m6A regulator-mediated RNA methylation modification patterns are involved in immune microenvironment regulation of periodontitis

CXCR4-mediated neutrophil dynamics in periodontitis

BACKGROUND AND OBJECTIVE

Periodontitis is a common oral disease closely related to immune response and this study is aimed to identify the key immune-related pathogenic genes and analyze the infiltration and function of immune cells in the disease using bioinformatics methods.

METHODS

Transcriptome datasets and single-cell RNA sequencing (scRNA-seq) datasets were downloaded from the GEO database. We utilized weighted correlation network analysis and least absolute selection and shrinkage operator, protein-protein interaction network construction to screen out key pathogenic genes as well as conducted the cell-type identification by estimating relative subsets of RNA transcripts algorithm to analyze and characterize immune cell types in periodontal tissues. In addition to bioinformatics validations, clinical and cell samples were collected and mouse periodontitis models were constructed to validate the important role of key genes in periodontitis.

RESULTS

Bioinformatics analysis pointed out the positive correlation between CXCR4 expression and periodontitis, and revealed the increased infiltration of neutrophils in periodontal inflammatory. Similar results were obtained from clinical samples and animal models. In addition, the clustering and functional enrichment results based on CXCR4 expression levels included activation of immune response and cell migration, implying the possible function of CXCR4 on regulating neutrophil dynamics, which might contribute to periodontitis. Subsequent validation experiments confirmed that the increased expression of CXCR4 in neutrophils under periodontitis, where cell migration-related pathways also were activated.

CONCLUSION

CXCR4 could be the key pathogenic gene of periodontitis and CXCR4/CXCL12 signal axial might contribute to the development of periodontitis by mediating neutrophil dynamics, suggesting that CXCR4 could be a potential target to help identify novel strategies for the clinical diagnosis and treatment of periodontitis.

Quercetin-Loaded Bioglass Injectable Hydrogel Promotes m6A Alteration of Per1 to Alleviate Oxidative Stress for Periodontal Bone Defects

Periodontal disease ranks third among noncommunicable illnesses, behind cancer and cardiovascular disease, and is closely related to the occurrence and progression of various systemic diseases. However, elucidating the processes of periodontal disease and promoting periodontal bone regeneration remains a challenge. Here, quercetin is demonstrated to reduce the oxidative stress state of orofacial mesenchymal stem cells (OMSCs) in vitro and to affect the osteogenic growth of OMSCs through molecular mechanisms that mediate the m6A change in Per1. Nevertheless, the limited therapeutic efficacy of systemic medication and the limitations of local medication resulting from the small, moist, and highly dynamic periodontal environment make it challenging to treat periodontal tissues with medication. Herein, a biosafe injectable hydrogel drug-controlled delivery system is constructed as a bone-enhancing factory and loaded with quercetin to treat oxidative stress injury in periodontal tissues. This drug-carrying system made up of nanoscale bioglass microspheres and a light-cured injectable hydrogel, allows effective drug particle loading and cementation in the dynamic and moist periodontal environment. Furthermore, the system demonstrates the ability to stimulate OMSCs osteogenic differentiation in a Per1-dependent manner, which ultimately promotes periodontal bone repair, suggesting that this system has potential for clinical periodontal therapy.

The role of WTAP in regulating macrophage-mediated osteoimmune responses and tissue regeneration in periodontitis

Periodontitis, delineated by the destruction of structures that support teeth, is predominantly propelled by intricate immune responses. Immunomodulatory treatments offer considerable promise for the management of this ailment; however, the modulation of the periodontal immune microenvironment to facilitate tissue regeneration presents a substantial biomedical challenge. Herein, our study investigates the role of Wilms' tumor 1-associating protein (WTAP), a critical m6A methyltransferase, in the immunomodulation of periodontitis and assesses its viability as a therapeutic target. We observed heightened expression of WTAP in macrophages extracted from gingival tissues impacted by periodontitis, with a strong association with M1 polarization. Via loss-of-function experiments, we demonstrated that diminishing WTAP expression precipitates a transition from M1 to M2 macrophage phenotypes amidst inflammatory conditions, thus improving the periodontal immune landscape. Further, RNA sequencing and indirect co-culture assays indicated that suppressing of WTAP expression modulates osteoimmune responses and enhances the osteogenic differentiation of bone marrow stromal cells. The local deployment of adeno-associated virus-shWTAP in murine models of periodontitis robustly validated the therapeutic promise of targeting WTAP in this disease. Collectively, our findings highlight the crucial role of WTAP in orchestrating macrophage-mediated osteoimmune responses and tissue regeneration in periodontitis, proposing novel avenues for immunotherapeutic interventions in its treatment.

Mechanisms and clinical landscape of N6-methyladenosine (m6A) RNA modification in gastrointestinal tract cancers

Epigenetics encompasses reversible and heritable chemical modifications of non-nuclear DNA sequences, including DNA and RNA methylation, histone modifications, non-coding RNA modifications, and chromatin rearrangements. In addition to well-studied DNA and histone methylation, RNA methylation has emerged as a hot topic in biological sciences over the past decade. N6-methyladenosine (m6A) is the most common and abundant modification in eukaryotic mRNA, affecting all RNA stages, including transcription, translation, and degradation. Advances in high-throughput sequencing technologies made it feasible to identify the chemical basis and biological functions of m6A RNA. Dysregulation of m6A levels and associated modifying proteins can both inhibit and promote cancer, highlighting the importance of the tumor microenvironment in diverse biological processes. Gastrointestinal tract cancers, including gastric, colorectal, and pancreatic cancers, are among the most common and deadly malignancies in humans. Growing evidence suggests a close association between m6A levels and the progression of gastrointestinal tumors. Global m6A modification levels are substantially modified in gastrointestinal tumor tissues and cell lines compared to healthy tissues and cells, possibly influencing various biological behaviors such as tumor cell proliferation, invasion, metastasis, and drug resistance. Exploring the diagnostic and therapeutic potential of m6A-related proteins is critical from a clinical standpoint. Developing more specific and effective m6A modulators offers new options for treating these tumors and deeper insights into gastrointestinal tract cancers.

Identification and validation of cuproptosis and disulfidptosis related genes in colorectal cancer

Colorectal cancer, the third most prevalent malignant cancer, is associated with poor prognosis. Recent studies have investigated the mechanisms underlying cuproptosis and disulfidptosis in colorectal cancer. However, whether genes linked to these processes impact the prognosis of colorectal cancer patients through analogous mechanisms remains unclear. In this study, we developed a model of cuproptosis and disulfidptosis in colorectal cancer and concurrently explored the role of the pivotal model gene HSPA8 in colorectal cancer cell lines. Our results revealed a positive correlation between cuproptosis and disulfidptosis, both of which are emerging as protective factors for the prognosis of CRC patients. Consequently, a prognostic model encompassing HSPA8, PDCL3, CBX3, ATP6V1G1, TAF1D, RPL4, and RPL14 was constructed. Notably, the key gene in our model, HSPA8, exhibited heightened expression and was validated as a protective prognostic factor in colorectal cancer, exerting inhibitory effects on colorectal cancer cell proliferation. This study offers novel insights into the interplay between cuproptosis and disulfidptosis. The application of the prognostic model holds promise for more effectively predicting the overall survival of colorectal cancer patients.

RUNX1/miR-429 feedback loop promotes growth, metastasis, and epithelial-mesenchymal transition in oral squamous cell carcinoma by targeting ITGB1

This study aimed to explore the role of miR-429 on the progression of oral squamous cell carcinoma (OSCC). OSCC cell lines were transfected with miR-429 mimic, pcDNA3.1-RUNX1, or pcDNA3.1-ITGB1, and their cell viability, apoptosis, migration, and invasion abilities were analyzed by cell counting, terminal deoxynucleotidyl transferase dUTP nick-end labeling staining, wound healing, and transwell assays, respectively. Furthermore, luciferase reporter assay, RNA pull-down, and ChIP were used to assess the regulation of miR-429, RUNX1, and ITGB1 expression in OSCC. Lastly, the biological role of the RUNX1/miR-429 feedback loop was explored in nude mice. The results revealed that miR-429 level was down-regulated, while RUNX1 and ITGB1 levels were up-regulated in OSCC tissues and that miR-429 was negatively correlated with RUNX1 and ITGB1 in OSCC tissues. Transfection of miR-429 mimic suppressed OSCC cell proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT). Moreover, we found that miR-429 participated in OSCC progression by directly targeting ITGB1. Additionally, we found that RUNX1 negatively regulated miR-429 expression by binding to its promoter. Our results also revealed that the RUNX1/miR-429 feedback loop regulated ITGB1 expression and that RUNX1 overexpression rescued the inhibitory effects of miR-429 mimic on OSCC cells. In addition, miR-429 mimic significantly suppressed tumor growth, inflammatory cell infiltration, EMT, and ITGB1 expression in vivo, which were inhibited by RUNX1 overexpression. Altogether, these results indicate that the RUNX1/miR-429 feedback loop promoted growth, metastasis, and EMT in OSCC by targeting ITGB1.

Molecular characterization of m6A RNA methylation regulators with features of immune dysregulation in IgA nephropathy

The role of RNA N6-methyladenosine (m6A) modification in immunity is being elucidated. This study aimed to explore the potential association between m6A regulators and the immune microenvironment in IgA nephropathy (IgAN). The expression profiles of 24 m6A regulators in 107 IgAN patients were obtained from the Gene Expression Omnibus (GEO) database. The least absolute shrinkage and selection operator (LASSO) regression and logistic regression analysis were utilized to construct a model for distinguishing IgAN from control samples. Based on the expression levels of m6A regulators, unsupervised clustering was used to identify m6A-induced molecular clusters in IgAN. Gene set enrichment analysis (GSEA) and immunocyte infiltration among different clusters were examined. The gene modules with the highest correlation for each of the three clusters were identified by weighted gene co-expression network analysis (WGCNA). A model containing 10 m6A regulators was developed using LASSO and logistic regression analyses. Three molecular clusters were determined using consensus clustering of 24 m6A regulators. A decrease in the expression level of YTHDF2 in IgAN samples was significantly negatively correlated with an increase in resting natural killer (NK) cell infiltration and was positively correlated with the abundance of M2 macrophage infiltration. The risk scores calculated by the nomogram were significantly higher for cluster-3, and the expression levels of m6A regulators in this cluster were generally low. Immunocyte infiltration and pathway enrichment results for cluster-3 differed significantly from those for the other two clusters. Finally, the expression of YTHDF2 was significantly decreased in IgAN based on immunohistochemical staining. This study demonstrated that m6A methylation regulators play a significant role in the regulation of the immune microenvironment in IgAN. Based on m6A regulator expression patterns, IgAN can be classified into multiple subtypes, which might provide additional insights into novel therapeutic methods for IgAN.

Importance of CD8 Tex cell-associated gene signatures in the prognosis and immunology of osteosarcoma

As a highly aggressive bone malignancy, osteosarcoma poses a significant therapeutic challenge, especially in the setting of metastasis or recurrence. This study aimed to investigate the potential of CD8-Tex cell-associated genes as prognostic biomarkers to reveal the immunogenomic profile of osteosarcoma and guide therapeutic decisions. mRNA expression data and clinical details of osteosarcoma patients were obtained from the TCGA database (TARGET-OS dataset). The GSE21257 dataset (from the GEO database) was used as an external validation set to provide additional information on osteosarcoma specimens. 84 samples from the TARGET-OS dataset were used as the training set, and 53 samples from the GSE21257 dataset served as the external validation cohort. Univariate Cox regression analysis was utilized to identify CD8 Tex cell genes associated with prognosis. The LASSO algorithm was performed for 1000 iterations to select the best subset to form the CD8 Tex cell gene signature (TRS). Final genes were identified using the multivariate Cox regression model of the LASSO algorithm. Risk scores were calculated to categorize patients into high- and low-risk groups, and clinical differences were explored by Kaplan-Meier survival analysis to assess model performance. Prediction maps were constructed to estimate 1-, 3-, and 5 year survival rates for osteosarcoma patients, including risk scores for CD8 Texcell gene markers and clinicopathologic factors. The ssGSEA algorithm was used to assess the differences in immune function between TRS-defined high- and low-risk groups. TME and immune cell infiltration were further assessed using the ESTIMATE and CIBERSORT algorithms. To explore the relationship between immune checkpoint gene expression levels and the two risk-defined groups. A CD8 Tex cell-associated gene signature was extracted from the TISCH database and prognostic markers including two genes were developed. The high-risk group showed lower survival, and model performance was validated by ROC curves and C-index. Predictive plots were constructed to demonstrate survival estimates, combining CD8 Tex cell gene markers and clinical factors. This study provides valuable insights into the molecular and immune characteristics of osteosarcoma and offers potential avenues for advances in therapeutic approaches.

Integrated analysis of m6A regulator-mediated RNA methylation modification patterns and immune characteristics in Sjögren's syndrome

The epigenetic modifier N6-methyladenosine (m6A), recognized as the most prevalent internal modification in messenger RNA (mRNA), has recently emerged as a pivotal player in immune regulation. Its dysregulation has been implicated in the pathogenesis of various autoimmune conditions. However, the implications of m6A modification within the immune microenvironment of Sjögren's syndrome (SS), a chronic autoimmune disorder characterized by exocrine gland dysfunction, remain unexplored. Herein, we leverage an integrative analysis combining public database resources and novel sequencing data to investigate the expression profiles of m6A regulatory genes in SS. Our cohort comprised 220 patients diagnosed with SS and 62 healthy individuals, enabling a comprehensive evaluation of peripheral blood at the transcriptomic level. We report a significant association between SS and altered expression of key m6A regulators, with these changes closely tied to the activation of CD4+ T cells. Employing a random forest (RF) algorithm, we identified crucial genes contributing to the disease phenotype, which facilitated the development of a robust diagnostic model via multivariate logistic regression analysis. Further, unsupervised clustering revealed two distinct m6A modification patterns, which were significantly associated with variations in immunocyte infiltration, immune response activity, and biological function enrichment in SS. Subsequently, we proceeded with a screening process aimed at identifying genes that were differentially expressed (DEGs) between the two groups distinguished by m6A modification. Leveraging these DEGs, we employed weight gene co-expression network analysis (WGCNA) to uncover sets of genes that exhibited strong co-variance and hub genes that were closely linked to m6A modification. Through rigorous analysis, we identified three critical m6A regulators - METTL3, ALKBH5, and YTHDF1 - alongside two m6A-related hub genes, COMMD8 and SRP9. These elements collectively underscore a complex but discernible pattern of m6A modification that appears to be integrally linked with SS's pathogenesis. Our findings not only illuminate the significant correlation between m6A modification and the immune microenvironment in SS but also lay the groundwork for a deeper understanding of m6A regulatory mechanisms. More importantly, the identification of these key regulators and hub genes opens new avenues for the diagnosis and treatment of SS, presenting potential targets for therapeutic intervention.

Integrating iron metabolism-related gene signature to evaluate prognosis and immune infiltration in nasopharyngeal carcinoma

BACKGROUND

Dysregulation of iron metabolism has been shown to have significant implications for cancer development. We aimed to investigate the prognostic and immunological significance of iron metabolism-related genes (IMRGs) in nasopharyngeal carcinoma (NPC).

METHODS

Multiple Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets were analyzed to identify key IMRGs associated with prognosis. Additionally, the immunological significance of IMRGs was explored.

RESULTS

A novel risk model was established using the LASSO regression algorithm, incorporating three genes (TFRC, SLC39A14, and ATP6V0D1).This model categorized patients into low and high-risk groups, and Kaplan-Meier analysis revealed significantly shorter progression-free survival for the high-risk group (P < 0.0001). The prognostic model's accuracy was additionally confirmed by employing time-dependent Receiver Operating Characteristic (ROC) curves and conducting Decision Curve Analysis (DCA). High-risk patients were found to correlate with advanced clinical stages, specific tumor microenvironment subtypes, and distinct morphologies. ESTIMATE analysis demonstrated a significant inverse relationship between increased immune, stromal, and ESTIMATE scores and lowered risk score. Immune analysis indicated a negative correlation between high-risk score and the abundance of most tumor-infiltrating immune cells, including dendritic cells, CD8+ T cells, CD4+ T cells, and B cells. This correlation extended to immune checkpoint genes such as PDCD1, CTLA4, TIGIT, LAG3, and BTLA. The protein expression patterns of selected genes in clinical NPC samples were validated through immunohistochemistry.

CONCLUSION

This study presents a prognostic model utilizing IMRGs in NPC, which could assist in assessing patient prognosis and provide insights into new therapeutic targets for NPC.

Identification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma

N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications have garnered significant attention in the field of epigenetic research due to their close association with human cancers. This study we focus on elucidating the expression patterns of m6A/m5C-related long non-coding RNAs (lncRNAs) in esophageal squamous cell carcinoma (ESCC) and assessing their prognostic significance and therapeutic potential. Transcriptomic profiles of ESCC were derived from public resources. m6A/m5C-related lncRNAs were obtained from TCGA using Spearman's correlations analysis. The m6A/m5C-lncRNAs prognostic signature was selected to construct a RiskScore model for survival prediction, and their correlation with the immune microenvironment and immunotherapy response was analyzed. A total of 606 m6A/m5C-lncRNAs were screened, and ESCC cases in the TCGA cohort were stratified into three clusters, which showed significantly distinct in various clinical features and immune landscapes. A RiskScore model comprising ten m6A/m5C-lncRNAs prognostic signature were constructed and displayed good independent prediction ability in validation datasets. Patients in the low-RiskScore group had a better prognosis, a higher abundance of immune cells (CD4 + T cell, CD4 + naive T cell, class-switched memory B cell, and Treg), and enhanced expression of most immune checkpoint genes. Importantly, patients with low-RiskScore were more cline benefit from immune checkpoint inhibitor treatment (P < 0.05). Our findings underscore the potential of RiskScore system comprising ten m6A/m5C-related lncRNAs as effective biomarkers for predicting survival outcomes, characterizing the immune landscape, and assessing response to immunotherapy in ESCC.

Immune patterns of cuproptosis in ischemic heart failure: A transcriptome analysis

Cuproptosis is a recently discovered programmed cell death pattern that affects the tricarboxylic acid (TCA) cycle by disrupting the lipoylation of pyruvate dehydrogenase (PDH) complex components. However, the role of cuproptosis in the progression of ischemic heart failure (IHF) has not been investigated. In this study, we investigated the expression of 10 cuproptosis-related genes in samples from both healthy individuals and those with IHF. Utilizing these differential gene expressions, we developed a risk prediction model that effectively distinguished healthy and IHF samples. Furthermore, we conducted a comprehensive evaluation of the association between cuproptosis and the immune microenvironment in IHF, encompassing infiltrated immunocytes, immune reaction gene-sets and human leukocyte antigen (HLA) genes. Moreover, we identified two different cuproptosis-mediated expression patterns in IHF and explored the immune characteristics associated with each pattern. In conclusion, this study elucidates the significant influence of cuproptosis on the immune microenvironment in ischemic heart failure (IHF), providing valuable insights for future mechanistic research exploring the association between cuproptosis and IHF.

Correlation analysis of disulfidptosis-related gene signatures with clinical prognosis and immunotherapy response in sarcoma

Disulfidptosis, a newly discovered type of programmed cell death, could be a mechanism of cell death controlled by SLC7A11. This could be closely associated with tumor development and advancement. Nevertheless, the biological mechanism behind disulfidptosis-related genes (DRGs) in sarcoma (SARC) is uncertain. This study identified three valuable genes (SLC7A11, RPN1, GYS1) associated with disulfidptosis in sarcoma (SARC) and developed a prognostic model. The multiple databases and RT-qPCR data confirmed the upregulated expression of prognostic DRGs in SARC. The TCGA internal and ICGC external validation cohorts were utilized to validate the predictive model capacity. Our analysis of DRG riskscores revealed that the low-risk group exhibited a more favorable prognosis than the high-risk group. Furthermore, we observed a significant association between DRG riskscores and different clinical features, immune cell infiltration, immune therapeutic sensitivity, drug sensitivity, and RNA modification regulators. In addition, two external independent immunetherapy datasets and clinical tissue samples were collected, validating the value of the DRGs risk model in predicting immunotherapy response. Finally, the SLC7A11/hsa-miR-29c-3p/LINC00511, and RPN1/hsa-miR-143-3p/LINC00511 regulatory axes were constructed. This study provided DRG riskscore signatures to predict prognosis and response to immunotherapy in SARC, guiding personalized treatment decisions.

Implication of m6A Methylation Regulators in the Immune Microenvironment of Bronchopulmonary Dysplasia

N6-methyladenosine (m6A) regulates gene expression and governs many important biological processes. However, the function of m6A in the development of bronchopulmonary dysplasia (BPD) remains poorly characterized. Thus, the purpose of this investigation was to evaluate the effects of m6A RNA methylation regulators on the development of BPD. BPD-related transcriptome data were downloaded from the GEO database. Differentially expressed m6A methylation regulators between BPD and control group were identified. Consensus clustering was conducted for the classification of BPD and association between clusters and BPD phenotypes were explored. Analysis of differentially expressed genes (DEGs) and immune-related DEGs was performed. The GSEA, GO and KEGG analyses were used to interpret the functional enrichments. The composition of immune cell subtypes in BPD subsets was predicted by CIBERSORT analysis. Compared with the control group, expression of most m6A regulators showed significant alteration, especially for IGF2BP1/2/3. BPD was classified into 2 subsets, and cluster 1 was correlated with severe BPD. Furthermore, the results of functional enrichment analyses showed a disturbed immune-related signaling pathway. Based on CIBERSORT analysis, we found that the proportion of immune cell subsets changed between cluster 1 and cluster 2. Our study revealed the implication of m6A methylation regulators in the development of BPD, which might provide a novel insight for the diagnosis and treatment of BPD.

Association between periodontitis and inflammatory comorbidities: The common role of innate immune cells, underlying mechanisms and therapeutic targets

Periodontitis, which is related to various systemic diseases, is a chronic inflammatory disease caused by periodontal dysbiosis of the microbiota. Multiple factors can influence the interaction of periodontitis and associated inflammatory disorders, among which host immunity is an important contributor to this interaction. Innate immunity can be activated aberrantly because of the systemic inflammation induced by periodontitis. This aberrant activation not only exacerbates periodontal tissue damage but also impairs systemic health, triggering or aggravating inflammatory comorbidities. Therefore, innate immunity is a potential therapeutic target for periodontitis and associated inflammatory comorbidities. This review delineates analogous aberrations of innate immune cells in periodontitis and comorbid conditions such as atherosclerosis, diabetes, obesity, and rheumatoid arthritis. The mechanisms behind these changes in innate immune cells are discussed, including trained immunity and clonal hematopoiesis of indeterminate potential (CHIP), which can mediate the abnormal activation and myeloid-biased differentiation of hematopoietic stem and progenitor cells. Besides, the expansion of myeloid-derived suppressor cells (MDSCs), which have immunosuppressive and osteolytic effects on peripheral tissues, also contributes to the interaction between periodontitis and its inflammatory comorbidities. The potential treatment targets for relieving the risk of both periodontitis and systemic conditions are also elucidated, such as the modulation of innate immunity cells and mediators, the regulation of trained immunity and CHIP, as well as the inhibition of MDSCs' expansion.

Significance of N6-methyladenosine RNA methylation regulators in diagnosis and subtype classification of primary Sjögren's syndrome

The importance of N6-methyladenine (m6A) in mRNA metabolism, physiology, pathology and other life processes is well recognized. However, the exact role of m6A regulators in primary Sjögren's syndrome (PSS) remains unclear. In this study, we used bioinformatics and machine learning random forest approach to screen eight key m6A regulators from the Gene Expression Omnibus GSE7451, GSE40611 and GSE84844 datasets. An accurate nomogram model for predicting PSS risk was established based on these regulators. And using consensus clustering, patients diagnosed with PSS were classified into two different m6A patterns. We found that patients in group B had higher m6A scores compared to those in group A: furthermore, both groups were closely related to immunity and possibly to other diseases. These results emphasise the important role of m6A regulators in the pathogenesis of PSS. Our study of m6A patterns may inform future immunotherapy strategies for PSS.

Identification of pyroptosis-related gene signature in nonalcoholic steatohepatitis

Non-alcoholic fatty liver disease (NAFLD) has emerged as one of the major causes of liver-related morbidity and mortality globally. It ranges from simple steatosis to non-alcoholic steatohepatitis (NASH) characterized by ballooning and hepatic inflammation. In the past few years, pyroptosis has been shown as a type of programmed cell death that triggers inflammation and plays a role in the development of NASH. However, the roles of pyroptosis-related genes (PRGs) in NASH remained unclear. In this study, we studied the expression level of pyroptosis-related genes (PRGs) in NASH and healthy controls, developed a diagnostic model of NASH based on PRGs and explored the pathological mechanisms associated with pyroptosis. We further compared immune status between NASH and healthy controls, analyzed immune status in different subtypes of NASH. We identified altogether twenty PRGs that were differentially expressed between NASH and normal liver tissues. Then, a novel diagnostic model consisting of seven PRGs including CASP3, ELANE, GZMA, CASP4, CASP9, IL6 and TP63 for NASH was constructed with an area under the ROC curve (AUC) of 0.978 (CI 0.965-0.99). Obvious variations in immune status between healthy controls and NASH cases were detected. Subsequently, the consensus clustering method based on differentially expressed PRGs was constructed to divide all NASH cases into two distinct pyroptosis subtypes with different immune and biological characteristics. Pyroptosis-related genes may play an important role in NASH and can provide new insights into the diagnosis and underlying mechanisms of NASH.

Analysis of m6A regulators related immune characteristics in ankylosing spondylitis by integrated bioinformatics and computational strategies

N6-methyladenosine (m6A) modification, as a common epigenetic modification, has been widely studied in autoimmune diseases. However, the role of m6A in the regulation of the immune microenvironment of ankylosing spondylitis (AS) remains unclear. Therefore, we aimed to investigate the effect of m6A modification on the immune microenvironment of AS. We first evaluated RNA modification patterns mediated by 26 m6A regulators in 52 AS samples and 20 healthy samples. Thereafter, an m6A related classifier composed of seven genes was constructed and could effectively distinguish healthy and AS samples. Then, the correlation between m6A regulators and immune characteristics were investigated, including infiltrating immunocytes, immune reactions activity, and human leukocyte antigen (HLA) genes expression. The results indicated that m6A regulators was closely correlated with immune characteristics. For example, EIF3A was significantly related to infiltrating immunocytes; IGF2BP2 and EIF3A were significant regulators in immune reaction of TGF-β family member, and the expression of HLA-DPA1 and HLA-E were affected by EIF3A and ALKBH5. Next, two distinct m6A expression patterns were identified through unsupervised clustering analysis, and diverse immune characteristics were found between them. A total of 5889 m6A phenotype-related genes were obtained between the two expression patterns, and their biological functions were revealed. Finally, we validated the expression status of m6A modification regulators using two additional datasets. Our findings illustrate that m6A modifications play a critical role in the diversity and complexity of the AS immune microenvironment.

Alkylation Repair Homolog 5 Regulates N(6)-methyladenosine (m6A) Methylation of Mitsugumin 53 to Attenuate Myocardial Infarction by Inhibiting Apoptosis and Oxidative Stress

ABSTRACT

N(6)-methyladenosine (m6A) methylation modification is involved in the progression of myocardial infarction (MI). In this study, we investigated the effects of demethylase alkylation repair homolog 5 (ALKBH5) on cell apoptosis and oxidative stress in MI. The ischemia/reperfusion (I/R) injury mouse model and hypoxia/reoxygenation (H/R) cell model were established. The levels of ALKBH5 and mitsugumin 53 (MG53) were measured by quantitative real-time polymerase chain reaction, immunohistochemical, and immunofluorescence analysis. Apoptosis was evaluated by TUNEL assay, flow cytometry, and western blot. Oxidative stress was assessed by antioxidant index kits. Methylation was analyzed by RNA binding protein immunoprecipitation (RIP), MeRIP, and dual-luciferase reporter assay. We observed that ALKBH5 and MG53 were highly expressed in MI. Overexpression of ALKBH5 inhibited H/R-induced cardiomyocyte apoptosis and oxidative stress in vitro, and it inhibited I/R-induced collagen deposition, cardiac function, and apoptosis in vivo. ALKBH5 could bind to MG53, inhibit m6A methylation of MG53, and increase its mRNA stability. Silencing of MG53 counteracted the inhibition of apoptosis and oxidative stress induced by ALKBH5. In conclusion, ALKBH5 suppressed m6A methylation of MG53 and inhibited MG53 degradation to inhibit apoptosis and oxidative stress of cardiomyocytes, thereby attenuating MI. The results provided a theoretical basis that ALKBH5 is a potential target for MI treatment.

Analysis and Regulatory Mechanisms of Platelet-Related Genes in Patients with Ischemic Stroke

It was found that ischemic stroke (IS) was associated with abnormal platelet activity and thrombosis. However, the potential significance of platelet-related genes (PRGs) in IS still needs to be more thorough. This study extracted IS-related transcriptome datasets from the Gene Expression Omnibus (GEO) database. The target genes were obtained by intersecting the differentially expressed genes (DEGs), the module genes related to IS, and PRGs, where the key genes of IS were screened by two machine learning algorithms. The key genes-based diagnostic model was constructed. Gene set enrichment analysis (GSEA) and the immune microenvironment analyses were analyzed targeting key genes in IS. The co-expression, TF-mRNA, and competitive endogenous RNAs (ceRNA) regulatory networks were constructed to reveal the potential regulation of key genes. Potential drugs targeting key genes were predicted as well. Totals of eight target genes were obtained and were associated with immune-related functions. Four platelet-related key genes were acquired, which were related to immunity and energy metabolism. The abnormal expressions of DOCK8, GIMAP5, ICOS were determined by the quantitative real-time polymerase chain reaction (qRT-PCR), and the significant correlations among these key genes were identified. Notably, hsa-miR-17-3p, hsa-miR-3158-3p, hsa-miR-423-3p, and hsa-miR-193a-8p could regulate all key genes at the same time. In addition, Caffeine, Carboplatin, and Vopratelimab were the targeted drugs of these key genes. This study identified four platelet-related key genes of IS, which might help to deepen the understanding of the role of platelet-related genes in the molecular mechanism of IS.

The essential roles of m6A modification in osteogenesis and common bone diseases

N6-methyladenosine (m6A) is the most prevalent modification in the eukaryotic transcriptome and has a wide range of functions in coding and noncoding RNAs. It affects the fate of the modified RNA, including its stability, splicing, and translation, and plays an important role in post-transcriptional regulation. Bones play a key role in supporting and protecting muscles and other organs, facilitating the movement of the organism, ensuring blood production, etc. Bone diseases such as osteoarthritis, osteoporosis, and bone tumors are serious public health problems. The processes of bone development and osteogenic differentiation require the precise regulation of gene expression through epigenetic mechanisms including histone, DNA, and RNA modifications. As a reversible dynamic epigenetic mark, m6A modifications affect nearly every important biological process, cellular component, and molecular function, including skeletal development and homeostasis. In recent years, studies have shown that m6A modification is involved in osteogenesis and bone-related diseases. In this review, we summarized the proteins involved in RNA m6A modification and the latest progress in elucidating the regulatory role of m6A modification in bone formation and stem cell directional differentiation. We also discussed the pathological roles and potential molecular mechanisms of m6A modification in bone-related diseases like osteoporosis and osteosarcoma and suggested potential areas for new strategies that could be used to prevent or treat bone defects and bone diseases.

USP39 Promotes the Viability and Migration of Head and Neck Squamous Cell Carcinoma Cell by Regulating STAT1

Objective: Ubiquitin-specific peptidase 39 (USP39) plays a carcinogenic role in many cancers, but little research has been conducted examining whether it is involved in head and neck squamous cell carcinoma (HNSCC). Therefore, this study explored the functional role of USP39 in HNSCC. Method: Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to identify differentially expressed proteins (DEPs) between the HNSCC tumor and adjacent healthy tissues. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to assess the functional enrichment of DEPs. Immunohistochemistry was used to detect protein expression. The viability and migration of two HNSCC cell lines, namely CAL27 and SCC25, were detected using the cell counting kit-8 assay and a wound healing assay, respectively. Quantitative real-time PCR was used to detect the expression level of signal transducer and activator of transcription 1 (STAT1) mRNA. Results: LC-MS/MS results identified 590 DEPs between HNSCC and adjacent tissues collected from 4 patients. Through GO and KEGG pathway analyses, 34 different proteins were found to be enriched in the spliceosome pathway. The expression levels of USP39 and STAT1 were significantly higher in HNSCC tumor tissue than in adjacent healthy tissue as assessed by LC-MS/MS analysis, and the increased expression of USP39 and STAT1 protein was confirmed by immunohistochemistry in clinical samples collected from 7 additional patients with HNSCC. Knockdown of USP39 or STAT1 inhibited the viability and migration of CAL27 and SCC25 cells. In addition, USP39 knockdown inhibited the expression of STAT1 mRNA in these cells. Conclusion: Our findings indicated that USP39 knockdown may inhibit HNSCC viability and migration by suppressing STAT1 expression. The results of this study suggest that USP39 may be a potential new target for HNSCC clinical therapy or a new biomarker for HNSCC.

METTL3 and METTL14 regulate IL-6 expression via RNA m6A modification of zinc transporter SLC39A9 and DNA methylation of IL-6 in periodontal ligament cells

The inflammatory response is a key process in periodontitis. The N6-methyladenosine (m6A) modification has been proven to be involved in various physiological and pathological processes. This study aims to investigate the role and downstream mechanism of N6-adenosine-enzyme subunits methyltransferase (METTL) 3 and 14 in the inflammatory response of periodontal ligament cells (PDLCs). The total m6A content and the expression of METTL3 and METTL14 were upregulated in lipopolysaccharide (LPS)-stimulated PDLCs. Knockdown of METTL3 or METTL14 suppressed the LPS-induced interleukin (IL)-6 expression, as shown by quantitative polymerase chain reaction (qPCR) and enzyme linked immunosorbent assay (ELISA). Mechanistically, conjoint analysis of m6A sequencing of METTL3-knockdown and METTL14-knockdown PDLCs revealed that the expression of solute carrier family 39 member 9 (SLC39A9) was mediated in a m6A-dependent manner. The suppression of LPS-induced IL-6 by METTL3 or METTL14 knockdown was partially counteracted by SLC39A9 knockdown, which induced downregulation of intracellular zinc via immunofluorescence staining. Amplicon bisulfite sequencing (AmpBS) demonstrated that METTL3/14 knockdown increased the methylation at one position of the IL-6 promoter, while SLC39A9 knockdown decreased it, which was basically consistent with the intracellular zinc concentration and negatively associated with IL-6 expression. Moreover, METTL3 or METTL14 knockdown attenuated the LPS-induced phosphorylation of p38 and JNK mitogen-activated protein kinase (MAPK), which was partially counteracted by SLC39A9 knockdown. These results revealed the "LPS-METTL3/14-SLC39A9-zinc-IL-6" axis and involvement of p38 and JNK MAPK signaling pathway in the inflammatory responses of PDLCs.

Decoding the role of m6A Regulators in identifying and characterizing molecular subtypes of rosacea

Rosacea is a common skin disease that predominantly affects individuals aged between 30 and 50 years. While the exact cause of the disease remains unclear, various factors have been shown to trigger or exacerbate its symptoms. N6-methyladenosine (m6A) modification is one of the most abundant epigenetic methylation modification in messenger RNA (mRNA) and non-coding RNA (ncRNA), plays a crucial role in RNA splicing, export, stability, and translation. In this study, we aimed to characterize m6A genes in rosacea, identify molecular subtypes based on m6A gene expression, characterize the immune features among subtypes, explore key molecules based on co-expression analysis, and identify potential targets and drugs. To achieve our objectives, we first compared the expression pattern and immune regulation of m6A genes between healthy and diseased groups. Then, we performed clustering to stratify disease samples into different subtypes and analyzed immune regulation and functional enrichment among the subtypes. Then, we conducted differential analysis between subtypes and applied weighted gene co-expression network analysis (WGCNA) in three subtypes. We found hub differential expression analysis (DEG) genes and their potential drug based on the WGCNA results and the drug-gene interaction database (DGIdb). Finally, in vivo and in vitro studies showed significant differences in m6A methyltransferase METTL3 levels in rosacea mice and control mice, as well as in the skin of rosacea patients and healthy people, while reducing METTL3 significantly inhibited the inflammatory response of human fibroblasts (HDFs) stimulated by LL37, suggesting that METTL3 may be associated with changes in overall m6A levels in rosacea. Taken together, our findings provide valuable insights into therapeutic targets and drug predictions for rosacea.

Dysregulated m6A methylation modification is associated with human peri-implantitis - A pilot study

BACKGROUND

N6-methyladenosine (m6A) RNA modification and its regulatory enzymes play important roles in the modulation of inflammation by regulating inflammation-related gene expression. Dysregulation of m6A has been associated with inflammatory diseases, including periodontitis. This study aimed to investigate the potential role of m6A modification and its master regulatory enzyme METTL3 in patients with peri‑implantitis.

MATERIALS AND METHODS

Peri-implant soft tissues from 20 subjects (10 healthy controls and 10 patients with peri‑implantitis) were enrolled in this study. Quantitative reverse transcription PCR (RT-qPCR) was used to detect METTL3 gene expression and western blotting was used to detect METTL3 protein expression. The m6A mRNA levels were measured using an m6A-RNA methylation quantification kit. Protein-protein interaction networks and in silico functional analyses were conducted using various bioinformatics tools.

RESULTS

m6A mRNA levels significantly increased in the peri‑implantitis group. Higher METTL3 mRNA and protein levels were observed in the peri‑implantitis group. High METTL3 expression might influence elevated levels of m6A RNA methylation. In addition, in silico functional analysis indicated that the METTL3 gene and protein were associated with inflammatory pathways.

CONCLUSIONS

Our data provide evidence, for the first time, that dysregulation of m6A modification is associated with peri‑implantitis and may represent a strong risk factor for this inflammatory disease.

The rosetta stone of successful ageing: does oral health have a role?

Ageing is an inevitable aspect of life and thus successful ageing is an important focus of recent scientific efforts. The biological process of ageing is mediated through the interaction of genes with environmental factors, increasing the body's susceptibility to insults. Elucidating this process will increase our ability to prevent and treat age-related disease and consequently extend life expectancy. Notably, centenarians offer a unique perspective on the phenomenon of ageing. Current research highlights several age-associated alterations on the genetic, epigenetic and proteomic level. Consequently, nutrient sensing and mitochondrial function are altered, resulting in inflammation and exhaustion of regenerative ability.Oral health, an important contributor to overall health, remains underexplored in the context of extreme longevity. Good masticatory function ensures sufficient nutrient uptake, reducing morbidity and mortality in old age. The relationship between periodontal disease and systemic inflammatory pathologies is well established. Diabetes, rheumatoid arthritis and cardiovascular disease are among the most significant disease burdens influenced by inflammatory oral health conditions. Evidence suggests that the interaction is bi-directional, impacting progression, severity and mortality. Current models of ageing and longevity neglect an important factor in overall health and well-being, a gap that this review intends to illustrate and inspire avenues for future research.

Significance of RNA N6-methyladenosine regulators in the diagnosis and subtype classification of coronary heart disease using the Gene Expression Omnibus database

Background

Many investigations have revealed that alterations in m6A modification levels may be linked to coronary heart disease (CHD). However, the specific link between m6A alteration and CHD warrants further investigation.

Methods

Gene expression profiles from the Gene Expression Omnibus (GEO) databases. We began by constructing a Random Forest model followed by a Nomogram model, both aimed at enhancing our predictive capabilities on specific m6A markers. We then shifted our focus to identify distinct molecular subtypes based on the key m6A regulators and to discern differentially expressed genes between the unique m6A clusters. Following this molecular exploration, we embarked on an in-depth analysis of the biological characteristics associated with each m6A cluster, revealing profound differences between them. Finally, we delved into the identification and correlation analysis of immune cell infiltration across these clusters, emphasizing the potential interplay between m6A modification and the immune system.

Results

In this research, 37 important m6Aregulators were identified by comparing non-CHD and CHD patients from the GSE20680, GSE20681, and GSE71226 datasets. To predict the risk of CHD, seven candidate m6A regulators (CBLL1, HNRNPC, YTHDC2, YTHDF1, YTHDF2, YTHDF3, ZC3H13) were screened using the logistic regression model. Based on the seven possible m6A regulators, a nomogram model was constructed. An examination of decision curves revealed that CHD patients could benefit from the nomogram model. On the basis of the selected relevant m6A regulators, patients with CHD were separated into two m6A clusters (cluster1 and cluster2) using the consensus clustering approach. The Single Sample Gene Set Enrichment Analysis (ssGSEA) and CIBERSORT methods were used to estimate the immunological characteristics of two separate m6A Gene Clusters; the results indicated a close association between seven candidate genes and immune cell composition. The drug sensitivity of seven candidate regulators was predicted, and these seven regulators appeared in numerous diseases as pharmacological targets while displaying strong drug sensitivity.

Conclusion

m6A regulators play crucial roles in the development of CHD. Our research of m6A clusters may facilitate the development of novel molecular therapies and inform future immunotherapeutic methods for CHD.

Multiplexed LC-MS/MS quantification of salivary RNA modifications in periodontitis

OBJECTIVE

To analyse the salivary epitranscriptomic profiles as periodontitis biomarkers using multiplexed mass spectrometry (MS).

BACKGROUND

The field of epitranscriptomics, which relates to RNA chemical modifications, opens new perspectives in the discovery of diagnostic biomarkers, especially in periodontitis. Recently, the modified ribonucleoside N6-methyladenosine (m6A) was revealed as a crucial player in the etiopathogenesis of periodontitis. However, no epitranscriptomic biomarker has been identified in saliva to date.

MATERIALS AND METHODS

Twenty-four saliva samples were collected from periodontitis patients (n = 16) and from control subjects (n = 8). Periodontitis patients were stratified according to stage and grade. Salivary nucleosides were directly extracted and, in parallel, salivary RNA was digested into its constituent nucleosides. Nucleoside samples were then quantified by multiplexed MS.

RESULTS

Twenty-seven free nucleosides were detected and an overlapping set of 12 nucleotides were detected in digested RNA. Among the free nucleosides, cytidine and three other modified nucleosides (inosine, queuosine and m6Am) were significantly altered in periodontitis patients. In digested RNA, only uridine was significantly higher in periodontitis patients. Importantly there was no correlation between free salivary nucleoside levels and the levels of those same nucleotides in digested salivary RNA, except for cytidine, m5C and uridine. This statement implies that the two detection methods are complementary.

CONCLUSION

The high specificity and sensitivity of MS allowed the detection and quantification of multiple nucleosides from RNA and free nucleosides in saliva. Some ribonucleosides appear to be promising biomarkers of periodontitis. Our analytic pipeline opens new perspectives for diagnostic periodontitis biomarkers.

Molecular subtypes based on N6-methyladenosine RNA methylation demonstrate the heterogeneity of immune and biological functions in pediatric septic shock

Introduction

Septic shock in children is a highly heterogeneous syndrome involving different immune states and biological processes. We used a bioinformatics approach to explore the relationship between N6-methyladenosine (m6A) methylation and septic shock in children.

Methods

A gene expression dataset including information on 98 children with septic shock was selected. To construct and evaluate a risk prediction model, machine learning was used to screen marker m6A regulators. Based on differentially expressed m6A regulators, molecular subtypes for paediatric septic shock were constructed. Subsequently, the differences in the m6Ascore, heterogeneity of immune cell infiltration, and heterogeneity of biological functions between the different subtypes were analyzed. Finally, real-time quantitative PCR (RT-qPCR) was performed to validate the expression of the marker m6A regulators.

Results

Fifteen differentially expressed m6A regulators were identified. Six marker m6A regulators, including LRPPRC, ELAVL1, RBM15, CBLL1, FTO, and RBM15B, were screened using the random forest method. The risk prediction model for paediatric septic shock constructed using m6A markers had strong consistency and high clinical practicability. Two subtypes of paediatric septic shock have been identified based on the differential expression pattern of m6A regulators. Significant differences were observed in RNA epigenetics, immune statuses, and biological processes between the two m6A subtypes. Differentially expressed genes between the two subtypes were enriched in cell number homeostasis, redox responses, and innate immune system responses. Finally, the six marker m6A regulators were verified in additional samples.

Conclusions

Based on the heterogeneity of m6A methylation-regulated genes, two different subtypes of septic shock in children with different RNA epigenetics, immune statuses, and biological processes were identified, revealing the heterogeneity of the disease largely attributable to differential m6A methylation. The findings will help explore and establish appropriate individualized treatments.

A Disulfidptosis-Related Gene Signature Associated with Prognosis and Immune Cell Infiltration in Osteosarcoma

Osteosarcoma (OS) stands as a leading aggressive bone malignancy that primarily affects children and adolescents worldwide. A recently identified form of programmed cell death, termed Disulfidptosis, may have implications for cancer progression. Yet, its role in OS remains elusive. To elucidate this, we undertook a thorough examination of Disulfidptosis-related genes (DRGs) within OS. This involved parsing expression data, clinical attributes, and survival metrics from the TARGET and GEO databases. Our analysis unveiled a pronounced association between the expression of specific DRGs, particularly MYH9 and LRPPRC, and OS outcome. Subsequent to this, we crafted a risk model and a nomogram, both honed for precise prognostication of OS prognosis. Intriguingly, risks associated with DRGs strongly resonated with immune cell infiltration levels, myriad immune checkpoints, genes tethered to immunotherapy, and sensitivities to systematic treatments. To conclude, our study posits that DRGs, especially MYH9 and LRPPRC, hold potential as pivotal architects of the tumor immune milieu in OS. Moreover, they may offer predictive insights into treatment responses and serve as reliable prognostic markers for those diagnosed with OS.

Comprehensive analyses of m6A RNA methylation patterns and related immune microenvironment in idiopathic pulmonary arterial hypertension

Idiopathic pulmonary arterial hypertension (IPAH) is a life-threatening disease with a poor prognosis and high heritability, characterized by elevated pulmonary vascular resistance (PVR) and pulmonary artery pressure. N6-methyladenosine (m6A) RNA modification influences many RNA metabolism pathways. However, the position of m6A methylation regulators in IPAH remains unknown. Therefore, the study aims to disclose the function m6A regulators exert in the pathological mechanisms of IPAH and the immune microenvironment involved. The GSE117261 dataset was downloaded from the Gene Expression Omnibus (GEO) to screen the differentially expressed genes (DEGs) between normal and IPAH samples. Functional and pathway enrichment analyses of DEGs were then conducted by Gene ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG). We also identified the differentially-expressed m6A (DEm6A) regulators between normal and IPAH samples. Key m6A regulators related to the prediction of IPAH were selected using the random forest model. The results showed that FMR1, RBM15, HNRNPA2B1 and IGFBP3 were upregulated in IPAH. In contrast, LRPPRC was downregulated. The single sample gene set enrichment analysis (ssGSEA) method was then adopted to estimate the immune microenvironment in distinct m6A clusters and m6A phenotype-related genes (PRGs) clusters, respectively. Furthermore, we calculated the m6A score via principal component analysis (PCA), and the Sankey diagram was selected to present the correlation among the m6A clusters, m6A PRGs clusters and m6A score. Finally, quantitative RT-PCR and Western blotting were used to validate the key genes in human pulmonary artery smooth muscle cells (HPASMCs) treated by human platelet-derived growth factor-BB (PDGF-BB). The relative mRNA and protein expression levels of FMR1 were significantly elevated, however, the relative mRNA and protein expression levels of LRPPRC were downregulated. Besides, the relative mRNA level of HNRNPA2B1 was increased. Generally, this bioinformatics analysis might provoke more insights into diagnosing and treating IPAH.

Diagnostic value and immune infiltration characterization of YTHDF2 as a critical m6A regulator in osteoarthritic synovitis

BACKGROUND

N6-methyladenosine (m6A) is a universal RNA modification pattern regulated by multiple m6A regulators. In osteoarthritis (OA), m6A regulators influence disease progression by regulating cartilage degradation. However, the function of m6A regulators in synovial tissue remains unclear. In this work, we investigated the biological significance of m6A regulators in osteoarthritic synovitis.

METHODS

Datasets were acquired from Gene Expression Omnibus. Differential analysis of merged data identified the differentially expressed m6A regulators. Machine learning models were used to evaluate genetic importance. To predict disease risk, a nomogram was constructed based on above m6A regulators. Cluster analysis divided the OA sample into different subgroups. Immune infiltration revealed the immune m6A regulators, which were validated using clinical samples. Eventually, a competing endogenous RNA (ceRNA) network was constructed.

RESULTS

We acquired five differentially expressed m6A regulators and a random forest model. The nomogram accurately predicted disease risk. We identified 122 differentially expressed genes between two m6A subgroups. The analysis of immune infiltration showed that YTHDF2 was an immune-related m6A regulator closely related with macrophages. In clinical samples, the protein and mRNA contents of YTHDF2 were consistent with the results of bioinformatic analysis. The ceRNA network based on YTHDF2 revealed 75 lncRNA nodes and 19 miRNA nodes.

CONCLUSION

YTHDF2 has a high diagnostic value in the synovitis of OA and significantly influences the immune status of patients. Hence, YTHDF2, a critical m6A regulator, may provide a biomarker for diagnosis and immune therapy of osteoarthritic synovitis.

Changes in N6-methyladenosine RNA methylomes of human periodontal ligament cells in response to inflammatory conditions

OBJECTIVE

To investigate the changes in the m6A methylation modification profile of human periodontal ligament cells (hPDLCs) in response to inflammatory conditions.

BACKGROUND

Periodontitis is an infectious disease of the periodontal support tissue that leads to the loss of alveolar bone. HPDLCs are primary cells that can repair periodontal tissue defects caused by periodontitis. However, the inflammatory conditions induce inflammatory damage and decrease ossification of hPDLCs. This inflammatory response depends on genetic and epigenetic mechanisms, including m6A methylation.

METHODS

HPDLCs were cultured with osteogenic induction medium (NC group), while TNF-α (10 ng/mL) and IL-1β (5 ng/mL) were added to simulate inflammatory conditions (Inflam group). Then RNA-seq and MeRIP-seq analyses were performed to identify m6A methylation modification in the transcriptome range of hPDLCs.

RESULTS

The results showed that the osteogenic differentiation of hPDLCs was inhibited under inflammatory conditions. RNA-seq analysis also revealed that the decreased genes in response to inflammatory conditions were primarily annotated in processes associated with ossification. Compared with the NC group, differentially m6A-methylated genes were primarily enriched in histone modification processes. Among 145 histone modification genes, 25 genes have been reported to be involved in the regulation of osteogenic differentiation, and they include KAT6B, EP300, BMI1, and KDMs (KDM1A, KDM2A, KDM3A, KDM4B, and KDM5A).

CONCLUSION

This study demonstrated that the m6A landscape of hPDLCs was changed in response to inflammation. M6A methylation differences among histone modification genes may act on the osteogenic differentiation of hPDLCs.

DNER and GNL2 are differentially m6A methylated in periodontitis in comparison with periodontal health revealed by m6A microarray of human gingival tissue and transcriptomic analysis

OBJECTIVE

This study aims to investigate the differences in the epigenomic patterns of N6-methyladenosine (m6A) methylation in gingival tissues between patients with periodontitis (PD) and healthy controls, identifying potential biomarkers.

BACKGROUND

As a multifactorial disease, PD involves multiple genetic and environmental effects. The m6A modification is the most prevalent internal mRNA modification and linked to various inflammatory diseases. However, the m6A modification pattern and m6A-related signatures in PD remain unclear.

MATERIALS AND METHODS

An m6A microarray of human gingival tissues was conducted in eight subjects: four diagnosed with PD and four healthy controls. Microarray analysis was performed to identify the differentially m6A methylated mRNAs (DMGs) and the differentially expressed mRNAs (DEGs). The differentially methylated and expressed mRNAs (DMEGs) were subjected to functional enrichment analysis by Metascape. The weighted gene co-expression network analysis (WGCNA) algorithm, the least absolute shrinkage and selection operator (LASSO) regression, and univariate logistic regression were performed to identify potential biomarkers. The cell type localization of the target genes was determined using single-cell RNA-seq (scRNA-seq) analysis. The m6A methylation level and gene expression of hub genes were subsequently verified by m6A methylated RNA immunoprecipitation (MeRIP) and quantitative real-time PCR (qRT-PCR).

RESULTS

In total, 458 DMGs, 750 DEGs, and 279 DMEGs were identified based on our microarray. Pathway analyses conducted for the DMEGs revealed that biological functions were mainly involved in the regulation of stem cell differentiation, ossification, circadian rhythm, and insulin secretion pathways. Besides, the genes involved in crucial biological processes were mainly expressed in fibroblast and epithelial cells. Furthermore, the m6A methylation and expression levels of two hub biomarkers (DNER and GNL2) were validated.

CONCLUSION

The current study exhibited a distinct m6A epitranscriptome, identified and verified two PD-related biomarkers (DNER and GNL2), which may provide novel insights into revealing the new molecular mechanisms and latent targets of PD.

Epithelial-mesenchymal transition-related gene prognostic index and phenotyping clusters for hepatocellular carcinoma patients

Epithelial-mesenchymal transition (EMT) contributes to high tumor heterogeneity and the immunosuppressive environment of the HCC tumor microenvironment (TME). Here, we developed EMT-related genes phenotyping clusters and systematically evaluated their impact on HCC prognosis, the TME, and drug efficacy prediction. We identified HCC specific EMT-related genes using weighted gene co-expression network analysis (WGCNA). An EMT-related genes prognostic index (EMT-RGPI) capable of effectively predicting HCC prognosis was then constructed. Consensus clustering of 12 HCC specific EMT-related hub genes uncovered two molecular clusters C1 and C2. Cluster C2 preferentially associated with unfavorable prognosis, higher stemness index (mRNAsi) value, elevated immune checkpoint expression, and immune cell infiltration. The TGF-β signaling, EMT, glycolysis, Wnt β-catenin signaling, and angiogenesis were markedly enriched in cluster C2. Moreover, cluster C2 exhibited higher TP53 and RB1 mutation rates. The TME subtypes and tumor immune dysfunction and exclusion (TIDE) score showed that cluster C1 patients responded well to immune checkpoint inhibitors (ICIs). Half-maximal inhibitory concentration (IC50) revealed that cluster C2 patients were more sensitive to chemotherapeutic and antiangiogenic agents. These findings may guide risk stratification and precision therapy for HCC patients.

Comprehensive analysis of m6A RNA methylation modification patterns and the immune microenvironment in osteoarthritis

Background

Osteoarthritis (OA) is the most common joint degenerative disease, and so far, there is no effective therapy to prevent or delay its development. Considerable attention is now being given to the impact of m6A RNA methylation modification on the disease immune regulation. However, much remains unknown about the function of m6A modification in OA.

Methods

A total of 63 OA and 59 healthy samples were applied to comprehensively examine the m6A regulators mediated RNA methylation modification pattern in OA, and evaluate the impacts of distinct patterns on the characteristics of OA immune microenvironment, including immune infiltration cells, immune responses and human leukocyte antigen (HLAs) genes expression. In addition, we screened out the m6A phenotype-related genes and further explored their potential biological functions. At last, we verified the expression of key m6A regulators and their associations with immune cells, in vitro.

Results

Most of m6A regulators was differentially expressed in OA samples compared to the normal tissues. Based on six hub-m6A regulators identified as abnormally expressed in OA samples, we developed a classifier to distinguish OA patients from healthy individuals. We noted that immune characteristics of OA were correlated with m6A regulators. For instance, YTHDF2 had a strongest significantly positive correlation with regulatory T cells (Tregs) and IGFBP2 was strongest negatively associated with dendritic cells (DCs), which were confirmed by the immunohistochemistry (IHC) staining. Two distinct m6A modification patterns were determined: pattern B had higher infiltrating immunocytes and more active immune responses than pattern A, and two patterns differed in the expression of HLA genes. We also identified 1,592 m6A phenotype-related genes that could mediate the OA synovitis and cartilage degradation by the PI3K-Akt signaling pathway. Quantitative real-time polymerase chain reaction (qRT-PCR) results indicated that IGFBP2 was significantly overexpressed, while YTHDF2 mRNA expression was decreased in OA samples, which was consistent with our findings.

Conclusion

Our research proves the essential impact of m6A RNA methylation modification on the OA immune microenvironment, and helps to explain the regulatory mechanism behind it, which may open up a new direction for more precise immunotherapy of osteoarthritis.

Landscape analysis of m6A modification regulators related biological functions and immune characteristics in myasthenia gravis

BACKGROUND

N6-methyladenosine (m6A) modification has been recognized to play fundamental roles in the development of autoimmune diseases. However, the implication of m6A modification in myasthenia gravis (MG) remains largely unknown. Thus, we aimed to systematically explore the potential functions and related immune characteristics of m6A regulators in MG.

METHODS

The GSE85452 dataset with MG and healthy samples was downloaded from Gene Expression Omnibus (GEO) database. m6A modification regulators were manually curated. The targets of m6A regulators were obtained from m6A2Target database. The differential expressed m6A regulators in GSE85452 dataset were identified by "limma" package and were validated by RT-PCR. Function enrichment analysis of dysregulated m6A regulators was performed using "clusterProfiler" package. Correlation analysis was applied for analyzing the relationships between m6A regulators and immune characteristics. Unsupervised clustering analysis was used to identify distinct m6A modification subtypes. The differences between subtypes were analyzed, including the expression level of all genes and the enrichment degree of immune characteristics. Weighted gene co-expression network analysis (WGCNA) was conducted to obtain modules associated with m6A modification subtypes.

RESULTS

We found that CBLL1, RBM15 and YTHDF1 were upregulated in MG samples of GSE85452 dataset, and the results were verified by RT-PCR in blood samples from19 MG patients and 19 controls. The targeted genes common modified by CBLL1, RBM15, and YTHDF1 were mainly enriched in histone modification and Wnt signaling pathway. Correlation analysis showed that three dysregulated m6A regulators were closely associated with immune characteristics. Among them, RBM15 possessed the strongest correlation with immune characteristics, including CD56dim natural killer cell (r = 0.77, P = 0.0023), T follicular helper cell (r = - 0.86, P = 0.0002), Interferon Receptor (r = 0.78, P = 0.0017), and HLA-DOA (r = 0.64, P = 0.0200). Further two distinct m6A modification patterns mediated by three dysregulated m6A regulators was identified. Bioinformatics analysis found that there were 3029 differentially expressed genes and different immune characteristics between two m6A modification patterns. Finally, WGCNA analysis obtained a total of 12 modules and yellow module was the most positively correlated to subtype-2.

CONCLUSION

Our findings suggested that m6A RNA modification had an important effect on immunity molecular mechanism of MG and provided a new perspective into understanding the pathogenesis of MG.

Role of N6-adenosine-methyltransferase subunits METTL3 and METTL14 in the biological properties of periodontal ligament cells

The N6-methyladenosine (m6A) modification has been proven to be involved in various physiological and pathological processes. The m6A is catalyzed by methyltransferase complex, which mainly consist of methyltransferase (METTL) 3 and 14 heterodimer. The present study aimed to investigate the role of METTL 3 and 14 in biological properties of periodontal ligament cells (PDLCs) via RNA-sequencing and specific cell assays. Firstly, the expressions of METTL3 and METTL14 were observed in PDLCs. Then, RNA-sequencing showed that cell properties were influenced after METTL3 or METTL14 was knocked down via short hairpin RNA (shRNA). In sh-METTL3 or METTL14 PDLCs, cell counting kit 8 (CCK8) and 5-ethynyl-2'-deoxyuridine (EdU) assays showed a down-regulated proliferation, transwell system indicated suppressed migration. Lastly, alkaline phosphatase (ALP) and alizarin red staining (ARS) staining, quantitative polymerase chain reaction (qPCR) and western blot demonstrated the inhibited osteogenic potentials. It could be concluded that METTL3 and METTL14 play indispensable roles in the regenerative potential of PDLCs.

Identification and experimental validation of key m6A modification regulators as potential biomarkers of osteoporosis

Osteoporosis (OP) is a severe systemic bone metabolic disease that occurs worldwide. During the coronavirus pandemic, prioritization of urgent services and delay of elective care attenuated routine screening and monitoring of OP patients. There is an urgent need for novel and effective screening diagnostic biomarkers that require minimal technical and time investments. Several studies have indicated that N6-methyladenosine (m6A) regulators play essential roles in metabolic diseases, including OP. The aim of this study was to identify key m6A regulators as biomarkers of OP through gene expression data analysis and experimental verification. GSE56815 dataset was served as the training dataset for 40 women with high bone mineral density (BMD) and 40 women with low BMD. The expression levels of 14 major m6A regulators were analyzed to screen for differentially expressed m6A regulators in the two groups. The impact of m6A modification on bone metabolism microenvironment characteristics was explored, including osteoblast-related and osteoclast-related gene sets. Most m6A regulators and bone metabolism-related gene sets were dysregulated in the low-BMD samples, and their relationship was also tightly linked. In addition, consensus cluster analysis was performed, and two distinct m6A modification patterns were identified in the low-BMD samples. Subsequently, by univariate and multivariate logistic regression analyses, we identified four key m6A regulators, namely, METTL16, CBLL1, FTO, and YTHDF2. We built a diagnostic model based on the four m6A regulators. CBLL1 and YTHDF2 were protective factors, whereas METTL16 and FTO were risk factors, and the ROC curve and test dataset validated that this model had moderate accuracy in distinguishing high- and low-BMD samples. Furthermore, a regulatory network was constructed of the four hub m6A regulators and 26 m6A target bone metabolism-related genes, which enhanced our understanding of the regulatory mechanisms of m6A modification in OP. Finally, the expression of the four key m6A regulators was validated in vivo and in vitro, which is consistent with the bioinformatic analysis results. Our findings identified four key m6A regulators that are essential for bone metabolism and have specific diagnostic value in OP. These modules could be used as biomarkers of OP in the future.

LRPPRC facilitates tumor progression and immune evasion through upregulation of m6A modification of PD-L1 mRNA in hepatocellular carcinoma

Objective

LRPPRC is a newly discovered N⁶-methyladenosine (m⁶A) modification reader, which potentially affects hepatocellular carcinoma (HCC) progression. PD-L1 in tumor cells is essential for tumor immune evasion. This work investigated the LRPPRC-mediated m⁶A-modification effect on PD-L1 mRNA and immune escape in HCC.

Methods

Expression and clinical implication of LRPPRC and PD-L1 were measured in human HCC cohorts. The influence of LRPPRC on malignant behaviors of HCC cells was investigated through in vitro assays and xenograft tumor murine models. The posttranscriptional mechanism of LRPPRC on PD-L1 and anti-tumor immunity was elucidated in HCC cells via RIP, MeRIP-qPCR, RNA stability, immunohistochemical staining, and so forth.

Results

LRPPRC exhibited the notable upregulated in human HCC tissues, which was in relation to advanced stage and worse overall survival and disease-free survival. Impaired proliferative capacity and G2/M phage arrest were found in LRPPRC-knockout cells, with increased apoptotic level, and attenuated migratory and invasive abilities. In HCC patients and murine models, LRPPRC presented a positive interaction with PD-L1, with negative associations with CD8+, and CD4+ T-cell infiltrations and chemokines CXCL9, and CXCL10. LRPPRC loss downregulated the expression of PD-L1 and its m⁶A level in HCC cells. Moreover, LRPPRC suppression mitigated tumor growth in murine models and improved anti-tumor immunity and immune infiltration in tumors.

Conclusion

This work unveiled that LRPPRC may posttranscriptionally upregulate PD-L1 partially with an m⁶A-dependent manner for heightening mRNA stabilization of PD-L1 and provided a new mechanism for m⁶A regulator-mediated immunosuppression in HCC.

N6-methyladenosine modulation classes and immune microenvironment regulation in ischemic stroke

N6-methyladenosine (m6A) modifications play an important role in the differentiation and regulation of immune cells. However, research on m6A in ischemic stroke (IS) is still in its infancy, and their role of the immune microenvironment remains unknown. In this study, we systematically assessed the modification classes of m6A regulators in IS based on the GEO database (GSE16561 and GSE22255). We found that in IS patients, IGF2BP2, IGF2BP1, and YTHDF2 expression was significantly upregulated, and ELAVL1, LRPPRC, METTL3, ALKBH5, CBLL1, and METTL14 expression was significantly downregulated. Seven IS-related genes (ELAVL1, IGF2BP2, LRPPRC, YTHDF2, ALKBH5, METTL14, and YTHDC1) were finally screened by logistic and least absolute shrinkage and selection operator (LASSO) regressions, and the AUC of the riskScore was 0.942, which was a good classification. For immune infiltration, there were highly significant differences in memory B cells, CD8 T cells, monocytes, activated dendritic cells, and mast cells between IS and normal samples. The IS samples were grouped into three classes by consistent clustering, and 15 m6A genes were differentially expressed in the different classes. Multiple infiltrating immune cells, immune-associated genes, and HLA-associated genes differed significantly across m6A modification classes, indicating the diversity and complexity of m6A modifications in the immune microenvironment of IS. Finally, 487 genes associated with the m6A modification class were identified, and 227 potential drugs were found. Our findings demonstrated that m6A modification plays a crucial role in the immune regulation of IS.

Diagnostic gene signatures and aberrant pathway activation based on m6A methylation regulators in rheumatoid arthritis

Purpose

Rheumatoid arthritis (RA) is a chronic autoimmune disease (AD) characterized by persistent synovial inflammation, bone erosion and progressive joint destruction. This research aimed to elucidate the potential roles and molecular mechanisms of N6-methyladenosine (m6A) methylation regulators in RA.

Methods

An array of tissues from 233 RA and 126 control samples was profiled and integrated for mRNA expression analysis. Following quality control and normalization, the cohort was split into training and validation sets. Five distinct machine learning feature selection methods were applied to the training set and validated in validation sets.

Results

Among the six models, the LASSO_λ-1se model not only performed better in the validation sets but also exhibited more stringent performance. Two m6A methylation regulators were identified as significant biomarkers by consensus feature selection from all four methods. IGF2BP3 and YTHDC2, which are differentially expressed in patients with RA and controls, were used to predict RA diagnosis with high accuracy. In addition, IGF2BP3 showed higher importance, which can regulate the G2/M transition to promote RA-FLS proliferation and affect M1 macrophage polarization.

Conclusion

This consensus of multiple machine learning approaches identified two m6A methylation regulators that could distinguish patients with RA from controls. These m6A methylation regulators and their target genes may provide insight into RA pathogenesis and reveal novel disease regulators and putative drug targets.

Diagnostic signature, subtype classification, and immune infiltration of key m6A regulators in osteomyelitis patients

Background: As a recurrent inflammatory bone disease, the treatment of osteomyelitis is always a tricky problem in orthopaedics. N6-methyladenosine (m6A) regulators play significant roles in immune and inflammatory responses. Nevertheless, the function of m6A modification in osteomyelitis remains unclear. Methods: Based on the key m6A regulators selected by the GSE16129 dataset, a nomogram model was established to predict the incidence of osteomyelitis by using the random forest (RF) method. Through unsupervised clustering, osteomyelitis patients were divided into two m6A subtypes, and the immune infiltration of these subtypes was further evaluated. Validating the accuracy of the diagnostic model for osteomyelitis and the consistency of clustering based on the GSE30119 dataset. Results: 3 writers of Methyltransferase-like 3 (METTL3), RNA-binding motif protein 15B (RBM15B) and Casitas B-lineage proto-oncogene like 1 (CBLL1) and three readers of YT521-B homology domain-containing protein 1 (YTHDC1), YT521-B homology domain-containing family 3 (YTHDF2) and Leucine-rich PPR motif-containing protein (LRPPRC) were identified by difference analysis, and their Mean Decrease Gini (MDG) scores were all greater than 10. Based on these 6 significant m6A regulators, a nomogram model was developed to predict the incidence of osteomyelitis, and the fitting curve indicated a high degree of fit in both the test and validation groups. Two m6A subtypes (cluster A and cluster B) were identified by the unsupervised clustering method, and there were significant differences in m6A scores and the abundance of immune infiltration between the two m6A subtypes. Among them, two m6A regulators (METTL3 and LRPPRC) were closely related to immune infiltration in patients with osteomyelitis. Conclusion: m6A regulators play key roles in the molecular subtypes and immune response of osteomyelitis, which may provide assistance for personalized immunotherapy in patients with osteomyelitis.

Analysis of m6A modulator-mediated methylation modification patterns and the tumor microenvironment in lung adenocarcinoma

Lung adenocarcinoma (LUAD) is the most common histological subtype of lung cancer. In the development and progression of LUAD, epigenetic aberration plays a crucial role. However, the function of RNA N6-methyladenosine (m⁶A) modifications in the LUAD progression is unknown. The m6A regulator modification patterns in 955 LUAD samples were analyzed comprehensively. Patterns were systematically correlated with the tumor microenvironment (TME) cell-infiltration characteristics. Using principal component analysis algorithms, the m6Ascore was generated to quantify m⁶A modification patterns in individual tumors. Then, their values for predicting prognoses and therapeutic response in LUAD patients were assessed. Three distinct m⁶A modification patterns in LUAD were identified. Among them, the prognosis of m6Acluster C was the best, while the prognosis of m⁶Acluster A was the worst. Interestingly, the characterization of TME cell infiltration and biological behavior differed among the three patterns. To evaluate m⁶A modification patterns within individual tumors, an m⁶Ascore signature was constructed. The results showed that the high m⁶Ascore group was associated with a better prognosis; tumor somatic mutations and tumor microenvironment differed significantly between the high- and low- m⁶Ascore groups. Furthermore, in the cohort with anti-CTLA-4 treatment alone, patients with a high m⁶Ascore had higher ICI scores, which indicated significant therapeutic advantage and clinical benefits.

Identification of immune characteristic landscapes related to autophagy in ischemic stroke

Ischemic stroke (IS) is a common and grievous nervous system disease. Both autophagy activation and immune response after cerebral ischemia play important roles in the development of IS. Many studies have revealed a close interplay between autophagy and immunity. However, little is known about how autophagy influences the immune characteristics of IS. Hence, the study aims to systematically explore the role of autophagy and its impact on immune characteristics in IS. We first compared the expression differences of autophagy genes in a training set and identified 20 dysregulated autophagy genes between healthy and IS samples. An autophagy-related classifier composed of seven genes was further established and could well distinguish healthy and IS samples. Then, the association between autophagy and immune characteristics, including infiltrating immunocytes, activity of immune reactions, and HLA gene expression, was investigated. The results showed that autophagy closely correlated with immune characteristics, such as NAMPT and ARNT significantly related to infiltrating immunocytes; PPP1R15A and CASP3 significantly related to activity of immune reactions; and NAMPT and ATG16L2 significantly related to HLA genes. Next, two distinct autophagy expression patterns were identified by unsupervised clustering analysis, and diverse immune characteristics were discovered between them. A total of 5481 autophagy phenotype-related genes were obtained between two expression patterns, and their biological functions revealed that these genes were involved in immune-related biological pathways. Finally, five dysregulated autophagy genes (FOS, MAP1LC3B, ERO1L, ARNT, and PPP1R15A) were proved between IS and healthy samples using another two validation sets. Our results illustrated that autophagy had a dramatic effect on the immunity of IS and provided a novel sight into understanding the pathogenesis of IS.

Characterization of immune microenvironment infiltration and m6A regulator-mediated RNA methylation modification patterns in osteoarthritis

Background

Few studies have been reported the potential role of N6-methyladenosine (m6A) modification in osteoarthritis (OA). We investigated the patterns of m6A modification in the immune microenvironment of OA.

Methods

We evaluated the m6A modification patterns based on 22 m6A regulators in 139 OA samples and systematically associated these modification patterns with immune cell infiltration characteristics. The function of m6A phenotype-related differentially expressed genes (DEGs) was investigated using gene enrichment analysis. An m6A score model was constructed using principal component analysis (PCA), and an OA prediction model was established based on the key m6A regulators. We used real-time PCR analysis to detect the changes of gene expression in the cell model of OA.

Results

Healthy and OA samples showed significant differences in the expression of m6A regulators. Nine key m6A regulators, two m6A modification patterns, m6A-related genes and two gene clusters were identified. Some m6A regulators had a strong correlation with each other. Gene clusters and m6A clusters have high similarity, and cluster A corresponds to a high m6A score. Immunocytes infiltration differed significantly between the two clusters, with the m6A cluster B and gene cluster B having more types of infiltrating immunocytes than cluster A. The predictive model can also predict the progression of OA through m6A regulators expression. The results of real-time PCR analysis showed that the gene expression in the cell model of OA is similar to that of the m6A cluster B.

Conclusions

Our study reveals for the first time the potential regulatory mechanism of m6A modification in the immune microenvironment of OA. This study also sheds new light on the pathogenesis of OA.

N6-Methyladenosine Regulator-Mediated RNA Methylation Is Involved in Primary Sjögren's Syndrome Immunoinfiltration

The crucial role of epigenetic regulation, especially the modifications of RNA N6-methyladenosine (m6A), in immunity is a current research hotspot. However, the m6A modifications in primary Sjögren's syndrome (pSS) and the immune infiltration pattern they govern remain unknown. Thus, the patterns of 23 m6A regulator-mediated RNA modifications in parotid or blood samples from pSS patients were evaluated by bioinformatics analysis in the current study. Comparing m6A regulators between control and pSS patients showed that m6A regulators are associated with pSS, and regulators also had differential correlations. Further clustering analysis and comparison of gene expression and immune cell infiltration between m6A modification patterns revealed that each modification pattern had its own unique genetic and immune profile. Multiple immune cell infiltrations were differentially expressed between the patterns. The enrichment of gene ontology between the two patterns in parotid was concentrated on RNA metabolism and processing. The KEGG pathway enrichment and weighted correlation network analysis further showed that the autophagy pathway might be involved in the m6A modification patterns in pSS. Together, these findings suggest that m6A regulators play a certain role in the immune cell infiltration of parotid tissue in pSS.

Identification and validation of a classifier based on hub aging-related genes and aging subtypes correlation with immune microenvironment for periodontitis

BACKGROUND

Periodontitis (PD), an age-related disease, is characterized by inflammatory periodontal tissue loss, and with the general aging of the global population, the burden of PD is becoming a major health concern. Nevertheless, the mechanism underlying this phenomenon remains indistinct. We aimed to develop a classification model for PD and explore the relationship between aging subtypes and the immune microenvironment for PD based on bioinformatics analysis.

MATERIALS AND METHODS

The PD-related datasets were acquired from the Gene Expression Omnibus (GEO) database, and aging-related genes (ARGs) were obtained from the Human Aging Genomic Resources (HAGR). Four machine learning algorithms were applied to screen out the hub ARGs. Then, an artificial neural network (ANN) model was constructed and the accuracy of the model was validated by receiver operating characteristic (ROC) curve analysis. The clinical effect of the model was evaluated by decision curve analysis (DCA). Consensus clustering was employed to determine the aging expression subtypes. A series of bioinformatics analyses were performed to explore the PD immune microenvironment and its subtypes. The hub aging-related modules were defined using weighted correlation network analysis (WGCNA).

RESULTS

Twenty-seven differentially expressed ARGs were dysregulated and a classifier based on four hub ARGs (BLM, FOS, IGFBP3, and PDGFRB) was constructed to diagnose PD with excellent accuracy. Subsequently, the mRNA levels of the hub ARGs were validated by quantitative real-time PCR (qRT-PCR). Based on differentially expressed ARGs, two aging-related subtypes were identified. Distinct biological functions and immune characteristics including infiltrating immunocytes, immunological reaction gene sets, the human leukocyte antigen (HLA) gene, and immune checkpoints were revealed between the subtypes. Additionally, the black module correlated with subtype-1 was manifested as the hub aging-related module and its latent functions were identified.

CONCLUSION

Our findings highlight the critical implications of aging-related genes in modulating the immune microenvironment. Four hub ARGs (BLM, FOS, IGFBP3, and PDGFRB) formed a classification model, and accompanied findings revealed the essential role of aging in the immune microenvironment for PD, providing fresh inspiration for PD etiopathogenesis and potential immunotherapy.

Role of the E3 ubiquitin-ligase Hakai in intestinal inflammation and cancer bowel disease

The E3 ubiquitin-ligases are important for cellular protein homeostasis and their deregulation is implicated in cancer. The E3 ubiquitin-ligase Hakai is involved in tumour progression and metastasis, through the regulation of the tumour suppressor E-cadherin. Hakai is overexpressed in colon cancer, however, the implication in colitis-associated cancer is unknown. Here, we investigated the potential role of Hakai in intestinal inflammation and cancer bowel disease. Several mouse models of colitis and associated cancer were used to analyse Hakai expression by immunohistochemistry. We also analysed Hakai expression in patients with inflamed colon biopsies from ulcerative colitis and Crohn's disease. By Hakai interactome analysis, it was identified Fatty Acid Synthase (FASN) as a novel Hakai-interacting protein. Moreover, we show that Hakai induces FASN ubiquitination and degradation via lysosome, thus regulating FASN-mediated lipid accumulation. An inverse expression of FASN and Hakai was detected in inflammatory AOM/DSS mouse model. In conclusion, Hakai regulates FASN ubiquitination and degradation, resulting in the regulation of FASN-mediated lipid accumulation, which is associated to the development of inflammatory bowel disease. The interaction between Hakai and FASN may be an important mechanism for the homeostasis of intestinal barrier function and in the pathogenesis of this disease.

Identification and verification of IGFBP3 and YTHDC1 as biomarkers associated with immune infiltration and mitophagy in hypertrophic cardiomyopathy

Background: Hypertrophic cardiomyopathy (HCM) is the main cause of sudden cardiac death among young adults, yet its pathogenesis remains vague. N6-methyladenosine (m6A) methylation modification was involved in various cardiovascular diseases such as coronary heart disease and heart failure, although its influence on HCM remains unclear. This study aimed to explore the potential role of m6A in the diagnosis and pathogenesis of HCM.

Methods: GSE36961 including 106 HCM and 39 controls was used in the study. The HCM-related m6A regulators were selected using support vector machine recursive feature elimination and random forest algorithm. A significant gene signature was then established using least absolute shrinkage and selection operator and then verified by GSE130036. Subgroup classification of HCM was performed based on the expression of m6A biomarkers. Gene set variation analysis was employed to explore the functional difference between distinct subgroups. Weighted gene co-expression network analysis was used to determine the m6A-related hub module. Single-sample gene set enrichment analysis was conducted to assess the immune and mitophagy features between subgroups. Besides, transfection of recombinant plasmids with targeted genes into H9c2 cells was performed to further verify the function of the significant biomarkers.

Results: Significant difference existed in m6A landscape between HCM and control patients, among which IGFBP3 and YTHDC1 were identified as the independent biomarkers of HCM. Highly infiltrated immune cells (MDSC, macrophages, etc.), more enriched immune-related pathways (TNFα signaling via NFκB and IL6-JAK-STAT3 signaling) and cardiac remodeling-associated pathways (epithelial mesenchymal transition, angiogenesis, etc.) were identified in the subgroup with higher IGFBP3. Consistently, overexpression of IGFBP3 in H9c2 cells led to upregulation of extracellular-matrix-related genes (COL1A2, COL3A1 and MMP9) and inflammation-related genes (TNFα and IL6). Besides, higher YTHDC1 expression seemed to be consistent with less-activated mitophagy (PINK1-PRKN mediated mitophagy) and energy metabolism. Further experiments demonstrated that overexpression of YTHDC1 resulted in up-regulation of PINK and PRKN in cardiomyocytes, which are essential genes mediating mitophagy.

Conclusion: Two m6A readers (IGFBP3 and YTHDC1) well distinguished HCM and may facilitate clinical diagnosis. IGFBP3 may play a role in the immune-microenvironments and remodeling of cardiac tissues, while YTHDC1 may influence mitophagy and energy metabolism in HCM.