018.00644 PMC6309127

20. Rodenhiser D , Mann M . Epigenetics and human disease: translating basic biology into clinical applications . Can Med Assoc J . 2006 ; 174 ( 3 ): 341 – 348 . 16446478 10.1503/cmaj.050774 PMC1373719

21. Marini F , Cianferotti L , Brandi ML . Epigenetic mechanisms in bone biology and osteoporosis: can they drive therapeutic choices? . Int J Mol Sci . 2016 ; 17 ( 8 ): 1329 . 27529237 10.3390/ijms17081329 PMC5000726

22. Tang J , Xiong Y , Zhou HH , Chen XP . DNA methylation and personalized medicine . J Clin Pharm Ther . 2014 ; 39 ( 6 ): 621 – 627 . 25230364 10.1111/jcpt.12206

23. Curtis EM , Fuggle NR , Cooper C , Harvey NC . Epigenetic regulation of bone mass . Best Practice Res Clinical Endocrinol Metabolism . 2022 ; 36 ( 2 ): 101612 . 10.1016/j.beem.2021.101612 PMC7614112 35120798

24. Ma J , Joehanes R , Liu C et al. Elucidating the genetic architecture of DNA methylation to identify promising molecular mechanisms of disease . Sci Rep . 15 2022 ; 12 ( 1 ): 19564 . 36380121 10.1038/s41598-022-24100-0 PMC9664436

25. Zhang X , Hu M , Lyu X , Li C , Thannickal VJ , Sanders YY . DNA methylation regulated gene expression in organ fibrosis . Biochimica et Biophysica Acta (BBA)—Molecular Basis Disease . 2017 ; 1863 ( 9 ): 2389 – 2397 . 10.1016/j.bbadis.2017.05.010 PMC5567836 28501566

26. Clabaut A , Grare C , Rolland-Valognes G et al. Adipocyte-induced transdifferentiation of osteoblasts and its potential role in age-related bone loss . PLoS One . 2021 ; 16 ( 1 ): e0245014 . 33497412 10.1371/journal.pone.0245014 PMC7837466

27. Loren P , Saavedra N , Saavedra K , Zambrano T , Moriel P , Salazar LA . Epigenetic Mechanisms Involved in Cisplatin-Induced Nephrotoxicity: an Update . Pharmaceuticals . 2021 ; 14 ( 6 ): 491 . 34063951 10.3390/ph14060491 PMC8223972

28. Chen ZX , Riggs AD . DNA methylation and demethylation in mammals . J Biol Chem . 2011 ; 286 ( 21 ): 18347 – 18353 . 21454628 10.1074/jbc.R110.205286 PMC3099650

29. Oton-Gonzalez L , Mazziotta C , Iaquinta MR et al. Genetics and epigenetics of bone remodeling and metabolic bone diseases . Int J Mol Sci . 2022 ; 23 ( 3 ): 1500 , 35163424 10.3390/ijms23031500 PMC8836080

30. Niu Q , Gao J , Wang L , Liu J , Zhang L . Regulation of differentiation and generation of osteoclasts in rheumatoid arthritis . Front Immunol . 2022 ; 13 : 1034050 . 36466887 10.3389/fimmu.2022.1034050 PMC9716075

31. Park-Min KH . Epigenetic regulation of bone cells . Connect Tissue Res . 2017 ; 58 ( 1 ): 76 – 89 . 27082893 10.1080/03008207.2016.1177037 PMC5498111

32. Liu H , Liu Z , Du J et al. Thymidine phosphorylase exerts complex effects on bone resorption and formation in myeloma . Sci Transl Med . 2016 ; 8 ( 353 ): 353ra113 . 10.1126/scitranslmed.aad8949 PMC5109917 27559096

33. Li L , Qu Y , Jin X et al. Protective effect of salidroside against bone loss via hypoxia-inducible factor-1α pathway-induced angiogenesis . Sci Rep . 2016 ; 6 :( 1 ): 32131 . 27558909 10.1038/srep32131 PMC4997314

34. Farshdousti Hagh M , Noruzinia M , Mortazavi Y et al. Different Methylation Patterns of RUNX2, OSX, DLX5 and BSP in Osteoblastic Differentiation of Mesenchymal Stem Cells . Cell J. Spring . 2015 ; 17 ( 1 ): 71 – 82 . 10.22074/cellj.2015.513 PMC4393674 25870836

35. Wang L , You X , Ruan D et al. TET enzymes regulate skeletal development through increasing chromatin accessibility of RUNX2 target genes . Nat Commun . 2022 ; 13 ( 1 ): 4709 . 35953487 10.1038/s41467-022-32138-x PMC9372040

36. Franklin S , Vondriska TM . Genomes, proteomes, and the central dogma . Circ Cardiovasc Genet . 2011 ; 4 ( 5 ): 576 . 22010165 10.1161/CIRCGENETICS.110.957795 PMC3200573

37. Lelli KM , Slattery M , Mann RS . Disentangling the many layers of eukaryotic transcriptional regulation . Annu Rev Genet . 2012 ; 46 :( 1 ): 43 – 68 . 22934649 10.1146/annurev-genet-110711-155437 PMC4295906

38. Hajheidari M , Koncz C , Bucher M . Chromatin evolution-key innovations underpinning morphological complexity . Front Plant Sci . 2019 ; 10 : 454 . 31031789 10.3389/fpls.2019.00454 PMC6474313

39. Clapier CR , Cairns BR . The biology of chromatin remodeling complexes . Annu Rev Biochem . 2009 ; 78 :( 1 ): 273 – 304 . 19355820 10.1146/annurev.biochem.77.062706.153223

40. Portela A , Esteller M . Epigenetic modifications and human disease . Nat Biotechnol . 2010 ; 28 ( 10 ): 1057 – 1068 . 20944598 10.1038/nbt.1685

41. Li CJ , Li RW . Bioinformatic Dissecting of TP53 Regulation Pathway Underlying Butyrate-induced Histone Modification in Epigenetic Regulation . Genet Epigenet . 2014 ; 6 : 1 – 7 . 25512709 10.4137/GEG.S14176 PMC4251064

42. Mittal R , Bencie N , Liu G et al. Recent advancements in understanding the role of epigenetics in the auditory system . Gene . 2020 ; 761 : 144996 . 32738421 10.1016/j.gene.2020.144996 PMC8168289

43. Liu R , Wu J , Guo H et al. Post-translational modifications of histones: mechanisms, biological functions, and therapeutic targets . MedComm . 2023 ; 4 ( 3 ): e292 . 37220590 10.1002/mco2.292 PMC10200003

44. Arora I , Sharma M , Tollefsbol TO . Combinatorial epigenetics impact of polyphenols and phytochemicals in cancer prevention and therapy . Int J Mol Sci . 2019 ; 20 ( 18 ): 4567 , 31540128 10.3390/ijms20184567 PMC6769666

45. Tong W , Zhang L . Fetal hypoxia and programming of matrix metalloproteinases . Drug Discovery Today . 2012 ; 17 ( 3-4 ): 124 – 134 . 21946060 10.1016/j.drudis.2011.09.011 PMC3248990

46. Marmorstein R , Zhou MM . Writers and readers of histone acetylation: structure, mechanism, and inhibition . Cold Spring Harb Perspect Biol . 2014 ; 6 ( 7 ): a018762 . 24984779 10.1101/cshperspect.a018762 PMC4067988

47. Seto E , Yoshida M . Erasers of histone acetylation: the histone deacetylase enzymes . Cold Spring Harb Perspect Biol . 2014 ; 6 ( 4 ): a018713 . 24691964 10.1101/cshperspect.a018713 PMC3970420

48. Wong JK , Zou H . Reshaping the chromatin landscape after spinal cord injury . Front Biol . 2014 ; 9 ( 5 ): 356 – 366 . 10.1007/s11515-014-1329-8 PMC4280023 25554728

49. Ling M , Huang P , Islam S et al. Epigenetic regulation of Runx2 transcription and osteoblast differentiation by nicotinamide phosphoribosyltransferase . Cell Biosci . 2017 ; 7 ( 1 ): 27 . 28546856 10.1186/s13578-017-0154-6 PMC5442704

50. Tang Z , Xu T , Li Y , Fei W , Yang G , Hong Y . Inhibition of CRY2 by STAT3/miRNA-7-5p Promotes Osteoblast Differentiation through Upregulation of CLOCK/BMAL1/P300 Expression . Molecular Therapy—Nucleic Acids . 2020 ; 19 : 865 – 876 . 31982773 10.1016/j.omtn.2019.12.020 PMC6994415

51. Jing H , Su X , Gao B et al. Epigenetic inhibition of Wnt pathway suppresses osteogenic differentiation of BMSCs during osteoporosis . Cell Death Dis . 2018 ; 9 ( 2 ): 176 . 29416009 10.1038/s41419-017-0231-0 PMC5833865

52. Zhang P , Liu Y , Jin C et al. Histone H3K9 acetyltransferase PCAF is essential for osteogenic differentiation through bone morphogenetic protein signaling and may be involved in osteoporosis . Stem Cells . 2016 ; 34 ( 9 ): 2332 – 2341 . 27300495 10.1002/stem.2424

53. Lin CH , Li NT , Cheng HS , Yen ML . Oxidative stress induces imbalance of adipogenic/osteoblastic lineage commitment in mesenchymal stem cells through decreasing SIRT1 functions . J Cellular Molecular Medi . 2018 ; 22 ( 2 ): 786 – 796 . 10.1111/jcmm.13356 PMC5783884 28975701

54. Wang J , Wang CD , Zhang N et al. Mechanical stimulation orchestrates the osteogenic differentiation of human bone marrow stromal cells by regulating HDAC1 . Cell Death Dis . 2016 ; 7 ( 5 ): e2221 . 27171263 10.1038/cddis.2016.112 PMC4917651

55. Tian Q , Gao S , Zhou X , Zheng L , Zhou Y . Histone acetylation in the epigenetic regulation of bone metabolism and related diseases . Stem Cells International . 2021 ; 2021 : 1 . 10.1155/2021/8043346 PMC8310436 34326880

56. Orogo AM , Gustafsson ÅB . Therapeutic targeting of autophagy: potential and concerns in treating cardiovascular disease . Circ Res . 2015 ; 116 ( 3 ): 489 – 503 . 25634972 10.1161/CIRCRESAHA.116.303791 PMC4313578

57. Kume S , Koya D . Autophagy: a novel therapeutic target for diabetic nephropathy . Diabetes Metab J . 2015 ; 39 ( 6 ): 451 – 460 . 26706914 10.4093/dmj.2015.39.6.451 PMC4696980

58. Rajendran R , Garva R , Krstic-Demonacos M , Demonacos C . Sirtuins: molecular traffic lights in the crossroad of oxidative stress, chromatin remodeling, and transcription . J Biomed Biotechnol . 2011 ; 2011 : 1 . 10.1155/2011/368276 PMC3168296 21912480

59. Ou X , Lee MR , Huang X , Messina-Graham S , Broxmeyer HE . SIRT1 positively regulates autophagy and mitochondria function in embryonic stem cells under oxidative stress . Stem Cells . 2014 ; 32 ( 5 ): 1183 – 1194 . 24449278 10.1002/stem.1641 PMC3991763

60. Yang G , Collins JM , Rafiee R et al. SIRT1 gene SNP rs932658 is associated with medication-related osteonecrosis of the jaw . J Bone Mineral Res . 2021 ; 36 ( 2 ): 347 – 356 . 10.1002/jbmr.4185 PMC8733933 32967053

61. Kim JH , Kim K , Youn BU et al. RANKL induces NFATc1 acetylation and stability via histone acetyltransferases during osteoclast differentiation . Biochem J . 2011 ; 436 ( 2 ): 253 – 262 . 21413932 10.1042/BJ20110062

62. Wang CY , Yang SF , Wang Z et al. PCAF acetylates Runx2 and promotes osteoblast differentiation . J Bone Miner Metab . 2013 ; 31 ( 4 ): 381 – 389 . 23468178 10.1007/s00774-013-0428-y

63. Lian WS , Ko JY , Chen YS et al. MicroRNA-29a represses osteoclast formation and protects against osteoporosis by regulating PCAF-mediated RANKL and CXCL12 . Cell Death Dis . 2019 ; 10 ( 10 ): 705 . 31543513 10.1038/s41419-019-1942-1 PMC6755134

64. Liu Y , Cheng W , Zhao Y et al. Cyclic mechanical strain regulates osteoblastic differentiation of mesenchymal stem cells on TiO(2) nanotubes through GCN5 and Wnt/β-Catenin . Front Bioeng Biotechnol . 2021 ; 9 : 735949 . 34869255 10.3389/fbioe.2021.735949 PMC8634263

65. Lu W , Zhang L , Ji K , Ding L , Wu G . Regulatory mechanisms of GCN5 in osteogenic differentiation of MSCs in periodontitis . Clinical & Exp Dental Res . 2023 ; 9 ( 3 ): 464 – 471 . 10.1002/cre2.695 PMC10280614 37021521

66. Misaghi A , Goldin A , Awad M , Kulidjian AA . Osteosarcoma: a comprehensive review . SICOT-J . 2018 ; 4 : 12 . 29629690 10.1051/sicotj/2017028 PMC5890448

67. Li J , Liu C , Li Y et al. TMCO1-mediated Ca(2+) leak underlies osteoblast functions via CaMKII signaling . Nat Commun . 2019 ; 10 ( 1 ): 1589 . 30962442 10.1038/s41467-019-09653-5 PMC6453895

68. Shakibaei M , Shayan P , Busch F et al. Resveratrol mediated modulation of Sirt-1/Runx2 promotes osteogenic differentiation of mesenchymal stem cells: potential role of Runx2 deacetylation . PLoS One . 2012 ; 7 ( 4 ): e35712 . 22539994 10.1371/journal.pone.0035712 PMC3335081

69. Kim HN , Han L , Iyer S et al. Sirtuin1 suppresses osteoclastogenesis by deacetylating FoxOs . Mol Endocrinol . 2015 ; 29 ( 10 ): 1498 – 1509 . 26287518 10.1210/me.2015-1133 PMC4588729

70. Yan S , Miao L , Lu Y , Wang L . Sirtuin 1 inhibits TNF-α-mediated osteoclastogenesis of bone marrow-derived macrophages through both ROS generation and TRPV1 activation . Mol Cell Biochem . 2019 ; 455 ( 1-2 ): 135 – 145 . 30456702 10.1007/s11010-018-3477-7

71. Alelú-Paz R , Ashour N , González-Corpas A , Ropero S . DNA methylation, histone modifications, and signal transduction pathways: a close relationship in malignant gliomas pathophysiology . J Signal Transduct . 2012 ; 2012 : 1 . 10.1155/2012/956958 PMC3407642 22852080

72. Lu C , Thompson CB . Metabolic regulation of epigenetics . Cell Metab . 2012 ; 16 ( 1 ): 9 – 17 . 22768835 10.1016/j.cmet.2012.06.001 PMC3392647

73. Ge K . Epigenetic regulation of adipogenesis by histone methylation . Biochimica et Biophysica Acta (BBA)—Gene Regulatory Mechanisms . 2012 ; 1819 ( 7 ): 727 – 732 . 22240386 10.1016/j.bbagrm.2011.12.008 PMC3328666

74. Wei Y , Gañán-Gómez I , Salazar-Dimicoli S , McCay SL , Garcia-Manero G . Histone methylation in myelodysplastic syndromes . Epigenomics . 2011 ; 3 ( 2 ): 193 – 205 . 22122281 10.2217/epi.11.9 PMC3758889

75. Sidler C , Kovalchuk O , Kovalchuk I . Epigenetic regulation of cellular senescence and aging . Front Genet . 2017 ; 8 : 138 . 29018479 10.3389/fgene.2017.00138 PMC5622920

76. Basta MD , Petruk S , Mazo A , Walker JL . Fibrosis-the tale of H3K27 histone methyltransferases and demethylases . Front Cell Dev Biol . 2023 ; 11 : 1193344 . 37476157 10.3389/fcell.2023.1193344 PMC10354294

77. Sun Y , Zhang H , Qiu T , Liao L , Su X . Epigenetic regulation of mesenchymal stem cell aging through histone modifications . Genes Diseases . 2023 ; 10 ( 6 ): 2443 – 2456 . 37554203 10.1016/j.gendis.2022.10.030 PMC10404871

78. Cakouros D , Gronthos S . Epigenetic Regulators of Mesenchymal Stem/Stromal Cell Lineage Determination . Curr Osteoporos Rep . 2020 ; 18 ( 5 ): 597 – 605 . 32794139 10.1007/s11914-020-00616-0 PMC7532954

79. Chen YS , Lian WS , Kuo CW et al. Epigenetic regulation of skeletal tissue integrity and osteoporosis development . Int J Mol Sci . 2020 ; 21 ( 14 ): 4923 . 32664681 10.3390/ijms21144923 PMC7404082

80. Yasui T , Hirose J , Tsutsumi S , Nakamura K , Aburatani H , Tanaka S . Epigenetic regulation of osteoclast differentiation: possible involvement of Jmjd3 in the histone demethylation of Nfatc1 . J Bone Miner Res . 2011 ; 26 ( 11 ): 2665 – 2671 . 21735477 10.1002/jbmr.464

81. Yang D , Okamura H , Nakashima Y , Haneji T . Histone demethylase Jmjd3 regulates osteoblast differentiation via transcription factors Runx2 and osterix . J Biol Chem . 2013 ; 288 ( 47 ): 33530 – 33541 . 24106268 10.1074/jbc.M113.497040 PMC3837102

82. Rummukainen P , Tarkkonen K , Dudakovic A et al. Lysine-specific Demethylase 1 (LSD1) epigenetically controls osteoblast differentiation . PLoS One . 2022 ; 17 ( 3 ): e0265027 . 35255108 10.1371/journal.pone.0265027 PMC8901060

83. Kim HJ , Park JW , Lee KH et al. Plant homeodomain finger protein 2 promotes bone formation by demethylating and activating Runx2 for osteoblast differentiation . Cell Res . 2014 ; 24 ( 10 ): 1231 – 1249 . 25257467 10.1038/cr.2014.127 PMC4185351

84. Kim K , Shin Y , Kim J , Ulmer TS , An W . H3K27me1 is essential for MMP-9-dependent H3N-terminal tail proteolysis during osteoclastogenesis . Epigenetics Chromatin . 2018 ; 11 ( 1 ): 23 . 29807539 10.1186/s13072-018-0193-1 PMC5971420

85. Ideno H , Nakashima K , Komatsu K et al. G9a is involved in the regulation of cranial bone formation through activation of Runx2 function during development . Bone . 2020 ; 137 : 115332 . 32344102 10.1016/j.bone.2020.115332

86. Cao X , He W , Rong K et al. DZNep promotes mouse bone defect healing via enhancing both osteogenesis and osteoclastogenesis . Stem Cell Res Ther . 2021 ; 12 ( 1 ): 605 . 34930462 10.1186/s13287-021-02670-6 PMC8686256

87. Qi Q , Wang Y , Wang X et al. Histone demethylase KDM4A regulates adipogenic and osteogenic differentiation via epigenetic regulation of C/EBPα and canonical Wnt signaling . Cell Mol Life Sci . 2020 ; 77 ( 12 ): 2407 – 2421 . 31515577 10.1007/s00018-019-03289-w PMC11105029

88. Munehira Y , Yang Z , Gozani O . Systematic Analysis of Known and Candidate Lysine Demethylases in the Regulation of Myoblast Differentiation . J Mol Biol . 2017 ; 429 ( 13 ): 2055 – 2065 . 27732873 10.1016/j.jmb.2016.10.004 PMC5388604

89. Deng P , Yuan Q , Cheng Y et al. Loss of KDM4B exacerbates bone-fat imbalance and mesenchymal stromal cell exhaustion in skeletal aging . Cell Stem Cell . 2021 ; 28 ( 6 ): 1057 – 1073 .. e7 . 33571444 10.1016/j.stem.2021.01.010 PMC8178178

90. Ye L , Fan Z , Yu B et al. Histone demethylases KDM4B and KDM6B promote osteogenic differentiation of human MSCs . Cell Stem Cell . 2018 ; 23 ( 6 ): 898 – 899 . 30526883 10.1016/j.stem.2018.11.002 PMC6335029

91. Li J , Xuan Z , Liu C . Long non-coding RNAs and complex human diseases . Int J Mol Sci . 2013 ; 14 ( 9 ): 18790 – 18808 . 24036441 10.3390/ijms140918790 PMC3794807

92. Vicentini C , Galuppini F , Corbo V , Fassan M . Current role of non-coding RNAs in the clinical setting . Non-coding RNA Research . 2019 ; 4 ( 3 ): 82 – 85 . 31891017 10.1016/j.ncrna.2019.09.001 PMC6926199

93. Rincón-Riveros A , Morales D , Rodríguez JA , Villegas VE , López-Kleine L . Bioinformatic tools for the analysis and prediction of ncRNA interactions . Int J Mol Sci . 2021 ; 22 ( 21 ): 11397 . 34768830 10.3390/ijms222111397 PMC8583695

94. Yang L , Wang H , Shen Q , Feng L , Jin H . Long non-coding RNAs involved in autophagy regulation . Cell Death Dis . 2017 ; 8 ( 10 ): e3073 . 28981093 10.1038/cddis.2017.464 PMC5680586

95. Yuan H , Xu X , Feng X et al. A novel long noncoding RNA PGC1β-OT1 regulates adipocyte and osteoblast differentiation through antagonizing miR-148a-3p . Cell Death Differ . 2019 ; 26 ( 10 ): 2029 – 2045 . 30728459 10.1038/s41418-019-0296-7 PMC6748127

96. Wang K , Wang Y , Hu Z et al. Bone-targeted lncRNA OGRU alleviates unloading-induced bone loss via miR-320-3p/Hoxa10 axis . Cell Death Dis . 2020 ; 11 ( 5 ): 382 . 32427900 10.1038/s41419-020-2574-1 PMC7237470

97. Wang H , Zhao W , Tian QJ , Xin L , Cui M , Li YK . Effect of lncRNA AK023948 on rats with postmenopausal osteoporosis via PI3K/AKT signaling pathway . Eur Rev Med Pharmacol Sci . 2020 ; 24 ( 5 ): 2181 – 2188 . 32196569 10.26355/eurrev_202003_20483

98. Cao L , Liu W , Zhong Y et al. Linc02349 promotes osteogenesis of human umbilical cord-derived stem cells by acting as a competing endogenous RNA for miR-25-3p and miR-33b-5p . Cell Prolif . 2020 ; 53 ( 5 ): e12814 . 32346990 10.1111/cpr.12814 PMC7260076

99. Chen L , Xiong Y , Yan C et al. LncRNA KCNQ1OT1 accelerates fracture healing via modulating miR-701-3p/FGFR3 axis . FASEB J . 2020 ; 34 ( 4 ): 5208 – 5222 . 32060985 10.1096/fj.201901864RR

100. Yi J , Liu D , Xiao J . LncRNA MALAT1 sponges miR-30 to promote osteoblast differentiation of adipose-derived mesenchymal stem cells by promotion of Runx2 expression . Cell Tissue Res . 2019 ; 376 ( 1 ): 113 – 121 . 30511267 10.1007/s00441-018-2963-2

101. Xiong Y , Chen L , Yan C , Endo Y , Mi B , Liu G . The lncRNA Rhno1/miR-6979-5p/BMP2 axis modulates osteoblast differentiation . Int J Biol Sci . 2020 ; 16 ( 9 ): 1604 – 1615 . 32226305 10.7150/ijbs.38930 PMC7097916

102. Chen Q , Wang M , Wu S . The lncRNA MCF2L-AS1 controls osteogenic differentiation by regulating miR-33a . Cell Cycle . 2020 ; 19 ( 9 ): 1059 – 1065 . 32255731 10.1080/15384101.2020.1747776 PMC7217350

103. Li G , Yun X , Ye K et al. Long non-coding RNA-H19 stimulates osteogenic differentiation of bone marrow mesenchymal stem cells via the microRNA-149/SDF-1 axis . J Cellular Molecular Medi . 2020 ; 24 ( 9 ): 4944 – 4955 . 10.1111/jcmm.15040 PMC7205807 32198976

104. Yang Q , Han Y , Liu P et al. Long noncoding RNA GAS5 promotes osteogenic differentiation of human periodontal ligament stem cells by regulating GDF5 and p38/JNK signaling pathway . Front Pharmacol . 2020 ; 11 : 701 . 32508644 10.3389/fphar.2020.00701 PMC7251029

105. Shen JJ , Zhang CH , Chen ZW et al. LncRNA HOTAIR inhibited osteogenic differentiation of BMSCs by regulating Wnt/β-catenin pathway . Eur Rev Med Pharmacol Sci . 2019 ; 23 ( 17 ): 7232 – 7246 . 31539110 10.26355/eurrev_201909_18826

106. He S , Yang S , Zhang Y et al. LncRNA ODIR1 inhibits osteogenic differentiation of hUC-MSCs through the FBXO25/H2BK120ub/H3K4me3/OSX axis . Cell Death Dis . 2019 ; 10 ( 12 ): 947 . 31827076 10.1038/s41419-019-2148-2 PMC6906393

107. Yan L , Liao L , Su X . Role of mechano-sensitive non-coding RNAs in bone remodeling of orthodontic tooth movement: recent advances . Prog Orthod. . 2022 ; 23 ( 1 ): 55 . 36581789 10.1186/s40510-022-00450-3 PMC9800683

108. Zhang RF , Liu JW , Yu SP et al. LncRNA UCA1 affects osteoblast proliferation and differentiation by regulating BMP-2 expression . Eur Rev Med Pharmacol Sci . 2019 ; 23 ( 16 ): 6774 – 6782 . 31486475 10.26355/eurrev_201908_18715

109. Ling L , Hu HL , Liu KY , Ram YI , Gao JL , Cao YM . Long noncoding RNA MIRG induces osteoclastogenesis and bone resorption in osteoporosis through negative regulation of miR-1897 . Eur Rev Med Pharmacol Sci . 2019 ; 23 ( 23 ): 10195 – 10203 . 31841172 10.26355/eurrev_201912_19654

110. Zhang Y , Chen XF , Li J , He F , Li X , Guo Y . lncRNA Neat1 stimulates osteoclastogenesis via sponging miR-7 . J Bone Mineral Res . 2020 ; 35 ( 9 ): 1772 – 1781 . 10.1002/jbmr.4039 32353178

111. Zhang R , Li J , Li G et al. LncRNA Nron regulates osteoclastogenesis during orthodontic bone resorption . Int J Oral Sci . 2020 ; 12 ( 1 ): 14 . 32385254 10.1038/s41368-020-0077-7 PMC7210890

112. Li L , Fang J , Liu Y , Xiao L . LncRNA LOC100506178 promotes osteogenic differentiation via regulating miR-214-5p-BMP2 axis in human bone marrow mesenchymal stem cells . PeerJ . 2020 ; 8 : e8909 . 32328347 10.7717/peerj.8909 PMC7166045

113. Liu SC , Sun QZ , Qiao XF et al. LncRNA TUG1 influences osteoblast proliferation and differentiation through the Wnt/β-catenin signaling pathway . Eur Rev Med Pharmacol Sci . 2019 ; 23 ( 11 ): 4584 – 4590 . 31210284 10.26355/eurrev_201906_18035

114. Wang X , Zhao D , Zhu Y , Dong Y , Liu Y . Long non-coding RNA GAS5 promotes osteogenic differentiation of bone marrow mesenchymal stem cells by regulating the miR-135a-5p/FOXO1 pathway . Mol Cell Endocrinol . 2019 ; 496 : 110534 . 31398367 10.1016/j.mce.2019.110534

115. Zhuang W , Ge X , Yang S et al. Upregulation of lncRNA MEG3 promotes osteogenic differentiation of mesenchymal stem cells from multiple myeloma patients by targeting BMP4 transcription . Stem Cells . 2015 ; 33 ( 6 ): 1985 – 1997 . 25753650 10.1002/stem.1989

116. Wu Y , Jiang Y , Liu Q , Liu CZ . lncRNA H19 promotes matrix mineralization through up-regulating IGF1 by sponging miR-185-5p in osteoblasts . BMC Mol Cell Biol . 2019 ; 20 ( 1 ): 48 . 31718549 10.1186/s12860-019-0230-3 PMC6852999

117. Gong ZM , Tang ZY , Sun XL . LncRNA PRNCR1 regulates osteogenic differentiation in osteolysis after hip replacement by targeting miR-211-5p . Biosci Rep . 2018 ; doi: 10.1042/bsr20180042 29752342

118. Peng W , Deng W , Zhang J , Pei G , Rong Q , Zhu S . Long noncoding RNA ANCR suppresses bone formation of periodontal ligament stem cells via sponging miRNA-758 . Biochem Biophys Res Commun . 2018 ; 503 ( 2 ): 815 – 821 . 29913147 10.1016/j.bbrc.2018.06.081

119. Chen RS , Zhang XB , Zhu XT , Wang CS . LncRNA Bmncr alleviates the progression of osteoporosis by inhibiting RANML-induced osteoclast differentiation . Eur Rev Med Pharmacol Sci . 2019 ; 23 ( 21 ): 9199 – 9206 . 31773670 10.26355/eurrev_201911_19411

120. Rachagani S , Macha MA , Heimann N et al. Clinical implications of miRNAs in the pathogenesis, diagnosis and therapy of pancreatic cancer . Adv Drug Deliv Rev . 2015 ; 81 : 16 – 33 . 25453266 10.1016/j.addr.2014.10.020 PMC4465296

121. Pelucchi P , Tria V , Martino V et al. A versatile tool for stable inhibition of microRNA activity . Biology . 2013 ; 2 ( 3 ): 861 – 871 . 24833050 10.3390/biology2030861 PMC3960870

122. O'Brien J , Hayder H , Zayed Y , Peng C . Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation . Front Endocrinol . 2018 ; 9 : 402 . 10.3389/fendo.2018.00402 PMC6085463 30123182

123. Zhang J , Tu Q , Bonewald LF et al. Effects of miR-335-5p in modulating osteogenic differentiation by specifically downregulating Wnt antagonist DKK1 . J of Bone & Mineral Res . 2011 ; 26 ( 8 ): 1953 – 1963 . 10.1002/jbmr.377 PMC3810406 21351149

124. Kim YJ , Bae SW , Yu SS , Bae YC , Jung JS . miR-196a regulates proliferation and osteogenic differentiation in mesenchymal stem cells derived from human adipose tissue . J Bone Mineral Res . 2009 ; 24 ( 5 ): 816 – 825 . 10.1359/jbmr.081230 19063684

125. Mizuno Y , Tokuzawa Y , Ninomiya Y et al. miR-210 promotes osteoblastic differentiation through inhibition of AcvR1b . FEBS Lett . 2009 ; 583 ( 13 ): 2263 – 2268 . 19520079 10.1016/j.febslet.2009.06.006

126. Wang X , Omar O , Vazirisani F , Thomsen P , Ekström K . Mesenchymal stem cell-derived exosomes have altered microRNA profiles and induce osteogenic differentiation depending on the stage of differentiation . PLoS One . 2018 ; 13 ( 2 ): e0193059 . 29447276 10.1371/journal.pone.0193059 PMC5814093

127. Sugatani T , Vacher J , Hruska KA . A microRNA expression signature of osteoclastogenesis . Blood . 2011 ; 117 ( 13 ): 3648 – 3657 . 21273303 10.1182/blood-2010-10-311415 PMC3072882

128. Guo LJ , Liao L , Yang L , Li Y , Jiang TJ . MiR-125a TNF receptor-associated factor 6 to inhibit osteoclastogenesis . Exp Cell Res . 2014 ; 321 ( 2 ): 142 – 152 . 24360988 10.1016/j.yexcr.2013.12.001

129. Ponzetti M , Rucci N . Osteoblast differentiation and signaling: established concepts and emerging topics . Int J Mol Sci . 2021 ; 22 ( 13 ): 6651 . 34206294 10.3390/ijms22136651 PMC8268587

130. Cao Z , Moore BT , Wang Y et al. MiR-422a as a potential cellular microRNA biomarker for postmenopausal osteoporosis . PLoS One . 2014 ; 9 ( 5 ): e97098 . 24820117 10.1371/journal.pone.0097098 PMC4018259

131. Kagiya T , Nakamura S . Expression profiling of microRNAs in RAW264.7 cells treated with a combination of tumor necrosis factor alpha and RANKL during osteoclast differentiation . J Periodontal Research . 2013 ; 48 ( 3 ): 373 – 385 . 23078176 10.1111/jre.12017

132. Rossi M , Pitari MR , Amodio N et al. miR-29b negatively regulates human osteoclastic cell differentiation and function: implications for the treatment of multiple myeloma-related bone disease . J Cellular Physiology . 2013 ; 228 ( 7 ): 1506 – 1515 . 10.1002/jcp.24306 23254643

133. Lee Y , Kim HJ , Park CK et al. MicroRNA-124 regulates osteoclast differentiation . Bone . 2013 ; 56 ( 2 ): 383 – 389 . 23867221 10.1016/j.bone.2013.07.007

134. Yin X , Zhou C , Li J et al. Autophagy in bone homeostasis and the onset of osteoporosis . Bone Res . 2019 ; 7 ( 1 ): 28 . 31666998 10.1038/s41413-019-0058-7 PMC6804951

135. Zhang QY , Jin HF , Chen S et al. Hydrogen sulfide regulating myocardial structure and function by targeting cardiomyocyte autophagy . Chin Med J (Engl) . 2018 ; 131 ( 7 ): 839 – 844 . 29578128 10.4103/0366-6999.228249 PMC5887743

136. Yin XM . Autophagy in liver diseases: a matter of what to remove and whether to keep . Liver Research . 2018 ; 2 ( 3 ): 109 – 111 . 32042470 10.1016/j.livres.2018.09.001 PMC7010265

137. Luo S , Li X , Zhang Y et al. Cargo recognition and function of selective autophagy receptors in plants . Int J Mol Sci . 2021 ; 22 ( 3 ): 1013 . 33498336 10.3390/ijms22031013 PMC7864022

138. Plotkin LI , Stains JP . Connexins and pannexins in the skeleton: gap junctions, hemichannels and more . Cell Mol Life Sci . 2015 ; 72 ( 15 ): 2853 – 2867 . 26091748 10.1007/s00018-015-1963-6 PMC4503509

139. Santos L , Elliott-Sale KJ , Sale C . Exercise and bone health across the lifespan . Biogerontology . 2017 ; 18 ( 6 ): 931 – 946 . 29052784 10.1007/s10522-017-9732-6 PMC5684300

140. Li Z , Li D , Su H , Xue H , Tan G , Xu Z . Autophagy: an important target for natural products in the treatment of bone metabolic diseases . Front Pharmacol . 2022 ; 13 : 999017 . 36467069 10.3389/fphar.2022.999017 PMC9716086

141. Polisetty N , Fatima A , Madhira SL , Sangwan VS , Vemuganti GK . Mesenchymal cells from limbal stroma of human eye . Mol Vis . 2008 ; 14 : 431 – 442 . 18334960 PMC2268845

142. Di GH , Liu Y , Lu Y , Liu J , Wu C , Duan HF . IL-6 secreted from senescent mesenchymal stem cells promotes proliferation and migration of breast cancer cells . PLoS One . 2014 ; 9 ( 11 ): e113572 . 25419563 10.1371/journal.pone.0113572 PMC4242635

143. Chen H , Liu X , Chen H et al. Role of SIRT1 and AMPK in mesenchymal stem cells differentiation . Ageing Res Rev . 2014 ; 13 : 55 – 64 . 24333965 10.1016/j.arr.2013.12.002

144. Geng W , Shi H , Zhang X , Tan W , Cao Y , Mei R . Substance P enhances BMSC osteogenic differentiation via autophagic activation . Mol Med Report . 2019 ; 20 ( 1 ): 664 – 670 . 10.3892/mmr.2019.10257 PMC6580032 31115537

145. Sotthibundhu A , McDonagh K , von Kriegsheim A et al. Rapamycin regulates autophagy and cell adhesion in induced pluripotent stem cells . Stem Cell Res Ther . 2016 ; 7 ( 1 ): 166 . 27846905 10.1186/s13287-016-0425-x PMC5109678

146. Rodan GA , Noda M . Gene expression in osteoblastic cells . Crit Rev Eukaryot Gene Expr . 1991 ; 1 ( 2 ): 85 – 98 . 1802105

147. Wang J , Zhang Y , Cao J et al. The role of autophagy in bone metabolism and clinical significance . Autophagy . 2023 ; 19 ( 9 ): 2409 – 2427 . 36858962 10.1080/15548627.2023.2186112 PMC10392742

148. Bartelt A , Behler-Janbeck F , Beil FT et al. Lrp1 in osteoblasts controls osteoclast activity and protects against osteoporosis by limiting PDGF-RANKL signaling . Bone Res . 2018 ; 6 ( 1 ): 4 . 29507818 10.1038/s41413-017-0006-3 PMC5826921

149. Dowell P , Otto TC , Adi S , Lane MD . Convergence of peroxisome proliferator-activated receptor gamma and Foxo1 signaling pathways . J Biol Chem . 2003 ; 278 ( 46 ): 45485 – 45491 . 12966085 10.1074/jbc.M309069200

150. Yang X , Karsenty G . ATF4, the osteoblast accumulation of which is determined post-translationally, can induce osteoblast-specific gene expression in non-osteoblastic cells . J Biol Chem . 2004 ; 279 ( 45 ): 47109 – 47114 . 15377660 10.1074/jbc.M410010200

151. Jacome-Galarza CE , Percin GI , Muller JT et al. Developmental origin, functional maintenance and genetic rescue of osteoclasts . Nature . 2019 ; 568 ( 7753 ): 541 – 545 . 30971820 10.1038/s41586-019-1105-7 PMC6910203

152. Rachner TD , Khosla S , Hofbauer LC . Osteoporosis: now and the future . Lancet North Am Ed . 2011 ; 377 ( 9773 ): 1276 – 1287 . 10.1016/S0140-6736(10)62349-5 PMC3555696 21450337

153. Zhao Y , Chen G , Zhang W et al. Autophagy regulates hypoxia-induced osteoclastogenesis through the HIF-1α/BNIP3 signaling pathway . J Cellular Physiol . 2012 ; 227 ( 2 ): 639 – 648 . 21465467 10.1002/jcp.22768

154. Montaseri A , Giampietri C , Rossi M , Riccioli A , Del Fattore A , Filippini A . The role of autophagy in osteoclast differentiation and bone resorption function . Biomolecules . 2020 ; 10 ( 10 ): 1398 . 33008140 10.3390/biom10101398 PMC7601508

155. Arai A , Kim S , Goldshteyn V et al. Beclin1 modulates bone homeostasis by regulating osteoclast and chondrocyte differentiation . J Bone Mineral Res . 2019 ; 34 ( 9 ): 1753 – 1766 . 10.1002/jbmr.3756 PMC9346192 31074883

156. Ishii T , Shimazu Y , Nishiyama I , Kikuta J , Ishii M . The role of sphingosine 1-phosphate in migration of osteoclast precursors; an application of intravital two-photon microscopy . Mol Cells . 2011 ; 31 ( 5 ): 399 – 404 . 21360199 10.1007/s10059-011-1010-x PMC3887611

157. Hsu LC , Reddy SV , Yilmaz Ö , Yu H . Sphingosine-1-phosphate receptor 2 controls podosome components induced by RANKL affecting osteoclastogenesis and bone resorption . Cells . 2019 ; 8 ( 1 ): 17 . 30609675 10.3390/cells8010017 PMC6357083

158. Ivashkiv LB . Metabolic-epigenetic coupling in osteoclast differentiation . Nat Med . 2015 ; 21 ( 3 ): 212 – 213 . 25742453 10.1038/nm.3815 PMC4795459

159. Fujita K , Xing Q , Khosla S , Monroe DG . Mutual enhancement of differentiation of osteoblasts and osteocytes occurs through direct cell-cell contact . J Cell Biochem . 2014 ; 115 ( 11 ). 10.1002/jcb.24880 PMC4169216 25043105

160. Bellido T , Saini V , Pajevic PD . Effects of PTH on osteocyte function . Bone . 2013 ; 54 ( 2 ): 250 – 257 . 23017659 10.1016/j.bone.2012.09.016 PMC3552098

161. Adachi T , Aonuma Y , Taira K , Hojo M , Kamioka H . Asymmetric intercellular communication between bone cells: propagation of the calcium signaling . Biochem Biophys Res Commun . 2009 ; 389 ( 3 ): 495 – 500 . 19737533 10.1016/j.bbrc.2009.09.010

162. Riquelme MA , Gu S , Hua R , Jiang JX . Mechanotransduction via the coordinated actions of integrins, PI3K signaling and Connexin hemichannels . Bone Res . 2021 ; 9 ( 1 ): 8 . 33531460 10.1038/s41413-020-00126-w PMC7854719

163. Xu H , Xia M , Sun L , Wang H , Zhang WB . Osteocytes enhance osteogenesis by autophagy-mediated FGF23 secretion under mechanical tension . Front Cell Dev Biol . 2021 ; 9 : 782736 . 35174158 10.3389/fcell.2021.782736 PMC8841855

164. Zhang B , Hou R , Zou Z et al. Mechanically induced autophagy is associated with ATP metabolism and cellular viability in osteocytes in vitro . Redox Biol . 2018 ; 14 : 492 – 498 . 29096322 10.1016/j.redox.2017.10.021 PMC5680519

165. Vrahnas C , Blank M , Dite TA et al. Author correction: increased autophagy in EphrinB2-deficient osteocytes is associated with elevated secondary mineralization and brittle bone . Nat Commun . 2019 ; 10 ( 1 ): 5073 . 31685818 10.1038/s41467-019-13040-5 PMC6828656

166. Wang XY , Gong LJ , Huang JM , Jiang C , Yan ZQ . Pinocembrin alleviates glucocorticoid-induced apoptosis by activating autophagy via suppressing the PI3K/Akt/mTOR pathway in osteocytes . Eur J Pharmacol . 2020 ; 880 : 173212 . 32470335 10.1016/j.ejphar.2020.173212

167. Manjithaya R , Subramani S . Autophagy: a broad role in unconventional protein secretion? . Trends Cell Biol . 2011 ; 21 ( 2 ): 67 – 73 . 20961762 10.1016/j.tcb.2010.09.009 PMC3025270

168. Denry I , Goudouri OM , Fredericks DC , Akkouch A , Acevedo MR , Holloway JA . Strontium-releasing fluorapatite glass-ceramic scaffolds: structural characterization and in vivo performance . Acta Biomater . 2018 ; 75 : 463 – 471 . 29859366 10.1016/j.actbio.2018.05.047 PMC6119524

169. Luo P , Gao F , Niu D et al. The role of autophagy in chondrocyte metabolism and osteoarthritis: a comprehensive research review . Biomed Res Int . 2019 ; 2019 : 1 . 10.1155/2019/5171602 PMC6487163 31111057

170. Gao M , Chen C , Zhang Q , Bian J , Qin L , Bao L . Research progress on the antiosteoarthritic mechanism of action of natural products . Evid-Based Complement Altern Med . 2021 ; 2021 : 1 . 10.1155/2021/7714533 PMC8497106 34630617

171. Huang Y , Seitz D , König F , Müller PE , Jansson V , Klar RM . Induction of articular chondrogenesis by chitosan/hyaluronic-acid-based biomimetic matrices using human adipose-derived stem cells . Int J Mol Sci . 2019 ; 20 ( 18 ): 4487 . 31514329 10.3390/ijms20184487 PMC6770472

172. Xiao SQ , Cheng M , Wang L et al. The role of apoptosis in the pathogenesis of osteoarthritis . International Orthopaedics (SICOT) . 2023 ; 47 ( 8 ): 1895 – 1919 . 10.1007/s00264-023-05847-1 37294429

173. Li J , Jiang M , Yu Z et al. Artemisinin relieves osteoarthritis by activating mitochondrial autophagy through reducing TNFSF11 expression and inhibiting PI3K/AKT/mTOR signaling in cartilage . Cell Mol Biol Lett . 2022 ; 27 ( 1 ): 62 . 35902802 10.1186/s11658-022-00365-1 PMC9331798

174. Jiang LB , Lee S , Wang Y , Xu QT , Meng DH , Zhang J . Adipose-derived stem cells induce autophagic activation and inhibit catabolic response to pro-inflammatory cytokines in rat chondrocytes . Osteoarthritis Cartilage . 2016 ; 24 ( 6 ): 1071 – 1081 . 26778531 10.1016/j.joca.2015.12.021

175. Lian LP , Xi XY . Long non-coding RNA XIST protects chondrocytes ATDC5 and CHON-001 from IL-1β-induced injury via regulating miR-653-5p/SIRT1 axis . J Biol Regul Homeost Agents . 2020 ; 34 ( 2 ): 379 – 391 . 32517436 10.23812/19-549-A-65

176. Wang Y , Huang M , Xu W , Li F , Ma C , Tang X . Calcitriol-enhanced autophagy in gingival epithelium attenuates periodontal inflammation in rats with type 2 diabetes mellitus . Front. Endocrinol. . 2022 ; 13 : 1051374 . 10.3389/fendo.2022.1051374 PMC9872194 36704029

177. Zhang P , Xiao J , Luo C et al. The effect of JAK inhibitor tofacitinib on chondrocyte autophagy . Inflammation . 2023 ; 46 ( 5 ): 1764 – 1776 . 37310645 10.1007/s10753-023-01840-3

178. Pan Y , Yang Y , Fan M et al. Progranulin regulation of autophagy contributes to its chondroprotective effect in osteoarthritis . Genes Diseases . 2023 ; 10 ( 4 ): 1582 – 1595 . 37397563 10.1016/j.gendis.2022.05.031 PMC10311031

179. He L , Xu Z , Niu X et al. GPRC5B protects osteoarthritis by regulation of autophagy signaling . Acta Pharmaceutica Sinica B . 2023 ; 13 ( 7 ): 2976 – 2989 . 37521864 10.1016/j.apsb.2023.05.014 PMC10372909

180. Li S , Gao L , Zhang W et al. MiR-152-5p suppresses osteogenic differentiation of mandible mesenchymal stem cells by regulating ATG14-mediated autophagy . Stem Cell Res Ther . 2022 ; 13 ( 1 ): 359 . 35883156 10.1186/s13287-022-03018-4 PMC9327198

181. Gravina GL , Festuccia C , Marampon F et al. Biological rationale for the use of DNA methyltransferase inhibitors as new strategy for modulation of tumor response to chemotherapy and radiation . Mol Cancer . 2010 ; 9 ( 1 ): 305 . 21108789 10.1186/1476-4598-9-305 PMC3001713

182. Nandy D , Rajam SM , Dutta D . A three layered histone epigenetics in breast cancer metastasis . Cell Biosci . 2020 ; 10 ( 1 ): 52 . 32257110 10.1186/s13578-020-00415-1 PMC7106732

183. Pargol M , Akbari M et al. Investigation the role of autophagy in non-small cell lung cancer . Asian Pac J Cancer Prev . 2021 ; 22 ( 3 ): 947 – 955 . 33773561 10.31557/APJCP.2021.22.3.947 PMC8286697

184. Biga PR , Latimer MN , Froehlich JM , Gabillard JC , Seiliez I . Distribution of H3K27me3, H3K9me3, and H3K4me3 along autophagy-related genes highly expressed in starved zebrafish myotubes . Biol Open . 2017 ; 6 ( 11 ): 1720 – 1725 . 29025701 10.1242/bio.029090 PMC5703616

185. Mushtaq A , Ashraf NU , Altaf M . The mTORC1-G9a-H3K9me2 axis negatively regulates autophagy in fatty acid-induced hepatocellular lipotoxicity . J Biol Chem . 2023 ; 299 ( 3 ): 102937 . 36690274 10.1016/j.jbc.2023.102937 PMC9957777

186. Li Y , Zhang M , Sheng M et al. Therapeutic potential of GSK-J4, a histone demethylase KDM6B/JMJD3 inhibitor, for acute myeloid leukemia . J Cancer Res Clin Oncol . 2018 ; 144 ( 6 ): 1065 – 1077 . 29594337 10.1007/s00432-018-2631-7 PMC5948279

187. Shogren-Knaak M , Ishii H , Sun JM , Pazin MJ , Davie JR , Peterson CL . Histone H4-K16 acetylation controls chromatin structure and protein interactions . Science . 2006 ; 311 ( 5762 ): 844 – 847 . 16469925 10.1126/science.1124000

188. Puri D , Subramanyam D . Stress—(self) eating: epigenetic regulation of autophagy in response to psychological stress . FEBS J . 2019 ; 286 ( 13 ): 2447 – 2460 . 30927484 10.1111/febs.14826 PMC7116062

189. Fabian MR , Sonenberg N , Filipowicz W . Regulation of mRNA translation and stability by microRNAs . Annu Rev Biochem . 2010 ; 79 ( 1 ): 351 – 379 . 20533884 10.1146/annurev-biochem-060308-103103

190. Dweep H , Kubikova N , Gretz N , Voskarides K , Felekkis K . Homo sapiens exhibit a distinct pattern of CNV genes regulation: an important role of miRNAs and SNPs in expression plasticity . Sci Rep . 2015 ; 5 ( 1 ): 12163 . 26178010 10.1038/srep12163 PMC4503977

191. Tan S , Shi H , Ba M et al. miR-409-3p sensitizes colon cancer cells to oxaliplatin by inhibiting Beclin-1-mediated autophagy . Int J Mol Med . 2016 ; 37 ( 4 ): 1030 – 1038 . 26935807 10.3892/ijmm.2016.2492

192. Zhang F , Wang B , Long H et al. Decreased miR-124-3p Expression Prompted Breast Cancer Cell Progression Mainly by Targeting Beclin-1 . Clin Lab . 2016 ; 62 ( 06/2016 ): 1139 – 1145 . 27468577 10.7754/clin.lab.2015.151111

193. Kovaleva V , Mora R , Park YJ et al. miRNA-130a targets ATG2B and DICER1 to inhibit autophagy and trigger killing of chronic lymphocytic leukemia cells . Cancer Res . 2012 ; 72 ( 7 ): 1763 – 1772 . 22350415 10.1158/0008-5472.CAN-11-3671

194. Zhang J , Chen LM , Zou Y , Zhang S , Xiong F , Wang CY . Implication of epigenetic factors in the pathogenesis of type 1 diabetes . Chin Med J (Engl) . 2021 ; 134 ( 9 ): 1031 – 1042 . 33813508 10.1097/CM9.0000000000001450 PMC8116022

195. Shu F , Xiao H , Li QN et al. Epigenetic and post-translational modifications in autophagy: biological functions and therapeutic targets . Sig Transduct Target Ther . 2023 ; 8 ( 1 ): 32 . 10.1038/s41392-022-01300-8 PMC9842768 36646695

196. Silwal P , Paik S , Jeon SM , Jo EK . Nuclear receptors as autophagy-based antimicrobial therapeutics . Cells . 2020 ; 9 ( 9 ): 1979 , 32867365 10.3390/cells9091979 PMC7563212

197. Reddy MA , Natarajan R . Recent developments in epigenetics of acute and chronic kidney diseases . Kidney Int . 2015 ; 88 ( 2 ): 250 – 261 . 25993323 10.1038/ki.2015.148 PMC4522401

198. Morris HA , Turner AG , Anderson PH . Vitamin-D regulation of bone mineralization and remodelling during growth . Front Biosci . 2012 ; E4 ( 1 ): 677 – 689 . 10.2741/409 22201904

199. Siris ES , Adler R , Bilezikian J et al. The clinical diagnosis of osteoporosis: a position statement from the National Bone Health Alliance Working Group . Osteoporos Int . 2014 ; 25 ( 5 ): 1439 – 1443 . 24577348 10.1007/s00198-014-2655-z PMC3988515

200. Gkastaris K , Goulis DG , Potoupnis M , Anastasilakis AD , Kapetanos G . Obesity, osteoporosis and bone metabolism . J Musculoskelet Neuronal Interact . 2020 ; 20 ( 3 ): 372 – 381 . 32877973 PMC7493444

201. Letarouilly JG , Broux O , Clabaut A . New insights into the epigenetics of osteoporosis . Genomics . 2019 ; 111 ( 4 ): 793 – 798 . 29730394 10.1016/j.ygeno.2018.05.001

202. Wang K , Niu J , Kim H , Kolattukudy PE . Osteoclast precursor differentiation by MCPIP via oxidative stress, endoplasmic reticulum stress, and autophagy . J Mol Cell Biol . 2011 ; 3 ( 6 ): 360 – 368 . 21990425 10.1093/jmcb/mjr021 PMC3234012

203. Sambandam Y , Townsend MT , Pierce JJ et al. Microgravity control of autophagy modulates osteoclastogenesis . Bone . 2014 ; 61 : 125 – 131 . 24463210 10.1016/j.bone.2014.01.004 PMC4384509

204. Sun KT , Chen MY , Tu MG , Wang IK , Chang SS , Li CY . MicroRNA-20a regulates autophagy related protein-ATG16L1 in hypoxia-induced osteoclast differentiation . Bone . 2015 ; 73 : 145 – 153 . 25485521 10.1016/j.bone.2014.11.026

205. Jin Y , Tymen SD , Chen D et al. MicroRNA-99 family targets AKT/mTOR signaling pathway in dermal wound healing . PLoS One . 2013 ; 8 ( 5 ): e64434 . 23724047 10.1371/journal.pone.0064434 PMC3665798

206. Wei F , Liu Y , Guo Y et al. miR-99b-targeted mTOR induction contributes to irradiation resistance in pancreatic cancer . Mol Cancer . 2013 ; 12 ( 1 ): 81 . 23886294 10.1186/1476-4598-12-81 PMC3726417

207. Jin Q , Martinez CA , Arcipowski KM et al. USP7 cooperates with NOTCH1 to drive the oncogenic transcriptional program in T-Cell leukemia . Clin Cancer Res . 2019 ; 25 ( 1 ): 222 – 239 . 30224337 10.1158/1078-0432.CCR-18-1740 PMC6320313

208. Zhou F , Li F , Fang P et al. Ubiquitin-specific protease 4 antagonizes osteoblast differentiation through dishevelled . J Bone Mineral Res . 2016 ; 31 ( 10 ): 1888 – 1898 . 10.1002/jbmr.2863 27128386

209. Lu X , Zhang Y , Zheng Y , Chen B . The miRNA-15b/USP7/KDM6B axis engages in the initiation of osteoporosis by modulating osteoblast differentiation and autophagy . J Cellular Molecular Medi . 2021 ; 25 ( 4 ): 2069 – 2081 . 10.1111/jcmm.16139 PMC7882933 33434305

210. Gao Y , Ge W . The histone methyltransferase DOT1L inhibits osteoclastogenesis and protects against osteoporosis . Cell Death Dis . 2018 ; 9 ( 2 ): 33 . 29348610 10.1038/s41419-017-0040-5 PMC5833786

211. Zhang L , Qi M , Chen J et al. Impaired autophagy triggered by HDAC9 in mesenchymal stem cells accelerates bone mass loss . Stem Cell Res Ther . 2020 ; 11 ( 1 ): 269 . 32620134 10.1186/s13287-020-01785-6 PMC7333327

212. Behera J , Ison J , Tyagi A , Mbalaviele G , Tyagi N . Mechanisms of autophagy and mitophagy in skeletal development, diseases and therapeutics . Life Sci . 2022 ; 301 : 120595 . 35504330 10.1016/j.lfs.2022.120595

213. Herrero-Beaumont G , Roman-Blas JA , Castañeda S , Jimenez SA . Primary osteoarthritis no longer primary: three subsets with distinct etiological, clinical, and therapeutic characteristics . Semin Arthritis Rheum . 2009 ; 39 ( 2 ): 71 – 80 . 19589561 10.1016/j.semarthrit.2009.03.006

214. Bijlsma JW , Berenbaum F , Lafeber FP . Osteoarthritis: an update with relevance for clinical practice . Lancet North Am Ed . 2011 ; 377 ( 9783 ): 2115 – 2126 . 10.1016/S0140-6736(11)60243-2 21684382

215. Liu-Bryan R , Terkeltaub R . Emerging regulators of the inflammatory process in osteoarthritis . Nat Rev Rheumatol . 2015 ; 11 ( 1 ): 35 – 44 . 25266449 10.1038/nrrheum.2014.162 PMC4374654

216. Caramés B , Taniguchi N , Otsuki S , Blanco FJ , Lotz M . Autophagy is a protective mechanism in normal cartilage, and its aging-related loss is linked with cell death and osteoarthritis . Arthritis Rheumatism . 2010 ; 62 ( 3 ): 791 – 801 . 20187128 10.1002/art.27305 PMC2838960

217. Shapiro IM , Layfield R , Lotz M , Settembre C , Whitehouse C . Boning up on autophagy: the role of autophagy in skeletal biology . Autophagy . 2014 ; 10 ( 1 ): 7 – 19 . 24225636 10.4161/auto.26679 PMC4028324

218. Hollander W , Meulenbelt I . DNA Methylation in Osteoarthritis . Curr Genomics . 2015 ; 16 ( 6 ): 419 – 426 . 27019616 10.2174/1389202916666150817212711 PMC4765529

219. Hashimoto K , Oreffo RO , Gibson MB , Goldring MB , Roach HI . DNA demethylation at specific CpG sites in the IL1B promoter in response to inflammatory cytokines in human articular chondrocytes . Arthritis Rheumatism . 2009 ; 60 ( 11 ): 3303 – 3313 . 19877066 10.1002/art.24882 PMC2788707

220. Takahashi A , de Andrés MC , Hashimoto K , Itoi E , Oreffo RO . Epigenetic regulation of interleukin-8, an inflammatory chemokine, in osteoarthritis . Osteoarthritis Cartilage . 2015 ; 23 ( 11 ): 1946 – 1954 . 26521741 10.1016/j.joca.2015.02.168 PMC4638192

221. Xue JF , Shi ZM , Zou J , Li XL . Inhibition of PI3K/AKT/mTOR signaling pathway promotes autophagy of articular chondrocytes and attenuates inflammatory response in rats with osteoarthritis . Biomed Pharmacother . 2017 ; 89 : 1252 – 1261 . 28320092 10.1016/j.biopha.2017.01.130

222. de Andrés MC , Imagawa K , Hashimoto K et al. Loss of methylation in CpG sites in the NF-κB enhancer elements of inducible nitric oxide synthase is responsible for gene induction in human articular chondrocytes . Arthritis Rheumatism . 2013 ; 65 ( 3 ): 732 – 742 . 23239081 10.1002/art.37806 PMC3937961

223. Martinez-Sanchez A , Dudek KA , Murphy CL . Regulation of human chondrocyte function through direct inhibition of cartilage master regulator SOX9 by microRNA-145 (miRNA-145) . J Biol Chem . 2012 ; 287 ( 2 ): 916 – 924 . 22102413 10.1074/jbc.M111.302430 PMC3256897

224. He L , Thomson JM , Hemann MT et al. A microRNA polycistron as a potential human oncogene . Nature . 2005 ; 435 ( 7043 ): 828 – 833 . 15944707 10.1038/nature03552 PMC4599349

225. He W , Cheng Y . Inhibition of miR-20 promotes proliferation and autophagy in articular chondrocytes by PI3K/AKT/mTOR signaling pathway . Biomed Pharmacother . 2018 ; 97 : 607 – 615 . 29101804 10.1016/j.biopha.2017.10.152

226. Li H , Li Z , Pi Y et al. MicroRNA-375 exacerbates knee osteoarthritis through repressing chondrocyte autophagy by targeting ATG2B . Aging . 2020 ; 12 ( 8 ): 7248 – 7261 . 32335541 10.18632/aging.103073 PMC7202526

227. Cai C , Min S , Yan B et al. MiR-27a promotes the autophagy and apoptosis of IL-1β treated-articular chondrocytes in osteoarthritis through PI3K/AKT/mTOR signaling . Aging . 2019 ; 11 ( 16 ): 6371 – 6384 . 31460867 10.18632/aging.102194 PMC6738432

228. D'Adamo S , Alvarez-Garcia O , Muramatsu Y , Flamigni F , Lotz MK . MicroRNA-155 suppresses autophagy in chondrocytes by modulating expression of autophagy proteins . Osteoarthritis Cartilage . 2016 ; 24 ( 6 ): 1082 – 1091 . 26805019 10.1016/j.joca.2016.01.005 PMC4875787

229. Wang J , Li X , Guo X et al. MicroRNA-34a-5p promotes the progression of osteoarthritis secondary to developmental dysplasia of the hip by restraining SESN2-induced autophagy . J Orthopaedic Res . 2024 ; 42 ( 1 ): 66 – 77 . 10.1002/jor.25639 37291947

230. Ni Z , Kuang L , Chen H et al. The exosome-like vesicles from osteoarthritic chondrocyte enhanced mature IL-1β production of macrophages and aggravated synovitis in osteoarthritis . Cell Death Dis . 2019 ; 10 ( 7 ): 522 . 31285423 10.1038/s41419-019-1739-2 PMC6614358

231. Taran SJ , Taran R , Malipatil NB . Pediatric osteosarcoma: an updated review . Indian J Med Paediatric Oncol . 2017 ; 38 ( 01 ): 33 – 43 . 10.4103/0971-5851.203513 PMC5398104 28469335

232. Lindsey BA , Markel JE , Kleinerman ES . Osteosarcoma overview . Rheumatol Ther . 2017 ; 4 ( 1 ): 25 – 43 . 27933467 10.1007/s40744-016-0050-2 PMC5443719

233. Wang P , Zhao ZQ , Guo SB et al. Roles of microRNA-22 in suppressing proliferation and promoting sensitivity of osteosarcoma cells via metadherin-mediated autophagy . Orthopaedic Surgery . 2019 ; 11 ( 2 ): 285 – 293 . 30932352 10.1111/os.12442 PMC6594522

234. Xie C , Liu S , Wu B et al. miR-19 promotes cell proliferation, invasion, migration, and EMT by inhibiting SPRED2-mediated autophagy in osteosarcoma cells . Cell Transplant . 2020 ; 29 : 096368972096246 . 10.1177/0963689720962460 PMC7784565 33023313

235. Bai Y , Chen Y , Chen X et al. Trichostatin A activates FOXO1 and induces autophagy in osteosarcoma . aoms . 2019 ; 15 ( 1 ): 204 – 213 . 10.5114/aoms.2018.73860 PMC6348367 30697272

236. Wu G , Yu W , Zhang M , Yin R , Wu Y , Liu Q . MicroRNA-145-3p suppresses proliferation and promotes apotosis and autophagy of osteosarcoma cell by targeting HDAC4 . Artificial Cells Nanomedicine Biotechnol . 2018 ; 46 ( sup2 ): 579 – 586 . 10.1080/21691401.2018.1464459 29893594

237. Song H , Liu J , Wu X et al. LHX2 promotes malignancy and inhibits autophagy via mTOR in osteosarcoma and is negatively regulated by miR-129-5p . Aging . 2019 ; 11 ( 21 ): 9794 – 9810 . 31724536 10.18632/aging.102427 PMC6874432

238. Wang Y , Zeng X , Wang N et al. Long noncoding RNA DANCR, working as a competitive endogenous RNA, promotes ROCK1-mediated proliferation and metastasis via decoying of miR-335-5p and miR-1972 in osteosarcoma . Mol Cancer . 2018 ; 17 ( 1 ): 89 . 29753317 10.1186/s12943-018-0837-6 PMC5948795

239. Dong S , Xiao Y , Ma X et al. miR-193b increases the chemosensitivity of osteosarcoma cells by promoting FEN1-mediated autophagy . Onco Targets Ther . 2019 ; 12 : 10089 – 10098 . 31819503 10.2147/OTT.S219977 PMC6878930

240. Mellado M , Martínez-Muñoz L , Cascio G , Lucas P , Pablos JL , Rodríguez-Frade JM . T cell migration in rheumatoid arthritis . Front Immunol . 2015 ; 6 : 384 . 26284069 10.3389/fimmu.2015.00384 PMC4515597

241. Scott DL . Evidence for early disease-modifying drugs in rheumatoid arthritis . Arthritis Res Ther . 2004 ; 6 ( 1 ): 15 – 18 . 14979927 10.1186/ar1030 PMC400421

242. Matteson EL , Weyand CM , Fulbright JW , Christianson TJ , McClelland RL , Goronzy JJ . How aggressive should initial therapy for rheumatoid arthritis be? Factors associated with response to ‘non-aggressive’ DMARD treatment and perspective from a 2-yr open label trial . Rheumatology (Oxford) . 2004 ; 43 ( 5 ): 619 – 625 . 14983105 10.1093/rheumatology/keh135

243. Grassi W , De Angelis R , Lamanna G , Cervini C . The clinical features of rheumatoid arthritis . Eur J Radiol . 1998 ; 27 ( Suppl 1 ): S18 – S24 . 9652497 10.1016/s0720-048x(98)00038-2

244. Smolen JS , Aletaha D , Gruben D , Zwillich SH , Krishnaswami S , Mebus C . Brief report: remission rates with tofacitinib treatment in rheumatoid arthritis: a comparison of various remission criteria . Arthritis Rheumatol . 2017 ; 69 ( 4 ): 728 – 734 . 27907269 10.1002/art.39996 PMC5396306

245. Mok CC , Tam LS , Chan TH , Lee GK , Li EK . Management of rheumatoid arthritis: consensus recommendations from the Hong Kong Society of Rheumatology . Clin Rheumatol . 2011 ; 30 ( 3 ): 303 – 312 . 21046421 10.1007/s10067-010-1596-y PMC3052444

246. Bottini N , Firestein GS . Epigenetics in rheumatoid arthritis: a primer for rheumatologists . Curr Rheumatol Rep . 2013 ; 15 ( 11 ): 372 . 24072602 10.1007/s11926-013-0372-9

247. Ribeiro ML , Reyes-Garau D , Armengol M , Fernández-Serrano M , Roué G . Recent advances in the targeting of epigenetic regulators in B-cell non-hodgkin lymphoma . Front Genet . 2019 ; 10 : 986 . 31681423 10.3389/fgene.2019.00986 PMC6807552

248. Wada TT , Araki Y , Sato K et al. Aberrant histone acetylation contributes to elevated interleukin-6 production in rheumatoid arthritis synovial fibroblasts . Biochem Biophys Res Commun . 2014 ; 444 ( 4 ): 682 – 686 . 24513290 10.1016/j.bbrc.2014.01.195

249. BJ , arthritis R : Autophagy: a dual role in the life and death of RASFs . Nat Rev Rheumatol . 2013 ; 9 ( 11 ): 637 . 10.1038/nrrheum.2013.148 24080860

250. Kato M , Ospelt C , Gay RE , Gay S , Klein K . Dual role of autophagy in stress-induced cell death in rheumatoid arthritis synovial fibroblasts . Arthritis Rheumatology . 2014 ; 66 ( 1 ): 40 – 48 . 24449574 10.1002/art.38190

251. Kukita A , Kukita T , Nagata K et al. The transcription factor FBI-1/OCZF/LRF is expressed in osteoclasts and regulates RANKL-induced osteoclast formation in vitro and in vivo . Arthritis Rheumatism . 2011 ; 63 ( 9 ): 2744 – 2754 . 21590684 10.1002/art.30455

252. Vomero M , Barbati C , Colasanti T et al. Autophagy and rheumatoid arthritis: current knowledges and future perspectives . Front Immunol . 2018 ; 9 : 1577 . 30072986 10.3389/fimmu.2018.01577 PMC6058034

253. Li G , Liu Y , Meng F et al. LncRNA MEG3 inhibits rheumatoid arthritis through miR-141 and inactivation of AKT/mTOR signalling pathway . J Cellular Molecular Medi . 2019 ; 23 ( 10 ): 7116 – 7120 . 10.1111/jcmm.14591 PMC6787440 31411001

254. Zhou H , Huang L , Zhan K , Liu X . Wenhua Juanbi recipe attenuates rheumatoid arthritis via inhibiting miRNA-146a-mediated autophagy . Biomed Res Int . 2022 ; 2022 : 1 . 10.1155/2022/1768052 PMC9683957 36440364

255. Yang S , Yin W , Ding Y , Liu F . Lnc RNA ZFAS1 regulates the proliferation, apoptosis, inflammatory response and autophagy of fibroblast-like synoviocytes via miR-2682-5p/ADAMTS9 axis in rheumatoid arthritis . Biosci Rep . 2020 ; 40 ( 8 ). doi: 10.1042/bsr20201273 . PMC7435024 32744323

256. Rodríguez-Paredes M , Esteller M . Cancer epigenetics reaches mainstream oncology . Nat Med . 2011 ; 17 ( 3 ): 330 – 339 . 21386836 10.1038/nm.2305

257. Yen CY , Huang HW , Shu CW et al. DNA methylation, histone acetylation and methylation of epigenetic modifications as a therapeutic approach for cancers . Cancer Lett . 2016 ; 373 ( 2 ): 185 – 192 . 26808576 10.1016/j.canlet.2016.01.036

258. Dhillon S . Decitabine/Cedazuridine: first Approval . Drugs . 2020 ; 80 ( 13 ): 1373 – 1378 . 32860582 10.1007/s40265-020-01389-7 PMC7708383

259. Suwanawiboon B , Sumida KN . 5-azacitidine: an alternative treatment of myelodysplastic syndromes in patient with refractory response to hematopoietic growth factor, a case report and review of literatures . Hawaii Med J . 2004 ; 63 ( 1 ): 14 – 16 ., 25 . 15011897

260. De Smedt E , Devin J , Muylaert C et al. G9a/GLP targeting in MM promotes autophagy-associated apoptosis and boosts proteasome inhibitor-mediated cell death . Blood Adv . 2021 ; 5 ( 9 ): 2325 – 2338 . 33938943 10.1182/bloodadvances.2020003217 PMC8114552

261. Rossetto D , Avvakumov N , Côté J . Histone phosphorylation: a chromatin modification involved in diverse nuclear events . Epigenetics . 2012 ; 7 ( 10 ): 1098 – 1108 . 22948226 10.4161/epi.21975 PMC3469451

262. Hottiger MO . Nuclear ADP-ribosylation and its role in chromatin plasticity, cell differentiation, and epigenetics . Annu Rev Biochem . 2015 ; 84 :( 1 ): 227 – 263 . 25747399 10.1146/annurev-biochem-060614-034506

263. Zhang Y . Transcriptional regulation by histone ubiquitination and deubiquitination . Genes Dev . 2003 ; 17 ( 22 ): 2733 – 2740 . 14630937 10.1101/gad.1156403

264. Shiio Y , Eisenman RN . Histone sumoylation is associated with transcriptional repression . Proc Natl Acad Sci USA . 2003 ; 100 ( 23 ): 13225 – 13230 . 14578449 10.1073/pnas.1735528100 PMC263760

265. Christophorou MA , Castelo-Branco G , Halley-Stott RP et al. Citrullination regulates pluripotency and histone H1 binding to chromatin . Nature . 2014 ; 507 ( 7490 ): 104 – 108 . 24463520 10.1038/nature12942 PMC4843970

266. Fujiki R , Hashiba W , Sekine H et al. GlcNAcylation of histone H2B facilitates its monoubiquitination . Nature . 2011 ; 480 ( 7378 ): 557 – 560 . 22121020 10.1038/nature10656 PMC7289526

267. Tsukada Y . Hydroxylation mediates chromatin demethylation . J Biochem . 2012 ; 151 ( 3 ): 229 – 246 . 22247561 10.1093/jb/mvs003

268. Howe FS , Boubriak I , Sale MJ et al. Lysine acetylation controls local protein conformation by influencing proline isomerization . Mol Cell . 2014 ; 55 ( 5 ): 733 – 744 . 25127513 10.1016/j.molcel.2014.07.004 PMC4157579

269. Li CJ , Cheng P , Liang MK et al. MicroRNA-188 regulates age-related switch between osteoblast and adipocyte differentiation . J Clin Invest . 2015 ; 125 ( 4 ): 1509 – 1522 . 25751060 10.1172/JCI77716 PMC4396470

270. Šmuc T , Ahn IY , Ulrich H . Nucleic acid aptamers as high affinity ligands in biotechnology and biosensorics . J Pharm Biomed Anal . 2013 ; 81-82 : 210 – 217 . 23666257 10.1016/j.jpba.2013.03.014

271. Liu J , Dang L , Li D et al. A delivery system specifically approaching bone resorption surfaces to facilitate therapeutic modulation of microRNAs in osteoclasts . Biomaterials . 2015 ; 52 : 148 – 160 . 25818421 10.1016/j.biomaterials.2015.02.007

272. Yao Y , Jia T , Pan Y et al. Using a novel microRNA delivery system to inhibit osteoclastogenesis . Int J Mol Sci . 2015 ; 16 ( 12 ): 8337 – 8350 . 25874760 10.3390/ijms16048337 PMC4425084