Comprehensive analysis of an lncRNA-miRNA-mRNA competing endogenous RNA network in pulpitis

Ferroptosis: A New Challenge and Target in Oral Diseases

OBJECTIVE

Ferroptosis, an iron-dependent intracellular programmed cell death mechanism discovered in the last decade, has emerged as a novel and intriguing concept in oral diseases, distinct from apoptosis, necrosis, and pyroptosis. This process plays a critical role in the pathophysiology of inflammation, trauma, and tumors, with evidence of its presence in multiple organ systems, including the liver, kidneys, and heart. In recent years, many studies have found that ferroptosis is closely related to oral diseases, and a number of pathogenic pathways and therapeutic strategies have been reported. However, ferroptosis remains an underexplored area in oral diseases, with multiple secrets waiting to be uncovered.

METHOD

We collected articles related to ferroptosis and oral diseases and analyzed the mechanisms and therapeutic strategies associated with ferroptosis in different oral diseases.

RESULTS

In this review, we present a comprehensive analysis of ferroptosis and oral diseases, emphasizing its core mechanisms and associated therapeutic approaches. Furthermore, we give an outlook for future explorations of ferroptosis related to oral diseases.

CONCLUSION

This review provides dental researchers and clinicians with a current state of ferroptosis in oral diseases, thereby inspiring noval investigations and discoveries.

Identification of pain-related long non-coding RNAs for pulpitis prediction

OBJECTIVES

We investigated the recently generated RNA-sequencing dataset of pulpitis to identify the potential pain-related lncRNAs for pulpitis prediction.

MATERIALS AND METHODS

Differential analysis was performed on the gene expression profile between normal and pulpitis samples to obtain pulpitis-related genes. The co-expressed gene modules were identified by weighted gene coexpression network analysis (WGCNA). Then the hypergeometric test was utilized to screen pain-related core modules. The functional enrichment analysis was performed on the up- and down-regulated genes in the core module of pulpitis pain to explore the underlying mechanisms. A pain-related lncRNA-based classification model was constructed using LASSO. Consensus clustering and gene set variation analysis (GSVA) on the infiltrating immunocytes was used for pulpitis subtyping. miRanda predicts miRNA-target relationship, which was filtered by expression correlation. Hallmark pathway and enrichment analysis was performed to investigate the candidate target pathways of the lncRNAs.

RESULTS

A total of 1830 differential RNAs were identified in pulpitis. WGCNA explored seven co-expressed modules, among which the turquoise module is pain-related with hypergeometric test. The up-regulated genes were significantly enriched in immune response related pathways. Down-regulated genes were significantly enriched in differentiation pathways. Eight lncRNAs in the pain-related module were related to inflammation. Among them, MIR181A2HG was downregulated while other seven lncRNAs were upregulated in pulpitis. The LASSO classification model revealed that MIR181A2HG and LINC00426 achieved outstanding predictive performances with perfect ROC-AUC score (AUC = 1). We differentiated the pulpitis samples into two progression subtypes and MIR181A2HG is a progressive marker for pulpitis. The miRNA-mRNA-lncRNA regulatory network of pulpitis pain was constructed, with GATA3 as a key transcription factor. NF-kappa B signaling pathway is a candidate pathway impacted by these lncRNAs.

CONCLUSIONS

PCED1B-AS1, MIAT, MIR181A2HG, LINC00926, LINC00861, LINC00528, LINC00426 and ITGB2-AS1 may be potential markers of pulpitis pain. A two-lncRNA signature of LINC00426 and MIR181A2HG can accurately predict pulpitis, which could facilitate the molecular diagnosis of pulpitis. GATA3 might regulate these lncRNAs and downstream NF-kappa B signaling pathway.

CLINICAL RELEVANCE

This study identified potential pain-related lncRNAs with underlying molecular mechanism analysis for the prediction of pulpitis. The classification model based on lncRNAs will facilitate the early diagnosis of pulpitis.

Developing a ceRNA-based lncRNA-miRNA-mRNA regulatory network to uncover roles in skeletal muscle development

The precise role of lncRNAs in skeletal muscle development and atrophy remain elusive. We conducted a bioinformatic analysis of 26 GEO datasets from mouse studies, encompassing embryonic development, postnatal growth, regeneration, cell proliferation, and differentiation, using R and relevant packages (limma et al.). LncRNA-miRNA relationships were predicted using miRcode and lncBaseV2, with miRNA-mRNA pairs identified via miRcode, miRDB, and Targetscan7. Based on the ceRNA theory, we constructed and visualized the lncRNA-miRNA-mRNA regulatory network using ggalluvial among other R packages. GO, Reactome, KEGG, and GSEA explored interactions in muscle development and regeneration. We identified five candidate lncRNAs (Xist, Gas5, Pvt1, Airn, and Meg3) as potential mediators in these processes and microgravity-induced muscle wasting. Additionally, we created a detailed lncRNA-miRNA-mRNA regulatory network, including interactions such as lncRNA Xist/miR-126/IRS1, lncRNA Xist/miR-486-5p/GAB2, lncRNA Pvt1/miR-148/RAB34, and lncRNA Gas5/miR-455-5p/SOCS3. Significant signaling pathway changes (PI3K/Akt, MAPK, NF-κB, cell cycle, AMPK, Hippo, and cAMP) were observed during muscle development, regeneration, and atrophy. Despite bioinformatics challenges, our research underscores the significant roles of lncRNAs in muscle protein synthesis, degradation, cell proliferation, differentiation, function, and metabolism under both normal and microgravity conditions. This study offers new insights into the molecular mechanisms governing skeletal muscle development and regeneration.

Current Insights into the Roles of LncRNAs and CircRNAs in Pulpitis: A Narrative Review

Pulpitis, an inflammation of the dental pulp, is generated by bacterial invasion through different ways as caries. In the establishment and development of this disease, different biological processes are involved. Long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are transcripts with regulatory capacity participating in different biological functions and have been implicated in different diseases. The aim of this narrative review is to critically analyze available evidence on the biological role of lncRNAs and circRNAs in pulpitis and discuss possible new research prospects. LncRNAs and circRNAs involved in pulpitis were explored, addressing their expression, molecular mechanisms, targets and biological effects studied in animal and in vitro models, as well as in studies in human patients. LncRNAs and circRNAs are emerging as key regulators of diverse biological functions in pulpitis including apoptosis, proliferation, differentiation, oxidative stress, autophagy, ferroptosis, inflammation and immune response. The molecular mechanisms performed by these non-coding RNAs (ncRNAs) involved interactions with miRNAs and the formation of regulatory networks in the context of pulpitis. Further studies more deeply analyzing the participation of lncRNAs and circRNAs in pulpitis will reveal the potential applications of these ncRNAs as biomarkers or their use in therapeutic strategies in pulp inflammation.

Osteopontin interacts with dendritic cells and macrophages in pulp inflammation: Comprehensive transcriptomic analysis and laboratory investigations

AIM

To investigate novel diagnostic markers for pulpitis and validate by clinical samples from normal and inflamed pulp. To explore the relationship between diagnostic markers and immune cells or their phenotypes during pulp inflammation.

METHODOLOGY

Two microarray datasets, GSE77459 and GSE92681, and identified differential expression genes were integrated. To understand immune features, gene functions, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Disease Ontology (DO) and ImmuneSigDB Gene Set Enrichment Analysis (GSEA) were analysed. For predictive purposes, machine learning techniques were applied to detect diagnostic markers. Immune infiltration in inflamed pulp was studied using CIBERSORT. The relationship between diagnostic markers and immune cells was investigated and validated their gene expression in clinical samples from the normal or inflamed pulp by qRT-PCR. Finally, the correlation between one marker, secreted phosphoprotein 1 (SPP1), encoding osteopontin (OPN), and dendritic cells (DCs)/macrophages was identified via HE staining and multiplex immunohistochemistry. An in vitro inflammatory dental pulp microenvironment model of THP-1 macrophages cocultured with dental pulp cells derived conditioned media (DPCs-CM) to investigate OPN production and macrophage phenotypes was established.

RESULTS

Analysis revealed unique immunologic features in inflamed pulp. Three diagnostic markers for pulpitis: endothelin-1 (EDN1), SPP1, and purine nucleoside phosphorylase (PNP), and validated them using qRT-PCR were predicted. Multiplex immunohistochemistry demonstrated OPN co-localized with activated DCs and M2 macrophages during pulp inflammation. In vitro experiments showed that THP-1 macrophages produced the highest levels of OPN when stimulated with DPCs-CM derived from the 20 μg/mL LPS pre-conditioned group, suggesting an M2b-like phenotype by increasing surface marker CD86 and expression of IL6, TNFα, IL10, and CCL1 but not CCL17 and MerTK. Levels of CCL1 and IL10 elevated significantly in the macrophages' supernatant from the 20 μg/mL LPS pre-conditioned CM group. OPN was proven co-localizing with CD86 in the inflamed pulp by immunofluorescence.

CONCLUSIONS

The current findings suggest that OPN can serve as a promising biomarker for pulpitis, correlated with DCs and macrophages. OPN+ macrophages in the inflamed pulp are associated with M2b-like phenotypes. These insights offer the potential for improved diagnosis and targeted therapy.

DUXAP8 Promotes LPS-Induced Cell Injury in Pulpitis by Regulating miR-18b-5p/HIF3A

BACKGROUND

The dysregulated long noncoding RNAs (lncRNAs) are implicated in progression of various diseases, including pulpitis. Double homeobox A pseudogene 8 (DUXAP8) has been found to be upregulated in pulpitis. Herein, the functional mechanism of DUXAP8 in lipopolysaccharide (LPS)-induced pulpitis was explored.

MATERIAL AND METHODS

DUXAP8, microRNA-18b-5p (miR-18b-5p), or hypoxia-inducible factor 3A (HIF3A) levels were examined through reverse transcription-quantitative polymerase chain reaction assay. Cell behaviours were determined by Cell Counting Kit-8 assay for cell viability, Ethynyl-2'-deoxyuridine (EdU) assay for cell proliferation, and flow cytometry for cell apoptosis. Protein levels were measured using western blot. Inflammatory reaction was analysed via enzyme-linked immunosorbent assay. Oxidative stress was assessed by commercial kits. Dual-luciferase reporter assay, RNA immunoprecipitation assay, and pull-down assay were used for validation of interaction between targets.

RESULTS

Cell apoptosis, inflammatory reaction, and oxidative stress were induced by LPS in human dental pulp cells (HDPCs). DUXAP8 upregulation and miR-18b-5p downregulation were found in pulpitis. LPS-induced cell injury was relieved after downregulation of DUXAP8. DUXAP8 interacted with miR-18b-5p. The regulation of DUXAP8 was related to miR-18b-5p sponging function in LPS-treated HDPCs. HIF3A served as a target of miR-18b-5p. MiR-18b-5p protected against LPS-induced cell injury through targeting HIF3A. DUXAP8 targeted miR-18b-5p to regulate HIF3A level.

CONCLUSIONS

Results demonstrated that LPS-induced cell injury in pulpitis was promoted by DUXAP8 through mediating miR-18b-5p/HIF3A axis.

Dysregulation of MicroRNA-152-3p is Associated with the Pathogenesis of Pulpitis by Modulating SMAD5

PURPOSE

To research the role of microRNA (miR)-152 in the pathogenesis of pulpitis using a cell model based on human dental pulp cells (HDPCs) treated with lipopolysaccharides (LPS).

MATERIALS AND METHODS

The biological activity of HDPCs infected by LPS was measured using a cell counting kit (CCK-8), Transwell test, flow cytometry, and fluorescent quantitative PCR. The concentration of superoxide dismutase (SOD) and malondialdehyde (MDA) was evaluated using an assay kit, the levels of interleukin (IL)-1β and IL-6 were measured by enzyme-linked immunosorbent assay (ELISA), and the targeting relationship between SMAD5 and miR-152 was measured by the double-luciferase report test. The expression of cell cycle-related CyclinD1 and BAX was assessed by PCR. By plotting a receiver operating characteristic (ROC) curve, the diagnostic value of miR-152 was shown.

RESULTS

The level of miR-152 in HDPCs induced by LPS decreased, while the level of SMAD5 increased. After overexpressing miR-152 in LPS-induced HDPCs, the viability was elevated, the apoptosis rate decreased, CyclinD1 was elevated, BAX diminished, the inflammatory cytokines (IL-6 and IL-1β) were inhibited, the activity of SOD increased, and the MDA content decreased. miR-152 targeted regulation of SMAD5, and SMAD5 modulated the effects of miR-152 on cell viability, apoptosis, inflammation, and the oxidative response of HDPCs. Reduced miR-152 expression was verified in patients with pulpitis, which could be a biomarker for pulpitis.

CONCLUSION

miR-152 was found to be a biomarker correlated with the pathogenesis of pulpitis and the biological behaviour of HDPCs.

Identification and characterization of the ferroptosis-related ceRNA network in irreversible pulpitis

Background

The role of ferroptosis in irreversible pulpitis (IP) remains unclear. The competing endogenous RNA (ceRNA) theory that has been widely investigated is rarely used studied in IP. Hub lncRNAs selected from a ceRNA network may provide a novel hypothesis for the interaction of ferroptosis and IP.

Methods

Differentially expressed genes (DEGs) were intersected with 484 ferroptosis markers to identify differentially expressed ferroptosis-related genes (DE-FRGs). Functional analysis and protein-protein interaction (PPI) networks were constructed to reveal the functions of DE-FRGs. Then, coexpression analyses were conducted between DE-FRGs and DElncRNAs to define ferroptosis-related DElncRNAs (FR-DElncRNAs). Predictions of DE-FRG- and FR-DElncRNA-related miRNAs were obtained, and members of both groups were selected. Additionally, two ceRNA networks consisting of FR-DElncRNAs, miRNAs and DE-FRGs from upregulated and downregulated groups were built. Finally, the hub lncRNAs of the ceRNA networks were used for immuno-infiltration analysis and qPCR verification.

Results

According to the results of PCA and clustering analysis, 5 inflamed and 5 healthy pulp tissue samples were selected for analysis. The intersection of DEGs with 484 ferroptosis marker genes identified 72 DE-FRGs. The response to stimulus, cellular process, signaling, localization, and biological regulation pathways related to DE-FRGs were enriched. In total, 161 downregulated and 40 upregulated FR-DElncRNAs were chosen by coexpression analysis for further investigation. The MultimiR package and starBase were used to predict miRNAs of DE-FRGs and FR-DElncRNAs, respectively. The upregulated ceRNA network contained 2 FR-DElncRNAs (↑), 19 miRNAs (↓) and 22 DE-FRGs (↑). The downregulated network contained 44 FR-DElncRNAs (↓), 251 miRNAs (↑) and 10 DE-FRGs (↓). Six hub lncRNAs were identified based on the MCC method (LUCAT1 and AC106897.1 ↑; LINC00943, AL583810.1, AC068888.1, and AC125257.1↓). In addition, strong relationships between hub lncRNAs and immune cells were shown by immune infiltration analysis. Finally, validated by qPCR assays of the pulp tissue of IP patients, the expression levels in clinical samples were consistent with the microarray data.

Conclusion

Two ceRNA networks were comprehensively constructed, and 6 hub lncRNAs were identified. These genes provide novel insights into the relationship between ferroptosis and IP. Intriguingly, the LINC00943/hsa-miR-29a-3p/PDK4 axis was deemed to be the key node in this network.

Establishment and validation of the autophagy-related ceRNA network in irreversible pulpitis

BACKGROUND

The molecular mechanisms underlying the onset and progression of irreversible pulpitis have been studied for decades. Many studies have indicated a potential correlation between autophagy and this disease. Against the background of the competing endogenous RNA (ceRNA) theory, protein-coding RNA functions are linked with long noncoding RNAs (lncRNAs) and microRNAs (miRNAs). This mechanism has been widely studied in various fields but has rarely been reported in the context of irreversible pulpitis. The hub genes selected under this theory may represent the key to the interaction between autophagy and irreversible pulpitis.

RESULTS

Filtering and differential expression analyses of the GSE92681 dataset, which contains data from 7 inflamed and 5 healthy pulp tissue samples, were conducted. The results were intersected with autophagy-related genes (ARGs), and 36 differentially expressed ARGs (DE-ARGs) were identified. Functional enrichment analysis and construction of the protein‒protein interaction (PPI) network of DE-ARGs were performed. Coexpression analysis was conducted between differentially expressed lncRNAs (DElncRNAs) and DE-ARGs, and 151 downregulated and 59 upregulated autophagy-related DElncRNAs (AR-DElncRNAs) were identified. StarBase and multiMiR were then used to predict related microRNAs of AR-DElncRNAs and DE-ARGs, respectively. We established ceRNA networks including 9 hub lncRNAs (HCP5 and AC112496.1 ↑; FENDRR, AC099850.1, ZSWIM8-AS1, DLX6-AS1, LAMTOR5-AS1, TMEM161B-AS1 and AC145207.5 ↓), which were validated by a qRT‒PCR analysis of pulp tissue from patients with irreversible pulpitis.

CONCLUSION

We constructed two networks consisting of 9 hub lncRNAs based on the comprehensive identification of autophagy-related ceRNAs. This study may provide novel insights into the interactive relationship between autophagy and irreversible pulpitis and identifies several lncRNAs that may serve as potential biological markers.

Identification of the characteristics of infiltrating immune cells in pulpitis and its potential molecular regulation mechanism by bioinformatics method

OBJECTIVE

The inflammation of dental pulp will also trigger an immune response. The purpose of this study is to demonstrate the immune cell's function and explore their regulatory molecules and signal pathways in pulpitis.

METHOD

The CIBERSORTx method was used to quantitatively analyze 22 types of immune cells infiltrating in the GSE77459 dataset of dental pulp tissues. The immune-related differential genes (IR-DEGs) were further screened and enriched for the GO and KEGG pathways. Protein-protein interaction (PPI) networks were constructed and the hub IR-DEGs were screened. Finally, we constructed the regulatory network of hub genes.

RESULTS

The GSE77459 dataset screened 166 IR-DEGs and was enriched for three signal pathways involved in pulpitis development: chemokine signaling, TNF signaling, and NF-κB signaling. Significant differences in immune cell infiltration were observed between normal and inflamed dental pulp. The proportions of M0 macrophages, neutrophils, and follicular helper T cells were significantly higher than that of the normal dental pulp, while the proportions of resting mast cells, resting dendritic cells, CD8 T cells, and monocytes were significantly lower. The random forest algorithm concluded that M0 macrophages and neutrophils were the two most important immune cells. We identified five immune-related hub genes IL-6, TNF-α, IL-1β, CXCL8, and CCL2. In addition, IL-6, IL-1β, and CXCL8 are highly correlated with M0 macrophages and neutrophils, and the five hub genes have many shared regulatory molecules: four miRNAs and two lncRNAs, three transcription factors.

CONCLUSION

Immune cell infiltration plays an important role in pulpitis among which M0 macrophages and neutrophils are the most significant immune cells. IL-6, TNF-α, IL-1, CXCL8, and CCL2 may be essential molecule of the immune response regulation network in pulpitis. This will help us understand the immune regulatory network in pulpitis.

Identification and Experimental Validation of LINC00582 Associated with B Cell Immune and Development of Pulpitis: Bioinformatics and In Vitro Analysis

BACKGROUND

Pulpitis is a common oral disease. Increasing evidence has demonstrated that long non-coding RNAs (lncRNAs) can regulate the immune response in pulpitis. This study focused on finding the key immune-related lncRNAs that regulate the development of pulpitis.

METHODS

Differentially expressed lncRNAs were analyzed. Enrichment analysis was performed to explore the function of differentially expressed genes. Immune cell infiltration was evaluated with Immune Cell Abundance Identifier. Cell Counting Kit-8 (CCK-8) and lactate dehydrogenase release assays were conducted to measure the viability of human dental pulp cells (HDPCs) and BALL-1 cells. Transwell assay was processed to prove migration and invasion of BALL-1 cells.

RESULTS

Our results revealed that 17 lncRNAs were significantly upregulated. Pulpitis-related genes were mainly enriched in inflammatory relative signal pathways. The abundance of various immune cells was significantly abnormal in pulpitis tissues, among which the expression of eight lncRNAs was significantly correlated with the expression of B cell marker protein CD79B. As the most relevant lncRNA for B cells, LINC00582 could regulate the proliferation, migration, invasion, and CD79B expression of BALL-1 cells.

CONCLUSIONS

Our study identified eight B cell immune-related lncRNAs. Meanwhile, LINC00582 has a positive effect on B cell immunity in the development of pulpitis.

Construction of an m6A-related lncRNA model for predicting prognosis and immunotherapy in patients with lung adenocarcinoma

N6-methyladenosine (m6A)-related lncRNAs could be involved in the development of multiple tumors with an unknown role in lung adenocarcinoma (LUAD). Hence, gene expression data and clinical data of LUAD patients were acquired from The Cancer Genome Atlas Database. The prognostic m6A-related lncRNAs were identified through differential lncRNA expression analysis and Spearman's correlation analysis. The least absolute shrinkage and selection operator regression was used to establish the prognostic risk model, so as to evaluate and validate the predictive performance with survival analysis and receiver operating characteristic curve analysis. The expression of immune checkpoints, immune cell infiltration and drug sensitivity of patients in different risk groups were analyzed separately. A total of 19 prognostic m6A-related lncRNAs were identified to set up the prognostic risk model. The patients were divided into high- and low-risk groups based on the median value of the risk scores. Compared with the patients in the low-risk group, the prognosis of the patients in the high-risk group was relatively worse. The receiver operating characteristic curves indicated that this model had excellent sensitivity and specificity. Multivariate Cox regression analysis demonstrated that the risk score could be supposed as an independent prognostic risk factor. We highlighted that the risk scores were correlated with immune cell infiltration and drug sensitivity for constructing a prognostic risk model in LUAD patients based on m6A-related lncRNAs.

Current understanding on long non-coding RNAs in immune response to COVID-19

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic threatening the lives and health of people worldwide. Currently, there are no effective therapies or available vaccines for COVID-19. The molecular mechanism causing acute immunopathological diseases in severe COVID-19 is being investigated. Long noncoding RNAs (lncRNAs) have been proven to be involved in many viral infections, such as hepatitis, influenza and acquired immune deficiency syndrome. Many lncRNAs present differential expression between normal tissue and virus-infected tissue. However, the role of lncRNAs in SARS-CoV-2 infection has not been fully elucidated. This study aimed to review the relationship between lncRNAs and viral infection, interferon and cytokine storms in COVID-19, hoping to provide novel insights into promising targets for COVID-19 treatment.

RNA-sequencing analysis reveals the potential molecular mechanism of RAD54B in the proliferation of inflamed human dental pulp cells

AIM

To investigate the role of RAD54B in the proliferation of inflamed human dental pulp cells (hDPCs) induced by lipopolysaccharide (LPS).

METHODOLOGY

Normal, carious and pulpitic human dental pulp tissues were collected. Total RNA was subjected to RNA-sequencing (seq) and gene expression profiles were studied by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Differentially expressed genes (DEGs) in homologous recombination repair (HRR) were validated with qRT-PCR. The expression of RAD54B and TNF-α in human dental pulp tissues was detected using immunohistochemistry. HDPCs were cultured and RAD54B level in hDPCs was detected after LPS stimulation using western blot. CCK-8 was used to investigate the proliferation of hDPCs transfected with negative control (Nc) small interfering RNA (siRNA), RAD54B siRNA, P53 siRNA or both siRNAs with or without LPS stimulation. Flow cytometry was used to detect the cell cycle distribution, and western blot and immunofluorescence were used to analyse the expression of RAD54B, P53 and P21 under the above treatments. One-way and two-way anova followed by least significant difference posttest were used for statistical analysis.

RESULTS

RNA-seq results identified DEGs amongst the three groups. KEGG pathway analysis revealed enrichment of DEGs in the replication and repair pathway. HRR and non-homologous end joining (NHEJ) components were further verified and qRT-PCR results were basically consistent with the sequencing data. RAD54B, an HRR accessory factor highly expressed in carious and pulpitic tissues as compared to that in normal pulps, was chosen as our gene of interest. High RAD54B expression was confirmed in inflamed human dental pulp tissues and LPS-stimulated hDPCs. Upon RAD54B knockdown, P53 and P21 expressions in hDPCs were upregulated whereas the proliferation was significantly downregulated, accompanied by increased G2/M phase arrest. After inhibiting P53 expression in RAD54B-knockdown hDPCs, P21 expression and cell proliferation were reversed.

CONCLUSIONS

Gene expression profiles of normal, carious and pulpitic human dental pulp tissues were revealed. HRR components were elucidated to function in dental pulp inflammation. Amongst the DEGs in HRR, RAD54B regulated the proliferation of inflamed hDPCs via P53/P21 signalling. This research deepens our understanding of dental pulp inflammation and provides new insight to clarify the underlying mechanisms.

MicroRNA expression in apical periodontitis and pulpal inflammation: a systematic review

Background

The aim of this systematic review is to determine microRNAs (miRs) that are differently expressed between diseased pulpal and periapical tissues.

Design

This systematic review used PubMed, Scopus, EBSCO, ProQuest, Cochrane database as well as manual searching to extract studies from January 2012 up to February 2022.

Results

A total of 12 studies met the eligibility criteria were included. All selected studies were of case-control type. Twenty-four miRNAs associated with apical periodontitis, 11 were found to be upregulatedand 13 were downregulated. Four out of the 44 miRs associated with pulpal inflammation were upregulated, whereas forty were downregulated. Six miRs, namely hsa-miR-181b, hsa-miR-181c,hsa-miR-455-3p,hsa-miR-128-3p, hsa-miR199a-5p, and hsa-miR-95, exhibited considerable downregulation in both periapical and pulp tissues.

Conclusion

MiRs have been investigated for their role in pulpal and periapical biology and may be utilised in diagnostic and therapeutic purposes. Further investigations are required to determine why certain irreversible pulpitis situations progress to apical periodontitis and others do not, based on the various miR expressions. Moreover, clinical and laboratory trials are needed to support this theory.

Wnt4 prevents apoptosis and inflammation of dental pulp cells induced by LPS by inhibiting the IKK/NF‑κB pathway

Wnt4 has been shown to promote the recovery of odontogenic differentiation of dental pulp stem cells under inflammatory conditions, but its role in inflammation and apoptosis of pulpitis remains to be elucidated. Lipopolysaccharide (LPS) (10 µg/ml) was applied to treat the human dental pulp cells (HDPCs) for 24 h. Western blotting measured the expressions of inflammatory cytokines and apoptosis-related proteins. Cell apoptosis was measured by flow cytometry. The level of Wnt4 was evaluated by reverse transcription-quantitative PCR and western blotting. The results indicated that LPS could promote inflammatory response and apoptosis in HDPCs and downregulated Wnt4 expression was found in LPS-HDPCs. Overexpression of Wnt4 ameliorated cell inflammatory response and apoptosis, presented by reduced expressions of IL-8, IL-6, TNF-α, IL-1β, Bax, cleaved-caspase 3 and enhanced Bcl-2 expression as well as decreased apoptosis rate. Moreover, overexpression of Wnt4 reduced the phosphorylation levels of IKK2, IκBα and p65 proteins upregulated by LPS. Finally, overexpression of IKK2 reversed the effects of Wnt4 on inflammation and apoptosis of LPS-HDPCs and NF-κB inhibitor reversed the effect of IKK2 overexpression in LPS-HDPCs. Wnt4 inhibited LPS-triggered inflammation and apoptosis in HDPCs via regulating the IKK/NF-κB signaling pathway, which provided a new viewpoint for understanding the pathological mechanism of pulpitis.

Exploring craniofacial and dental development with microRNAs

microRNAs (miRs) are small RNA molecules that regulate many cellular and developmental processes. They control gene expression pathways during specific developmental time points and are required for tissue homeostasis and stem cell maintenance. miRs as therapeutic reagents in tissue regeneration and repair hold great promise and new technologies are currently being designed to facilitate their expression or inhibition. Due to the large amount of miR research in cells and cancer many cellular processes and gene networks have been delineated however, their in vivo response can be different in complex tissues and organs. Specifically, this report will discuss animal developmental models to understand the role of miRs as well as xenograft, disease, and injury models. We will discuss the role of miRs in clinical studies including their diagnostic function, as well as their potential ability to correct craniofacial diseases.

Long Non-coding RNA PVT1 is Involved in the Pathological Mechanism of Pulpitis by Regulating miR-128-3p

PURPOSE

Pulpitis is a common disease in stomatology, which is caused by dental pulp infection. It was found that long non-coding RNA regulates inflammation and repair responses through competitively sponging microRNAs. This study explored the expression and clinical significance of PVT1 in pulpitis patients, and further investigated the possible regulatory mechanism of PVT1 on pulpitis through in-vitro experiments.

MATERIALS AND METHODS

The expression of PVT1 and miR-128-3p was detected through RT-qPCR. An ROC curve was drawn to estimate the diagnostic significance of PVT1 and miR-128-3p for pulpitis. An in-vitro pulpitis cell model was constructed to evaluate the effects of PVT1 or miR-128-3p on cell proliferation, apoptosis, and inflammatory response. The Luciferase reporter gene explored the interaction between PVT1 and miR-128-3p.

RESULTS

The expression of PVT1 increased, while the miR-128-3p level decreased, in the saliva of pulpitis patients. ROC curves showed that both PVT1 and miR-128-3p had the potential to diagnose pulpitis. This in-vitro study revealed that the expression of PVT1 was increased in the pulpitis cell model. A low level of PVT1 suppressed the hDPCs injury induced by LPS. The Luciferase reporter gene verified the targeting relationship between PVT1 and miR-128-3p, and the latter was negatively regulated by PVT1. Further in-vitro studies showed that inhibition of miR-128-3p could reverse the effect of si-PVT1 on cell viability, cell apoptosis and inflammatory response.

CONCLUSION

This study revealed that knockdown of PVT1 may suppress the damage in pulpitis cell models induced by LPS via targeting miR-128-3p.

Analysis of circRNAs profile in TNF-α treated DPSC

Background

Pulpitis often are characterized as sustained inflammation and impaired pulp self-repair. Circular RNAs (circRNAs) have been reported to be involved in the development of inflammation, but their influence in pulpitis is still unidentified, which was examined in our research.

Methods

In this study, TNF-α (20 ng/mL) was used to treat DPSCs, then MTS identified cell proliferation. The circRNAs profile in DPSCs with or without TNF-α treatment was evaluated using RNA sequencing and subsequently by bioinformatics analysis. After that, the circular structure was assessed using agarose gel electrophoresis, followed by Sanger sequencing. And the circRNAs expression was ratified using quantitative real-time polymerase chain reaction in cell and tissues samples. Additionally, the plausible mechanism of circRNAs was envisaged, and the circRNA-miRNA-mRNA linkage was plotted using Cytoscape.

Results

The treatment of TNF-α inhibited cell proliferation capabilities in DPSCs, which also made 1195 circRNA expressions undergo significant alterations. Among these changes, 11 circRNAs associated with inflammation were chosen for circular structure verification, and only seven circRNAs (hsa_circ_0001658, hsa_circ_0001978, hsa_circ_0003910, hsa_circ_0004314, hsa_circ_0004417, hsa_circ_0035915, and hsa_circ_0002545) had circular structure. Additionally, five circRNAs expressions (hsa_circ_0001978, hsa_circ_0003910, hsa_circ_0004314, hsa_circ_0004417, and hsa_circ_0035915) had significantly altered between with or without TNF-α treated DPSCs. Furthermore, hsa_circ_0001978 and hsa_circ_0004417 were increased in patients suffering from pulpitis. Furthermore, their ceRNA linkage and Kyoto Encyclopedia of Genes and Genomes analysis suggested that these two circRNAs may participate in the inflammation development of pulpitis via mitogen-activated protein kinase and the Wnt signaling pathway.

Conclusion

This study revealed that the circRNAs profile was altered in TNF-α treated DPSCs. Also, hsa_circ_0001978 and hsa_circ_0004417 may be involved in the inflammation progress of pulpitis. These outcomes provided the latest information for additional research on pulpitis.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12903-022-02267-2.

Identification of Immune-Related lncRNA Regulatory Network in Pulpitis

Background. Long noncoding RNAs (lncRNAs) are emerging as critical regulators of various biological processes, including immune regulation. Methods. Due to the critical significance of immunological responses in the development and progression of pulpitis, we used an integrated algorithm to identify immune-related lncRNAs and then examined the lncRNA-immunity regulation network in pulpitis. Before identifying immune-related lncRNAs, the data from GEO datasets were precleaned. ConsensusClusterPlus was used to differentiate immune-related pulpitis subgroups. Enrichment analysis using GO and MSigDB databases was employed to determine the differences in molecular function, cellular component, and biological process between the two pulpitis subtypes. Results. An integrated algorithm was designed to filtrate immune-related lncRNAs accurately. 790 immune-related lncRNAs were found in 17 immunological categories, with 38 of them perturbated in pulpitis. The Cytoscape software was used to visualize the relationship between representative immune regulatory pathways and immune-related lncRNAs. Two immune-related pulpitis subtypes were discovered using differentially expressed immune-related lncRNAs. Subtype 2 has a stronger association with immune-related pathways than subtype 1 does. Conclusions. Our study identified many immune-related lncRNAs and investigated potential lncRNA regulation networks; meanwhile, the molecular subtypes of pulpitis were identified, all of which will be relevant for further research into inflammatory and immunological processes in pulpitis.

Comprehensive analysis of GSEC/miR-101-3p/SNX16/PAPOLG axis in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most lethal malignancies. A growing number of studies have shown that competitive endogenous RNA (ceRNA) regulatory networks might play important roles during HCC process. The present study aimed to identify a regulatory axis of the ceRNA network associated with the development of HCC. The roles of SNX16 and PAPOLG in HCC were comprehensively analyzed using bioinformatics tools. Subsequently, the “mRNA-miRNA-lncRNA” model was then used to predict the upstream miRNAs and lncRNAs of SNX16 and PAPOLG using the miRNet database, and the miRNAs with low expression and good prognosis in HCC and the lncRNAs with high expression and poor prognosis in HCC were screened by differential expression and survival analysis. Finally, the risk-prognosis models of ceRNA network axes were constructed by univariate and multifactorial Cox proportional risk analysis, and the immune correlations of ceRNA network axes were analyzed using the TIMER and GEPIA database. In this study, the relevant ceRNA network axis GSEC/miR-101-3p/SNX16/PAPOLG with HCC prognosis was constructed, in which GSEC, SNX16, and PAPOLG were highly expressed in HCC with poor prognosis, while miR-101-3p was lowly expressed in HCC with good prognosis. The risk-prognosis model predicted AUC of 0.691, 0.623, and 0.626 for patient survival at 1, 3, and 5 years, respectively. Immuno-infiltration analysis suggested that the GSEC/miR-101-3p/SNX16/PAPOLG axis might affect macrophage polarization. The GSEC/miR-101-3p/SNX16/PAPOLG axis of the ceRNA network axis might be an important factor associated with HCC prognosis and immune infiltration.

Specific microRNAs regulate dental pulp stem cell behavior

INTRODUCTION

MicroRNAs (miRNAs), small non-coding RNA, control the translation of messenger RNAs into proteins. miRNAs have a crucial role in regulating the diverse biological processes of many physiological and pathological activities. The aim of this systematic review is to explore various functions of miRNAs in the regulation of dental pulp stem cells (DPSCs) behavior.

METHODS

The articles were searched in PubMed, SCOPUS and ISI Web of Science database using designated keywords. Full-length manuscripts published in English in peer-reviewed journals relevant to the role of miRNAs in DPSC functions were included and reviewed by 2 independent researchers.

RESULTS

The original search of the database generated 299 studies. One hundred and two duplicate studies were removed. After their exclusion, 48 studies were selected for review. miRNAs have shown to modulate the stemness and differentiation of various mesenchymal stem cells. The miRNAs expression profiles in DPSCs were differed compared with other cell types and have been demonstrated to regulate the levels of proteins crucial for promoting or inhibiting DPSC proliferation as well as differentiation. Further, miRNAs also modulate inflammatory processes in dental pulp.

CONCLUSION

miRNAs have various function upon the regulation of DPSCs and understanding these roles of miRNAs is crucial for the development of new therapeutics in regenerative dental medicine. With the advancing technologies, the utilization of miRNA technology could revolutionarily change the future of regenerative endodontics.

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.

NUTM2A-AS1 silencing alleviates LPS-induced apoptosis and inflammation in dental pulp cells through targeting let-7c-5p/HMGB1 axis

BACKGROUND

Long non-coding RNA (lncRNA) NUTM2A antisense RNA 1 (NUTM2A-AS1) has been reported to be abnormally up-regulated in pulpitis tissues. However, the function of NUTM2A-AS1 in pulpitis remains unclear. The aim of this study was to investigate the role and working mechanism of NUTM2A-AS1 in pulpitis using lipopolysaccharide (LPS)-treated human dental pulp cells (HDPCs).

METHODS

3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, flow cytometry and lactate dehydrogenase (LDH) release detection assay were conducted to analyze the viability of HDPCs. Cell inflammatory response was analyzed through measuring the protein levels of interleukin-6 (IL-6) and IL-8. Western blot assay and quantitative real-time polymerase chain reaction (qRT-PCR) were applied to measure protein expression and RNA expression, respectively. Bioinformatic database StarBase was used to predict the possible targets of NUTM2A-AS1 and let-7c-5p, and dual-luciferase reporter assay was conducted to verify these intermolecular interactions.

RESULTS

LPS stimulation restrained cell viability and induced cell apoptosis and inflammation of HDPCs. LPS exposure up-regulated the expression of NUTM2A-AS1 and High-Mobility Group Box 1 (HMGB1) and down-regulated the level of let-7c-5p. LPS-induced injury in HDPCs was partly attenuated by the silencing of NUTM2A-AS1 or HMGB1. Let-7c-5p was confirmed as a direct target of NUTM2A-AS1, and let-7c-5p bound to the 3' untranslated region (3'UTR) of HMGB1 messenger RNA (mRNA) in HDPCs. HMGB1 overexpression largely overturned NUTM2A-AS1 silencing-mediated effects in LPS-induced HDPCs.

CONCLUSION

NUTM2A-AS1 knockdown attenuated LPS-induced damage in HDPCs partly through targeting let-7c-5p/HMGB1 axis.

Predicting the Key Genes Involved in Aortic Valve Calcification Through Integrated Bioinformatics Analysis

Background: Valvular heart disease is obtaining growing attention in the cardiovascular field and it is believed that calcific aortic valve disease (CAVD) is the most common valvular heart disease (VHD) in the world. CAVD does not have a fully effective treatment to delay its progression and the specific molecular mechanism of aortic valve calcification remains unclear.

Materials and Methods: We obtained the gene expression datasets GSE12644 and GSE51472 from the public comprehensive free database GEO. Then, a series of bioinformatics methods, such as GO and KEGG analysis, STING online tool, Cytoscape software, were used to identify differentially expressed genes in CAVD and healthy controls, construct a PPI network, and then identify key genes. In addition, immune infiltration analysis was used via CIBERSORT to observe the expression of various immune cells in CAVD.

Results: A total of 144 differential expression genes were identified in the CAVD samples in comparison with the control samples, including 49 up-regulated genes and 95 down-regulated genes. GO analysis of DEGs were most observably enriched in the immune response, signal transduction, inflammatory response, proteolysis, innate immune response, and apoptotic process. The KEGG analysis revealed that the enrichment of DEGs in CAVD were remarkably observed in the chemokine signaling pathway, cytokine-cytokine receptor interaction, and PI3K-Akt signaling pathway. Chemokines CXCL13, CCL19, CCL8, CXCL8, CXCL16, MMP9, CCL18, CXCL5, VCAM1, and PPBP were identified as the hub genes of CAVD. It was macrophages that accounted for the maximal proportion among these immune cells. The expression of macrophages M0, B cells memory, and Plasma cells were higher in the CAVD valves than in healthy valves, however, the expression of B cells naïve, NK cells activated, and macrophages M2 were lower.

Conclusion: We detected that chemokines CXCL13, CXCL8, CXCL16, and CXCL5, and CCL19, CCL8, and CCL18 are the most important markers of aortic valve disease. The regulatory macrophages M0, plasma cells, B cells memory, B cells naïve, NK cells activated, and macrophages M2 are probably related to the occurrence and the advancement of aortic valve stenosis. These identified chemokines and these immune cells may interact with a subtle adjustment relationship in the development of calcification in CAVD.

The Genetic and Epigenetic Mechanisms Involved in Irreversible Pulp Neural Inflammation

AIM

To identify the critical genetic and epigenetic biomarkers by constructing the long noncoding RNA- (lncRNA-) related competing endogenous RNA (ceRNA) network involved in irreversible pulp neural inflammation (pulpitis).

MATERIALS AND METHODS

The public datasets regarding irreversible pulpitis were downloaded from the gene expression omnibus (GEO) database. The differential expression analysis was performed to identify the differentially expressed genes (DEGs) and DElncRNAs. Functional enrichment analysis was performed to explore the biological processes and signaling pathways enriched by DEGs. By performing a weighted gene coexpression network analysis (WGCNA), the significant gene modules in each dataset were identified. Most importantly, DElncRNA-DEmRNA regulatory network and DElncRNA-associated ceRNA network were constructed. A transcription factor- (TF-) DEmRNA network was built to identify the critical TFs involved in pulpitis.

RESULT

Two datasets (GSE92681 and GSE77459) were selected for analysis. DEGs involved in pulpitis were significantly enriched in seven signaling pathways (i.e., NOD-like receptor (NLR), Toll-like receptor (TLR), NF-kappa B, tumor necrosis factor (TNF), cell adhesion molecules (CAMs), chemokine, and cytokine-cytokine receptor interaction pathways). The ceRNA regulatory relationships were established consisting of three genes (i.e., LCP1, EZH2, and NR4A1), five miRNAs (i.e., miR-340-5p, miR-4731-5p, miR-27a-3p, miR-34a-5p, and miR-766-5p), and three lncRNAs (i.e., XIST, MIR155HG, and LINC00630). Six transcription factors (i.e., GATA2, ETS1, FOXP3, STAT1, FOS, and JUN) were identified to play pivotal roles in pulpitis.

CONCLUSION

This paper demonstrates the genetic and epigenetic mechanisms of irreversible pulpitis by revealing the ceRNA network. The biomarkers identified could provide research direction for the application of genetically modified stem cells in endodontic regeneration.

Long noncoding RNA MEG3 expressed in human dental pulp regulates LPS-Induced inflammation and odontogenic differentiation in pulpitis

Pulpitis refers to inflammation of the inner pulp by invading microbes, and tissue repair occurs due to odontogenic differentiation of human dental pulp cells (hDPCs) with multidifferentiation potential. Long noncoding RNAs (lncRNAs) can modulate numerous pathological and biological processes; however, the role of lncRNAs in the inflammation and regeneration of the dentin-pulp complex in pulpitis is unclear. Here, we performed high-throughput sequencing to identify differentially expressed lncRNAs between human normal and inflamed pulp and concluded that lncMEG3 (lncRNA maternally expressed gene 3, MEG3) was significantly upregulated in both inflamed pulp and LPS-treated hDPCs. MEG3 expression in the pulp tissue was detected using the RNAscope® technique. RNA pulldown assays identified the MEG3-interacting proteins and the potential mechanisms. With MEG3 knockdown, we investigated the role of MEG3 in the secretion of inflammatory cytokines in LPS-treated hDPCs and odontogenic differentiation of hDPCs. MEG3 downregulation inhibited the secretion of TNF-α, IL-1β and IL-6 in LPS-treated hDPCs, and the p38/MAPK signaling pathway may be related to this effect. MEG3 knockdown promoted odontogenic differentiation of hDPCs by regulating the Wnt/β-catenin signaling pathway. Our study suggested that MEG3 has a negative effect on inflammation and regeneration of the dentin-pulp complex in pulpitis.

Computational gene expression profiling in the exploration of biomarkers, non-coding functional RNAs and drug perturbagens for COVID-19

The coronavirus disease, caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), is a global health crisis that is being endured with an increased alarm of transmission each day. Though the pandemic has activated innumerable research attention to decipher an antidote, fundamental understanding of the molecular mechanisms is necessary to halt the disease progression. The study focused on comparison of the COVID-19 infected lung tissue gene expression datasets -GSE155241 and GSE150316 with the GEO2R-limma package. The significant up- and downregulated genes were annotated. Further evaluation of the enriched pathways, transcription factors, kinases, noncoding RNAs and drug perturbations revealed the significant molecular mechanisms of the host response. The results revealed a surge in mitochondrial respiration, cytokines, neurodegenerative mechanisms and deprived oxygen, iron, copper, and glucose transport. Hijack of ubiquitination by SARS-CoV-2, hox gene differentiation, histone modification, and miRNA biogenesis were the notable molecular mechanisms inferred. Long non-coding RNAs such as C058791.1, TTTY15 and TPTEP1 were predicted to be efficient in regulating the disease mechanisms. Drugs-F-1566-0341, Digoxin, Proscillaridin and Linifanib that reverse the gene expression signatures were predicted from drug perturbations analysis. The binding efficiency and interaction of proscillaridin and digoxin as obtained from the molecular docking studies confirmed their therapeutic potential. Two overlapping upregulated genes MDH1, SGCE and one downregulated gene PFKFB3 were appraised as potential biomarkers candidates. The upregulation of PGM5, ISLR and ANK2 as measured from their expressions in normal lungs affirmed their possible prognostic biomarker competence. The study explored significant insights for better diagnosis, and therapeutic options for COVID-19.

Communicated by Ramaswamy H. Sarma

Diagnostic biomarker candidates for pulpitis revealed by bioinformatics analysis of merged microarray gene expression datasets

Background

Pulpitis is an inflammatory disease, the grade of which is classified according to the level of inflammation. Traditional methods of evaluating the status of dental pulp tissue in clinical practice have limitations. The rapid and accurate diagnosis of pulpitis is essential for determining the appropriate treatment. By integrating different datasets from the Gene Expression Omnibus (GEO) database, we analysed a merged expression matrix of pulpitis, aiming to identify biological pathways and diagnostic biomarkers of pulpitis.

Methods

By integrating two datasets (GSE77459 and GSE92681) in the GEO database using the sva and limma packages of R, differentially expressed genes (DEGs) of pulpitis were identified. Then, the DEGs were analysed to identify biological pathways of dental pulp inflammation with Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and Gene Set Enrichment Analysis (GSEA). Protein–protein interaction (PPI) networks and modules were constructed to identify hub genes with the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and Cytoscape.

Results

A total of 470 DEGs comprising 394 upregulated and 76 downregulated genes were found in pulpitis tissue. GO analysis revealed that the DEGs were enriched in biological processes related to inflammation, and the enriched pathways in the KEGG pathway analysis were cytokine-cytokine receptor interaction, chemokine signalling pathway and NF-κB signalling pathway. The GSEA results provided further functional annotations, including complement system, IL6/JAK/STAT3 signalling pathway and inflammatory response pathways. According to the degrees of nodes in the PPI network, 10 hub genes were identified, and 8 diagnostic biomarker candidates were screened: PTPRC, CD86, CCL2, IL6, TLR8, MMP9, CXCL8 and ICAM1.

Conclusions

With bioinformatics analysis of merged datasets, biomarker candidates of pulpitis were screened and the findings may be as reference to develop a new method of pulpitis diagnosis.

Investigation of the underlying genes and mechanism of familial hypercholesterolemia through bioinformatics analysis

Background

Familial hypercholesterolemia (FH) is one of the commonest inherited metabolic disorders. Abnormally high level of low-density lipoprotein cholesterol (LDL-C) in blood leads to premature atherosclerosis onset and a high risk of cardiovascular disease (CVD). However, the specific mechanisms of the progression process are still unclear. Our study aimed to investigate the potential differently expressed genes (DEGs) and mechanism of FH using various bioinformatic tools.

Methods

GSE13985 and GSE6054 were downloaded from the Gene Expression Omnibus (GEO) database for bioinformatic analysis in this study. First, limma package of R was used to identify DEGs between blood samples of patients with FH and those from healthy individuals. Then, the functional annotation of DEGs was carried out by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis and Gene Ontology (GO) analysis. Based on Search Tool for the Retrieval of Interacting Genes (STRING) tool, we constructed the Protein-Protein Interactions (PPIs) network among DEGs and mined the core genes as well.

Results

A total of 102 communal DEGs (49 up-regulated and 53 down-regulated) are identified in FH samples compared with control samples. The functional changes of DEGs are mainly associated with the focal adhere and glucagon signaling pathway. Ten genes (ITGAL, TLN1, POLR2A, CD69, GZMA, VASP, HNRNPUL1, SF1, SRRM2, ITGAV) were identified as core genes. Bioinformatic analysis showed that the core genes are mainly enriched in numerous processes related to cell adhesion, integrin-mediated signaling pathway and cell-matrix adhesion. In the transcription factor (TF) target regulating network, 219 nodes were detected, including 214 DEGs and 5 TFs (SP1, EGR3, CREB, SEF1, HOX13). In conclusion, the DEGs and hub genes identified in this study may help us understand the potential etiology of the occurrence and development of AS.

Conclusion

Up-regulated ITGAL, TLN1, POLR2A, VASP, HNRNPUL1, SF1, SRRM2, and down-regulated CD69, GZMA and ITGAV performed important promotional effects for the formation of atherosclerotic plaques those suffering from FH. Moreover, SP1, EGR3, CREB, SEF1 and HOX13 were the potential transcription factors for DEGs and could serve as underlying targets for AS rupture prevention. These findings provide a theoretical basis for us to understand the potential etiology of the occurrence and development of AS in FH patients and we may be able to find potential diagnostic and therapeutic targets.

Long non‑coding RNAs are novel players in oral inflammatory disorders, potentially premalignant oral epithelial lesions and oral squamous cell carcinoma (Review)

In recent years, a large number of studies have shown that the abnormal expression of long non‑coding (lnc)RNAs can lead to a variety of different diseases, including inflammatory disorders, cardiovascular disease, nervous system diseases, and cancers. Recent research has demonstrated the biological characteristics of lncRNAs and the important functions of lncRNAs in oral inflammation, precancerous lesions and cancers. The present review aims to explore and discuss the potential roles of candidate lncRNAs in oral diseases by summarizing multiple lncRNA profiles in diseased and healthy oral tissues to determine the altered lncRNA signatures. In addition, to highlight the exact regulatory mechanism of lncRNAs in oral inflammatory disorders, potentially premalignant oral epithelial lesions and oral squamous cell carcinoma. The detection of lncRNAs in oral samples has the potential to be used as a diagnostic and an early detection tool for oral diseases. Furthermore, lncRNAs are promising future therapeutic targets in oral diseases, and research in this field may expand in the future.

The prognostic value of COL3A1/FBN1/COL5A2/SPARC-mir-29a-3p-H19 associated ceRNA network in Gastric Cancer through bioinformatic exploration

Increasing studies on malignant tumors have proposed a new competing endogenous RNA (ceRNA) regulatory mechanism that mRNA, miRNA and lncRNA interact with each other. However, the mRNA-miRNA-lncRNA associated ceRNA network in gastric cancer remains unknown. We used online bioinformatic softwares to predict the hub genes and their upstream miRNAs and lncRNAs in gastric cancer, and then performed survival analyses. After collecting gastric cancer tissue samples and performing PCR experiments, the correlations among predicted mRNA, miRNA and lncRNA were further verified. A total of 101 up-regulated significant differentially expressed genes (DEGs) and 219 down-regulated significant DEGs in gastric cancer were confirmed. Functional enrichment analyses of these significant DEGs indicated that they were potentially enriched in some pathways involved in tumor malignant biological processes or metabolism. Then, we identified 20 hub genes in the PPI networks. Combined with expression and survival analyses, 8 up-regulated genes and 1 down-regulated gene were identified as central genes and acted as important prognostic roles in gastric cancer. 17 miRNAs were confirmed that might potentially regulate the expressions of these central genes. But only 8 out of them indicated better outcome in gastric cancer. Further, 79 lncRNAs were predicted that might have the potence to combine with the 8 central miRNAs. The lncRNA H19 was eventually defined as a central lncRNA by survival analyses. Stimultaneously, we found that there were certain interactions among lncRNA, miRNA and mRNAs in 50 gastric cancer tissues by qRT-PCR. Moreover, the high expression of H19 is associated with advanced TNM stage, primary tumor and lymph nodes, indicating a poor prognosis. In summary, we uncovered the prognostic value of COL3A1/FBN1/COL5A2/SPARC-mir-29a-3p-H19 ceRNA network in gastric cancer.

The long non-coding RNA LOC285758 promotes invasion of acute myeloid leukemia cells by down-regulating miR-204-5p

Acute myeloid leukemia (AML) is the second most common type of leukemia worldwide. It was previously reported that expression of the long noncoding RNA LOC285758 is positively associated with AML cell proliferation, but the underlying mechanisms have not previously been reported. Here, we report that LOC285758 expression is higher in clinical AML blood samples and cultured AML cells. miR‐204‐5p was confirmed to be a target gene of LOC285758 by bioinformatics analysis and luciferase assay. LOC285758 overexpression promoted AML cell viability and invasion abilities, which were effectively inhibited by miR‐204‐5p overexpression; moreover, miR‐204‐5p overexpression also regulated the expression of E‐cadherin, N‐cadherin and Twist1. The data also showed that increased LOC285758 expression could effectively suppress the earlier effects of miR‐204‐5p on AML cells. Our findings suggest that targeting of miR‐204‐5p by LOC285758 promotes the cell viability and invasion of AML cells, and thus LOC285758 may have potential as a therapeutic target for AML treatment.

Expression levels and associations of five long non-coding RNAs in gastric cancer and their clinical significance

Gastric cancer (GC) is a type of cancer that is commonly diagnosed worldwide due to a lack of early diagnostic, prognostic and therapeutic targets for this disease. The aim of the present study was to examine the expression levels of five long non-coding RNAs, namely PTPRG antisense RNA 1 (PTPRG-AS1), forkhead box P4 antisense RNA 1 (FOXP4-AS1), bladder cancer-associated transcript 2 (BLACAT2), ZXF2 and upregulated in colorectal cancer (UCC), to study their associations with patient characteristics and assess their prognostic efficacy, in order to determine the possibility of their application as GC biomarkers. The expression levels of long non-coding RNAs (lncRNAs) were determined by reverse transcription-quantitative PCR analysis of 61 pairs of GC tissues and adjacent healthy gastric mucosa tissues and GC cell lines. The Chi-square test was conducted to assess the associations of lncRNA expression levels with clinical characteristics of patients. The effect of UCC on GC cell proliferation was determined using in vitro functional experiments. The prognostic efficacy of FOXP4-AS1, BLACAT2 and UCC were examined in the Gene Expression Profiling Interactive Analysis database and those of PTPRG-AS1 were examined in the Kaplan Meier Plot database. Gene alteration frequencies of PTPRG-AS1 and BLACAT2 in GC were identified using the cBioPortal for Cancer Genomics. PTPRG-AS1, FOXP4-AS1, BLACAT2, ZXF2 and UCC were found to be upregulated in GC cell lines and GC tissues compared with adjacent normal tissues. PTPRG-AS1 and ZXF2 expression levels were associated with the expression status of the cell proliferation marker Ki67. UCC promoted the proliferation of GC cells in vitro and was associated with lymph node metastasis. Increased expression of FOXP4-AS1 indicated a favorable outcome in terms of disease-free survival, whereas high expression of PTPRG-AS1 was associated with poor survival rates for patients in different GC risk groups. BLACAT2 gene mutation was associated with poor disease-free survival outcome for patients with GC. The results suggest that PTPRG-AS1, FOXP4-AS1, BLACAT2, ZXF2 and UCC are potential biomarkers for the detection of GC at the molecular level and may be used as potential targets for GC therapy. The individual roles of these lncRNAs may be utilized for prognostic predictions.