starBase Database Research Articles

Identification of aberrant plasma vesicles containing AAK1 and CCDC18-AS1 in adolescents with major depressive disorder and preliminary exploration of treatment efficacy.

Major depressive disorder (MDD) during adolescence significantly jeopardizes both mental and physical health. However, the etiology underlying MDD in adolescents remains unclear. A total of 74 adolescents with MDD and 40 health controls (HCs) who underwent comprehensive clinical and cognitive assessments were enrolled. Differential expression analysis was conducted on plasma extracellular vesicles (EVs) carrying long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) by microarray analysis. Two possible lncRNA-miR-mRNA networks were established and candidate regulatory axes were generated using the StarBase, miRDB, and TargetScan bioinformatics databases. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the candidate molecules and signaling axes in a clinical cohort. A total of 3752 dysregulated lncRNAs and 1789 dysfunctional mRNAs were identified. Two candidate regulatory axes (AC156455.1/miR-126-5p/AAK1 and CCDC18-AS1/miR-6835-5p/CCND2) with potential connections with MDD were selected. The candidate molecules exhibit differential expression patterns among adolescents with MDD and HCs, as well as before and after treatment with sertraline in adolescents with MDD. Furthermore, AAK1, CCDC18-AS1, and miR-6835-5p expressions exhibited significant differences between the response and non-response groups. Baseline expression of CCDC18-AS1, miR-6835-5p, and CCND2 could predict the therapeutic effect of sertraline, which may be associated with reducing suicidal ideation and improving cognitive function. Our study may provide insights into the understanding of the underlying pathological mechanisms in adolescents with MDD.

New insights into roles of IL-7R gene as a diagnostic biomarker for post-stroke depression

BackgroundPost-stroke depression (PSD) is the most prevalent neuropsychiatric complication following a stroke. The inflammatory theory suggests that PSD may be associated with an overactive inflammatory response. However, research findings regarding inflammation-related indicators in PSD remain inconsistent and elusive. This study aimed to screen the diagnostic markers that helps to distinguish between PSD and post-stroke non-depressed (PSND) patients.MethodsTwo GEO datasets, including patients with major depression disease (MDD) and controls (CON, GSE98793), ischemic stroke (IS) and CON (GSE16561), were used to analyzed differentially expressed genes (DEGs) and perform enrichment analysis. Protein-protein interaction (PPI) network and Random Forest analysis were used to screen the candidate hub genes. CIBERSORT was performed to analyze the immune infiltration. We analyzed the proteins that interact with the hub genes using string database, circRNA-miRNA-mRNA ceRNA network of the hub genes using RNAInter, miRWalk, miRDB and Starbase databases, and the drugs that regulate the hub genes by DSigDB database. We further verified the expression of the hub genes using Quantitative Real-Time PCR from the blood of patients and CON.ResultsFrom the screened 394 DEGs, the DEGs were found primarily related to activation of immune response. PPI network and random forest analysis obtained the hub genes: IL-7R. ROC analysis showed that IL-7R had a good diagnostic and predictive effect on MDD and IS patients. The proportions of macrophages M0 and monocytes in patients were significantly higher than those in CON. We constructed PPI network and ceRNA network that related to IL-7R. The perturbagen signatures and computational drug signatures were found that can target IL-7R. The expression of IL-7R in MDD, PSND and PSD patients was lower than that in CON, and the expression of IL-7R in PSD patients was lower than that in PSND patients.ConclusionThese findings indicate that IL-7R may serve as a diagnostic marker to distinguish between PSD and PSND patients, and targeting IL-7R as a therapeutic target could potentially improve treatment outcomes for PSD.

CircMYH9/miR-133a-3p/CXCR4 axis: a novel regulatory network in sperm fertilization and embryo development

This study aimed to investigate the influence of sperm miRNAs on fertilization rates (FR) in in vitro fertilization (IVF) and to explore potential regulatory mechanisms in sperm-mediated fertilization and embryo development. Through high-throughput sequencing, we identified differentially expressed miRNAs in sperm, with miR-133a-3p significantly upregulated in samples associated with low FR and available embryo rate (AER). Key regulatory circRNAs and mRNAs were further identified via the Starbase database, intersected with differentially expressed RNA, and analyzed through GO, KEGG, and PPI analyses. The circMYH9/miR-133a-3p/CXCR4 axis emerged as a critical regulatory network. In vitro assays using the GC-2 spd mouse spermatogenic cell line revealed that miR-133a-3p inhibited cell growth and proliferation while promoting apoptosis. circMYH9, acting as a competing endogenous RNA (ceRNA) for miR-133a-3p, modulated CXCR4 expression, enhancing GC-2 spd cell growth and inhibiting apoptosis through the miR-133a-3p/CXCR4 axis. In vivo experiments using a mouse model confirmed that circMYH9 overexpression increased IVF success rates and promoted embryo development via this axis. Mechanistically, miR-133a-3p suppresses sperm fertilization and embryo development by targeting the circMYH9/miR-133a-3p/CXCR4 axis. These findings suggest that this regulatory network could serve as a novel biomarker for assessing fertilization potential and embryo quality in clinical settings and as a potential therapeutic target to improve IVF outcomes and address infertility. This study provides valuable insights into the molecular mechanisms governing sperm function and early embryonic development.

Ferroptosis-related lncRNA AL136084.3 is associated with NUPR1 in bladder cancer

BackgroundLncRNAs are critical regulators of bladder cancer (BLCA), and ferroptosis is a newly discovered cell death responsible for mediating apoptosis and tumorigenesis. The present study aims to establish a prognostic signature of differentially expressed ferroptosis-related lncRNAs (DEFRlncRNAs) and explore the DEFRlncRNA associated with NUPR1 in BLCA.MethodsDEFRlncRNAs in BLCA patients were screened using univariate and multivariate Cox and LASSO regression analyses. In vitro experiments were performed to detect the regulatory effects of DEFRlncRNAs on BLCA cells. A prognostic signature of DEFRlncRNAs in BLCA was created and validated. Moreover, we used RNA-binding protein immunoprecipitation (RIP) to evaluate the correlated DEFRlncRNA with NUPR1.ResultsA prognostic signature involving 18 DEFRlncRNAs in BLCA was created. Overexpression of AL355353.2 or knockdown of AL136084.3 promoted apoptosis in 5637 and T24 cells in vitro. Results from Starbase database estimated that AL136084.3 was positively associated with NUPR1 (R = 0.229, p < 0.001). RIP analysis revealed the reciprocal binding of NUPR1 and AL136084.3 in BLCA.ConclusionThe identified FRlncRNA pair signature has a good prognostic and clinical predictive value. The ferroptosis-related lncRNA AL136084.3 is correlated with NUPR1 in BLCA.

Multi-omics analysis of the biological function of the VEGF family in colon adenocarcinoma

The vascular endothelial growth factor (VEGF) family plays a crucial role in cancer progression, but the prognostic significance and biological functions of VEGF family members in colon adenocarcinoma (COAD) remain unclear. Using data from The Cancer Genome Atlas, Gene Expression Omnibus, Gene Set Cancer Analysis, cBioPortal, GeneMANIA, String, MethSurv and starBase database, we identified vascular endothelial growth factor B (VEGFB) as a key gene associated with COAD prognosis, with its abnormal expression linked to methylation dysregulation. In vitro experiments confirmed VEGFB expression was significantly higher in colon cancer tissues compared to normal tissues, as shown by Real-time quantitative PCR and immunohistochemistry. Cell Counting Kit-8 and colony formation assay showed that decreased VEGFB expression in SW480 cells resulted in decreased cell viability and proliferation ability. Scratch assay showed that VEGFB downregulation impaired SW480 cell migration. In addition, our research suggests that VEGFB not only promotes angiogenesis but is also involved in the tumor microenvironment and immune regulation. The SHNG17-miR-375-VEGFB regulatory axis provides a potential therapeutic target for COAD, highlighting VEGFB’s role in immune activation during anti-angiogenic therapy and potential reversal of drug resistance.

Mesenchymal stem cell-derived exosomes carrying miR-486-5p inhibit glycolysis and cell stemness in colorectal cancer by targeting NEK2

Colorectal cancer (CRC) is a major global concern. Mesenchymal stem cell-derived exosomes (MSC-EXOs) have demonstrated efficacy as a therapeutic approach for colorectal cancer. However, the precise mechanism by which MSC-EXOs treat colorectal cancer remains unclear. Human umbilical cord (hUC)-MSC-EXOs were isolated and identified. Cell Counting Kit-8 (CCK-8), Transwell, and colony formation assays were used to assess the activity of CRC cells. Glucose consumption, lactic acid production, and extracellular acidification rate (ECAR) were measured to assess glycolytic activity. Cell stemness was assessed using a sphere-formation assay. Furthermore, MSC-exosomal microRNAs (miRNAs) in CRC tissues were analyzed using the EVmiRNA database, and aberrantly expressed miRNAs in CRC cells were obtained from the Gene Expression Omnibus (GEO) database. The binding relationship between miR-486-5p and the never in mitosis gene A-related kinase 2 (NEK2) was predicted using the Starbase database and validated through RNA binding protein immunoprecipitation (RIP) and dual luciferase assays. These results showed that hUC-MSC-EXOs inhibited the proliferation and metastasis of CRC cells. Moreover, glycolysis and stemness abilities of CRC cells also decreased after treatment with hUC-MSC-EXOs. miR-486-5p was found to be enriched in hUC-MSC-EXOs and significantly downregulated in CRC cells. miR-486-5p directly bound to NEK2. Overexpression of NEK2 reversed the inhibitory effect of miR-486-5p on CRC cell glycolysis and stemness. Our study highlights that hUC-MSC-EXO miR-486-5p inhibits glycolysis and cell stemness in CRC by targeting NEK2. This finding offers compelling evidence supporting the potential application of hUC-MSC-EXOs in the treatment of CRC.

MiR-148b Caused Liver Injury in Rats with Traumatic Hemorrhagic Shock by Inhibiting SIRT6 Expression.

The purpose of this study was to investigate the role of miR- 148b in liver injury in rats with traumatic hemorrhagic shock (THS) and to elucidate its potential mechanism. The levels of alanine aminotransferase (ALT) and aspartate aminotransferase (AST) in the serum of rats were detected by enzyme-linked immune sorbent assay (ELISA), and the injury of rat liver was analyzed by hematoxylin-eosin (H&E) staining. Apoptosis of rat hepatocytes and normal rat liver cell line (BRL3A) was identified by terminal deoxynucleotidyl transferase-mediated dUTP-biotin nick end labeling (TUNEL) assay and flow cytometry, respectively. MiR-148b and sirtuin 6 (SIRT6) expression was measured by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Western blot. Lactate dehydrogenase (LDH) content and cell viability were measured by commercial kits and cell counting kit-8 (CCK-8) assay, respectively. The binding sites of miR-148b and SIRT6 were predicted by the Starbase database and verified by dual luciferase reporter assay. MiR-148b expression in THS rats or ischemia-reperfusion (I/R)-treated cells was higher than in the control group. Overexpression of miR-148b further promoted the effects of I/R, which enhanced the levels of ALT, AST and LDH, cell apoptosis of liver tissue or BRL3A cells and decreased the expression of SITR6. Besides, miR-148b negatively correlated with SIRT6, and upregulated the expression of SIRT6 could partly reverse the effect of miR-148b. Hepatocyte injury induced by I/R was achieved by regulating miR-148b /SIRT6 axis.

Scinderin Promotes Hydrogen Peroxide-induced Lens Epithelial Cell Injury in Age-related Cataract.

Scinderin (SCIN) is a calcium-dependent protein implicated in cell growth and apoptosis by regulating actin cleavage and capping. In this study, we investigated the role of SCIN in hydrogen peroxide-induced lens epithelial cell (LEC) injury related to age-related cataract (ARC). Anterior lens capsules from ARC patients were collected to examine SCIN expression levels. Immortalized human LEC cell line SRA01/04 and lens capsules freshly isolated from mice were induced by H2O2 to mimic the oxidative stress in ARC. The role of SCIN was investigated by gain-of-function (overexpression) and loss-offunction (knockdown) experiments. Flow cytometry (FCM) and Western-blot (WB) assays were performed to investigate the effect of SCIN on apoptosis. The oxidative stress (OS) was examined by detecting malondialdehyde (MDA) level, superoxide dismutase (SOD) and catalase (CAT) activity. The interaction between SCIN mRNA and miR-489-3p was predicted by StarBase and miRDB databases and validated by luciferase reporter activity assay. SCIN was significantly elevated in cataract samples, and the expression levels were positively correlated with the nuclear sclerosis grades. SCIN overexpression promoted OS and apoptosis in H2O2-induced SRA01/04 cells, while SCIN silencing showed the opposite effect. We further showed that miR-489-3p was a negative regulator of SCIN. miR-489-3p overexpression suppressed apoptosis and OS in H2O2-induced SRA01/04 cells by targeting SCIN. Our study identified SCIN as an upregulated gene in ARC, which is negatively regulated by miR-489-3p. Targeting miR-489-3p/SCIN axis could attenuate OS-induced apoptosis in LECs.

Role of hsa-miR-543-KIF5C/CALM3 pathway in neuron differentiation of embryonic mesenchymal stem cells.

Human umbilical cord mesenchymal stem cells (hUC-MSCs) have the ability to differentiate into nerve cells, which offers promising options for treating neurodegenerative diseases. To explore the important regulatory molecules of hUC-MSCs differentiation into neurons. In this research, the neural differentiation of hUC-MSCs was induced by a low-serum DMSO/BHA/DMEM medium. The GEO database was used to retrieve the relevant datasets. The starBase and miEAA databases were used for bioinformatics analysis. RT-qPCR was used to detect the hsa-miR-543 level and the mRNA levels of NSE, NeuN, NF-M, KIF5C, and CALM3. The protein levels of KIF5C and CALM3 were checked by western blotting. The expression levels of NSE, NeuN, NF-M, KIF5C, and CALM3 were elevated, while hsa-miR-543 was under-expressed in neuro-induced hUC-MSCs. The increase in NSE, NeuN, and NF-M mRNA levels induced by DMSO/BHA/DMEM was partially reversed by the knockdown of KIF5C and CALM3 in hUC-MSCs. Moreover, the transfection of hsa-miR-543 mimic partially countered the DMSO/BHA/DMEM-induced elevation in NSE, NeuN, NF-M, KIF5C, and CALM3 mRNA levels. KIF5C and CALM3 facilitated the neuronal differentiation of hUC-MSCs, whereas hsa-miR-543 exerted an opposing effect by negatively regulating KIF5C and CALM3.

CircRNA_SLC8A1 alleviates hypertrophic scar progression by mediating the Nrf2-ARE pathway.

Hypertrophic scar (HS) is associated with cosmetic defects, mobility, and functional impairments, pruritus, and pain. Previous circRNA microarray analysis identified reduced expression of circRNA_SLC8A1 in HS tissues. Therefore, this study aims to investigate the role of circRNA_SLC8A1 in modulating the abnormal behavior of HS-derived fibroblasts (HSFs) in vitro. RT-qPCR and FISH assays were used to assess the differential expression and localization of circRNA_SLC8A1 in normal and HS tissues. Following modulation of circRNA_SLC8A1 expression, CCK-8, flow cytometry, Transwell, and wound healing assays were employed to evaluate the effects of circRNA_SLC8A1 on the biological behaviors of HSFs. The Starbase database, dual-luciferase reporter assays, and Ago2-RIP assays were utilized to predict and validate the interaction between circRNA_SLC8A1 and downstream miRNAs. CircRNA_SLC8A1 was found to be downregulated in HS tissues and was primarily localized in the cytoplasm. Overexpression of circRNA_SLC8A1 reduced cell viability, cell invasion, wound healing, and the expression of Vimentin, N-cadherin, Col I, and Col III, while enhancing apoptosis and E-cadherin expression in HSFs. CircRNA_SLC8A1 activates the Nrf2-ARE pathway by competitively binding to miRNA-27a-3p. miRNA-27a-3p and Nrf2 exhibited high and low expression, respectively in HS tissues, with an inverse correlation between their levels. Overexpression of miRNA-27a-3p counteracted the effects of circRNA_SLC8A1 in HSF proliferation, apoptosis, migration, EMT, collagen deposition, and Nrf2-ARE pathway activity. CircRNA_SLC8A1 inhibits the proliferation, migration, EMT, and collagen deposition of HSF through competitive binding with miRNA-27a-3p, thereby activating the Nrf2-ARE pathway. The circRNA_SLC8A1/miRNA-27a-3p/Nrf2-ARE axis may offer a promising molecular target for HS therapy.

CircLPHN3 correlates with prognosis in colorectal cancer and regulates cellular processes by targeting miR-142-5p.

Colorectal cancer (CRC) is often diagnosed late and has a poor prognosis. Circular RNAs (circRNAs) have been identified as prognostic biomarkers in various cancers, including CRC. The objective was to elucidate the role of circLPHN3 (hsa_circ_0069865) in CRC progression and to provide a promising prognostic marker for CRC. CircLPHN3 was identified through bioinformatics analysis of the GSE121842 dataset. The levels of circLPHN3 in CRC samples were analyzed by real time-quantitative polymerase chain reaction. Its clinical significance was assessed using the Kaplan-Meier curve and multivariate Cox regression. Downstream microRNAs of circLPHN3 were predicted with the RNAhybrid, Circular RNA Interactome, and starBase online databases. The target of miR-142-5p was predicted using miRDB, TargetScanHuman, starBase, and miRWalk databases. The relationship between circLPHN3, miR-142-5p, and LDB2 was verified by dual luciferase reporter assay. The function of circLPHN3 on CRC cell growth and metastasis was measured using Transwell and the cell counting kit-8 assay. Significant downregulation of circLPHN3 was found in CRC. CircLPHN3 was closely related to higher tumor node metastasis stage, lymph node metastasis, and predicted unfavorable prognosis. miR-142-5p was highly expressed in CRC and its expression was negatively regulated by circLPHN3. Overexpression of circLPHN3 curbed CRC cell growth, migration, and invasion, mediated by miR-142-5p. Moreover, LDB2 was identified as a target of miR-142-5p. CircLPHN3 acted as a prognostic biomarker and tumor suppressor for CRC via modulating miR-142-5p.

RBM15B Promotes Prostate Cancer Cell Proliferation via PCNA m6A Modification.

Prostate cancer (PC) is the most frequently occurring cancer in men, characterized by the abnormal proliferation of cells within the prostate gland. This study explores the role of RNA binding motif protein 15B (RBM15B) in PC. RBM15B expression levels in PC patients were predicted using the Starbase database. The expression of RBM15B and proliferating cell nuclear antigen (PCNA) expression in PC cells was detected. Following RBM15B knockdown, cell proliferation assays were conducted. N6-methyladenosine (m6A) levels in PC cells were quantified, and RNA immunoprecipitation was performed to analyze the binding of m6A and YTH N-methyladenosine RNA binding protein 1 (YTHDF1) on PCNA mRNA. The stability of PCNA mRNA was assessed after treatment with actinomycin D. An in vivo nude mouse xenograft model was created to validate the role of RBM15B. The findings revealed the upregulation of RBM15B in PC. RBM15B knockdown resulted in decreased proliferation, colony formation, and EdU-positive cells. Mechanical analysis showed that RBM15B facilitated m6A modification of PCNA mRNA, leading to increasing m6A methylation. YTHDF1 bound to these m6A sites on PCNA mRNA, thus stabilizing it. Furthermore, PCNA overexpression mitigated the effects of RBM15B knockdown on PC cell proliferation. In conclusion, RBM15B promotes PC cell proliferation by enhancing the stability of PCNA mRNA through YTHDF1-mediated m6A modification.

SNX4 Is Correlated With Immune Infiltration and Prognosis in Clear Cell Renal Cell Carcinoma.

Clear cell renal cell carcinoma (ccRCC) is known as the most common and malignant histologic subtype of renal carcinoma. Sorting nexin 4 (SNX4) plays a regulatory role in recycling from endosomes to the plasma membrane and promotes autophagosome assembly and transport, which may exert the cancerous growth and progression. This study aimed to assess the biological role of SNX4 in ccRCC and their clinical association via public biological data platforms combined with experimental verification. In our study, we analyzed the mRNA and protein expression of SNX4 in ccRCC under different clinicopathological characteristics through The Cancer Genome Atlas (TCGA), Human Protein Atlas (HPA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) databases. We used the Gene Expression Profiling Interactive Analysis (GEPIA) platform to conduct the survival analysis and figure out the immune cell infiltration level under different expression levels of SNX4 combined with Tumor Immune Estimation Resource (TIMER) database. Furthermore, we predicted competing endogenous RNA (ceRNA) regulatory network using TargetScan, miRDB, starBase and miRTarBase online databases. We totally collected six paired ccRCC tissues and adjacent tissues and applied quantitative real-time polymerase chain reaction (qRT-PCR) and western blot (WB) to detect the expression of SNX4 in the collected clinical specimens. The mRNA and protein expression level of SNX4 was significantly lower in ccRCC than those in normal tissues. The results proposed that lower SNX4 was expressed in patients with higher histologic grade and in male patients. Kaplan-Meier analysis demonstrated that lower mRNA expression level of SNX4 was correlated with poorer prognosis. SNX4 had positive correlation with immune cell infiltrating levels and programmed cell death-ligand 1 (PD-L1) expression. Furthermore, we constructed the SNX4/miR-221-3p/miR-222-3p/DHRS4-AS1 axis, which may be the underlying ceRNA interaction network. Finally, we verified the reduced expression of SNX4 in ccRCC by qRT-PCR and WB. The expression of SNX4 in ccRCC was lower than adjacent tissues and its downregulated expression was associated with poor prognosis of ccRCC patients. SNX4 may exert critical roles in the tumorigenesis, development and migration of ccRCC via various mechanisms.

Effect and mechanism of the PTMAP5–hsa-miR-22-3p–KIF2C regulatory axis on the occurrence and development of hepatocellular carcinoma

Hepatocellular carcinoma (HCC), a primary liver cancer, is known for its high malignancy potential. Despite extensive research, the etiology of HCC remains elusive, with numerous molecular mechanisms yet to be deciphered. This study delves into the influence and mechanism of the PTMAP5&amp;ndash;hsa-miR-22-3p&amp;ndash;KIF2C regulatory axis in HCC pathogenesis. A comparative analysis of gene expression profiles between the GSE87630 and GSE45267 datasets unveiled a cohort of 346 differentially expressed genes. Protein&amp;ndash;protein interaction networks were established using the STRING database, and key genes were identified through receiver operating characteristic curve analysis and LASSO regression analysis. The expression and prognostic value of these key genes were further evaluated using GEPIA and Kaplan&amp;ndash;Meier analysis. Upstream miRNAs were predicted using the MiRTarBase and StarBase databases, facilitating the construction of the PTMAP5&amp;ndash;hsa-miR-22-3p&amp;ndash;KIF2C regulatory axis. Co-expression analysis of KIF2C was performed through UALCAN and StarBase, and the regulatory axis was found to play a pivotal role in HCC development through the cell cycle, oocyte meiosis, and FOXO signaling, as revealed by DAVID enrichment analysis. Furthermore, the expression and prognostic significance of KIF2C in various cancer types were assessed using TIMER and GEPIA, while TISIDB analysis revealed correlations between KIF2C expression and relevant major histocompatibility complex molecules, immunomodulators, chemokines, receptors, and immune variants in HCC. These findings also extended to HCC molecular subtypes. In conclusion, we constructed a novel PTMAP5&amp;ndash;hsa-miR-22-3p&amp;ndash;KIF2C regulatory subnetwork, which could provide valuable therapeutic targets and diagnostic markers for HCC.

An abnormal metabolism-related gene, ALG3, is a potential diagnostic and prognostic biomarker for lung adenocarcinoma.

To explore the abnormal metabolism-related genes that affect the prognosis of patients with lung adenocarcinoma (LUAD), and analyze the relationship with immune infiltration and competing endogenous RNA (ceRNA) network. Transcriptome data of LUAD were downloaded from the Cancer Genome Atlas database. Abnormal metabolism-related differentially expressed genes in LUAD were screened by the R language. Cox analysis was used to construct LUAD prognostic risk model. Kaplan-Meier test, ROC curve and nomograms were used to evaluate the predictive ability of metabolic related gene prognostic model. CIBERSORT algorithm was used to analyze the relationship between risk score and immune infiltration. The starBase database constructed a regulatory network consistent with the ceRNA hypothesis. IHC experiments were performed to verify the differential expression of ALG3 in LUAD and paracancerous samples. In this study, 42 abnormal metabolism-related differential genes were screened. After survival analysis, the final 5 metabolism-related genes were used as the construction of prognosis model, including ALG3, COL7A1, KL, MST1, and SLC52A1. In the model, the survival rate of LUAD patients in the high-risk subgroup was lower than that in the low-risk group. In addition, the risk score of the constructed LUAD prognostic model can be used as an independent prognostic factor for patients. According to the analysis of CIBERSORT algorithm, the risk score is related to the infiltration of multiple immune cells. The potential ceRNA network of model genes in LUAD was constructed through the starBase database. IHC experiments revealed that ALG3 expression was upregulated in LUAD. The prognostic model of LUAD reveals the relationship between metabolism and prognosis of LUAD, and provides a novel perspective for diagnosis and research of LUAD.

Circ_0114866 promotes the progression and EMT of non-small cell lung cancer via miR-653-5p/MYL6B axis

BackgroundNon-small-cell lung cancer (NSCLC) is the most prevalent form of lung cancer. Circular RNA (circRNA) has emerged as a key player in the development of NSCLC by acting as miRNA sponges. However, the precise role of circ_0114866 in regulating NSCLC process is yet to be elucidated. MethodsThe expression of circ_0114866, miR-653-5p, and MYL6B were assessed by qPCR. Cell viability, proliferation, invasion, and migration were investigated using CCK-8, colony formation, Transwell, and wound healing assays. The protein levels of MYL6B, MMP-2, N-cadherin, E-cadherin, and vimentin were evaluated through Western blot analysis. Xenograft tumor model were selected to analyze the impact of circ_0114866 on NSCLC tumor growth. Through circBank or Starbase databases, the binding interactions between miR-653-5p and circ_0114866 or MYL6B were predicted. Subsequently, these interactions were verified by dual-luciferase reporter assay. ResultsThe expression of circ_0114866 and MYL6B were clearly elevated, while miR-653-5p expression was notably reduced in NSCLC tissues and cells. Notably, circ_0114866 knockdown obviously suppressed the proliferation, metastasis, and EMT process in NSCLC cells. Additionally, circ_0114866 functioned as a sponge for miR-653-5p, leading to an increase in MYL6B expression by absorbing miR-653-5p. Furthermore, the inhibitory effects on biological behaviors and EMT process of NSCLC cells induced by circ_0114866 knockdown were reversed by miR-653-5p inhibitor. Moreover, in vivo experiments demonstrated that silencing circ_0114866 resulted in a repression of tumor growth. ConclusionOur findings indicate that circ_0114866 knockdown upregulated MYL6B transcription by sponging miR-653-5p, leading to hinder the progression and EMT process of NSCLC.

Identification and Validation of Aging- and Endoplasmic Reticulum Stress-Related Genes in Periodontitis Using a Competing Endogenous RNA Network.

Periodontitis is a multifactorial chronic inflammatory disease that destroy periodontium. Apart from microbial infection and host immune responses, emerging evidence shows aging and endoplasmic reticulum stress (ER stress) play a key role in periodontitis pathogenesis. The aim of this study is to identify aging-related genes (ARGs) and endoplasmic reticulum stress-related genes (ERGs) in periodontitis. Data were obtained from the Gene Expression Omnibus (GEO), Human Ageing Genomic Resources (HAGR) and GeneCards databases to identify differentially expressed mRNAs/miRNAs/lncRNAs (DEmRNAs/DEmiRNAs/DElncRNAs), ARGs and ERGs, respectively. We used the MultiMiR database for the reverse prediction of miRNAs and predicted miRNA-lncRNA interactions using the STARBase database. Afterwards, we constructed a mRNA-miRNA-lncRNA ceRNA network. A total of 10 hub genes, namely LCK, LYN, CXCL8, IL6, HCK, IL1B, BTK, CXCL12, GNAI1 and FCER1G, and 5 DEmRNAs-ARGs-ERGs were then discovered. Further, weighted gene co-expression network analysis (WGCNA) and single sample gene set enrichment analysis (ssGSEA) were performed to explore co-expression modules and immune infiltration respectively. Finally, we used transmission electron microscope (TEM), inverted fluorescence microscopy, quantitative real-time polymerase chain reaction (qRT-PCR) and Western Blot to verify the bioinformatic results in periodontal ligament stem cells (PDLSCs) infected with Porphyromonas gingivalis (P. gingivalis). The experimental results broadly confirmed the accuracy of bioinformatic analysis. The present study established an aging- and ER stress-related ceRNA network in periodontitis, contributing to a deeper understanding of the pathogenesis of periodontitis.

Knockdown of long non-coding RNA SBF2-AS1 inhibits calcium oxalate-induced HK-2 cell injury by regulating the miR-302e/NLRP3 pathway.

Long non-coding ribose nucleic acids (lncRNAs) have been implicated in the development of nephrolithiasis. The study aims to investigate the interplay of lncRNA SBF2-AS1 (SETbinding factor 2 antisense RNA 1) and NLR family pyrin domain containing 3 (NLRP3) in regulating the calcium oxalate monohydrate (COM)-induced human kidney HK-2 cell injury. HK-2 cells were treated with COM (100µg/mL) to create a cellular model of kidney injury. Gene and protein expression was assessed by quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) and Western blot. Proliferation and apoptosis rates, as well as levels of malondialdehyde (MDA), lactate dehydrogenase (LDH), superoxide dismutase (SOD), tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6 were measured. Additionally, potential miRNAs interacting with SBF2-AS1 and NLRP3 were predicted utilizing the starBase and TargetScan databases. The interference of SBF2-AS1 resulted in increased cell proliferation and SOD levels in HK-2 cells after COM induction. SBF2-AS1 silencing also reduced COM-induced cell death and inflammatory cytokine production by down-regulating NLRP3 protein expression. Conversely, forced upregulation of NLRP3 abrogated the effect of SBF2-AS1 interference. Notably, SBF2-AS1 interference on COM-induced oxidative stress and COM-induced cellular damage was rescued by antioxidant, indicating the involvement of oxidative burden in COM-induced damage. miR-302e acted as a mediator miRNA linking the functional association of SBF2-AS1 and NLRP3. Silencing SBF2-AS1 promoted miR-302e level and miR-302e reduced NLRP3 expression in HK-2 cells to protect against COM-induced damage. In summary, these findings suggest that downregulation of lncRNA SBF2-AS1 can potentially protect HK-2 cells from COM-induced injury by modulating the miR-302e/NLRP3 pathway.

Exploratory Study of Differentially Expressed Genes of Peripheral Blood Monocytes in Patients with Carotid Atherosclerosis.

The abundance of circulating monocytes is closely associated with the development of atherosclerosis in humans. This study aimed to further research into diagnostic biomarkers and targeted treatment of carotid atherosclerosis (CAS). We performed transcriptomics analysis through weighted gene co-expression network analysis (WGCNA) of monocytes from patients in public databases with and without CAS. Differentially expressed genes (DEGs) were screened by R package limma. Diagnostic molecules were derived by the least absolute shrinkage and selection operator (LASSO) and support vector machine recursive feature elimination (SVM-RFE) algorithms. NetworkAnalyst, miRWalk, and Star- Base databases assisted in the construction of diagnostic molecule regulatory networks. The Drug- Bank database predicted drugs targeting the diagnostic molecules. RT-PCR tested expression profiles. From 14,369 hub genes and 61 DEGs, six differentially expressed monocyte-related hub genes were significantly associated with immune cells, immune responses, monocytes, and lipid metabolism. LASSO and SVM-RFE yielded five genes for CAS prediction. RT-PCR of these genes showed HMGB1 was upregulated, and CCL3, CCL3L1, CCL4, and DUSP1 were downregulated in CAS versus controls. Then, we constructed and visualized the regulatory networks of 9 transcription factors (TFs), which significantly related to 5 diagnostic molecules. About 11 miRNAs, 19 lncRNAs, and 39 edges centered on four diagnostic molecules (CCL3, CCL4, DUSP1, and HMGB1) were constructed and displayed. Eleven potential drugs were identified, including ibrutinib, CTI-01, roflumilast etc. Conclusion: A set of five biomarkers were identified for the diagnosis of CAS and for the study of potential therapeutic targets.

MiR-21-5p modulates LPS-induced acute injury in alveolar epithelial cells by targeting SLC16A10

Sepsis is a systemic inflammatory response syndrome resulting from the invasion of the human body by bacteria and other pathogenic microorganisms. One of its most prevalent complications is acute lung injury, which places a significant medical burden on numerous countries and regions due to its high morbidity and mortality rates. MicroRNA (miRNA) plays a critical role in the body's inflammatory response and immune regulation. Recent studies have focused on miR-21-5p in the context of acute lung injury, but its role appears to vary in different models of this condition. In the LPS-induced acute injury model of A549 cells, there is differential expression, but the specific mechanism remains unclear. Therefore, our aim is to investigate the changes in the expression of miR-21-5p and SLC16A10 in a type II alveolar epithelial cell injury model induced by LPS and explore the therapeutic effects of their targeted regulation. A549 cells were directly stimulated with 10 µg/ml of LPS to construct a model of LPS-induced cell injury. Cells were collected at different time points and the expression of interleukin 1 beta (IL-1β), tumor necrosis factor-α (TNF-α) and miR-21-5p were measured by RT-qPCR and western blot. Then miR-21-5p mimic transfection was used to up-regulate the expression of miR-21-5p in A549 cells and the expression of IL-1β and TNF-α in each group of cells was measured by RT-qPCR and western blot. The miRDB, TargetScan, miRWalk, Starbase, Tarbase and miR Tarbase databases were used to predict the miR-21-5p target genes and simultaneously, the DisGeNet database was used to search the sepsis-related gene groups. The intersection of the two groups was taken as the core gene. Luciferase reporter assay further verified SLC16A10 as the core gene with miR-21-5p. The expression of miR-21-5p and SLC16A10 were regulated by transfection or inhibitors in A549 cells with or without LPS stimulation. And then the expression of IL-1β and TNF-α in A549 cells was tested by RT-qPCR and western blot in different groups, clarifying the role of miR-21-5p-SLC16A10 axis in LPS-induced inflammatory injury in A549 cells. (1) IL-1β and TNF-α mRNA and protein expression significantly increased at 6, 12, and 24 h after LPS stimulation as well as the miR-21-5p expression compared with the control group (P < 0.05). (2) After overexpression of miR-21-5p in A549 cells, the expression of IL-1β and TNF-α was significantly reduced after LPS stimulation, suggesting that miR-21-5p has a protection against LPS-induced injury. (3) The core gene set, comprising 51 target genes of miR-21-5p intersecting with the 1448 sepsis-related genes, was identified. This set includes SLC16A10, TNPO1, STAT3, PIK3R1, and FASLG. Following a literature review, SLC16A10 was selected as the ultimate target gene. Dual luciferase assay results confirmed that SLC16A10 is indeed a target gene of miR-21-5p. (4) Knocking down SLC16A10 expression by siRNA significantly reduced the expression of IL-1β and TNF-α in A549 cells after LPS treatment (P < 0.05). (5) miR-21-5p inhibitor increased the expression levels of IL-1β and TNF-α in A549 cells after LPS stimulation (P < 0.05). In comparison to cells solely transfected with miR-21-5p inhibitor, co-transfection of miR-21-5p inhibitor and si-SLC6A10 significantly reduced the expression of IL-1β and TNF-α (P < 0.05). MiR-21-5p plays a protective role in LPS-induced acute inflammatory injury of A549 cells. By targeting SLC16A10, it effectively mitigates the inflammatory response in A549 cells induced by LPS. Furthermore, SLC16A10 holds promise as a potential target for the treatment of acute lung injury.