KinomeMETA: a web platform for kinome-wide polypharmacology profiling with meta-learning.

Kinase-targeted inhibitors hold promise for new therapeutic options, with multi-target inhibitors offering the potential for broader efficacy while minimizing polypharmacology risks. However, comprehensive experimental profiling of kinome-wide activity is expensive, and existing computational approaches often lack scalability or accuracy for understudied kinases. We introduce KinomeMETA, an artificial intelligence (AI)-powered web platform that significantly expands the predictive range with scalability for predicting the polypharmacological effects of small molecules across the kinome. By leveraging a novel meta-learning algorithm, KinomeMETA efficiently utilizes sparse activity data, enabling rapid generalization to new kinase tasks even with limited information. This significantly expands the repertoire of accurately predictable kinases to 661 wild-type and clinically-relevant mutant kinases, far exceeding existing methods. Additionally, KinomeMETA empowers users to customize models with their proprietary data for specific research needs. Case studies demonstrate its ability to discover new active compounds by quickly adapting to small dataset. Overall, KinomeMETA offers enhanced kinome virtual profiling capabilities and is positioned as a powerful tool for developing new kinase inhibitors and advancing kinase research. The KinomeMETA server is freely accessible without registration at https://kinomemeta.alphama.com.cn/.

Application of Natural Medicinal Plants Active Ingredients in Oral Squamous Cell Carcinoma.

Oral squamous cell carcinoma (OSCC) is the most common malignant cancer of the head and neck, with high morbidity and mortality, ranking as the sixth most common cancer in the world. The treatment of OSCC is mainly radiotherapy, chemotherapy and surgery, however, the prognosis of patients is still poor and the recurrence rate is high. This paper reviews the range of effects of natural medicinal plant active ingredients (NMPAIs) on OSCC cancer, including the types of NMPAIs, anti-cancer mechanisms, involved signaling pathways, and clinical trials. The NMPAIs include terpenoids, phenols, flavonoids, glycosides, alkaloids, coumarins, and volatile oils. These active ingredients inhibit proliferation, induce apoptosis and autophagy, inhibit migration and invasion of OSCC cells, and regulate cancer immunity to exert anti-cancer effects. The mechanism involves signaling pathways such as mitogen-activated protein kinase, phosphatidylinositol 3 kinase/protein kinase B, nuclear factor kappa B, miR-22/WNT1/ß-catenin and Nrf2/Keap1. Clinically, NMPAIs can inhibit the growth of OSCC, and the combined drug is more effective. Natural medicinal plants are promising candidates for the treatment of OSCC.

KinomeMETA: meta-learning enhanced kinome-wide polypharmacology profiling.

Kinase inhibitors are crucial in cancer treatment, but drug resistance and side effects hinder the development of effective drugs. To address these challenges, it is essential to analyze the polypharmacology of kinase inhibitor and identify compound with high selectivity profile. This study presents KinomeMETA, a framework for profiling the activity of small molecule kinase inhibitors across a panel of 661 kinases. By training a meta-learner based on a graph neural network and fine-tuning it to create kinase-specific learners, KinomeMETA outperforms benchmark multi-task models and other kinase profiling models. It provides higher accuracy for understudied kinases with limited known data and broader coverage of kinase types, including important mutant kinases. Case studies on the discovery of new scaffold inhibitors for membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase and selective inhibitors for fibroblast growth factor receptors demonstrate the role of KinomeMETA in virtual screening and kinome-wide activity profiling. Overall, KinomeMETA has the potential to accelerate kinase drug discovery by more effectively exploring the kinase polypharmacology landscape.

Current advances in niosomes applications for drug delivery and cancer treatment.

The advent of nanotechnology has led to an increased interest in nanocarriers as a drug delivery system that is efficient and safe. There have been many studies addressing nano-scale vesicular systems such as liposomes and niosome is a newer generation of vesicular nanocarriers. The niosomes provide a multilamellar carrier for lipophilic and hydrophilic bioactive substances in the self-assembled vesicle, which are composed of non-ionic surfactants in conjunction with cholesterol or other amphiphilic molecules. These non-ionic surfactant vesicles, simply known as niosomes, can be utilized in a wide variety of technological applications. As an alternative to liposomes, niosomes are considered more chemically and physically stable. The methods for preparing niosomes are more economic. Many reports have discussed niosomes in terms of their physicochemical properties and applications as drug delivery systems. As drug carriers, nano-sized niosomes expand the horizons of pharmacokinetics, decreasing toxicity, enhancing drug solvability and bioavailability. In this review, we review the components and fabrication methods of niosomes, as well as their functionalization, characterization, administration routes, and applications in cancer gene delivery, and natural product delivery. We also discuss the limitations and challenges in the development of niosomes, and provide the future perspective of niosomes.

Evaluation of the competence of an artificial intelligence-assisted colonoscopy system in clinical practice: A post hoc analysis.

Background: Artificial intelligence-assisted colonoscopy (AIAC) has been proposed and validated in recent years, but the effectiveness of clinic application remains unclear since it was only validated in some clinical trials rather than normal conditions. In addition, previous clinical trials were mostly concerned with colorectal polyp identification, while fewer studies are focusing on adenoma identification and polyps size measurement. In this study, we validated the effectiveness of AIAC in the clinical environment and further investigated its capacity for adenoma identification and polyps size measurement. Methods: The information of 174 continued patients who went for coloscopy in Chongqing Rongchang District People's hospital with detected colon polyps was retrospectively collected, and their coloscopy images were divided into three validation datasets, polyps dataset, polyps/adenomas dataset (all containing narrow band image, NBI images), and polyp size measurement dataset (images with biopsy forceps and polyps) to assess the competence of the artificial intelligence system, and compare its diagnostic ability with endoscopists with different experiences. Results: A total of 174 patients were included, and the sensitivity of the colorectal polyp recognition model was 99.40%, the accuracy of the colorectal adenoma diagnostic model was 93.06%, which was higher than that of endoscopists, and the mean absolute error of the polyp size measurement model was 0.62 mm and the mean relative error was 10.89%, which was lower than that of endoscopists. Conclusion: Artificial intelligence-assisted model demonstrated higher competence compared with endoscopists and stable diagnosis ability in clinical use.

Anticancer Activity of Diosgenin and Its Molecular Mechanism.

Diosgenin, a steroidal sapogenin, obtained from Trigonella foenum-graecum, Dioscorea, and Rhizoma polgonati, has shown high potential and interest in the treatment of various cancers such as oral squamous cell carcinoma, laryngeal cancer, esophageal cancer, liver cancer, gastric cancer, lung cancer, cervical cancer, prostate cancer, glioma, and leukemia. This article aims to provide an overview of the in vivo, in vitro, and clinical studies reporting the diosgenin's anticancer effects. Preclinical studies have shown promising effects of diosgenin on inhibiting tumor cell proliferation and growth, promoting apoptosis, inducing differentiation and autophagy, inhibiting tumor cell metastasis and invasion, blocking cell cycle, regulating immunity and improving gut microbiome. Clinical investigations have revealed clinical dosage and safety property of diosgenin. Furthermore, in order to improve the biological activity and bioavailability of diosgenin, this review focuses on the development of diosgenin nano drug carriers, combined drugs and the diosgenin derivatives. However, further designed trials are needed to unravel the diosgenin's deficiencies in clinical application.

Identification of Potential Antimicrobial Targets of Pseudomonas aeruginosa Biofilms through a Novel Screening Approach.

Pseudomonas aeruginosa is an opportunistic pathogen of considerable medical importance, owing to its pronounced antibiotic tolerance and association with cystic fibrosis and other life-threatening diseases. The aim of this study was to highlight the genes responsible for P. aeruginosa biofilm tolerance to antibiotics and thereby identify potential new targets for the development of drugs against biofilm-related infections. By developing a novel screening approach and utilizing a public P. aeruginosa transposon insertion library, several biofilm-relevant genes were identified. The Pf phage gene (PA0720) and flagellin gene (fliC) conferred biofilm-specific tolerance to gentamicin. Compared with the reference biofilms, the biofilms formed by PA0720 and fliC mutants were completely eliminated with a 4-fold-lower gentamicin concentration. Furthermore, the mreC, pprB, coxC, and PA3785 genes were demonstrated to play major roles in enhancing biofilm tolerance to gentamicin. The analysis of biofilm-relevant genes performed in this study provides important novel insights into the understanding of P. aeruginosa antibiotic tolerance, which will facilitate the detection of antibiotic resistance and the development of antibiofilm strategies against P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogen of high medical importance and is one of the main pathogens responsible for the mortality of patients with cystic fibrosis. In addition to inherited antibiotic resistance, P. aeruginosa can form biofilms, defined as communities of microorganisms embedded in a self-produced matrix of extracellular polymeric substances adhering to each other and/or to a surface. Biofilms protect bacteria from antibiotic treatments and represent a major reason for antibiotic failure in the treatment of chronic infections caused by cystic fibrosis. Therefore, it is crucial to develop new therapeutic strategies aimed at specifically eradicating biofilms. The aim of this study was to generalize a novel screening method for biofilm research and to identify the possible genes involved in P. aeruginosa biofilm tolerance to antibiotics, both of which could improve the understanding of biofilm-related infections and allow for the identification of relevant therapeutic targets for drug development.

Geniposide ameliorates glucocorticoid-induced osteoblast apoptosis by activating autophagy.

Long-term exposure to glucocorticoid (GC) contributes to the development of osteoporosis (OP), which is correlated with the risk of fracture. Pathologically, GC-induced bone loss is associated with osteoblast apoptosis. Geniposide (GEN), a natural occurring compound derived from Eucommia ulmoides, has been reported to ameliorate dexamethasone (DEX)-induced OP. Our previous study shows that GEN exhibits protective activity against DEX-induced OP by attenuating endoplasmic reticulum stress and decreasing apoptosis in osteoblasts. However, the molecular mechanisms of GEN in inhibiting DEX-induced osteoblast apoptosis still need further elucidation. In this article, a molecular target network of GEN against OP was screened. It was found that GEN might interact with OP by mediating PI3K/AKT pathway, which is the upstream factor in regulating autophagy. GEN exhibited protective activity against DEX-induced apoptosis by activating autophagy in vivo and in vitro. Blockage of autophagy, activation of PI3K/AKT/mTOR pathway, or inhibition of GLP-1R activity could eliminate the protective effects of GEN against DEX-induced apoptosis. Collectively, GEN ameliorated DEX-induced osteoblast apoptosis by activating autophagy through GLP-1R/PI3K/AKT/mTOR pathway.

7-Ketocholesterol Induces Oxiapoptophagy and Inhibits Osteogenic Differentiation in MC3T3-E1 Cells.

7-Ketocholesterol (7KC) is one of the oxysterols produced by the auto-oxidation of cholesterol during the dysregulation of cholesterol metabolism which has been implicated in the pathological development of osteoporosis (OP). Oxiapoptophagy involving oxidative stress, autophagy, and apoptosis can be induced by 7KC. However, whether 7KC produces negative effects on MC3T3-E1 cells by stimulating oxiapoptophagy is still unclear. In the current study, 7KC was found to significantly decrease the cell viability of MC3T3-E1 cells in a concentration-dependent manner. In addition, 7KC decreased ALP staining and mineralization and down-regulated the protein expression of OPN and RUNX2, inhibiting osteogenic differentiation. 7KC significantly stimulated oxidation and induced autophagy and apoptosis in the cultured MC3T3-E1 cells. Pretreatment with the anti-oxidant acetylcysteine (NAC) could effectively decrease NOX4 and MDA production, enhance SOD activity, ameliorate the expression of autophagy-related factors, decrease apoptotic protein expression, and increase ALP, OPN, and RUNX2 expression, compromising 7KC-induced oxiapoptophagy and osteogenic differentiation inhibition in MC3T3-E1 cells. In summary, 7KC may induce oxiapoptophagy and inhibit osteogenic differentiation in the pathological development of OP.

Blood-brain barrier penetration prediction enhanced by uncertainty estimation.

Blood-brain barrier is a pivotal factor to be considered in the process of central nervous system (CNS) drug development, and it is of great significance to rapidly explore the blood-brain barrier permeability (BBBp) of compounds in silico in early drug discovery process. Here, we focus on whether and how uncertainty estimation methods improve in silico BBBp models. We briefly surveyed the current state of in silico BBBp prediction and uncertainty estimation methods of deep learning models, and curated an independent dataset to determine the reliability of the state-of-the-art algorithms. The results exhibit that, despite the comparable performance on BBBp prediction between graph neural networks-based deep learning models and conventional physicochemical-based machine learning models, the GROVER-BBBp model shows greatly improvement when using uncertainty estimations. In particular, the strategy combined Entropy and MC-dropout can increase the accuracy of distinguishing BBB + from BBB - to above 99% by extracting predictions with high confidence level (uncertainty score < 0.1). Case studies on preclinical/clinical drugs for Alzheimer' s disease and marketed antitumor drugs that verified by literature proved the application value of uncertainty estimation enhanced BBBp prediction model, that may facilitate the drug discovery in the field of CNS diseases and metastatic brain tumors.

The pharmacokinetic property and pharmacological activity of acteoside: A review.

Acteoside (AC), a phenylpropanoid glycoside isolated from many dicotyledonous plants, has been demonstrated various pharmacological activities, including anti-oxidation, anti-inflammation, anti-cancer, neuroprotection, cardiovascular protection, anti-diabetes, bone and cartilage protection, hepatoprotection, and anti-microorganism. However, AC has a poor bioavailability, which can be potentially improved by different strategies. The health-promoting characteristics of AC can be attributed to its mediation in many signaling pathways, such as MAPK, NF-κB, PI3K/AKT, TGFß/Smad, and AMPK/mTOR. Interestingly, docking simulation study indicates that AC can be an effective candidate to inhibit the activity of SARS-CoV2 main protease and protect against COVID-19. Many clinical trials for AC have been investigated, and it shows great potentials in drug development.

[Evaluation of the effect of repairing unilateral cleft lip nose deformity with autogenous concha cartilage].

PURPOSE: To explore the effect of nasal deformity correction after unilateral cleft lip repair with autogenous concha cartilage transplantation. METHODS: Thirteen patients with nasal deformity after unilateral cleft lip surgery were collected, who were treated with autogenous concha cartilage and nasal septum deviation correction at the same time. Their chin-lifting photos were taken before operation, five days, one month and six months after operation. The nasal morphology was evaluated by subjective evaluation and objective measurement, and statistical analysis was performed using SPSS 21.0 software package. RESULTS: Subjective evaluation showed that there was significant difference in nasal morphology between prior to operation and 5 days postoperatively (P=0.000), but there was no significant difference between 5 days postoperatively and 1 month and 6 months postoperatively(P=0.110, 0.053). In objective measurement, there was no significant difference in the symmetry rate of nasal tip between prior to operation and 5 days, 1 month and 6 months after operation(P=0.051, 0.136, 0.204), but there was significant difference in the symmetry rate of nasal base, nasal columella, extranasal convex angle and nasal alar base inclination angle between prior to operation and 5 days postoperatively(P=0.000, 0.000, 0.000, 0.000). However, there was no significant difference in symmetry rate of the above four indexes between 5 days after operation and 1 month and 6 months after operation(P＞0.05). CONCLUSIONS: Autogenous concha cartilage transplantation can effectively improve the symmetry of nasal floor, columella and alar after operation, and the effect is stable half a year after operation.

Role of the flagellar hook in the structural development and antibiotic tolerance of Pseudomonas aeruginosa biofilms.

Pseudomonas aeruginosa biofilms exhibit an intrinsic resistance to antibiotics and constitute a considerable clinical threat. In cystic fibrosis, a common feature of biofilms formed by P. aeruginosa in the airway is the occurrence of mutants deficient in flagellar motility. This study investigates the impact of flagellum deletion on the structure and antibiotic tolerance of P. aeruginosa biofilms, and highlights a role for the flagellum in adaptation and cell survival during biofilm development. Mutations in the flagellar hook protein FlgE influence greatly P. aeruginosa biofilm structuring and antibiotic tolerance. Phenotypic analysis of the flgE knockout mutant compared to the wild type (WT) reveal increased fitness under planktonic conditions, reduced initial adhesion but enhanced formation of microcolony aggregates in a microfluidic environment, and decreased expression of genes involved in exopolysaccharide formation. Biofilm cells of the flgE knock-out mutant display enhanced tolerance towards multiple antibiotics, whereas its planktonic cells show similar resistance to the WT. Confocal microscopy of biofilms demonstrates that gentamicin does not affect the viability of cells located in the inner part of the flgE knock-out mutant biofilms due to reduced penetration. These findings suggest that deficiency in flagellar proteins like FlgE in biofilms and in cystic fibrosis infections represent phenotypic and evolutionary adaptations that alter the structure of P. aeruginosa biofilms conferring increased antibiotic tolerance.

Effect of auto flash margin on superficial dose in breast conserving radiotherapy for breast cancer.

PURPOSE: To investigate the dose-effect of Auto Flash Margin (AFM) on breast cancer's superficial tissues based on the Treatment Planning System (TPS) in the breast-conserving radiotherapy plan. METHODS: A total of 16 breast-conserving patients with early stage breast cancer were selected, using the X-ray Voxel Monte Carlo (XVMC) algorithm. Then, every included case plan was designed using a 2 cm-AFM (the value of AFM is 2 cm) and N-AFM (without AFM). Under the condition of ensuring the same configuration of #MU and collimator, the absorbed dose after a simulated inspiratory motion was calculated again using the new plan center, which moved backward to the linac source. The dose difference between the measurement points between AFM and N-AFM groups was compared. RESULTS: In the dose results, PTVV50Gy of the AFM group was superior to that of the N-AFM group, PTVD2% , PTVDmean , Lung_IpsiV20Gy , Lung_IpsiDmean , and BodyDmax . Also, the dose results of the N-AFM group were significantly higher than those of the AFM group. However, there was no significant difference between Lung_ContraV5Gy , HeartDmean , and Breast_ContraV10Gy in the two groups. In the collimator alignments at the same angle between groups, the AFM group formed an apparent air region outside the collimator compared with the N-AFM group. In the XVMC algorithm feature parameter, the AFM group had less #MU, higher QE, and slightly longer optimization time. The #segments of both groups were close to the 240 control points preset by the plan. The validation results of EBT3 film in both groups were more significant than 95%, meeting the clinical plan's application requirements. The difference in film results between groups was mainly reflected in the dose distribution at the near-source. 4DCT was used to summarize the maximum and minimum inspiratory motion distances of 7.31 ± 0.45 and 3.42 ± 0.91 mm respectively. CONCLUSIONS: These results suggest that the AFM function application could significantly reduce the possibility of insufficient tumor target caused by inspiratory motion and ensure sufficient tumor target exposure.

Inorganic nanohybrids combat antibiotic-resistant bacteria hiding within human macrophages.

Bacterial infections are one of the main health concerns humanity faces today and bacterial resistances and protection mechanisms are set to aggravate the issue in the coming years. An increasing number of bacterial strains evades antibiotic treatment by hiding inside cells. Conventional antimicrobial agents are unable to penetrate or be retained in the infected mammalian cells. Recent approaches to overcome these limitations have focused on load-carrier systems, requiring a triggered discharge leading to complex release kinetics. The unison of potent antimicrobial activity with high mammalian cell compatibility is a prerequisite for intracellular activity, which is not well-met by otherwise well-established inorganic systems, such as silver-based nanoparticles. In this work, load and carrier are combined into one functional inorganic nanoparticle system, which unites antimicrobial activity with mammalian cell compatibility. These multicomponent nanohybrids based on cerium oxide are produced in one step, yet unite complex materials. The nanoparticles form suprastructures of similar size and surface charge as bacteria, therefore facilitating the uptake into the same subcellular compartments, where they unleash their antibacterial effect. Such intrinsically antibacterial nanohybrids significantly reduce bacterial survival inside macrophages without harming the latter. Furthermore, blocking of nanoparticle endocytosis and subcellular electron microscopy elucidate the mechanism of action. Taken together, this work presents the first demonstration of antibacterial activity of ceria-based nanoparticles inside of mammalian cells and offers a route to straightforward and robust intracellular antibacterial agents that do not depend on payload delivery or biological constituents.

Pharmacological effects and mechanisms of muscone.

Musk, the dried secretion from the preputial follicles of the male musk deer (genus Moschus), possesses various pharmacological activities and has been used extensively in traditional Chinese medicine for thousands of years. Muscone is the main active ingredient of musk and exerts pharmacological effects similar to those of musk. Although muscone was notably used to treat various disorders and diseases, such as neurological disorders, chronic inflammation and ischemia-reperfusion injury, most of the mechanisms of the pharmacological action of muscone remain unclear because of slow progress in research before the 21st century. In recent years, the pharmacological activities and mechanisms of muscone have been clarified. The present article summarizes the pharmacological and biological studies on cerebrovascular disease, cardiovascular disease, neurological effects, cancer and others and the associated mechanisms of the action of muscone to date.

Antibacterial, Cytocompatible, Sustainably Sourced: Cellulose Membranes with Bifunctional Peptides for Advanced Wound Dressings.

Progressive antibiotic resistance is a serious condition adding to the challenges associated with skin wound treatment, and antibacterial wound dressings with alternatives to antibiotics are urgently needed. Cellulose-based membranes are increasingly considered as wound dressings, necessitating further functionalization steps. A bifunctional peptide, combining an antimicrobial peptide (AMP) and a cellulose binding peptide (CBP), is designed. AMPs affect bacteria via multiple modes of action, thereby reducing the evolutionary pressure selecting for antibiotic resistance. The bifunctional peptide is successfully immobilized on cellulose membranes of bacterial origin or electrospun fibers of plant-derived cellulose, with tight control over peptide concentrations (0.2 ± 0.1 to 4.6 ± 1.6 µg mm-2 ). With this approach, new materials with antibacterial activity against Staphylococcus aureus (log4 reduction) and Pseudomonas aeruginosa (log1 reduction) are developed. Furthermore, membranes are cytocompatible in cultures of human fibroblasts. Additionally, a cell adhesive CBP-RGD peptide is designed and immobilized on membranes, inducing a 2.2-fold increased cell spreading compared to pristine cellulose. The versatile concept provides a toolbox for the functionalization of cellulose membranes of different origins and architectures with a broad choice in peptides. Functionalization in tris-buffered saline avoids further purification steps, allowing for translational research and multiple applications outside the field of wound dressings.

Detection of microbial colonization of the urinary tract of patients prior to secondary ureterorenoscopy is highly variable between different types of assessment: results of a prospective observational study.

This study compares the findings of different detection methods for microorganisms in patients with ureteral stents undergoing secondary ureterorenoscopy including the use of a novel validated examination pipeline for biofilms on ureteral stents. Of the included 94 patients, 21.3% showed bacteriuria in preoperative urine cultures. Intraoperative urine culture showed bacteriuria in four (4.3%) of the patients. Stent biofilm cultures were positive in 12.9% and qPCR detected bacterial DNA in 18.1%. The findings of the different examinations were poorly correlated with each other. Detection of microorganisms in the urinary tract of patients with indwelling ureteral stents is highly dependent on timing (i.e. pre- vs intraoperative) and method of assessment. Preoperative routine urine cultures are not predictive for intraoperative urine- and stent culture. These results cast doubt on the clinical relevance of enterococcal species, staphylococci, and streptococci if identified preoperatively prior to stent removal. The timing of oral preoperative antibiotic prophylaxis might need to be reconsidered.

LAT, HOXD3 and NFE2L3 identified as novel DNA methylation-driven genes and prognostic markers in human clear cell renal cell carcinoma by integrative bioinformatics approaches.

Background: Abnormal DNA methylation of is one of the important mechanisms leading to tumor pathogenesis. The purpose of this study was to explore differentially methylated genes that may drive the development of renal clear cell carcinoma through a comprehensive analysis of the TCGA database. Materials and methods: Methylation data and RNA-seq data for clear cell renal cell carcinoma were downloaded from The Cancer Genome Atlas (TCGA). Differentially methylated genes and the differential genes associated with survival were then screened by MethylMix R package and univariate Cox proportional-hazards model, respectively. Their common genes were then intersected and obtained for further analysis. Correlation of gene expression and methylation levels, gene set enrichment analysis (GSEA) enrichments, survival curve, and ROC curve plotting for DNA methylation-driven genes were finally performed. The methylation alterations of the three genes were validated via two GEO datasets (GSE70303 and GSE113501), and the genes expression level was verified through two GEO datasets (GSE6344 and GSE53757). Results: Three novel DNA methylation-driven genes LAT, HOXD3 and NFE2L3 were identified in clear cell renal cell carcinoma. Expression analysis further revealed that hypomethylation levels of LAT and NFE2L3 showed higher gene expression levels, while HOXD3 exhibited opposite methylation-expression pattern. The CpG sites of LAT (cg16462073), HOXD3 (cg24000528) and NFE2L3 (cg16882373) that may affect respective gene expressions were also identified. For the survival analysis, we found that hypomethylation and over-expression of LAT and NFE2L3 were correlated with poor survival, while hypermethylation and low-expression HOXD3 was correlated with poor survival of clear cell renal cell carcinoma patients. In addition, GSEA KEGG analysis and biological processes of these genes were also enriched for functional analysis. Kaplan-Meier survival and ROC analyses of these genes showed an average risk score of 0.9140593, AUC = 0.692, which suggested a good clinical application value. Finally, the opposite methylation-expression pattern of these three genes were verified in GEO datasets. Conclusions: In this study, we successfully exhibited the potential DNA methylation-driven genes LAT, HOXD3, and NFE2L3 involved in clear cell renal cell carcinoma. Moreover, gene functions and prognostic risk models were also elucidated, which facilitated the expansion of the current study on the role of methylation in the pathology process of clear cell renal cell carcinoma.

Integrative gene expression profiling reveals that dysregulated triple microRNAs confer paclitaxel resistance in non-small cell lung cancer via co-targeting MAPT.

BACKGROUND: Paclitaxel has shown significant anti-tumor activity against non-small cell lung cancer (NSCLC); however, resistance to paclitaxel frequently occurs and represents a significant clinical problem and its underlying molecular mechanism remains elusive. METHODS: Long-term treatment of culture cell with paclitaxel was carried out to mimic the development of acquired drug resistance in NSCLC. Cell proliferation and clonogenic assay and apoptosis evaluation were carried out to determine the efficacy of paclitaxel on NSCLC cells. Western blot analyses were performed to determine the expression and activation of proteins. Apoptosis enzyme-linked immunosorbent assay was used to quantify cytoplasmic histone-associated DNA fragments. Microarray analyses were applied to explore both mRNA and miRNA expression profiles in NSCLC cells followed by integrative analysis. qRT-PCR was carried out to verify the differentially expressed mRNAs and miRNAs. RESULTS: The expression of 652 genes was shown to be changed at least 2-fold in paclitaxel-resistant NSCLC (H460_TaxR) cells with 511 upregulated and 141 downregulated as compared with that in parental H460 cells. The differentially expressed genes were functionally enriched in regulating the cell proliferation, cell death, and response to endogenous stimulus, and clustered in pathways such as cancer and signaling by the G protein-coupled receptor (GPCR). Moreover, 43 miRNAs were shown to be differentially expressed in H460_TaxR cells with 15 upregulated and 28 downregulated as compared with parental H460 cells. A total of 289 pairs of miRNA-potential target gene were revealed in H460_TaxR cells by bioinformatics analysis. Furthermore, integrative analysis of miRNAs and gene expression profiles revealed that dysregulated miR-362-3p, miR-766-3p, and miR-6507-3p might confer paclitaxel resistance in NSCLC via targeting MAPT simultaneously. CONCLUSION: Our findings suggested that specific manipulation of MAPT-targeting miRNAs may be a novel strategy to overcome paclitaxel resistance in patients with NSCLC especially large-cell lung carcinoma.