Gene Ontology Biological Process Enrichment Research Articles

VCAM-1 Promotes Angiogenesis of Bone Marrow Mesenchymal Stem Cells Derived from Patients with Trauma-Induced Osteonecrosis of the Femoral Head by Regulating the Apelin/CCN2 Pathway.

Trauma-induced osteonecrosis of the femoral head (TI-ONFH) is a pathological process in which the destruction of blood vessels supplying blood to the femoral head causes the death of bone tissue cells. Vascular cell adhesion molecule 1 (VCAM-1) has been shown to have potent proangiogenic activity, but the role in angiogenesis of TI-ONFH is unclear. In this work, we discovered that VCAM-1 was significantly downregulated in the bone marrow mesenchymal stem cells (BMSCs) derived from patients with TI-ONFH. Subsequently, we constructed BMSCs overexpressing VCAM-1 using a lentiviral vector. VCAM-1 enhances the migration and angiogenesis of BMSCs. We further performed mRNA transcriptome sequencing to explore the mechanisms by which VCAM-1 promotes angiogenesis. Gene ontology biological process enrichment analysis demonstrated that upregulated differentially expressed genes (DEGs) were related to blood vessel development. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed that upregulated DEGs were engaged in the Apelin signaling pathway. Apelin-13 is the endogenous ligand of the APJ receptor and activates this G protein-coupled receptor. Treatment with Apelin-13 activated the Apelin signaling pathway and suppressed the expression of cellular communication network factor 2 in BMSCs. Furthermore, Apelin-13 also inhibits the migration and angiogenesis of VCAM-1-BMSCs. In summary, VCAM-1 plays an important role in vascular microcirculation disorders of TI-ONFH, which provides a new direction for the molecular mechanism and treatment of TI-ONFH.

P904 Genetic Variants in IBD Chilean Patients are related to clinical outcomes

Abstract Background IBD has emerged as a worldwide disease with an increased incidence in newly industrialized countries such as Chile. This population has been underrepresented in genome-wide association studies (GWAS) because IBD genetics studies have focused mainly on North America and European populations. In addition, specific IBD risk alleles have been related to different races and ethnicities. Aim: To investigate the association of IBD risk variants reported in previous GWAS studies with clinical outcomes in our Chilean patients. Methods 192 Chilean individuals with IBD (145 UC and 47 CD) were genotyped using Illumina GSA Arrays. From IBD GWAS (Jostin et al. and Liu et al.), we selected gene variants with pGWAS value < 5x10-8 and looked for them in our Chilean IBD group. Then, we built a Chilean dataset (clinical-genotype information). Using this dataset, we performed a Spearman correlation matrix to correlate clinical outcomes with IBD variants. Further, we built regression models to predict the clinical outcomes using the variants obtained from the correlation matrix (p <0.05). Then, we selected the best models using significance testing (P values) or likelihood-based information criterion, such as the Akaike Information Criterion (AIC) and plotted the models using a Receiver Operating Characteristic Curve (ROC). Finally, to evaluate the association among variants in each model, we perform a Gene Ontology biological process enrichment analysis using PANTHER (Fisher, FDR). Results As shown in Figure 1 and Table 1, the best predictive regression models (more than 80%) for the clinical outcomes were surgery, Clinical/Endoscopy remission for more than five years, and Naïve anti-TNF. Association with genetic variants was observed significantly (p<0.05) in the enrichment analysis for the model Clinical/endoscopy remission (Table 2). Conclusion Conclusion. Candidates’ genes related to clinical outcomes in our Chilean IBD cohort were related to epithelial, innate, and adaptative immune responses and host-microbial interactions. Future research is needed to validate these findings.

Downregulation of ACAN is Associated with the Growth hormone pathway and Induces short stature.

ACAN heterozygous mutations can cause short stature in patients with or without advanced bone age and have recently attracted researchers' attention. Growth hormone can be used to treat short stature induced by ACAN mutations; however, few studies have focused on the underlying mechanism of this treatment. Four patients with new mutations were reported based on clinical data and genetic tests. We investigated the expression and Gene Ontology biological process enrichment of ACAN and GH pathways based on GTEx databases through bioinformatics analyses. The effect of ACAN on the growth hormone response evaluated in ATDC5 cells with a growth hormone stimulation test. Four mutations were reported in this study: c.619C > A, c.1967A > G, c.1888G > A, and c.1308_1309del. All patients' heights were under -2.5 SD, with one had advanced bone age, and two had GH deficiency. Two individuals received growth hormone therapy acquired variable levels of height SD score improvement. ACAN and the GH pathway were strongly associated; ACAN does not affect GHR but regulates the response to GH. Downregulating ACAN inhibited ATDC5 cell proliferation induced by GH. ACAN is associated with the GH pathway, revealing the potential mechanism underlying GH-targeted treatment for ACAN mutation-induced short stature. GH-promoting therapies may increase patients' heights.

Exploring the Mechanism of the Baishao Luoshi Formula against Poststroke Spasticity by Network Pharmacology and Experimental Validation.

Post-stroke spasticity (PSS) is a major cause of disability, leading to severely impaired upper-limb flexibility and ability to walk and move, significantly affecting the quality of life of cerebral infarction patients. There is currently no recognized effective therapy. Alternatively, Chinese traditional medicine has shown promise for PSS treatment. In this regard, the BSLSF has been reported to be effective; however, its underlying mechanism remains unclear. The objective of this study is to clarify the main targets and pathways of Baishao Luoshi Formula (BSLSF) during PSS treatment, laying the foundation for further research on its pharmacological effects. In this study, network pharmacology and experimental verification were conducted to explore the potential mechanism of BSLSF systematically. After obtaining active ingredients of BSLSF from the TCMSP database, SwissTarget-Prediction and PharMapper were used to uncover BSLSF targets. PSS-related targets were gathered with GeneCards and Online Mendelian Inheritance in Man. The differentially expressed genes between BSLSF and PSS were identified by a Venn plot. The drugactive ingredient-target interaction network and Protein-protein interaction (PPI) were constructed using Cytoscape and further analyzed using the MCC algorithm of CytoHubba plugin. Then, Pathway enrichment and GO biological process enrichment analyses were performed. Subsequently, a mice model of middle cerebral artery occlusion (MCAO) was established for the in vivo experiments. We found that AKT1, TNF, CASP3, VEGFA, and CREB1 were potential targets during PSS treatment. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses showed that the mechanism of PSS was closely related to synaptic plasticity. And the immunohistochemical staining showed that BSLSF protected against ischemic stroke via the CCR5/CREB signaling pathway and probably affected synaptic plasticity. our study validated that treatment with BSLSF protected against ischemic stroke via the CCR5/CREB signaling pathway and could affect synaptic plasticity. In a sense, this study provides the basis for further extensive and in-depth analysis of BSLSF, enabling the quest for new drug targets at the same time.

Analysis of primary synchronous breast invasive ductal carcinoma and lung adenocarcinoma with next-generation sequencing: A case report.

Multiple primary cancers (MPCs) have an increasing incidence rate due to the detection of early stages of cancer and the development of effective therapeutic strategies. MPCs are less common compared with metachronous cancers. Therefore, distinguishing synchronous primary tumors from metastasis and developing an individualized treatment strategy can be challenging. In the present study, the case of a 70-year-old female who was referred to The First Hospital of Jilin University (Changchun, China) with an enlarged left cervical lymph node and no other clinical manifestations is reported. Radiography revealed distinct lesions in the left breast, left cervical lymph node and bilateral lungs. Subsequently, a biopsy was performed in all three lesions and then each specimen was subjected to immunohistochemistry, fluorescence in situ hybridization, amplification refractory mutation system-PCR and next-generation sequencing (NGS). Disease-related enrichment of lymph node mutant genes and Gene Ontology Biological Process enrichment of breast, as well as lung, mutant genes were performed using the Database for Annotation, Visualization and Integrated Discovery. Based on the molecular assessment, the patient was finally diagnosed with breast invasive ductal carcinoma, primary lung adenocarcinoma and cervical lymph node metastatic lung adenocarcinoma. Since primary synchronous breast and lung cancer (SBLC) is rare, a molecular assessment, particularly using NGS, could provide important information for both the diagnosis and treatment of SBLC.

Prediction of the Mechanism of Shaoyao Gancao Decoction in the Treatment of Alopecia Areata by Network Pharmacology and Its Preliminary Verification Study.

Objective To explore the mechanism of Shaoyao Gancao decoction (SGD) in treatment of alopecia areata (AA) by network pharmacology and animal experiments. Methods Based on the traditional Chinese medicine systems pharmacology database and analysis platform (TCMSP), the components and targets of SGD were determined. Then, the related targets of AA were retrieved from DrugBank, GeneCards, OMIM, and DisGeNET databases. The intersection of drug targets and disease targets was determined, and the key targets of the protein-protein interaction network were obtained with the String database. Gene Ontology (GO) biological process enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of potential key targets were carried out using the DAVID database using AutoDock for molecular docking verification. Finally, the key pathway was validated by animal experiments. Results A total of 102 active components, 212 predicted targets, and 812 AA disease-related targets were obtained. Topological analysis yielded 45 key targets of SGD in the treatment of AA, including IL-6, PTGS2, TNF, VEGFA, CCL2, IL-1B, CXCL8, CASP3, MPO, and IL-10. There were 324 GO entries obtained through GO biological process enrichment analysis, and 20 pathways were obtained through KEGG pathway enrichment analysis, involving the PI3K-Akt signaling pathway, osteoclast differentiation, and Jak-STAT signaling pathway. The molecular docking results showed effective ingredients (quercetin, kaempferol, and 7-methoxy-2-methyl isoflavone) have good docking results with targets (IL-6, PTGS2, and TNF). The results of animal experiments showed that SGD can effectively upregulate the expression of PI3K and AKT proteins. Conclusion This is the first in-depth study on the mechanism of SGD's treatment effect in AA using network pharmacology, and preliminary animal experiments verified that it is closely related to the PI3K/AKT signaling pathway. This finding may provide a new basis for SGD's clinical application in AA.

The Changes of Amygdala Transcriptome in Autism Rat Model After Arginine Vasopressin Treatment

BackgroundSome studies have shown that arginine vasopressin (AVP) can significantly improve the social interaction disorder of autism, but the mechanism remains unclear.MethodsFemale Wistar rats were intraperitoneally injected with VPA or normal saline at embryonic day 12.5 to establish an autism model or normal control in their offspring. Male offspring prenatally exposed to VPA were randomly assigned to two groups: the VPA-induced autism model group and the AVP group. The rats in the AVP group were treated with intranasal AVP at postnatal day (PND) 21 and for 3 weeks. The VPA-induced autism model group was given the same dose of normal saline in the same way. Behavioral responses were evaluated in the open field and three-chambered social test apparatus; the expression levels of AVP in serum were detected by enzyme-linked immunosorbent assay kit, and the gene expression levels on the amygdala were measured by RNA-seq at PND42.ResultsIntranasal administration of AVP can significantly improve the social interaction disorder and elevate the levels of AVP in serum. Transcriptome sequencing results showed that 518 differently expressed genes (DEGs) were identified in the VPA-induced autism model group compared with the control in this study. Gene Ontology biological process enrichment analysis of DEGs showed that the VPA-induced autism model group had significant nervous system developmental impairments compared with the normal group, particularly in gliogenesis, glial cell differentiation, and oligodendrocyte differentiation. Gene Set Enrichment Analysis (GSEA) enrichment analysis also showed that biological process of oligodendrocyte differentiation, axoneme assembly, and axon ensheathment were inhibited in the VPA-induced autism model group. Pathway enrichment analysis of DEGs between the control and VPA-induced autism model group showed that the PI3K/AKT and Wnt pathways were significantly dysregulated in the VPA-induced autism model group. Few DEGs were found when compared with the transcriptome between the VPA-induced autism model group and the AVP treatment group. GSEA enrichment analysis showed deficits in oligodendrocyte development and function were significantly improved after AVP treatment; the pathways were mainly enriched in the NOTCH, mitogen-activated protein kinase, and focal adhesion signaling pathways, but not in the PI3K/AKT and Wnt pathways. The expression patterns analysis also showed the same results.ConclusionAVP can significantly improve the social interaction disorder of VPA-induced autism model, and AVP may target behavioral symptoms in autism by modulating the vasopressin pathways, rather than primary disease mechanisms.

Network Pharmacology Integrated with Molecular Docking Explores the Mechanisms of Naringin against Osteoporotic Fracture by Regulating Oxidative Stress.

Naringin (NG), as the most abundant component of Drynariae Rhizoma (Chinese name: Gusuibu), has been proved to be an antioxidant flavonoid on promoting osteoporotic fracture (OF) healing, but relevant research is scanty on the underlying mechanisms. We adopted target prediction, protein-protein interaction (PPI) analysis, Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and molecular docking to establish a system pharmacology database of NG against OF. Totally 105 targets of naringin were obtained, including 26 common targets with OF. A total of 415 entries were obtained through GO Biological Process enrichment analysis (P < 0.05), and 37 entries were obtained through KEGG pathway enrichment analysis with seven signaling pathways included (P < 0.05), which were primarily concerned with p53, IL-17, TNF, estrogen, and PPAR signaling pathways. According to the results of molecular docking, naringin is all bound in the active pockets of the core targets with 3–9 hydrogen bonds through some connections such as hydrophobic interactions, Pi-Pi stacked interactions, and salt bridge, demonstrating that naringin binds tightly to the core targets. In general, naringin may treat OF through multiple targets and multiple pathways via regulating oxidative stress, etc. Notably, it is first reported that NG may regulate osteoclast differentiation and oxidative stress through the expression of the core targets so as to treat OF.

1046P - Identification of a RNA-Seq based signature to improve prognostic for uterine sarcoma

BackgroundUterine sarcoma (US) is a highly malignant cancer with poor prognosis and high mortality. This study focused on identification of RNA-Seqexpressionsignature for prognosis prediction of Uterine Sarcoma. MethodsWe obtained RNA-Seqexpression profiles from The Cancer Genome Atlas (TCGA) database and differential expressed genes (DEGs) were identified between US tissues and normal tissues. Univariate Cox proportional hazards regression analysis was performed to identify Prognosis associated DEGscorrelated with survival of US patients.The RNA-Seqbased prognostic signature was identified by least absolute shrinkage and selection operator (LASSO) Cox model. The cohort was randomly divided into training and testing groups. Thebiological pathway and processof putative RNA targets was also analyzed by bioinformatics. ResultsThis study identified a RNA-Seq signature based on 11 genes, AP000320.1, HNRNPA1P33, RPL21P10, AC067773.1, AC011933.3, STX19, AC091133.4, HIST1H3A, AC004988.1, AL356585.1 and HNRNPA3P1. In the training group, the median OS in the high-risk and low-risk groups were 13.7 vs 88.1 months (HR, 0.204, 95% CI, 0.08589 - 0.4846; P<0.0001), respectively. In the testing group, the median OS in the high-risk and low-risk groups were 11.9 vs 67.2 months (HR, 0.04315, 95% CI, 0.004845 - 0.3842; P<0.0001) respectively. Genes in the model were put into gene ontology biological process enrichment and Kyoto Encyclopedia of Genes and Genomes signaling pathways analysis, which suggested that these genes might contribute to cancer-associated processes such as the nuclear nucleosome and DNA packaging complex. ConclusionsThis 11-genebased prognostic signature may improve prognosis prediction of US. Legal entity responsible for the studyThe authors. FundingHas not received any funding. DisclosureAll authors have declared no conflicts of interest.Linguistic correction

Prediction of Recurrence in Cervical Cancer Using a Nine-lncRNA Signature.

Background and ObjectiveAs a common cancer type in women, cervical cancer remains one of the leading causes of cancer-associated mortalities word wide. Recent evidence has demonstrated the regulatory role of a large number of long non-coding RNAs (lncRNAs) in cervical cancer. Here, we aimed to identify new biomarkers that related with the recurrence through comprehensive bioinformatics analysis.MethodsFirstly, we collected online lncRNA expression data of cervical cancer patients which were divided into training, validation, and test set. Then we developed a nine-lncRNA signature from training set by conducting LASSO Cox regression model along with 10-fold cross validation. The prognostic value of this risk score was validated in all the three sets using Kaplan–Meier analysis, C-index, time-dependent ROC curves and dynamic AUC. Biological function of these lncRNAs in cervical cancer cells were evaluated by performing gene ontology biological process enrichment and Kyoto Encyclopedia of Genes and Genomes signaling pathways analysis.ResultsAccording to the results, a higher predict accuracy was observed in the nine-lncRNA signature than that of FIGO stage in all the three sets. Stratified analysis also demonstrated that the nine-lncRNA signature can predict the recurrence of cervical cancer within FIGO stage. The potential mechanisms underlying the nine-lncRNAs from the signature were also identified according to the gene enrichment analysis.ConclusionIn the present article, we provided a reliable prognostic tool to facilitate the individual management of patients with cervical cancer after treatment.

Identification of a 26-lncRNAs Risk Model for Predicting Overall Survival of Cervical Squamous Cell Carcinoma Based on Integrated Bioinformatics Analysis.

As a common malignancy in women, cervical squamous cell carcinoma is a major cause of cancer-related mortality globally. Recent studies have demonstrated that long non-coding RNA (lncRNA) can function as potential biomarkers in cancer prognosis; however, little is known about its role in cervical cancer. In this study, we downloaded the gene expression profiles along with the clinical data of patients with cervical squamous cell carcinoma from The Cancer Genome Atlas. By applying bioinformatics analysis including random forest selection and Least Absolute Shrinkage and Selection Operator (LASSO) cox regression model along with 10-fold cross-validation, we constructed a 26-lncRNAs risk model that can be used to predict the overall survival of cervical squamous cell carcinoma. After that, Kaplan-Meier analysis combined with log-rank p test was applied to assess the predictive accuracy of the 26-lncRNAs risk model. Further analysis showed that the prognostic value of 26-lncRNAs risk model was independent of other clinicopathological factors. At last, lncRNAs in the model were put into gene ontology biological process enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathways analysis, which suggested that these lncRNAs might contribute to cancer-associated processes such as cell cycle and apoptosis. This study indicated that lncRNAs signature could be a useful marker to predict the prognosis of cervical squamous cell carcinoma.

Protein-protein interaction network and significant gene analysis of osteoporosis

This study used DNA microarray data to identify differentially expressed genes of osteoporosis and provide useful information for treatments of the disease. We downloaded gene expression data of Osteoporosis GSE35956 from the Gene Expression Omnibus database, which included five normal and five osteoporosis samples. We then identified the differentially expressed genes between normal and disease samples using the R language software, and constructed the protein interaction network. DAVID was used to perform the biological process enrichment and KEGG pathway cluster analyses. We used the Cytoscape plug-in unit, Cluster ONE, to perform cluster module analysis to find hub proteins of the network module and to analyze their Gene Ontology (GO) functions. A total of 294 genes were found to be differentially expressed between normal and disease samples, which were used to construct the differential gene-protein interaction network. GO function analysis revealed that the genes' functions were mainly involved in the intracellular signaling cascade. KEGG pathway analysis suggested that the main metabolic pathways of these genes were those of cancer: the neurotrophin/T cell/Fc epsilon RI/B cell/ ErbB/p53 signaling pathway, the cell cycle pathway, and the chronic myeloid leukemia pathway. Screening analysis of hub proteins revealed that KRT18 had the highest hub degree. In conclusion, we found differentially expressed genes related to osteoporosis. GO biological process enrichment and KEGG pathway enrichment analyses identified significant osteoporosis genes and their molecular functions. Finally, module analysis of hub proteins in interaction networks showed that cell death was one of the main biological processes of osteoporosis genes.