Transcriptome-Wide Identification of m6A Writers, Erasers and Readers and Their Expression Profiles under Various Biotic and Abiotic Stresses in Pinus massoniana Lamb.

N6-methyladenosine (m6A) RNA modification is the most prevalent form of RNA methylation and plays a crucial role in plant development. However, our understanding of m6A modification in Masson pine (Pinus massoniana Lamb.) remains limited. In this study, a complete analysis of m6A writers, erasers, and readers in Masson pine was performed, and 22 m6A regulatory genes were identified in total, including 7 m6A writers, 7 m6A erases, and 8 readers. Phylogenetic analysis revealed that all m6A regulators involved in Masson pine could be classified into three distinct groups based on their domains and motifs. The tissue expression analysis revealed that the m6A regulatory gene may exert a significant influence on the development of reproductive organs and leaves in Masson pine. Moreover, the results from stress and hormone expression analysis indicated that the m6A regulatory gene in Masson pine might be involved in drought stress response, ABA-signaling-pathway activation, as well as resistance to Monochamus alternatus. This study provided valuable and anticipated insights into the regulatory genes of m6A modification and their potential epigenetic regulatory mechanisms in Masson pine.

Differential network analysis reveals the key role of the ECM-receptor pathway in α-particle-induced malignant transformation.

Space particle radiation is a major environmental factor in spaceflight, and it is known to cause body damage and even trigger cancer, but with unknown molecular etiologies. To examine these causes, we developed a systems biology approach by focusing on the co-expression network analysis of transcriptomics profiles obtained from single high-dose (SE) and multiple low-dose (ME) α-particle radiation exposures of BEAS-2B human bronchial epithelial cells. First, the differential network and pathway analysis based on the global network and the core modules showed that genes in the ME group had higher enrichment for the extracellular matrix (ECM)-receptor interaction pathway. Then, collagen gene COL1A1 was screened as an important gene in the ME group assessed by network parameters and an expression study of lung adenocarcinoma samples. COL1A1 was found to promote the emergence of the neoplastic characteristics of BEAS-2B cells by both in vitro experimental analyses and in vivo immunohistochemical staining. These findings suggested that the degree of malignant transformation of cells in the ME group was greater than that of the SE, which may be caused by the dysregulation of the ECM-receptor pathway.

Advances in Foxp3+ regulatory T cells (Foxp3+ Treg) and key factors in digestive malignancies.

Foxp3+ regulatory T cells (Foxp3+ Treg) play a role in regulating various types of tumors, but uncertainty still exists regarding the exact mechanism underlying Foxp3+ Treg activation in gastrointestinal malignancies. As of now, research has shown that Foxp3+ Treg expression, altered glucose metabolism, or a hypoxic tumor microenvironment all affect Foxp3+ Treg function in the bodies of tumor patients. Furthermore, it has been demonstrated that post-translational modifications are essential for mature Foxp3 to function properly. Additionally, a considerable number of non-coding RNAs (ncRNAs) have been implicated in the activation of the Foxp3 signaling pathway. These mechanisms regulating Foxp3 may one day serve as potential therapeutic targets for gastrointestinal malignancies. This review primarily focuses on the properties and capabilities of Foxp3 and Foxp3+Treg. It emphasizes the advancement of research on the regulatory mechanisms of Foxp3 in different malignant tumors of the digestive system, providing new insights for the exploration of anticancer treatments.

The coordination of bimaxillary alveolar arch widths in subjects with normal occlusion or posterior crossbite: A CBCT retrospective study.

OBJECTIVES: To propose a method for evaluating the coordination of maxillomandibular alveolar arch in transverse dimension with cone-beam computed tomography (CBCT) and to apply this method to subjects with normal occlusion at different dentition stages or transverse discrepancy. MATERIALS AND METHODS: Digital data of 130 patients with normal occlusion at different dentition stages or transverse discrepancy were collected for three-dimensional reconstruction. The patients with normal occlusion were divided into Group 1 (>16 years) and Group 2 (≤16 years) based on their age. Adult patients with posterior crossbite were divided into the Group 3. According to the proposed method, the average alveolar arch coordination angle (AACA) and other parameters were analysed in each group. Group 1 was considered as the control group and compared with Group 2 and Group 3. RESULTS: Significant differences were observed in the maxillary posterior segment width among patients with normal occlusion. Group 3 demonstrated increased AACA and mandibular alveolar arch width compared with the normal occlusion group. Pearson correlation analysis indicated a positive relationship between maxillomandibular alveolar arch widths in the normal occlusion groups, with a strong correlation between AACA and the disparity in maxillomandibular widths. CONCLUSION: Adults with normal occlusion exhibit significantly wider maxillary posterior alveolar arches than adolescents, with no marked difference in mandibular widths. The posterior crossbite group showed broader mandibular alveolar arches. There was a strong correlation between AACA and the difference in maxillomandibular widths. This study's method shows potential value for orthodontic transverse diagnosis.

Discovery of novel covalent inhibitors of DJ-1 through hybrid virtual screening.

Background: DJ-1 is a ubiquitously expressed protein with multiple functions. Its overexpression has been associated with the occurrence of several cancers, positioning DJ-1 as a promising therapeutic target for cancer treatment. Methods: To find novel inhibitors of DJ-1, we employed a hybrid virtual screening strategy that combines structure-based and ligand-based virtual screening on a comprehensive compound library. Results: In silico study identified six hit compounds as potential DJ-1 inhibitors that were assessed in vitro at the cellular level. Compound 797780-71-3 exhibited antiproliferation activity in ACHN cells with an IC50 value of 12.18 µM and was able to inhibit the Wnt signaling pathway. This study discovers a novel covalent inhibitor for DJ-1 and paves the way for further optimization.

An EPR study of the cognitive processes underlying the impact of self-relevant information on emotional word processing.

Using the event-related potentials (ERPs) technique, this study successively presented names (in either a supra- or subthreshold manner) and emotional words to examine how self-relevant cue (self-name) affects emotional word processing in word class judgment task (to determine whether an emotional word is a noun or adjective) and valence judgment task (to determine whether an emotional word is positive or negative). At the suprathreshold condition, self-relevant positive words elicited a more significant Early posterior negativity (EPN) than negative words only in the valence judgment task. In contrast, at the subthreshold condition, self-relevant negative words elicited an enhanced Late positive potential (LPP) than positive words only in the word class judgment task. These results indicate that self-relevant cue affects emotional word processing at both suprathreshold and subthreshold conditions; nevertheless, the effect manifests as self-positive bias at the suprathreshold condition and self-negative bias at the subthreshold condition. The experimental task modulates these dynamics.

Role of Cue Training, Context, and Stimulus Intensity on Fear Generalization in Humans.

Fear generalization is a crucial mechanism underlying maladaptive behavior, but factors influencing this process are not fully understood. We investigated the effects of cue training and context on fear generalization and how cognitive rules influence responses to different conditions. We also examined the role of stimulus intensity in fear generalization to provide insight into fear generalization mechanisms. Participants (n = 104) completed a fear emotion task with two stages: acquisition and generalization testing. Subjective fear expectancy ratings were used as outcome measures. Participants who received single threat cue training exhibited stronger fear generalization responses than those who received discrimination training with threat and safe cues. Participants who received discrimination training and used linear rules had the strongest fear response to the largest stimulus. Therefore, a safe cue may mitigate fear generalization but could increase fear responses to more intense stimuli. Altering context did not change the fear generalization response because fear generalization is mainly governed by the association between the conditioned stimulus and the unconditioned fear stimulus. The present study emphasizes the multifaceted nature of fear generalization and the importance of examining multiple factors to understand this phenomenon. These findings elucidate fear learning and provide insights needed for effective interventions for maladaptive behavior.

Probing distribution and dynamics of lithium ions in supermolecule ß-CD-PEO/Li+ solid polymer electrolytes via solid-state NMR.

In this work, the distribution and dynamics of Li+ ions in ß-CD-PEO/Li+ (ß-CD, ß-cyclodextrin; PEO, polyethylene-oxides) crystalline polymer electrolytes were investigated by solid-state NMR to enlighten the ionic conduction mechanism. Specifically, 7Li-6Li REDOR NMR and variable-contact-time 1H-6Li CP/MAS NMR were adopted for the study. The results demonstrate that Li+ ions coordinated by polymer chains have relatively compact spatial density and fast dynamics, which facilitate the improvement of the electrochemical properties. Additionally, the variation of the distribution and dynamics of the Li+ ions and the ionic conduction mechanism were studied and discussed by altering the amount of the Li+ ions. This work deepens our understanding of the distribution and dynamics of Li+ ions in ß-CD-PEO/Li+ crystals and demonstrates possible future applications of solid-state NMR on the study of the polymer electrolytes.

METTL3-Mediated lncRNA m6A Modification in the Osteogenic Differentiation of Human Adipose-Derived Stem Cells Induced by NEL-Like 1 Protein.

OBJECTIVES: This study aimed to explore the regulatory mechanism of methyltransferase3 (METTL3) -mediated long non-coding RNA (lncRNA) N6-methyladenosine (m6A) modification in the osteogenic differentiation of human adipose-derived stem cells (hASCs) induced by NEL-like 1 protein (NELL-1). MATERIALS AND METHODS: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and high- throughput sequencing for RNA (RNA-seq) were performed on hASCs. Osteogenic ability was detected by alkaline phosphatase (ALP) staining, Alizarin Red S(ARS) staining, ALP quantification and Quantitative real-time polymerase chain reaction analysis (qRT-PCR). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis predicted the osteogenesis-related pathways enriched for the lncRNAs and identified the target lncRNAs. After overexpression and knockdown of METTL3, methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) and qRT-PCR were used to detect the levels of m6A modification and the expression of the target lncRNA, and the binding of both was confirmed by RNA binding protein immunoprecipitation (RIP) assay. The effects of lncRNA and METTL3 on phosphorylation of the key proteins of the pathway were detected by western blot analysis. RESULTS: In vitro experiments showed that METTL3 can promote osteogenic differentiation and that its expression level is upregulated. KEGG pathway analysis predicted that lncRNAs with differentially upregulated methylated peaks were enriched mostly in the mitogen-activated protein kinase (MAPK) signaling pathway, in which Serine/threonine protein kinase 3 (STK3) was the predicted target gene of the lncRNA RP11-44 N12.5. The m6A modification and expression of RP11-44 N12.5 were both regulated by METTL3. Subsequently, lncRNA RP11-44 N12.5 and METTL3 were found to regulate the phosphorylation levels of three key proteins in the MAPK signaling pathway, ERK, JNK and p38. CONCLUSIONS: This study shows, for the first time, that METTL3 can activate the MAPK signaling pathway by regulating the m6A modification and expression of a lncRNA, thereby enhancing the osteogenic differentiation of hASCs.

Transcriptome-wide m6A methylome during osteogenic differentiation of human adipose-derived stem cells.

OBJECTIVES: Adipose-derived stem cells are frequently used for bone regeneration both in vitro and in vivo. N6-methyladenosine (m6A) is the most abundant post-transcriptional modification on eukaryotic RNAs and plays multifaceted roles in development and diseases. However, the regulatory mechanisms of m6A in osteogenic differentiation of human adipose-derived stem cells (hASCs) remain elusive. The present study aimed to build the transcriptome-wide m6A methylome during the osteogenic differentiation of hASCs. MATERIALS AND METHODS: hASCs were harvested after being cultured in a basic or osteogenic medium for 7 days, and the osteogenic differentiation was validated by alkaline phosphatase (ALP) and Alizarin Red S staining, ALP activity assay, and qRT-PCR analysis of ALP, RUNX2, BGLAP, SPP1, SP7, and COL1A1 genes. The m6A level was colorimetrically measured, and the expression of m6A regulators was confirmed by qRT-PCR and western blot. Moreover, m6A MeRIP-seq and RNA-seq were performed to build the transcriptome and m6A methylome. Furthermore, bioinformatic analyses including volcano plots, Venn plots, clustering analysis, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, gene sets enrichment analysis, and protein-protein interaction analysis were conducted. RESULTS: In total, 1145 differentially methylated peaks, 2261 differentially expressed genes, and 671 differentially methylated and expressed genes (DMEGs) were identified. GO and KEGG pathway analyses conducted for these DMEGs revealed extensive and osteogenic biological functions. The "PI3K-Akt signaling pathway"; "MAPK signaling pathway"; "parathyroid hormone synthesis, secretion, and action"; and "p53 signaling pathway" were significantly enriched, and the DMEGs in these pathways were identified as m6A-specific key genes. A protein-protein interaction network based on DMEGs was built, and VEGFA, CD44, MMP2, HGF, and SPARC were speculated as the hub DMEGs. CONCLUSIONS: The total m6A level was reduced with osteogenic differentiation of hASCs. The transcriptome-wide m6A methylome built in the present study indicated quite a few signaling pathways, and hub genes were influenced by m6A modification. Future studies based on these epigenetic clues could promote understanding of the mechanisms of osteogenic differentiation of hASCs.

The relevance between the immune response-related gene module and clinical traits in head and neck squamous cell carcinoma.

PURPOSE: Head and neck squamous cell carcinoma (HNSCC) is the sixth most prevalent cancer in the world, accounting for more than 90% of head and neck malignant tumors. However, its molecular mechanism is largely unknown. To help elucidate the potential mechanism of HNSCC tumorigenesis, we investigated the gene interaction patterns associated with tumorigenesis. METHODS: Weighted gene co-expression network analysis (WGCNA) can help us to predict the intrinsic relationship or correlation between gene expression. Additionally, we further explored the combination of clinical information and module construction. RESULTS: Sixteen modules were constructed, among which the key module most closely associated with clinical information was identified. By analyzing the genes in this module, we found that the latter may be related to the immune response, inflammatory response and formation of the tumor microenvironment. Sixteen hub genes were identified-ARHGAP9, SASH3, CORO1A, ITGAL, PPP1R16B, TBC1D10C, IL10RA, ITK, AKNA, PRKCB, TRAF3IP3, GIMAP4, CCR7, P2RY8, GIMAP7, and SP140. We further validated these genes at the transcriptional and translation levels. CONCLUSION: The innovative use of a weighted network to analyze HNSCC samples provides new insights into the molecular mechanism and prognosis of HNSCC. Additionally, the hub genes we identified can be used as biomarkers and therapeutic targets of HNSCC, laying the foundation for the accurate diagnosis and treatment of HNSCC in clinical and research in the future.

Analysis of methylation-driven genes for predicting the prognosis of patients with head and neck squamous cell carcinoma.

To help provide evidence for prognosis prediction and personalized targeted therapy for patients with head and neck squamous cell carcinoma (HNSCC), we investigated prognosis-specific methylation-driven genes in HNSCC. Survival time data, RNA sequencing data, and methylation data for HNSCC patients were downloaded from The Cancer Genome Atlas. The MethylMix R package based on the ß mixture model was utilized to screen genes with different methylation statuses in tumor tissues and adjacent normal tissues, and a total of 182 HNSCC-related methylation-driven genes were then identified. A survival prediction scoring model based on multivariate Cox analysis was developed to screen the genes related to the prognosis of HNSCC, and a linear risk model of the methylation status of six genes (INA, LINC01354, TSPYL4, MAGEB2, EPHX3, and ZNF134) was constructed. The prognostic values of the six genes were further independently explored by survival analysis combined with methylation and gene expression analyses. The 5-year survival rate in the high-risk group of patients in the test set was 30.4% (95% CI: 22.7%-40.8%) and that in the low-risk group of patients was 65.5% (95% CI: 56.1%-76.5%). The area under the receiver operating characteristic curve for the model was 0.723, which further verified the specificity and sensitivity of the model. In addition, subsequent combined survival analysis revealed that all six genes could be used as independent prognostic markers and thus might be potential drug targets. The innovative method provides new insight into the molecular mechanism and prognosis of HNSCC.

Functional analysis of lncRNAs based on competitive endogenous RNA in tongue squamous cell carcinoma.

BACKROUND: Tongue squamous cell carcinoma (TSCC) is the most common malignant tumor in the oral cavity. An increasing number of studies have suggested that long noncoding RNA (lncRNA) plays an important role in the biological process of disease and is closely related to the occurrence and development of disease, including TSCC. Although many lncRNAs have been discovered, there remains a lack of research on the function and mechanism of lncRNAs. To better understand the clinical role and biological function of lncRNAs in TSCC, we conducted this study. METHODS: In this study, 162 tongue samples, including 147 TSCC samples and 15 normal control samples, were investigated and downloaded from The Cancer Genome Atlas (TCGA). We constructed a competitive endogenous RNA (ceRNA) regulatory network. Then, we investigated two lncRNAs as key lncRNAs using Kaplan-Meier curve analysis and constructed a key lncRNA-miRNA-mRNA subnetwork. Furthermore, gene set enrichment analysis (GSEA) was carried out on mRNAs in the subnetwork after multivariate survival analysis of the Cox proportional hazards regression model. RESULTS: The ceRNA regulatory network consists of six differentially expressed miRNAs (DEmiRNAs), 29 differentially expressed lncRNAs (DElncRNAs) and six differentially expressed mRNAs (DEmRNAs). Kaplan-Meier curve analysis of lncRNAs in the TSCC ceRNA regulatory network showed that only two lncRNAs, including LINC00261 and PART1, are correlated with the total survival time of TSCC patients. After we constructed the key lncRNA-miRNA -RNA sub network, the GSEA results showed that key lncRNA are mainly related to cytokines and the immune system. High expression levels of LINC00261 indicate a poor prognosis, while a high expression level of PART1 indicates a better prognosis.

One-Dimensional Zinc-Based Coordination Polymer as a Higher Capacity Anode Material for Lithium Ion Batteries.

A zinc-based one-dimensional (1D) coordination polymer ([Zn(H2mpca)2(tfbdc)(H2O)], Zn-ODCP) has been synthesized and characterized by spectroscopic and physicochemical methods, single-crystal X-ray diffraction, and thermogravimetric analysis (H2mpca = 3-methyl-1H-pyrazole-4-carboxylic acid; H2tfbdc = 2,3,5,6-tetrafluoroterephthalic acid). Zn-ODCP shows blue luminescence in the solid state. When Zn-ODCP acts as an anode material for lithium ion batteries, it exhibits a good cyclic stability and a higher reversible capacity of 300 mAh g-1 at 50 mA g-1 after 50 cycles. The higher capacity may be mainly ascribed to the metal ion and ligand all taking part in lithium storage. Searching for electrode materials of lithium ion batteries from 1D metal coordination polymers is a new route.