lncRNA ADAMTS9-AS2 Controls Human Mesenchymal Stem Cell Chondrogenic Differentiation and Functions as a ceRNA

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

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

The Role of Selenitetriglycerides in Enhancing Antioxidant Defense Mechanisms in Peripartum Holstein-Friesian Cows

The transition period in high-yielding dairy cows is a critical phase marked by an elevated risk of oxidative stress. This study evaluated the effect of oral selenitetriglyceride supplementation on oxidative stress management in periparturient cows. A controlled experiment was conducted on 12 cows, divided into two groups: the experimental group (STG) received selenitetriglycerides (0.5 mg Se/kg BW), while the control group (CON) was given a placebo, starting 12 days before calving until the calving day. Blood and liver tissue samples were collected at predetermined intervals around the time of parturition. The study observed a significant increase in serum selenium levels and NEFA stabilization in the STG group compared with the control. Antioxidant parameters indicated elevated GSH-Px and CAT concentrations in the STG group. Liver gene expression analysis revealed a significant increase in SOD2 mRNA levels in the STG group (FC = 4.68, p < 0.01). Conversely, GSH-Px3 expression significantly decreased (FC = 0.10, p < 0.05) on the 7th day postpartum in the CON group. However, SOD1, SOD3, and CAT expressions remained stable in both groups. These findings highlight the beneficial role of selenitetriglycerides in enhancing antioxidant capacity and influencing specific gene expressions associated with oxidative stress management in dairy cows during the peripartum period.

miR-20a-5p regulated SMAD6 to inhibit chondrogenesis of hDPSCs

OBJECTIVES

Chondrogenic differentiation of human dental pulp stem cells (hDPSCs) is highly promising for cartilage repair. The specific mechanism, however, still needs to be explicated.

MATERIALS AND METHODS

In this study, we isolated hDPSCs and transfected cells with lentiviruses containing an over-expression, knock-down, or negative control of miR-20a-5p. Three-D pellet cultures of hDPSCs were used for the chondrogenic induction. Following the pellet culture period, chondrogenesis was assessed by histological and immunohistochemical analysis and expression of chondrogenic-related genes. Dual-luciferase report assay was performed to determine potential targeted genes of miR-20a-5p, and the phosphorylation levels of P65 and IκBα were explored. Animal experiments were performed to determine the effect of miR-20a-5p on cartilage regeneration.

RESULTS

miR-20a-5p was showed to repress the expression of SMAD6 to inhibit the chondrogenic differentiation of hDPSCs. Accordingly, the knock-down of miR-20a-5p promoted cartilage regeneration in the osteochondral defects of rats. Mechanically, it is indicated that NF-κB signaling is the potential down-stream network of miR-20a-5p/Smad6 crosstalk during chondrogenic differentiation.

CONCLUSIONS

miR-20a-5p could target SMAD6 to activate NF-κB signaling pathway, and thus inhibit chondrogenesis of hDPSCs, which provided promising therapeutic target for cartilage defects clinically.

Unveiling Mesenchymal Stem Cells' Regenerative Potential in Clinical Applications: Insights in miRNA and lncRNA Implications

It is now widely recognized that mesenchymal stem cells (MSCs) possess the capacity to differentiate into a wide array of cell types. Numerous studies have identified the role of lncRNA in the regulation of MSC differentiation. It is important to elucidate the role and interplay of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the regulation of signalling pathways that govern MSC function. Furthermore, miRNAs and lncRNAs are important clinical for innovative strategies aimed at addressing a wide spectrum of existing and emerging disease. Hence it is important to consider their impact on MSC function and differentiation. Examining the data available in public databases, we have collected the literature containing the latest discoveries pertaining to human stem cells and their potential in both fundamental research and clinical applications. Furthermore, we have compiled completed clinical studies that revolve around the application of MSCs, shedding light on the opportunities presented by harnessing the regulatory potential of miRNAs and lncRNAs. This exploration of the therapeutic possibilities offered by miRNAs and lncRNAs within MSCs unveils exciting prospects for the development of precision therapies and personalized treatment approaches. Ultimately, these advancements promise to augment the efficacy of regenerative strategies and produce positive outcomes for patients. As research in this field continues to evolve, it is imperative to explore and exploit the vast potential of miRNAs and lncRNAs as therapeutic agents. The findings provide a solid basis for ongoing investigations, fuelling the quest to fully unlock the regenerative potential of MSCs.

Research progress on the regulation of bone marrow stem cells by noncoding RNAs in adolescent idiopathic scoliosis

Adolescent idiopathic scoliosis (AIS) is a common spinal deformity in young women, but its pathogenesis remains unclear. The primary pathogenic factors contributing to its development include genetics, abnormal bone metabolism, and endocrine factors. Bone marrow stem cells (BMSCs) play a crucial role in the pathogenesis of AIS by regulating its occurrence and progression. Noncoding RNAs (ncRNAs) are also involved in the pathogenesis of AIS, and their role in regulating BMSCs in patients with AIS requires further evaluation. In this review, we discuss the relevant literature regarding the osteogenic, chondrogenic, and lipogenic differentiation of BMSCs. The corresponding mechanisms of ncRNA-mediated BMSC regulation in patients with AIS, recent advancements in AIS and ncRNA research, and the importance of ncRNA translation profiling and multiomics are highlighted.

Knockdown of long noncoding RNA SAN rejuvenates aged adipose-derived stem cells via miR-143-3p/ADD3 axis

BACKGROUND

Senescent adipose-derived stem cells (ASCs) exhibit reduced therapeutic efficacy during wound healing. Transcriptional regulation factors including long noncoding RNAs (lncRNAs) reportedly have essential roles in stem cell aging. However, the mechanisms of which lncRNAs influence mesenchymal stem cell aging and how it works need further investigation.

METHODS

The expression patterns of lncRNA senescence-associated noncoding RNA (SAN) and miR-143-3p in ASCs obtained from old and young volunteer donors were detected by quantitative polymerase chain reaction. ASCs with overexpression or knockdown of SAN and γ-adducin (ADD3) were constructed by lentiviral transduction. Mimic and inhibitor were used to manipulate the cellular level of miR-143-3p in ASCs. The effects of these RNAs on ASCs proliferation, migration and cellular senescence were examined by EdU, transwell and senescence-activated β-galactosidase (SA-β-gal) staining assays. Wound scratch and tube formation assays were conducted to evaluate the capacities of ASCs in promoting fibroblasts migration and endothelial cells angiogenesis. Furthermore, dual-luciferase assays and rescue experiments were performed to identify the RNA interactions. Finally, the therapeutic effects of SAN-depleted aged ASCs were evaluated in a skin injury model.

RESULTS

The lncRNA SAN (NONHSAT035482.2) was upregulated in aged ASCs; it controlled cellular senescence in ASCs. lncRNA SAN knockdown in ASCs led to ASC functional enhancement and the inhibition of cellular senescence; it also promoted the effects of conditioned medium (CM) on endothelial cell tube formation and fibroblast migration. Mechanistic analysis showed that SAN serves as a sponge for miR-143-3p, thereby regulating the expression of ADD3. The application of SAN-depleted aged ASCs increased re-epithelialization, collagen deposition, neovascularization and led to accelerated skin wound closure, compared with transplantation of aged ASCs.

CONCLUSION

The lncRNA SAN mediates ASC senescence by regulating the miR-143-3p/ADD3 pathway, providing a potential target for rejuvenation of senescent ASCs and enhancement of wound repair.

LncRNA MRF drives the regulatory function on monocyte recruitment and polarization through HNRNPD-MCP1 axis in mesenchymal stem cells

Background

Mesenchymal stem cells (MSCs) exhibit two bidirectional immunomodulatory abilities: proinflammatory and anti-inflammatory regulatory effects. Long noncoding RNAs (lncRNAs) have important functions in the immune system. Previously, we performed high-throughput sequencing comparing lncRNA expression profiles between MSCs cocultured with or without CD14+ monocytes and screened out a new lncRNA termed lncRNA MCP1 regulatory factor (MRF). However, the mechanism of MRF in MSCs is still unknown.

Methods

MRF expression was quantified via qRT–PCR. RNA interference and lentiviruses were used to regulate MRF expression. The immunomodulatory effects of MSCs on monocytes were evaluated via monocyte migration and macrophage polarization assays. RNA pull-down and mass spectrometry were utilized to identify downstream factors of MRF. A dual-luciferase reporter assay was applied to analyze the transcription factors regulating MRF. qRT–PCR, western blotting and ELISAs were used to assess MCP1 expression. A human monocyte adoptive transfer mouse model was applied to verify the function of MRF in vivo.

Results

MRF was upregulated in MSCs during coculture with CD14+ monocytes. MRF increased monocyte recruitment by upregulating the expression of monocyte chemotactic protein (MCP1). Knockdown of MRF enhanced the regulatory effect of MSCs on restraining M1 polarization and facilitating M2 polarization. Mechanistically, MRF bound to the downstream protein heterogeneous nuclear ribonucleoprotein D (HNRNPD) to upregulate MCP1 expression, and the transcription factor interferon regulatory factor 1 (IRF1) activated MRF transcription early during coculture. The human monocyte adoptive transfer model showed that MRF downregulation in MSCs inhibited monocyte chemotaxis and enhanced the effects of MSCs to inhibit M1 macrophage polarization and promote M2 polarization in vivo.

Conclusion

We identified the new lncRNA MRF, which exhibits proinflammatory characteristics. MRF regulates the ability of MSCs to accelerate monocyte recruitment and modulate macrophage polarization through the HNRNPD-MCP1 axis and initiates the proinflammatory regulatory process in MSCs, suggesting that MRF is a potential target to improve the clinical effect of MSC-based therapy or correct MSC-related immunomodulatory dysfunction under pathological conditions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12929-022-00858-3.

YY1-induced lncRNA XIST inhibits cartilage differentiation of BMSCs by binding with TAF15 to stabilizing FUT1 expression

Introduction

The functional roles and mechanism of the XIST in osteoarthritis and the chondrogenic differentiation of BMSCs were clarified.

Methods

The expression levels of XIST, TAF15, FUT1 and YY1 were detected through quantitative RT-PCR. The protein expression of Sox9, ACAN, COL2A1 and FUT1 were detected by western blot and immunohistochemistry. The damage of cartilage tissue was detected by HE staining, and Safranin O-fast green. Alcian-Blue and Alizarin red S staining were performed to evaluate BMSCs chondrogenic differentiation. The relationship between XIST and TAF15, XIST and TAF15 were analyzed by RNA immunoprecipitation assay. Luciferase reporter assays and chromatin immunoprecipitation were performed to detect the interaction relationship between XIST and YY1. In addition, osteoarthritis mice were built to assess the function of XIST in vivo.

Results

The levels of XIST, TAF15 and FUT1 were upregulated in cartilage tissues from osteoarthritis patient. The level of XIST was decreased in BMSCs during chondrogenic differentiation. XIST overexpression inhibited the chondrogenic differentiation of BMSCs. Moreover, silencing of FUT1 reversed the effects of XIST overexpression on BMSCs chondrogenic differentiation. Mechanistically, in BMSCs, YY1 induced the expression of XIST in BMSCs, and XIST regulated FUT1 mRNA stability through targeting TAF15. Furthermore, silencing of XIST alleviated the symptoms of cartilage injury in OA mice.

Conclusion

Taken together, these results suggested that YY1 induced XIST was closely related to the chondrogenic differentiation of BMSCs and the progression of osteoarthritis by TAF15/FUT1 axis, and may be a new OA therapeutic target.

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XIST and TAF15 expression were upregulated in osteoarthritis.

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Overexpression of XIST suppressed the chondrogenic differentiation of BMSCs.

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XIST regulated BMSCs chondrogenic differentiation through enhancing FUT1 mRNA stability via TAF15.

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XIST silencing relieved cartilage damage in OA mice.

Whole Transcriptome Mapping Identifies an Immune- and Metabolism-Related Non-coding RNA Landscape Remodeled by Mechanical Stress in IL-1β-Induced Rat OA-like Chondrocytes

Background: Osteoarthritis (OA) is a common degenerative joint disease. The aims of this study are to explore the effects of mechanical stress on whole transcriptome landscape and to identify a non-coding transcriptome signature of mechanical stress.

Methods: Next-generation RNA sequencing (RNA-seq) was performed on IL-1β-induced OA-like chondrocytes stimulated by mechanical stress. Integrated bioinformatics analysis was performed and further verified by experimental validations.

Results: A total of 5,022 differentially expressed mRNAs (DEMs), 88 differentially expressed miRNAs (DEMIs), 1,259 differentially expressed lncRNAs (DELs), and 393 differentially expressed circRNAs (DECs) were identified as the transcriptome response to mechanical stress. The functional annotation of the DEMs revealed the effects of mechanical stress on chondrocyte biology, ranging from cell fate, metabolism, and motility to endocrine, immune response, and signaling transduction. Among the DELs, ∼92.6% were identified as the novel lncRNAs. According to the co-expressing DEMs potentially regulated by the responsive DELs, we found that these DELs were involved in the modification of immune and metabolism. Moreover, immune- and metabolism-relevant DELs exhibited a notable involvement in the competing endogenous RNA (ceRNA) regulation networks. Silencing lncRNA TCONS_00029778 attenuated cellular senescence induced by mechanical stress. Moreover, the expression of Cd80 was elevated by mechanical stress, which was rescued by silencing TCONS_00029778.

Conclusion: The transcriptome landscape of IL-1β-induced OA-like chondrocytes was remarkably remodeled by mechanical stress. This study identified an immune- and metabolism-related ncRNA transcriptome signature responsive to mechanical stress and provides an insight of ncRNAs into chondrocyte biology and OA.

Scrapie-Responsive Gene 1 Promotes Chondrogenic Differentiation of Umbilical Cord Mesenchymal Stem Cells via Wnt5a

Objective

Repair of cartilage defects, a common condition resulting from many factors, is still a great challenge. Based on their chondrogenic differentiation ability, mesenchymal stem cell- (MSC-) based cartilage regeneration is a promising approach for cartilage defect repair. However, MSC differentiation into chondroblasts or related cell lineages is elaborately controlled by stem cell differentiation stage factors and affected by an array of bioactive elements, which may impede the efficient production of target cells. Thus, identifying a single transcription factor to promote chondrogenic differentiation is critical. Herein, we explored the mechanism by which scrapie-responsive gene 1 (SCRG1), a candidate gene for cartilage regeneration promotion, regulates chondrogenic differentiation of MSCs.

Methods

Expression of SCRG1 was detected in umbilical cord-derived MSCs (UCMSCs) by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and immunohistochemical analysis during chondrogenic differentiation. The function of SCRG1 in chondrogenic potential was evaluated after gene knockdown or overexpression by lentiviral vectors. Finally, a rabbit cartilage defect model was established to evaluate the effect of SCRG1 on cartilage repair in vivo.

Results

Expression of SCRG1 was upregulated during in vitro chondrogenic differentiation of UCMSCs. SCRG1 knockdown inhibited chondrogenic differentiation of UCMSCs, while SCRG1 overexpression promoted chondrogenic differentiation of UCMSCs in vitro. In addition, UCMSC overexpressing SCRG1 promoted cartilage repair in vivo. Mechanistically, SCRG1 promoted chondrogenic differentiation via upregulation of Wnt5a expression and subsequent inhibition of β-catenin.

Conclusion

Our results showed that SCRG1 promotes chondrogenic differentiation of UCMSCs by inhibiting canonical Wnt/β-catenin signaling through Wnt5a. Our findings provide a future target for chondrogenic differentiation and cartilage regeneration.

Role of lncRNAs into Mesenchymal Stromal Cell Differentiation

Currently, findings support that 75% of the human genome is actively transcribed, but only 2% is translated into a protein, according to databases such as ENCODE (Encyclopedia of DNA Elements) [1]. The development of high-throughput sequencing technologies, computational methods for genome assembly and biological models have led to the realization of the importance of the previously unconsidered non-coding fraction of the genome. Along with this, noncoding RNAs have been shown to be epigenetic, transcriptional and post-transcriptional regulators in a large number of cellular processes [2]. Within the group of non-coding RNAs, lncRNAs represent a fascinating field of study, given the functional versatility in their mode of action on their molecular targets. In recent years, there has been an interest in learning about lncRNAs in MSC differentiation. The aim of this review is to address the signaling mechanisms where lncRNAs are involved, emphasizing their role in either stimulating or inhibiting the transition to differentiated cell. Specifically, the main types of MSC differentiation are discussed: myogenesis, osteogenesis, adipogenesis and chondrogenesis. The description of increasingly new lncRNAs reinforces their role as players in the well-studied field of MSC differentiation, allowing a step towards a better understanding of their biology and their potential application in the clinic.

The non-coding RNA interactome in joint health and disease

Non-coding RNAs have distinct regulatory roles in the pathogenesis of joint diseases including osteoarthritis (OA) and rheumatoid arthritis (RA). As the amount of high-throughput profiling studies and mechanistic investigations of microRNAs, long non-coding RNAs and circular RNAs in joint tissues and biofluids has increased, data have emerged that suggest complex interactions among non-coding RNAs that are often overlooked as critical regulators of gene expression. Identifying these non-coding RNAs and their interactions is useful for understanding both joint health and disease. Non-coding RNAs regulate signalling pathways and biological processes that are important for normal joint development but, when dysregulated, can contribute to disease. The specific expression profiles of non-coding RNAs in various disease states support their roles as promising candidate biomarkers, mediators of pathogenic mechanisms and potential therapeutic targets. This Review synthesizes literature published in the past 2 years on the role of non-coding RNAs in OA and RA with a focus on inflammation, cell death, cell proliferation and extracellular matrix dysregulation. Research to date makes it apparent that 'non-coding' does not mean 'non-essential' and that non-coding RNAs are important parts of a complex interactome that underlies OA and RA.

Integrated Analysis of Stemness-Related LncRNAs Helps Predict the Immunotherapy Responsiveness of Gastric Cancer Patients

The immune microenvironment plays a critical role in tumor biology. As a critical feature of cancers, stemness is acknowledged as a contributor to the development of drug resistance in gastric cancers (GCs). Long non-coding RNAs (lncRNAs) have been revealed to participate in this process. In this study, we aimed to develop a stemness-related lncRNA signature (SRLncSig) with guiding significance for immunotherapy. Three cohorts (TCGA, Zhongshan, and IMvigor210) were enrolled for analysis. A list of stemness-related lncRNAs (SRlncRNAs) was collected by co-expression strategy under the threshold of coefficient value >0.35 and p-value < 0.05. Cox and Lasso regression analysis was further applied to find out the SRlncRNAs with prognosis-predictive value to establish the SRLncSig in the TCGA cohort. IPS and TIDE algorithms were further applied to predict the efficacy of SRLncSig in TCGA and Zhongshan cohorts. IMvigor210 was composed of patients with clinical outcomes of immunotherapy. The results indicated that SRLncSig not only was confirmed as an independent risk factor for GCs but also identified as a robust indicator for immunotherapy. The patient with a lower SRLncSig score was more likely to benefit from immunotherapy, and the results were highly consistent in three cohorts. In conclusion, our study not only could clarify the correlations between stemness and immunotherapy in GC patients but also provided a model to guide the applications of immunotherapy in clinical practice.

Effects of miRNAs, lncRNAs and circRNAs on osteoporosis as regulatory factors of bone homeostasis (Review)

Osteoporosis is a common metabolic bone disorder typically characterized by decreased bone mass and an increased risk of fracture. At present, the detailed molecular mechanism underlying the development of osteoporosis remains to be elucidated. Accumulating evidence shows that non-coding (nc)RNAs, such as microRNAs (miRNAs), long ncRNAs (lncRNAs) and circular RNAs (circRNAs), play significant roles in osteoporosis through the post-transcriptional regulation of gene expression as regulatory factors. Previous studies have demonstrated that ncRNAs participate in maintaining bone homeostasis by regulating physiological and developmental processes in osteoblasts, osteoclasts and bone marrow stromal cells. In the present review, the latest research investigating the involvement of miRNAs, lncRNAs and circRNAs in regulating the differentiation, proliferation, apoptosis and autophagy of cells that maintain the bone microenvironment in osteoporosis is summarized. Deeper insight into the aspects of osteoporosis pathogenesis involving the deregulation of ncRNAs could facilitate the development of therapeutic approaches for osteoporosis.

The impact of non-coding RNAs on normal stem cells

Self-renewal and differentiation into diverse cells are two main characteristics of stem cells. These cells have important roles in development and homeostasis of different tissues and are supposed to facilitate tissue regeneration. Function of stem cells is regulated by dynamic interactions between external signaling, epigenetic factors, and molecules that regulate expression of genes. Among the highly appreciated regulators of function of stem cells are long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). Impact of miR-342-5p, miR-145, miR-1297, miR-204-5p, miR-132, miR-128-3p, hsa-miR-302, miR-26b-5p and miR-10a are among miRNAs that regulate function of stem cells. Among lncRNAs, AK141205, ANCR, MEG3, Pnky, H19, TINCR, HULC, EPB41L4A-AS1 and SNHG7 have important roles in the regulation of stem cells. In the current paper, we aimed at reviewing the importance of miRNAs and lncRNAs in differentiation of stem cells both in normal and diseased conditions. For this purpose, we searched PubMed/Medline and google scholar databases using "stem cell" AND "lncRNA", or "long non-coding RNA", or "microRNA" or "miRNA".

Comprehensive Analysis of Differentially Expressed Genes in Clinically Diagnosed Irreversible Pulpitis by Multiplatform Data Integration Using a Robust Rank Aggregation Approach

INTRODUCTION

Molecular diagnosis may overcome the limitations of clinical and histologic diagnosis in pulpitis, thereby benefiting many treatment techniques, such as vital pulp therapies. In this study, integrated microarray data on pulpitis were used to obtain a list of normalized differentially expressed (DE) genes for analyzing the molecular mechanisms underlying pulpitis and identifying potential diagnostic biomarkers.

METHODS

A systematic search of public microarray and sequencing databases was performed to obtain expression data of pulpitis. Robust rank aggregation (RRA) was used to obtain DE gene lists (RRA_DEmRNAs and RRA_DElncRNAs) between inflamed pulp and normal samples. DE genes were evaluated by functional enrichment analyses, correlation analyses for inflammation-related RRA_DEmRNAs, and protein-protein interaction and competing endogenous RNA network construction. Quantitative real-time polymerase chain reaction validation was applied in snap-frozen pulp tissues.

RESULTS

Using the GSE77459 and GSE92681 data sets, 280 RRA_DEmRNAs and 90 RRA_DElncRNAs were identified. RRA_DEmRNAs were significantly enriched in inflammation-related biological processes and osteoclast differentiation and tumor necrosis factor, chemokine, and B-cell receptor signaling pathways. The molecular complex detection and cytoHubba methods identified 2 clusters and 10 hub genes in the protein-protein interaction network. The competing endogenous RNA network was composed of 2 long noncoding RNAs (ADAMTS9-AS2 and LINC00290), 2 microRNAs (hsa-miR-30a-5p and hsa-miR-128-3p), and 3 messenger RNAs (ABCA1, FBLN5, and SOCS3). The expression between most top inflammation-related RRA_DEmRNAs in pulpitis showed positive correlations. Quantitative real-time polymerase chain reacation validated the expression trends of selected genes, including ITGAX, TREM1, CD86, FCGR2A, ADAMTS9-AS2, LINC00290, hsa-miR-30a-5p, hsa-miR-128-3p, RASGRP3, IL3RA, CCDC178, CRISPLD1, LINC01857, AC007991.2, ARHGEF26-AS1, and AL021408.1.

CONCLUSIONS

The identified biomarkers provide insight into the pathology and may aid in the molecular diagnosis of pulpitis.

IRF2-mediated upregulation of lncRNA HHAS1 facilitates the osteogenic differentiation of bone marrow-derived mesenchymal stem cells by acting as a competing endogenous RNA

BACKGROUND

Mesenchymal stem cells (MSCs) are the major source of osteoblasts. Long noncoding RNAs (lncRNAs) are abundantly expressed RNAs that lack protein-coding potential and play an extensive regulatory role in cellular biological activities. However, the regulatory network of lncRNAs in MSC osteogenesis needs further investigation.

METHODS

QRT-PCR, western blot, immunofluorescence, and immunohistochemistry assays were used to determine the levels of relevant genes. The osteogenic differentiation capability was evaluated by using Alizarin Red S (ARS) staining, alkaline phosphatase activity assays, hematoxylin & eosin staining or micro-CT. RNA fluorescence in situ hybridization (FISH) and RNAscope were used to detect HHAS1 expression in cells and bone tissue. A microarray assay was performed to identify differentially expressed microRNAs. RNA immunoprecipitation and RNA pull-down were used to explore the interactions between related proteins and nucleic acids.

RESULTS

The level of lncRNA HHAS1 increased during bone marrow-derived MSC (BMSC) osteogenesis and was positively related to the levels of osteogenic genes and ARS intensity. HHAS1 was located in both the cytoplasm and the nucleus and was expressed in human bone tissue. HHAS1 facilitated BMSC osteogenic differentiation by downregulating miR-204-5p expression and enhancing the level of RUNX family transcription factor 2 (RUNX2). In addition, interferon regulatory factor 2 (IRF2) was increased during BMSC osteogenic differentiation and interacted with the promoter of HHAS1, which resulted in the transcriptional activation of HHAS1. Furthermore, IRF2 and HHAS1 helped improve bone defect repair in vivo.

CONCLUSIONS

Our study identified a novel lncRNA, HHAS1, that facilitates BMSC osteogenic differentiation and proposed a role for the IRF2/HHAS1/miR-204-5p/RUNX2 axis in BMSC osteogenesis regulation. These findings help elucidate the regulatory network of BMSC osteogenesis and provide potential targets for clinical application.

Global transcriptomic analysis reveals Lnc-ADAMTS9 exerting an essential role in myogenesis through modulating the ERK signaling pathway

Background

Long non-coding RNAs (lncRNAs) are emerging key regulators involved in a variety of biological processes such as cell differentiation and development. The balance between myogenesis and adipogenesis is crucial for skeletal muscle homeostasis in humans and meat quality in farm animals. The present study aimed to reveal the global transcriptomic profiles of adipogenic (Adi-) and myogenic (Myo-) precursors derived from porcine skeletal muscle and identify lncRNAs involved in the modulation of myogenesis homeostasis in porcine skeletal muscle.

Results

In this study, a total of 655 novel individual lncRNAs including differentially expressed 24 lncRNAs, and 755 differentially expressed mRNAs were identified (fold change ≥2 or ≤ 0.5 and adjusted P < 0.05). Integrated results of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis accompanied by the variation of intracellular Ca²⁺ concentration highlighted Lnc-ADAMTS9 involved in the modulation of myogenesis homeostasis in porcine skeletal muscle. Although Lnc-ADAMTS9 knock-down did not alter the mRNA expression of ADAMTS9, we demonstrated that Lnc-ADAMTS9 can promote myogenic proliferation and myogenic differentiation of myogenic precursors through inhibiting the ERK/MAPK signaling pathway.

Conclusion

We deciphered a comprehensive catalog of mRNAs and lncRNAs that might be involved in the regulation of myogenesis and adipogenesis homeostasis in the skeletal muscle of pigs. The Lnc-ADAMTS9 exerts an essential role in myogenesis through the ERK signaling pathway.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40104-020-00524-4.

Characterization of exosomal long non-coding RNAs in chondrogenic differentiation of human adipose-derived stem cells

The exosomes derived from chondrogenic stem cells and long non-coding RNAs (lncRNAs) play a key role in cartilage regeneration. Here, we investigated the expression profile of exosomal lncRNAs in chondrogenesis of human adipose derived stem cells (hADSCs). hADSCs were induced to differentiate into chondrocytes in vitro. Exosomes from undifferentiated hADSCs and chondrogenic hADSCs were isolated. LncRNA and mRNA expression profiles in the isolated exosomes were analyzed by RNA sequencing. The resultant data were subjected to gene ontology (GO) terms and KEGG pathway analysis to identify differentially expressed lncRNAs. We identified 23 upregulated and 163 downregulated lncRNAs in exosomes derived from chondrogenic hADSCs compared to that in exosomes from undifferentiated hADSCs. In addition, analysis of mRNA expression data revealed 968 upregulated genes and 572 downregulated genes in exosomes of chondrogenic hADSCs. Lncrna and mRNA expression levels were further validated by qRT-PCR. Differentially expressed lncRNAs and mRNAs were utilized to construct a coding-non-coding gene co-expression network (CNC network). GO terms and KEGG pathway enrichment analysis revealed several significant processes differentially regulated between undifferentiated hADSCs and chondrogenic hADSCs. Taken together, this study revealed the differential expression of exosomal lncRNAs of chondrogenic hADSCs and provided a foundation for future study on the cartilage recovery mechanism of exosomes derived from chondrogenic stem cells.

The Current State of Research Regarding the Role of Non-Coding RNAs in Cutaneous Squamous Cell Carcinoma

Skin cancers, including those of both both melanoma and non-melanoma subtypes, remain among the most common forms of human cancer. Non-melanoma skin cancers are typically further differentiated into the basal cell carcinoma and cutaneous squamous cell carcinoma (cSCC) categories. Current approaches to diagnosing and treating cSCC remain unsatisfactory, and the prognosis for patients with this disease is relatively poor. Recent advances in high-throughput sequencing have led to an increasingly robust understanding of the diversity of non-coding RNAs (ncRNAs) expressed in both physiological and pathological contexts. These ncRNAs include microRNAs, long ncRNAs, and circular RNAs, all of which have been found to play key functional roles and/or to have value as diagnostic biomarkers or therapeutic targets in a range of different disease contexts. The number of ncRNAs associated with cSCC continues to rise, and as such, there is clear value in comprehensively reviewing the functional roles of these molecules in this form of cancer in order to highlight future avenues for research and clinical development.

Regulation of bone marrow mesenchymal stem cell fate by long non-coding RNA

Bone mesenchymal stem cells (BMSCs) are progenitor cells isolated from bone marrow, which keep potential to differentiate into several kinds of cells including osteoblasts and adipocytes. A dynamic mutual regulation exists between osteogenesis and adipogenesis processes. Long non-coding RNA (lncRNA) performs diverse functions in biological activities including regulation of BMSCs commitment. Evidence has shown that lncRNA regulates key signaling pathways including TGFβ/BMP, Wnt and Notch pathways, and several transcription factors in BMSCs differention. Dysregulation of lncRNA in BMSCs leads to disruption of osteo-adipogenesis difffrentiation and results in impairment of bone homeostasis. In this review, we focus on the role of lncRNA in several critical signaling pathways that involved in regulation of osteo-adipogenesis of BMSC and prospects the potential clinical application of lncRNA.

Down-Regulation of Lnc-CYP7A1-1 Rejuvenates Aged Human Mesenchymal Stem Cells to Improve Their Efficacy for Heart Repair Through SYNE1

Background

Several long non-coding RNAs (lncRNAs) have been associated with cell senescence, termed senescence-associated lncRNAs (SAL-RNAs). However, the mechanisms involved for SAL-RNAs in aging are not fully elucidated. In the present study, we investigated the effects of SAL-RNAs on aged human bone marrow-derived mesenchymal stem cells (hBM-MSCs), and the possible means to counteract such effects to improve the regenerative capacity of aged hBM-MSCs.

Methods

By comparing the lncRNAs expression of hBM-MSCs derived from young and old individuals, lnc-CYP7A1-1 was identified as being significantly increased with age. Using predictive software, the expression of Spectrin Repeat Containing Nuclear Envelope Protein 1 (SYNE1), was found to be decreased with age. Next, through lentiviral constructs, we downregulated the expression of lnc-CYP7A1-1 or SYNE1 in hBM-MSCs separately. Additionally, hBM-MSCs proliferation, survival, migration, and senescence were investigated in vitro. In vivo, lnc-CYP7A1-1 downregulated aged hBM-MSCs were implanted into infarcted mouse hearts after myocardial infarction (MI), and cardiac function was measured. Through lentivirus-mediated downregulation of lnc-CYP7A1-1 in aged hBM-MSCs, we revealed that cell senescence was decreased, whereas cell proliferation, migration, and survival were increased. On the other hand, downregulation of SYNE1, the target gene of lnc-CYP7A1-1, in young hBM-MSCs increased cell senescence, yet decreased cell proliferation, migration, and survival. Downregulation of lnc-CYP7A1-1 in aged hBM-MSCs induced cell rejuvenation, yet this effect was attenuated by repression of SYNE1. In vivo, transplantation of lnc-CYP7A1-1 downregulated old hBM-MSCs improved cardiac function after MI.

Conclusion

Down-regulation of lnc-CYP7A1-1 rejuvenated aged hBM-MSCs and improved cardiac function when implanted into the infarcted mouse hearts, possibly through its target gene SYNE1.

Platelet lysate induces chondrogenic differentiation of umbilical cord-derived mesenchymal stem cells by regulating the lncRNA H19/miR-29b-3p/SOX9 axis

Platelet lysate (PL) has been shown to induce chondrogenic differentiation of human umbilical cord‐derived mesenchymal stem cells (hUCMSCs). However, the underlying mechanism is still not clear. The aim of this study was to investigate whether long noncoding RNA H19 is involved in this process. hUCMSCs were isolated, identified and cultured in 5% PL‐supplemented chondrogenic differentiation medium. Chondrogenic differentiation was assessed by Alcian blue staining. The expressions of H19, miR‐29b‐3p, SRY‐related high‐mobility‐group box 9 (SOX9), collagen II and aggrecan were determined by quantitative real‐time PCR and western blot. The interaction between miR‐29b‐3p and H19 or SOX9 was analyzed by luciferase reporter assay. During PL‐induced chondrogenic differentiation of hUCMSCs, expressions of H19 and SOX9 were increased, whereas miR‐29b‐3p expression was decreased. H19 overexpression promoted, whereas H19 silencing attenuated the PL‐induced chondrogenic differentiation of hUCMSCs. SOX9 was identified as a direct target of miR‐29b‐3p, and H19 was observed to act as a sponge of miR‐29b‐3p to up‐regulate SOX9 expression. The chondrogenic differentiation‐promoting effect of H19 overexpression was negated when miR‐29b‐3p expression was up‐regulated by Lenti‐miR‐29b‐3p infection. In conclusion, PL induced chondrogenic differentiation of hUCMSCs by regulating the H19/miR‐29b‐3p/SOX9 axis.

DLX5 and HOXC8 enhance the chondrogenic differentiation potential of stem cells from apical papilla via LINC01013

BACKGROUND

Mesenchymal stem cell (MSC)-based cartilage tissue regeneration is a treatment with great potential. How to enhance the MSC chondrogenic differentiation is a key issue involved in cartilage formation. In the present study, we seek to expound the phenotypes and mechanisms of DLX5 in chondrogenic differentiation function in MSCs.

METHODS

Stem cells from apical papilla (SCAPs) were used. The Alcian Blue staining, pellet culture system, and cell transplantation in rabbit knee cartilage defect were used to evaluate the chondrogenic differentiation function of MSCs. Western blot, real-time RT-PCR, and ChIP assays were used to evaluate the molecular mechanisms.

RESULTS

DLX5 and HOXC8 expressions were upregulated during chondrogenic differentiation. In vitro results showed that DLX5 and HOXC8 enhanced the expression of chondrogenic markers including collagen II (COL2), collagen V (COL5), and sex-determining region Y box protein 9 (SOX9) and promoted the chondrogenic differentiation and the formation of cartilage clumps in the pellet culture system. Mechanically, DLX5 and HOXC8 formed protein complexes and negatively regulated the LncRNA, LINC01013, via directly binding its promoter. In vivo transplantation experiment showed that DLX5 and HOXC8 could restore the cartilage defect in the rabbit knee model. In addition, knock-down of LINC01013 enhanced the chondrogenic differentiation of SCAPs.

CONCLUSIONS

In conclusion, DLX5 and HOXC8 enhance the chondrogenic differentiation abilities of SCAPs by negatively regulating LINC01013 in SCAPs, and provided the potential target for promoting cartilage tissue regeneration.

lncRNA LIFR-AS1 suppresses invasion and metastasis of non-small cell lung cancer via the miR-942-5p/ZNF471 axis

Background

MicroRNA 942-5p (miR-942-5p) has been reported to promote migration and invasion in non-small cell lung cancer (NSCLC), but the underlying mechanism is not completely understood. The interplay between long non-coding RNAs (lncRNAs) and miRNAs plays a crucial role in tumor progression.

Methods

In the present study, we performed bioinformatic and biochemical analyses to identify miR-942-5p-interacting lncRNAs. The function and clinical significance of the candidate lncRNA(s) in NSCLC were determined.

Results

We identified LIFR-AS1 as a pivotal miR-942-5p-interacting lncRNA. Overexpression of miR-942-5p caused a reduction of LIFR-AS1 in NSCLC cells. LIFR-AS1 showed the ability to sponge miR-942-5p, leading to derepression of ZNF471. Functionally, LIFR-AS1 overexpression inhibited NSCLC cell migration and invasion, whereas LIFR-AS1 silencing yielded an opposite effect. In vivo studies confirmed that LIFR-AS1 overexpression suppressed lung metastasis of NSCLC cells. Rescue experiments demonstrated that enforced expression of miR-942-5p or depletion of ZNF471 restored the migration and invasion capacity of LIFR-AS1-overexpressing cells. Moreover, overexpression of ZNF471 restrained NSCLC cell invasion. Clinically, LIFR-AS1 downregulation was significantly correlated with TNM stage, lymph node metastasis, and reduced overall survival in NSCLC patients.

Conclusions

we provide first evidence for the involvement of the LIFR-AS1/miR-942-5p/ZNF471 axis in NSCLC invasion and metastasis. LIFR-AS1 may represent a novel target for the treatment of NSCLC.

Long noncoding RNA RUSC1-AS1 promotes tumorigenesis in cervical cancer by acting as a competing endogenous RNA of microRNA-744 and consequently increasing Bcl-2 expression

The expression of a long noncoding RNA termed RUSC1-AS1 is dysregulated in breast cancer and laryngeal squamous cell carcinoma, and this dysregulation affects various tumor-associated biological processes. To our knowledge, the expression status and detailed roles of RUSC1-AS1 in cervical cancer as well as its regulatory mechanisms of action remain unknown. Therefore, the objectives of this study were to measure RUSC1-AS1 expression in cervical cancer, investigate the effects of RUSC1-AS1 on cervical cancer cells, and identify the mechanism underlying these effects. Herein, RUSC1-AS1 was found to be highly expressed in cervical cancer tissues and cell lines. High RUSC1-AS1 expression significantly correlated with the International Federation of Gynecology and Obstetrics (FIGO) stage, lymph node metastasis, and shorter overall survival among the patients with cervical cancer. Functional assays revealed that interference with RUSC1-AS1 expression suppressed cervical cancer cell proliferation, migration, and invasion in vitro; induced apoptosis in vitro; and impeded tumor growth in vivo. In addition, RUSC1-AS1 was demonstrated to act as a competing endogenous RNA of microRNA-744 (miR-744) and consequently increase B-cell lymphoma 2 (Bcl-2 or BCL2) expression levels in cervical cancer cells. Furthermore, either inhibition of miR-744 or restoration of Bcl-2 expression neutralized the effects of the RUSC1-AS1 silencing on the malignant characteristics of cervical cancer cells. Thus, RUSC1-AS1 promotes the aggressiveness of cervical cancer in vitro and in vivo by upregulating miR-744-Bcl-2 axis output. The RUSC1-AS1-miR-744-Bcl-2 pathway may be involved in cervical cancer pathogenesis and could serve as a novel target for anticancer therapies.

The role and mechanism of lncRNA NEAT1 in the fibrosis of pulmonary epithelial cell

Background

Pulmonary fibrosis is a serious clinical fatal disease. Epithelial–mesenchymal transition (EMT) and lncRNA NEAT1 have been implied in its development and progression.

Objective

To study the role of lncRNA NEAT1 in the progression of fibrosis in human pulmonary epithelial cells (BEAS-2B). Specifically, BEAS-2B was transfected with NEAT1 and miR-29c, EMT and cell proliferation were measured and the expression level of relevant genes was determined by Western blot.

Result

Results showed that NEAT1 promotes fibrosis and proliferation of BEAS-2B cells via the up-regulation of α-SMA, Vimentin, Snail and proliferation-related genes including Cyclin D1 and Cyclin E; miR-29c is a target gene of NEAT1 and through which NEAT1 regulates EMT and expression of proliferation-related genes.

Conclusion

This study investigated the mechanism of pulmonary fibrosis progression by elucidating the role of NEAT1/miR-29c in the fibrosis and proliferation of BEAS-2B cells, thus providing a basis for the new therapeutic targets of pulmonary fibrosis.

Microarray expression profiles and bioinformatics analysis of mRNAs, lncRNAs, and circRNAs in the secondary temozolomide-resistant glioblastoma

Temozolomide is a first line anti-tumor drug used for the treatment of patients with Glioblastoma multiforme (GBM). However, the drug resistance to temozolomide limits its clinical application. Therefore, novel strategies to overcome chemoresistance are desperately needed for improved treatment of human GBM. Here, we simultaneously detected, for the first time, the expression profiles of mRNAs, lncRNAs, and circRNAs in three pairs of secondary temozolomide-resistant glioblastoma (STRG) and matched primary glioblastoma tissues by microarrays. Using these data, we discovered a total of 92 mRNA, 299 lncRNAs and 53 circRNAs were altered in human glioma tissue after chemotherapy with temozolomide. The functions of differentially expressed lncRNAs, circRNAs were annotated by analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). The results showed that the highest enriched GO terms of the upregulated lncRNAs were embryonic forelimb morphogenesis (BP), extracellular space (CC), and serine-type endopeptidase activity (MF). Meanwhile, GO:0035360(BP), PRC1 complex (CC), and ubiquitin-protein transferase activity (MF) were the highest enriched GO terms targeted by downregulated lncRNAs. The NF-kappa B signaling pathway were significantly enriched in the STRG. However, circRNAs highest enriched GO term was viral process, chromosome, and protein transporter activity, respectively. KEGG pathway analysis showed that circRNAs in the network were enriched in ErbB signaling pathway. Furthermore, we also predicted the potential role of these differentially expressed ncRNAs and constructed a network of lncRNAs-mRNAs and circRNAs-miRNAs to show their interactions. After a series of bioinformatics analyses, we found that low expression of NONHSAT163779 and high expression of circ_0043949 are closely related to the chemoresistance of STRG. Our findings revealed the alteration of expression patterns of mRNAs, lncRNAs, and circRNAs in the secondary temozolomide-resistant glioblastoma for the first time. NONHSAT163779 and hsa_circ_0043949 might be potential therapeutic targets and prognostic biomarkers for the treatment of glioblastoma.

Retracted Article: Long non-coding RNA MEG3 inhibits cell proliferation, migration, invasion and enhances apoptosis in non-small cell lung cancer cells by regulating the miR-31-5p/TIMP3 axis

Non-small cell lung cancer (NSCLC) is a malignant lung cancer and accounts for 80% of lung cancer-related deaths. Long non-coding RNA maternally expressed gene 3 (MEG3) has been identified as a tumor suppressor in multiple cancers. However, the regulatory mechanism of MEG3 in NSCLC development is still largely unknown. The expression levels of MEG3, microRNA-31-5p (miR-31-5p) and tissue inhibitor of metalloproteinase 3 (TIMP3) in NSCLC tumors and cells were measured by quantitative real time polymerase chain reaction (qRT-PCR). Cell viability, apoptosis, migration and invasion were detected by cell counting kit-8 (CCK-8), flow cytometry, western blotting and transwell assays, respectively. Xenograft mouse models were established by subcutaneously injecting NSCLC cells stably transfected with Lenti-pcDNA or Lenti-MEG3. The interaction between miR-31-5p and MEG3 or TIMP3 was validated by luciferase reporter and RNA immunoprecipitation (RIP) assays. MEG3 and TIMP3 levels were up-regulated, whereas miR-31-5p expression was down-regulated in NSCLC tumors and cells compared with normal tissues and cells. Overexpression of MEG3 repressed cell proliferation, migration and invasion, but induced apoptosis in NSCLC cells. More importantly, MEG3 effectively hindered tumor growth in vivo. Next, luciferase reporter and RIP assays confirmed the interaction between miR-31-5p and MEG3 or TIMP3. Pearson's correlation coefficient revealed that miR-31-5p was inversely correlated with MEG3 or TIMP3. Rescue experiments indicated that MEG3 regulated TIMP3 expression by sponging miR-31-5p in NSCLC cells. Thus, MEG3 inhibited cell proliferation, migration and invasion, but enhanced apoptosis in NSCLC cells through up-regulating TIMP3 expression by regulating miR-31-5p, indicating novel biomarkers for the therapy of NSCLC.

Non-small cell lung cancer (NSCLC) is a malignant lung cancer and accounts for 80% of lung cancer-related deaths.