Aloe vera: capacidad antioxidante y uso potencial como agente terapéutico en el tratamiento del Alzheimer mediante evaluación in silico / Aloe vera: antioxidant capacity and potential use as therapeutic agent in the treatment of Alzheimer's through in silico evaluation

Resumen: El gel de Aloe vera es considerado una fuente natural de múltiples beneficios, originados por la acción combinada de vitaminas, aminoácidos, compuestos fenólicos, enzimas, minerales, ácidos orgánicos, lípidos y carbohidratos, que se relacionan con la mejora de enfermedades neuro-degenerativas como Alzheimer. Los ensayos in vitro e in silico permiten confirmar e identificar posibles beneficios de esta planta y sus compuestos en enfermedades. El objetivo del presente trabajo fue evaluar la actividad antioxidante del gel de A. vera y mediante análisis in silico, establecer el potencial terapéutico de sus compuestos bioactivos en la enfermedad de Alzheimer. Se obtuvieron hojas de A. vera, de las que se extrajo el gel, retirando el exocarpio, se liofilizó y almacenó hasta su uso. Se caracterizó la capacidad antioxidante, se cuantificaron los compuestos fenólicos y flavonoides y se analizó la relación que existe entre los parámetros mediante correlación de Pearson. Mediante análisis in silico se evaluó el potencial de interacción de 8 compuestos del gel con la proteína gamma secretasa. El gel de A. vera obtuvo alta capacidad antioxidante por ABTS, DPPH, radical OH y poder reductor, usando bajas concentraciones para inhibir el 50 % de los radicales, y correlaciones positivas con fenoles totales y flavonoides. En el estudio in silico el compuesto que presentó mejor unión con gamma secretasa fue aloe-emodina, con menor energía libre de unión y menor concentración de constante de inhibición, sugiriendo su potencial uso como coadyuvante en el tratamiento de la enfermedad de Alzheimer.

Abstract: Aloe vera gel is considered a natural source of multiple benefits, originated by the combined action of vitamins, amino acids, phenolic compounds, enzymes, minerals, organic acids, lipids and carbohydrates, which are related to the improvement of neuro-degenerative diseases such as Alzheimer's. In vitro and in silico tests allow us to confirm and identify possible benefits of this plant and its compounds in diseases. The objective of the present study was to evaluate the antioxidant activity of A. vera gel and, through in silico analysis, to establish the therapeutic potential of its bioactive compounds in Alzheimer's disease. A. vera leaves were obtained, from which the gel was extracted, removing the exocarp, lyophilized and stored until use. The antioxidant capacity was characterized, the phenolic compounds and flavonoids were quantified, and the relationship between the parameters was analyzed using Pearson correlation. The interaction potential of 8 compounds in the gel with the gamma secretase protein was evaluated through in silico analysis. The A. vera gel obtained high antioxidant capacity due to ABTS, DPPH, OH radical and reducing power, using low concentrations to inhibit 50 % of the radicals, and positive correlations with total phenols and flavonoids. In the in silico study, the compound that showed the best binding with gamma secretase was aloe-emodin, with lower binding free energy and lower inhibition constant concentration, suggesting its potential use as an adjuvant in the treatment of Alzheimer's disease.

Natural treasures from Picrorhiza kurrooa: a computational exploration of drug-like properties and bioactivity of kutkin, cucurbitacin, apocynin and lupanine

Background: To analyse and predict the basic pharmacokinetic and toxicological properties of four compounds of interest found in Picrorhiza kurroa (Kutkin, cucurbitacin, apocynin and lupanine) using computational bioinformatics tools. Methods: The chemical structures and molecular properties of the compounds were obtained from authentic sources and processed for data profiling. 2D structures were converted to 3D structures using ChemSketch software and PHASE module. In silico screening of the 3D structures was performed using bioinformatics prediction software to assess drug-likeness, absorption, blood-brain barrier penetration, enzyme interaction potential, skin penetration, and acute oral toxicity. Results: Kutkin exhibited poor drug-likeness and low oral absorption, while the other three compounds showed promising drug-like properties and good oral absorption. Cucurbitacin and lupanine were predicted to cross the blood-brain barrier, while Kutkin and Apocynin were not. None of the compounds were substrates for P-glycoprotein, but Kutkin and cucurbitacin were substrates for CYP3A4. All four compounds had low skin penetration. Acute oral toxicity varied, with cucurbitacin classified as highly toxic and the others as slightly toxic. Conclusions: Cucurbitacin, apocynin, and lupanine have potential for further development as therapeutic agents due to their favorable drug-like properties and good absorption. Kutkin's poor drug-likeness and low absorption make it less suitable for oral drug development. This information provides valuable insights for further research on the medicinal properties of Picrorhiza kurroa and the development of new drugs based on its active compounds.

Mining of Gene Modules and Identification of Key Genes for Early Diagnosis of Gastric Cancer

Gastric cancer (GC) is one of the most common malignant tumors with high incidence and mortality rates. Most patients with GC are not diagnosed until the advanced stage of cancer or during tumor screening, resulting in missing the best treatment time. This study identified key modules and hub genes associated with GC by weighted gene co-expression network analysis (WGCNA). The "limma" package in R was used to identify differentially expressed genes (DEGs) in GC samples from TCGA, and a total of 4892 DEGs were identified. GO enrichment and KEGG pathway enrichment analyses were conducted to detect the related pathways and functions of DEGs. These DEGs were primarily associated with extracellular matrix organization, DNA replication, cell cycle, and p53 signaling pathway. Gene modules associated with clinical characteristics were identified with WGCNA in tumor and normal samples. Six gene modules were obtained in the WGCNA network, of which two modules were significantly correlated with GC. Hub genes of key modules were identified using survival analysis and expression analysis. Finally, one-way ANOVA was used to explore the relationship between hub gene expression in normal tissues and different pathological stages of GC. Through survival and expression analysis, a total of 19 genes with good prognosis and significantly differential expressed were identified. The hub genes were significantly differential expressed in normal tissues and different pathological stages of GC, indicating that these genes have important diagnostic value for early GC and can be used as auxiliary indicators in the diagnosis of early GC.

Decoding potential targets and pharmacologic mechanisms of curcumin in treating non-small cell lung carcinoma via bioinformatics and molecular docking

Emerging evidence demonstrates that curcumin has an inhibitory effect on non-small cell lung cancer (NSCLC), and its targets and mechanism of action need further exploration. The goal of this study was to explore the potential targets and mechanism of curcumin against NSCLC by network pharmacology, bioinformatics, and experimental validation, thereby providing more insight into combination treatment with curcumin for NSCLC in preclinical and clinical research. Curcumin targets against NSCLC were predicted based on HIT2.0, STD, CTD, and DisGeNET, and the core targets were analyzed via protein-protein interaction network construction (PPI), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and molecular docking. The gene expression levels of samples in A549 cells, NCI-H460, and curcumin treated groups were detected by real-time quantitative PCR. A total of 67 common targets between curcumin and NSCLC were collected by screening public databases. GO and KEGG analysis suggested that curcumin treatment of NSCLC mainly involves cancer-related pathways, such as PI3K-AKT signaling pathway, Foxo signaling pathway, microRNAs, MAPK signaling pathway, HIF-1 signaling pathway, etc. The targets with the highest degree were identified through the PPI network, namely CASP3, CTNNB1, JUN, IL6, MAPK3, HIF1A, STAT3, AKT1, TP53, CCND1, VEGFA, and EGFR. The results of the in vitro experiments showed that curcumin treatment of NSCLC down-regulated the gene expressions of CCND1, CASP3, HIF1A, IL-6, MAPK3, STAT3, AKT1, and TP53. Our findings revealed that curcumin functions as a potential therapeutic candidate for NSCLC by suppressing multiple signaling pathways and interacting with multiple gene targets.

Potential biomarkers as a predictive factor of response to primary chemotherapy in breast cancer patients

In this study, we identified miRNAs and their potential mRNA targets that are intricately linked to primary chemotherapy response in patients with invasive ductal carcinomas. A cohort of individuals diagnosed with advanced invasive breast ductal carcinoma who underwent primary chemotherapy served as the cornerstone of our study. We conducted a comparative analysis of microRNA expression among patients who either responded or did not respond to primary systemic therapy. To analyze the correlation between the expression of the whole transcriptome and the 24 differentially expressed (DE) miRNAs, we harnessed the extensive repository of The Cancer Genome Atlas (TCGA) database. We mapped molecular mechanisms associated with these miRNAs and their targets from TCGA breast carcinomas. The resultant expression profile of the 24 DE miRNAs emerged as a potent and promising predictive model, offering insights into the intricate dynamics of chemotherapy responsiveness of advanced breast tumors. The discriminative analysis based on the principal component analysis identified the most representative miRNAs across breast cancer samples (miR-210, miR-197, miR-328, miR-519a, and miR-628). Moreover, the consensus clustering generated four possible clusters of TCGA patients. Further studies should be conducted to advance these findings.

Integrative analyses of genetic characteristics associated with skeletal endothelial cells

Abstract The osseous vascular endothelium encompasses a vast intricate framework that regulates bone remodeling. Osteoporosis, an age-associated systemic bone disease, is characterized by the degeneration of the vascular architecture. Nevertheless, the precise mechanisms underpinning the metamorphosis of endothelial cells (ECs) with advancing age remain predominantly enigmatic. In this study, we conducted a systematic analysis of differentially expressed genes (DEGs) and the associated pathways in juvenile and mature femoral ECs, utilizing data sourced from the Gene Expression Omnibus (GEO) repositories (GSE148804) and employing bioinformatics tools. Through this approach, we successfully discerned six pivotal genes, namely Adamts1, Adamts2, Adamts4, Adamts14, Col5a1, and Col5a2. Subsequently, we constructed a miRNA-mRNA network based on miRNAs displaying differential expression between CD31hiEMCNhi and CD31lowEMCNlow ECs, utilizing online repositories for prediction. The expression of miR-466i-3p and miR-466i-5p in bone marrow ECs exhibited an inverse correlation with age. Our in vivo experiments additionally unveiled miR-466i-5p as a pivotal regulator in osseous ECs and a promising therapeutic target for age-related osteoporosis.

CLCA1 is Poorly Expressed in Stomach Adenocarcinoma and Correlates with Immune Infiltration / CLCA1 se Expresa Deficientemente en el Adenocarcinoma de Estómago y se Correlaciona con la Infiltración Inmune

SUMMARY: Calcium-activated chloride channel regulator 1 (CLCA1) is associated with cancer progression. The expression and immunologic function of CLCA1 in stomach adenocarcinoma (STAD) remain unclear. In this investigation, the expression of CLCA1 in STAD tissues and its involvement in the progression and immune response of STAD were examined using databases such as cBioPortal, TISIDB, and UALCAN. In order to validate the expression level of CLCA1 protein in gastric adenocarcinoma, thirty clinical tissue specimens were gathered for immunohistochemical staining. The findings indicated a downregulation of CLCA1 in STAD patients, which was correlated with race, age, cancer grade, Helicobacter pylori infection, and molecular subtype. Through the examination of survival analysis, it was identified that diminished levels of CLCA1 within gastric cancer cases were linked to decreased periods of post-progression survival (PPS), overall survival (OS), and first progression (FP) (P<0.05). The CLCA1 mutation rate was lower in STAD, but the survival rate was higher in the variant group. The correlation between the expression level of CLCA1 and the levels of immune infiltrating cells in STAD, as well as the immune activating molecules, immunosuppressive molecules, MHC molecules, chemokines, and their receptor molecules, was observed. Gene enrichment analysis revealed that CLCA1 may be involved in STAD progression through systemic lupus erythematosus (SLE), proteasome, cell cycle, pancreatic secretion, and PPAR signaling pathways. In summary, CLCA1 is anticipated to function as a prognostic marker for patients with STAD and is linked to the immunization of STAD.

El regulador 1 del canal de cloruro activado por calcio (CLCA1) está asociado con la progresión del cáncer. La expresión y la función inmunológica de CLCA1 en el adenocarcinoma de estómago (STAD) aún no están claras. En esta investigación, se examinó la expresión de CLCA1 en tejidos STAD y su participación en la progresión y respuesta inmune de STAD utilizando bases de datos como cBioPortal, TISIDB y UALCAN. Para validar el nivel de expresión de la proteína CLCA1 en el adenocarcinoma gástrico, se recolectaron treinta muestras de tejido clínico para tinción inmunohistoquímica. Los hallazgos indicaron una regulación negativa de CLCA1 en pacientes con STAD, que se correlacionó con la raza, la edad, el grado del cáncer, la infección por Helicobacter pylori y el subtipo molecular. Mediante el examen del análisis de supervivencia, se identificó que los niveles reducidos de CLCA1 en los casos de cáncer gástrico estaban relacionados con períodos reducidos de supervivencia posterior a la progresión (PPS), supervivencia general (OS) y primera progresión (FP) (P <0,05). La tasa de mutación CLCA1 fue menor en STAD, pero la tasa de supervivencia fue mayor en el grupo variante. Se observó la correlación entre el nivel de expresión de CLCA1 y los niveles de células inmunes infiltrantes en STAD, así como las moléculas activadoras inmunes, moléculas inmunosupresoras, moléculas MHC, quimiocinas y sus moléculas receptoras. El análisis de enriquecimiento genético reveló que CLCA1 puede estar involucrado en la progresión de STAD a través del lupus eritematoso sistémico (LES), el proteasoma, el ciclo celular, la secreción pancreática y las vías de señalización de PPAR. En resumen, se prevé que CLCA1 funcione como un marcador de pronóstico para pacientes con STAD y está vinculado a la inmunización de STAD.

Identification and Expression Pattern of Salvia miltiorrhiza Terpenoid Synthase Gene Family / 中国实验方剂学杂志

ObjectiveBioinformatics methods were used to systematically identify the Salvia miltiorrhiza terpenoid synthase （SmTPS） gene family members and predict their functions from the perspective of the genome. MethodThe genome and transcriptome data of S. miltiorrhiza， Arabidopsis thaliana， and tomato were obtained from the national genomics data center （NGDC）， national center for biotechnology information （NCBI）， the Arabidopsis information resource （TAIR）， and tomato functional genomics database （TFGD）， and the whole genome identification and bioinformatics analysis of the SmTPS gene family member were carried out with the help of Perl language programming， Tbtools， and other bioinformatics tools. ResultA total of 52 TPS gene family members were identified， and they were distributed on eight chromosomes of S. miltiorrhiza. Their coding amino acid number was 207-822 aa. The isoelectric points were 4.76-9.16. The molecular mass was 24.11-94.81 kDa， and all members are hydrophilic proteins. Gene structure analysis showed that there were significant differences in the number of introns among different subfamilies. The number of introns in 72.6% of TPS-a， b， and g subfamilies was 6， and that in 88.9% of TPS-c and e/f subfamilies was more than 10. Protein motifs were conserved among TPS subfamilies. The analysis of promoter cis-acting elements showed that all promoters of the SmTPSs contained a large number of light-responsive elements， and most of them had hormone-responsive elements. Gene expression analysis showed that SmTPS gene family members exhibited tissue-specific expression， and 24 of them responded to exogenous methyl jasmonate. ConclusionBased on the published S. miltiorrhiza genome， 52 SmTPS gene family members were identified， and their functions were predicted based on the phylogenetic analysis and expression patterns. This paper provides reference information for the further biosynthesis pathway and regulatory mechanism analysis of terpenoids in S. miltiorrhiza.

Identification and Analysis of NnOMT and NnNMT Gene Families in Nelumbo nucifera / 中国实验方剂学杂志

ObjectiveThe biosynthetic pathways of benzylisoquinoline alkaloids（BIAs） in Nelumbo nucifera are of great theoretical and economic value. In this paper， N. nucifera O-methyltransferase（NnOMT） and N. nucifera N-methyltransferase（NnNMT） gene families were identified and analyzed by bioinformatics in order to facilitate the biosynthetic pathway of BIAs in N. nucifera. MethodBased on the whole genome of N. nucifera， UniPort and National Center for Biotechnology Information（NCBI） databases were used to identify the NnOMT and NnNMT gene families of N. nucifera， and analyze their physicochemical properties and subcellular localization， then TBtools， MEME， MEGA 11.0， FigTree 1.4.4 and other tools were used to analyze the phylogeny， sequence characteristics， gene structure， functional annotation and cis-acting elements of NnOMT and NnNMT genes identified in the previous stage. ResultA total of 61 NnOMT and NnNMT genes were identified in this paper， the number of amino acids encoded by these genes ranged from 168 aa to 580 aa， the isoelectric point ranged from 4.76 to 9.16， and the relative molecular weight ranged from 18 699.52 Da to 64 934.53 Da， most of which showed acidic and mostly hydrophilic proteins. There were 10 conserved motifs， Kyoto Encyclopedia of Genes and Genomes（KEGG） analysis enriched a total of 12 pathways， including metabolism， biosynthesis of phenylpropane and isoquinoline alkaloids， etc. And Visualization of Gene Ontology（GO） enrichment results showed that 61 NnOMT and NnNMT genes were annotated to 32 items， which included 16 molecular functions［such as reduced nicotinamide adenine dinucleotide（NADH） activity and exopeptidase activity］ and 16 biological processes（such as metabolic process of carbon tetrachloride， anaerobic carbon tetrachloride metabolic process and responses to exogenous biological stimuli）. There were a variety of cis-acting elements in the promoter regions of NnOMT and NnNMT genes， mainly promoter and enhancer regions element， light responsive element and methyl jasmonate responsive element. ConclusionIn this study， a comprehensive bioinformatics analysis of 61 NnOMT and NnNMT genes is carried out based on the genome data of N. nucifera， which lays a foundation for research on the gene structure and function of NnOMT and NnNMT gene families， and provides a reference for biosynthetic pathway elucidation of BIAs in N. nucifera.

Screening and bioinformatics analysis of key autophagy-related genes in alcoholic hepatitis / 器官移植

Objective To screen key autophagy-related genes in alcoholic hepatitis (AH) and investigate potential biomarkers and therapeutic targets for AH. Methods Two AH gene chips in Gene Expression Omnibus (GEO) and autophagy-related data sets obtained from MSigDB and GeneCards databases were used, and the key genes were verified and obtained by weighted gene co-expression network analysis (WGCNA). The screened key genes were subject to gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein-protein interaction (PPI) and immune infiltration analyses. Messenger RNA (mRNA)- microRNA (miRNA) network was constructed to analyze the expression differences of key autophagy-related genes during different stages of AH, which were further validated by real-time fluorescence quantitative polymerase chain reaction (RT-qPCR) in the liver tissues of AH patients and mice. Results Eleven autophagy-related genes were screened in AH (EEF1A2, CFTR, SOX4, TREM2, CTHRC1, HSPB8, TUBB3, PRKAA2, RNASE1, MTCL1 and HGF), all of which were up-regulated. In the liver tissues of AH patients and mice, the relative expression levels of SOX4, TREM2, HSPB8 and PRKAA2 in the AH group were higher than those in the control group. Conclusions SOX4, TREM2, HSPB8 and PRKAA2 may be potential biomarkers and therapeutic targets for AH.

Identification and expression analysis of cellulose synthase family genes in Aquilaria sinensis / 药学学报

Cellulose synthase (CesA), one of the key enzymes in the biosynthesis of cellulose in plants, plays an important role in plant growth and plant resistance. In this study, a total of 21 AsCesA genes from Aquilaria sinensis were systematically identified and the physico-chemical characteristics were analyzed based on genome database and bioinformatical methods. The phylogenetic tree was constructed and the gene location on chromosome, cis-acting elements in the 2 000 basepairs upstream regulatory regions and conservative motifs were analyzed. The AsCesA proteins were mainly located on the plasma membrane. The number of amino acids of the proteins ranged from 390 to 1 261. The isoelectric point distributed from 5.67 to 8.86. All of the 21 AsCesA proteins possessed the transmembrane domains, the number of which was from 6 to 8. The genes were classified into 3 groups according to the phylogenetic relationship. Obvious differences were observed in motif composition in genes from different groups. However, motif2, motif6, motif7 and motif10 were observed in all of AsCesA proteins. Analysis of cis-acting elements indicated that AsCesA genes family has cis-acting elements related to plant hormones, abiotic stresses, and biological processes. Seven AsCesA genes with differential expression were selected according to the calli transcriptome data induced by NaCl at different times and their expression levels under different abiotic stresses were analyzed by quantitative real-time PCR. The results indicated that salt, low temperature, drought, and heavy metal stresses could affect the expression level of AsCesA genes, and the abundance of AsCesA1, AsCesA3 and AsCesA20 showed a significant change, implying their potential important roles to the abiotic stresses. The accumulation pattern of cellulose content under different abiotic stresses was similar to the expression trend of AsCesA genes. Our results provide valuable insights into the role of cellulose synthase in A.sinensis in plant defense.

Mechanism of Tumor T Cell Exhaustion from Perspective of ''Sanjiao-Yingwei'' Qi Transformation Malfunction / 中国实验方剂学杂志

In order to promote the innovative application of Sanjiao theory and Yingwei theory， this paper tries to apply the ''Sanjiao-Yingwei'' Qi transformation theory to the treatment of tumor diseases， integrating it with T cell exhaustion mechanism to elaborate on its scientific connotation and using network pharmacology and bioinformatics to elucidate the correlation between the anti-tumor mechanism of ''Sanjiao-Yingwei'' Qi transformation and T cell exhaustion. The ''Sanjiao-Yingwei'' Qi transformation function is closely related to the immunometabolic ability of the human body， and the ''Sanjiao-Yingwei'' Qi transformation system constitutes the immunometabolic exchange system within and outside the cellular environment. Cancer toxicity is generated by the fuzzy Sanjiao Qi， and the long-term fuzzy Sanjiao Qi is the primary factor leading to T cell exhaustion， which is related to the long-term activation of T cell receptors by the high tumor antigen load in the tumor microenvironment. Qi transformation malfunction of the Sanjiao produces phlegm and collects stasis， which contributes to T cell exhaustion and is correlated with nutrient deprivation， lipid accumulation， and high lactate levels in the immunosuppressed tumor microenvironment， as well as with the release of transforming growth factor-β and upregulated expression of programmed death receptor-1 by tumor-associated fibroblasts and platelets in the tumor microenvironment. Ying and Wei damage due to Sanjiao Qi transformation malfunction is similar to the abnormal manifestations such as progressive loss of exhausted T cell effector function and disturbance of cellular energy metabolism. Guizhi decoction， Shengming decoction， and Wendan decoction can correct T cell exhaustion and exert anti-tumor effects through multi-target and multi-pathways by regulating ''Sanjiao-Yingwei'' Qi transformation， and hypoxia inducible factor-1α （HIF-1α） may be one of the main pathways to correct T cell exhaustion. It was found that HIF-1α may be one of the important prognostic indicators in common tumors by bioinformatics. The use of the ''Sanjiao-Yingwei'' Qi transformation method may play an important part in improving the prognosis of tumor patients in clinical practice.

Mechanism of Xiezhuo Jiedu Recipe in Preventing Colorectal Adenoma in Mice Through miRNA-34a-5p/PI3K/Akt Signalling Pathway / 中国实验方剂学杂志

ObjectiveKey microRNAs （miRNAs） of colorectal adenoma （CRA） were identified and analyzed by bioinformatics methods， and differentially expressed genes （DEGs） were screened to construct regulatory relationships. The mechanism of Xiezhuo Jiedu recipe in preventing CRA was speculated and verified by animal experiments. MethodThe miRNAs dataset GSE50194 was obtained from the Gene Expression Omnibus （GEO） database of intestinal mucosal tissue of CRA patients， and the differentially expressed miRNAs were screened by GEO2R and Excel. TargetScan， miRTarbase， and miRDB databases were used to predict the target genes of the differentially expressed miRNAs， and an intersection was obtained. Key DEGs were screened through the STRING database and Cytoscape software， and the TRRUST database was used to predict downstream binding transcription factors （TFs）. The mRNA intersection was enriched by gene ontology （GO） and Kyoto encyclopedia of genes and genomes （KEGG） in the Metascape database. DIANA TOOLS were applied to perform KEGG enrichment analysis of key miRNAs， and the key signaling pathways were selected for animal experiments. In animal experiments， the CRA mice model was established by using sodium glycan sulfate （DSS） drinking combined with intraperitoneal injection of azomethane oxide （AOM）， and Xiezhuo Jiedu recipe and aspirin were given by intragastric administration at the same time. The experiment lasted for nine weeks. The pathological changes in intestinal tissue were observed by hematoxylin-eosin （HE） staining. Real-time fluorescence quantitative polymerase chain reaction （Real-time PCR） was used to detect the mRNA expression of miR-34a-5p in adenoma tissue. Protein expression levels of phosphatidylinositol 3-kinase （PI3K）， protein kinase B （Akt）， phosphoryl-PI3K （p-PI3K）， phosphoryl-Akt （p-Akt）， and B cell lymphoma （Bcl）-2 were detected by Western blot. The expression of Cyclin D1 （CCND1） was detected by immunohistochemistry （IHC）. In situ terminal transferase labeling （TUNEL） was used to detect apoptosis of adenoma tissue cells. ResultThe GEO database screened the GSE50194 dataset， and miR-34a-5p was selected as the research object from CRA and normal tissue. A total of 93 DEGs were selected. Among them， GO and KEGG enrichment analyses were closely related to biological processes such as transcriptional regulatory complex， RNA polymerase Ⅱ transcriptional regulatory complex， enzyme-linked receptor protein signaling pathway， and DNA-binding transcriptional activator activity， cancer pathway， PI3K/Akt pathway， etc. miR-34a-5p is mainly enriched in PI3K/Akt， cell cycle， and colorectal cancer pathways. Five key DEGs were screened out through the Matescape database， among which Bcl-2 and CCND1 were the key DEGs of miR-34a-5p. Further screening of the TFs of key DEGs revealed that E2F transcription factor 1 （E2F1） and tumor protein P53 （TP53） were the main TFs of Bcl-2 and CCND1. Animal experiments showed that Xiezhuo Jiedu recipe could effectively up-regulate mRNA level of miR-34a-5p， down-regulate the expression of PI3K， Akt， Bcl-2， p-PI3K， and p-Akt proteins in the intestinal tissue of CRA mice， down-regulate the positive expression rate of CCND1， and increase the apoptosis rate of intestinal epithelial cells. ConclusionIt is speculated that Xiezhuo Jiedu recipe may inhibit the abnormal proliferation and promote the apoptosis of intestinal epithelial cells in CRA mice by regulating the miR-34a-5p/PI3K/Akt signaling pathway， thus playing a role in the prevention of CRA.

Mechanism of Xiezhuo Jiedu Recipe Regulating Ferroptosis in Treatment of Ulcerative Colitis Based on Bioinformatics and Animal Experiments / 中国实验方剂学杂志

ObjectiveThe bioinformatics method was used to screen ferroptosis differential genes （FRGs） closely related to ulcerative colitis （UC）， and animal experiments were conducted to verify whether the mechanism of Xiezhuo Jiedu recipe in treating UC is related to the regulation of ferroptosis. MethodThe differentially expressed genes （DEGs） of colonic mucosa tissue of UC patients were obtained from the GEO database， and the intersection of the genes with ferroptosis genes was used to obtain FRGs. The core FRGs were obtained by cluster analysis， minimum absolute contraction and selection operator （LASSO） regression， and receiver operating characteristic curve （ROC） curve analysis. In animal experiments， the UC mouse model was prepared by making the mouse freely drink 2.5% dextran sodium sulfate （DSS）. Xiezhuo Jiedu recipe and mesalazine were given by gavage for seven days， and the inflammatory infiltration of colonic mucosa was observed by hematoxylin-eosin （HE） staining. Real-time fluorescence quantitative polymerase chain reaction （Real-time PCR） was used to detect the mRNA expression levels of E3 ubiquitin ligase （FBXW7）， zinc finger protein （ZFP36）， solute carrier family 7 member 11 （SLC7A11）， and Toll-like receptor 4 （TLR4） in colon tissue. The protein expression levels of FBXW7， ZFP36， SLC7A11， and TLR4 in colon tissue were detected by Western blot. ResultDataset GSE87466 was screened from the GEO database， and its intersections with the ferroptosis gene were analyzed to obtain 21 FRGs. After cluster analysis， LASSO regression， and ROC analysis， core FRGs （FBXW7， ZFP36， SLC7A11， and TLR4） were obtained. Immunoinfiltration analysis showed significant differences in the expression of initial B cells， M1 macrophages， plasma cells， and M2 macrophages in the colonic mucosa tissue of UC mice， and there was a significant correlation between core FRGs and these immune cells. Further animal experiments showed that the colonic mucosa tissue of mice in the model group was disorganized and infiltrated by a large number of inflammatory cells. The inflammation of the colonic mucosa tissue of mice in each group was relieved to varying degrees after treatment with Xiezhuo Jiedu recipe and mesalazine， while the colonic mucosa tissue of mice in the high-dose group of Xiezhuo Jiedu recipe showed almost no inflammatory changes. Compared with the normal group， the protein and mRNA expressions of FBXW7， ZFP36， SLC7A11， and TLR4 in the model group were significantly increased， and the expression of core FRGs in colonic mucosa tissue of mice in all groups was significantly down-regulated after treatment with Xiezhuo Jiedu recipe and mesalazine. ConclusionFBXW7， ZFP36， SLC7A11， and TLR4 are ferroptosis genes closely related to the pathogenesis of UC， and Xiezhuo Jiedu recipe can significantly alleviate colonic mucosa inflammation in mice by down-regulating core ferroptosis genes.

Improvement of Colonic Mucosa Inflammatory Response in Mice with Ulcerative Colitis by Xiezhuo Jiedu Recipe Through miRNA-155-5p/JAK2/STAT3 Pathway / 中国实验方剂学杂志

ObjectiveThe differential expression of microRNAs （miRNAs） between the active stage and the remission stage of ulcerative colitis （UC） was analyzed by bioinformatics method， and the regulatory relationship was constructed by screening the differentially expressed genes （DEGs）. The mechanism of Xizhuo Jiedu recipe in the treatment of UC was speculated and verified by animal experiments. MethodThe miRNAs data set of colonic mucosa tissue of UC patients was obtained from the gene expression database （GEO）， and the most differentially expressed miRNAs were screened by GEO2R， Excel， and other tools as research objects. TargetScan， miRTarbase， miRDB， STRING， TRRUST， and Matescape databases were used to screen key DEGs， predict downstream transcription factors （TFs）， gene ontology （GO）， and conduct Kyoto Encyclopedia of Genes and Genomes （KEGG） enrichment analysis. The key signaling pathways were selected for animal experiments. In animal experiments， the UC mouse model was prepared by making the mouse freely drink 2.5% dextran sodium sulfate （DSS）. Xiezhu Jiedu recipe and mesalazine were given by gavage for seven days， and the inflammatory infiltration of colonic mucosa was observed by hematoxylin-eosin （HE） staining. Real-time fluorescence quantitative polymerase chain reaction （Real-time PCR） was used to detect the mRNA expression of miR-155-5p in colon tissue. Immunohistochemistry and Western blot were used to detect the protein expression levels of cytokine signal transduction inhibitor （SOCS1）， phosphorylated transcriptional signal transductor and activator 3 （p-STAT3）， phosphorylated Janus kinase 2 （p-JAK2）， and retinoic acid-associated orphan receptor-γt （ROR-γt）. The expression levels of transforming growth factor-β （TGF-β）， interleukin-17 （IL-17）， interleukin-6 （IL-6）， and interleukin-10 （IL-10） in serum were detected by enzyme linked immunosorbent assay （ELISA）. ResultThe GSE48957 dataset was screened from the GEO database， and miR-155-5p was selected as the research object from the samples in the active and remission stages. 131 DEGs were screened. The GO/KEGG enrichment analysis was closely related to biological processes such as positive regulation of miRNA transcription and protein phosphorylation， as well as signaling pathways such as stem cell signaling pathway， IL-17 signaling pathway， and helper T cell 17 （Th17） cell differentiation. The Matescape database was used to screen out 10 key DEGs， among which SOCS1 was one of the key DEGs of miR-155-5p. Further screening of the TFS of key DEGs revealed that STAT3 was one of the main TFs of SOCS1. The results of animal experiments showed that Xiezhu Jiedu Recipe could effectively down-regulate the mRNA expression of miR-155-5p and protein expression of p-STAT3， p-JAK2， and ROR-γt in colon tissue of UC mice and the expression of IL-17 and IL-6 in serum of UC mice， up-regulate the protein expression of SOCS1 and the expression of TGF-β and IL-10， increase the level of anti-inflammatory factors， and reduce inflammatory cell infiltration. ConclusionIt is speculated that Xizhuo Jiedu recipe may interfere with SOCS1 by regulating the expression of miR-155-5p in UC mice， inhibit the phosphorylation of STAT3， inhibit the differentiation of CD4+ T cells into Th17 cells， reduce the levels of pro-inflammatory factors （IL-17 and IL-6）， and increase the levels of anti-inflammatory factors （TGF-β and IL-10）. As a result， the inflammation of colon mucosa in UC mice was alleviated.

Bioinformatics analysis based on pelvic organ prolapse related aging genes of GEO Database and LASSO regression algorithm / 吉林大学学报(医学版)

Objective:To screen the aging genes closely associated with pelvic organ prolapse(POP)by bioinformatics techniques,and to clarify the potential clinical significance and value of key genes.Methods:Gene Expression Omnibus(GEO)Database was used to download the datasets GSE53868 and GSE151188 for POP-related genes with the keyword"pelvic organ prolapse".The aging-related genes were obtained from Aging Atlas,CellAge,and the Human Ageing Genomic Resources(HAGR)Databases;the intersection of genes related with POP in two groups provided a list of differentially expressed genes(DEGs)associated with aging in POP;gene Set Enrichment Analysis(GSEA)was conducted with R software version 4.2.1;Gene Ontology(GO)functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)signaling pathway enrichment analysis of DEGs were conducted by the Database for Annotation,Visualization and Integrated Discovery(DAVID);the protein-protein interaction(PPI)network was constructed with Cytoscape 3.9.1 software;the top 10 Hub genes were selected by cytoHubba plugin;the infiltration of 22 types of immune cells in the patients in POP group and control group was analyzed by CIBERSORT deconvolution method using R software;the key genes were further screened by LASSO regression algorithm;the correlation and diagnostic efficacy between key genes and immune cell infiltration were analyzed.Results:From the Aging Atlas,CellAge,and HAGR Databases,724 aging-related genes were identified.Intersection with the POP expression profile yielded an aging gene expression matrix related to POP containing 624 genes,and 29 POP-related DEGs were identified after differential analysis,including 2 upregulated genes and 27 downregulated genes.The GSEA results showed that the upregulated pathways were mainly related to diabetes and cellular senescence,whereas the downregulated pathways included Alzheimer's disease and hypoxia-inducible factor-1(HIF-1)signaling pathways.The GO functional enrichment analysis mainly enriched in the biological processes such as the response of the cells to lipopolysaccharide,inflammatory response,and negative regulation of cell proliferation.The KEGG signaling pathway enrichment analysis mainly enriched in interleukin-17(IL-17),tumor necrosis factor(TNF),and nuclear factor-kappa B(NF-κB)signaling pathways.The PPI network analysis got 10 Hub genes including interleukin-6(IL-6),interleukin-1B(IL-1B),prostaglandin-endoperoxide synthase 2(PTGS2),and NF-kappa-B inhibitor alpha(NFKBIA).The CIBERSORT deconvolution method results showed a relatively higher infiltration proportion of neutrophils and activated mast cells in the patients in POP group,the activated mast cells had a positive correlation with most of the DEGs(r>0.5)and the macrophages had a significant positive correlation with IL-1B(r>0.6).The key genes Jun D proto-oncogene(JUND),Snail homolog 1(SNAI1),amphiregulin(AREG),Lamin A/C(LMNA),and superoxide dismutase 2(SOD2)selected by LASSO regression analysis had high diagnostic efficacies,and the area under receiver operating characteristic curve(ROC)(AUC)were all greater than 0.75.Conclusion:During the aging process,the genes such as JUND,SNAI1,AREG,LMNA,and SOD2 may participate in the pathophysiology of POP through various pathways,including inflammation-related pathways,transcription regulation,and affecting collagen secretion and metabolism,thereby influence the connective tissue support function and promote the occurrence and development of POP.

Bioinformatics analysis on molecular subtypes and clinical characteristics of head and neck squamous cell carcinoma based on genes associated with lactate metabolism / 吉林大学学报(医学版)

Objective:To select the differential prognostic lactic acid metabolism-related genes(LRGs)of the head and neck squamous cell carcinoma(HNSCC)to construct the LRGs prognostic model of HNSCC,and to clarify the potential mechanism.Methods:The HNSCC gene expression and clinical data were obtained from The Cancer Genome Atlas(TCGA)and Gene Expression Omnibus(GEO)Databases,the LRGs were identified through GeneCards Database,and R software was used to screen out the LRGs of HNSCC;univariate Cox regression analysis was used to identify prognosis-related genes;two different subtypes were identified based on the prognostis-related LRGs;Kaplan-Meier(K-M)curve analysis was used to compare the prognosis of the patients between two groups;CIBERSORT algorithm was used to perform the immuno-correlation analysis between two groups;multivariate Cox regression analysis and LASSO regression analysis were used to construct the prognostic model;receiver operating characteristic curve(ROC)and K-M survival curve were used to assess the relationship between LRGs and survival and prognosis of the HNSCC patients.The prognostic model was validated by GSE27020,GSE41613,and GSE65858 datasets.The experiment were grouped based on risk score,and immune-related analysis and tumor score analysis were performed.Results:The TCGA Database differential analysis results showed that 1 196 LRGs were identified from HNSCC samples;univariate Cox regression analysis selected 27 differentially expressed genes(DEGs)associated with the prognosis of the HNSCC patients.Two different LRGs subtypes(Group 1 and Group 2)were identified according to the prognosis-related genes.The K-M survival curves results showed that the overall survival(OS)of the patients in Group 2 was significantly higher than that in Group 1,and the immune cell expression amount of the patients in Group 2 was also higher than that in group 1.The multivariate Cox regression and LASSO regression analysis results screened out 9 LRGs,including hypoxanthine phosphoribosyltransferase 1(HPRT1),amyloid precursor protein(APP),glycogen phosphorylase L(PYGL),urokinase-type plasminogen activator(PLAU),cannabinoid receptor 2(CNR2),stanniocalcin 2(STC2),nucleotide binding oligomerization domain-like receptor protein 1(NLRP1),integrin-linked kinase(ILK),and forkhead box B1(FOXB1);the prognostic model was constructed.The K-M and ROC curve results indicated that the expression levels of above 9 genes were associated with the survival and prognosis of the HNSCC patients,providing good 1-year,2-year,and 3-year survival prediction effect,and the area under ROC curve(AUC)values were all greater than 0.650.Furthermore,the predictive ability of the prognosis model was validated in GSE27020,GSE41613,and GSE65858 datasets.The patients classified based on the risk scores had distinguishable immune statuses.Conclusion:The differentially expressed LRGs of HNSCC screened by bioinformatics methods are related to the survival and prognosis of the HNSCC patients;the prognostic model constructed by 9 LRGs can predict the survival status and treatment response of the HNSCC patients.

Discussion on the relationship between irritable bowel syndrome and premature ejaculation from 5-HT and prediction of natural drugs / 国际中医中药杂志

Objective:To explore the relationship between irritable bowel syndrome (IBS) and premature ejaculation (PE) from 5-HT; To predict the natural drugs with therapeutic effect.Methods:Targets related to IBS and PE were screened in the GeneCards, DisGeNET, TTD, OMIM, DrugBank databases. After removing duplicates, the two disease targets were intersected and imported into STRING platform, and the protein interaction network between IBS and PE targets related to 5-HT receptor was obtained. GO enrichment analysis was carried out on the intersected targets by R language, and Coremine Medical platform was used for predicting natural drugs.Results:5-HT1A, 5-HT1B, 5-HT2A, 5-HT2C and 5-HT3A were the common targets related to 5-HT in IBS and PE. GO function enrichment yielded 250 gene function related information, mainly enriched in serotonin receptor signaling pathways, cell response to dopamine, and response to dopamine. The prediction of natural drugs obtained 14 kinds of Chinese materia medica, including Nelumbinis Semen, Nelumbinis Rhizomatis Nodus, Nelumbinis Receptaculum, Nelumbinis Stamen, Nelumbinis Folium, Nelumbinis Plumula, Ginkgo Semen, and Ginkgo Folium.Conclusions:Abnormal 5-HT levels can affect gastrointestinal motility, ejaculation latency, and glans sensitivity. Elevated central 5-HT levels are a common pathogenesis of IBS and PE. The interaction between receptors such as 5-HT1A and 5-HT3A and 5-HT can regulate gastrointestinal motility and secretion activities, intestinal nervous system, and reduce intestinal hypersensitivity; increasing the sensitivity of the 5-HT1A receptor can reduce the ejaculation threshold and promote ejaculation, while increasing the sensitivity of the 5-HT2C receptor can increase the ejaculation threshold.

Discussion on the mechanism of Ganwei Baihe Decoction in treating gastric ulcer based on bioinformatics and experimental validation / 国际中医中药杂志

Objective:To study the potential mechanism of Ganwei Baihe Decoction in the treatment of gastric ulcer (GU) based on bioinformatics and validate it through animal experiments.Methods:TCMSP, DisGeNET, and GeneCards databases were used to retrieved active components and action targets of Ganwei Baihe Decoction. After obtaining the intersection, protein interaction data of the intersection genes were obtained through the STRING database. A PPI network was constructed by Cytoscape 3.10.0 software and the key genes and key components were obtained. DAVID online analysis database was used for GO functional enrichment and KEGG pathway enrichment analysis of key targets. Animal experiments were used for verification. Totally 36 SD rats were divided into blank group, model group, Omeprazole group and Ganwei Baihe Decoction group according to the random number table method, with 9 rats in each group. After 7 days of gavage of the corresponding drugs to each group of rats, they fasted and but with water for 24 hours, and then re-gavaged once. After 1 hour of administration, a gastric ulcer rat model was prepared by gavage of 80 mg/kg of indomethacin. After 3 hours of administration, anesthesia was used to extract the sample. The expression level of Caspase-3 protein in the gastric tissue of rats was to be determined by Western blot method.Results:There were 234 effective active components with 290 targets in Ganwei Baihe Decoction, and 6 496 therapeutic targets for GU. 213 potential targets for GU were screened out. There were 437 GO function and 153 KEGG pathway enriched entries. Compared with the model group, the protein expression of Caspase-3 in the Ganwei Baihe Decoction group and Omeprazole group decreased ( P<0.05). Conclusion:The mechanism of Ganwei Baihe Decoction in treating GU may be through key components such as quercetin and β-sitosterol acting on key targets such as AKT1 and CASP3, regulating the Apoptosis pathway, PI3K-Akt signaling pathway, MAPK signaling pathway, etc. to exert inhibitory effects on apoptosis.

Identification of Atrial Fibrillation-related Inflammatory Genes and Their Association with Immune Cell Infiltration Based on Comprehensive Bioinformatic Analysis / 昆明医科大学学报

Objective To identify inflammation-related genes in atrial fibrillation(AF)and explore the possible role and mechanism of these genes and infiltrating immune cells in the development of AF.Methods A series of bioinformatics analysis combined with machine learning algorithms to identify biomarkers of AF,the receiver operating characteristic(ROC)curves were used to verify the prediction and diagnostic value of key genes,and Spearman correlation analysis was used to clarify the correlation between key genes and infiltrating immune cells.Results 593 differential genes(| log2(fold change,FC)|>1,P<0.05),7 immune cell subtypes(P<0.05)were selected,190 immune-related differential genes were obtained,3 biomarkers(IGF1,PTGS 2 and PPARG),and the correlation analysis showed that 3 markers were significantly associated with infiltrating immune cells(P<0.05).Conclusion IGF1,PTGS2 and PPARG are inflammation-related genes of AF,which are speculated to be closely related to the process and pathway of immune cell infiltration.