The Screening and Identification of Key Biomarkers in Adrenocortical Carcinoma: Evidence from a Bioinformatics Analysis

<sec> <title>Objective:</title> This study aimed to identify the potential key genes associated with the progression and prognosis of adrenocortical carcinoma (ACC). </sec> <sec> <title>Methods:</title> Differentially expressed genes (DEGs) in ACC cells and normal adrenocortical cells were assessed by microarray from the Gene Expression Omnibus database. The biological functions of the classified DEGs were examined by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analyses and a protein–protein interaction (PPI) network was mapped using Cytoscape software. MCODE software was also used for the module analysis and then 4 algorithms of cytohubba software were used to screen hub genes. The overall survival (OS) examination of the hub genes was then performed by the ualcan online tool. </sec> <sec> <title>Results:</title> Two GSEs (GSE12368, GSE33371) were downloaded from GEO including 18 and 43 cases, respectively. One hundred and sixty-nine DEGs were identified, including 57 upregulated genes and 112 downregulated genes. The Gene Ontology (GO) analyses showed that the upregulated genes were significantly enriched in the mitotic cytokines is, nucleus and ATP binding, while the downregulated genes were involved in the positive regulation of cardiac muscle contraction, extracellular space, and heparin-binding (P < 0.05). The Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) pathway examination showed significant pathways including the cell cycle and the complement and coagulation cascades. The protein– protein interaction (PPI) network consisted of 162 nodes and 847 edges, including mitotic nuclear division, cytoplasmic, protein kinase binding, and cell cycle. All 4 identified hub genes (FOXM1, UBE2C, KIF11, and NDC80) were associated with the prognosis of adrenocortical carcinoma (ACC) by survival analysis. </sec> <sec> <title>Conclusions:</title> The present study offered insights into the molecular mechanism of adrenocortical carcinoma (ACC) that may be beneficial in further analyses. </sec>

LCN2 as a Potential Diagnostic Biomarker for Ulcerative Colitis-Associated Carcinogenesis Related to Disease Duration

BackgroundPatients with long-duration ulcerative colitis (UC) had a higher risk of developing ulcerative colitis-associated carcinogenesis (UCAC) when compared to those with short-duration UC. This study aimed to discover the biomarker for cancer surveillance related to disease duration.MethodsThe microarrays were divided into short-duration (&lt;10 years) UC, long-duration (≥10 years) UC, UCAC, and normal groups in the Gene Expression Omnibus (GEO) datasets. Differentially expressed genes (DEGs) of GEO and the hub genes of the selected weighted gene co-expression network analysis (WGCNA) were intersected to obtain the overlapping genes. Among these genes, the key gene was identified by using the protein–protein interaction (PPI) network, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, the cytoHubba of Cytoscape, and the expression levels. Also, immunofluorescence of human colonic mucosa and animal experiment were used to validate the expression trend of the key gene in the progress of UC developing into UCAC.ResultsLipocalin-2 (LCN2) was more relevant with disease duration of UC and significantly negatively correlated with the risk of UCAC. The expression level of LCN2 in short-duration UC was higher than that of long-duration UC (P &lt; 0.01), long-duration UC was higher than that of UCAC (P = 0.001), and UC and UCAC were all higher than that of the normal (P &lt; 0.001). We then discovered that the expression trend of LCN2 in blood and stool samples was consistent with that in colorectal mucosa.ConclusionThe research indicates that LCN2 could be a novel biomarker to evaluate cancer surveillance related to disease duration of developing UC into UCAC. Compared with that of blood samples, stool detection of LCN2 may have more advantages for diagnosis value of early stage of UCAC as a complement to colonoscopy surveillance.

Network Analysis for the Identification of Hub Genes and Related Molecules as Potential Biomarkers Associated With the Differentiation of Bone Marrow-derived Stem Cells Into Hepatocytes

The incidence of liver diseases has been increasing steadily. However, it has some shortcomings, such as high cost and organ donor scarcity. The application of stem cell research has brought new ideas for the treatment of liver diseases. Therefore, it is particularly important to clarify the molecular and regulatory mechanisms of differentiation of bone marrow-derived stem cells (BMSCs) into liver cells. Herein, we screened differentially expressed genes between hepatocytes and untreated BMSCs to identify the genes responsible for the differentiation of BMSCs into hepatocytes. GSE30419 gene microarray data of BMSCs and GSE72088 gene microarray data of primary hepatocytes were obtained from the Gene Expression Omnibus database. Transcriptome Analysis Console software showed that 1896 genes were upregulated and 2506 were downregulated in hepatocytes as compared with BMSCs. Hub genes were analyzed using the STRING, revealing that two hub genes, Cat and Cyp2e1, play a pivotal role in oxidation-reduction process. The results indicate that the lncRNA-miRNA-mRNA interaction chain may play an important role in the differentiation of BMSCs into hepatocytes, which provides a new therapeutic target for liver disease treatment.

The Immunological Role of CDK4/6 and Potential Mechanism Exploration in Ovarian Cancer

BackgroundOvarian cancer (OC) is one of the most lethal gynecologic cancers. Growing evidence has proven that CDK4/6 plays a key role in tumor immunity and the prognosis of many cancers. However, the expression and function of CDK4/6 in OC remain unclear. Therefore, we aimed to explore the influence of CDK4/6 in OC, especially on immunity.MethodsWe analyzed CDK4/6 expression and prognosis using The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO) and Genotype Tissue Expression (GTEx) data. Subsequently, we used the cytoHubba plug-in of Cytoscape software and starBase to identify the noncoding RNAs (ncRNAs) regulating CDK4/6. Finally, we verified the effect of CDK4/6 on immunity in OC cell lines and animal models.ResultsCDK4/6 expression was higher in OC tissues than in normal ovarian tissues, and the high expression levels of CDK4/6 contributed to the immunosuppressive state of OC and were thus related to the poor prognosis of OC patients. This was also in general agreement with the results of OC cell line and animal experiments. Mechanistically, the CDK4/6 inhibitor palbociclib increased the secretion of interferon (IFN)-γ and the interferon-stimulated gene (ISG) response, thereby upregulating the expression of antigen-presenting molecules; this effect was partly dependent on the STING pathway and thus activated immunity in OC. Additionally, according to public data, the LRRC75A-AS1-hsa-miR-330-5p axis could inhibit the immune response of OC patients by upregulating CDK4/6, leading to a poor prognosis.ConclusionCDK4/6 affects the immune microenvironment of OC and correlates with the prognosis of OC patients.

MicroRNA-92a-3p Enhances Cisplatin Resistance by Regulating Krüppel-Like Factor 4-Mediated Cell Apoptosis and Epithelial-to-Mesenchymal Transition in Cervical Cancer

Recent studies have confirmed the existence and key roles of microRNA (miRNAs) in cancer drug resistance, including cervical cancer (CC). The present study aims to establish a novel role for miR-92a-3p and its associated gene networks in cisplatin (DDP) resistance of CC. First, the disparities in miRNA expression between CC tissues and adjacent normal tissues were screened based on GSE19611 microarray data that retrieved from Gene Expression Omnibus (GEO), and we identified several miRs that were significantly downregulated or upregulated in CC tissues including miR-92a-3p. Moreover, miR-92a-3p was significantly up-regulated in DDP-resistant cells and was the most differently expressed miRNA. Functionally, knockdown of miR-92a-3p increased the sensitivity of DDP-resistant cells to DDP via inhibiting cell proliferation, migration and invasion, and promoting apoptosis. Conversely, overexpression of miR-92a-3p significantly induced DDP resistance in CC parental cells including HeLa and SiHa cells. Moreover, Krüppel-like factor 4 (KLF4) was identified as a direct target of miR-92a-3p, and an obvious inverse correlation was observed between the expression of miR-92a-3p and KLF4 in 40 pairs of cancer tissues. Furthermore, KLF4 knockdown reversed the promoting effect of miR-92a-3p inhibition on DDP sensitivity in DDP-resistant CC cells. Besides, high expression of miR-92a-3p was associated with DDP resistance, as well as a short overall survival in clinic. Taken together, these findings provide important evidence that miR-92a-3p targets KLF4 and is significant in DDP resistance in CC, indicating that miR-92a-3p may be an attractive target to increase DDP sensitivity in clinical CC treatment.

The Downregulation of PTGS2 Mediated by ncRNAs is Tightly Correlated with Systemic Sclerosis-Interstitial Lung Disease

Background: Interstitial lung disease in systemic sclerosis (SSc-ILD) is one of the most severe complications of systemic sclerosis (SSc) and is the main cause of mortality. In this study, we aimed to explore the key genes in SSc-ILD and analyze the relationship between key genes and immune cell infiltration as well as the key genes relevant to the hallmarks of cancer.Methods: Weighted gene co-expression network analysis (WGCNA) algorithm was implemented to explore hub genes in SSc-ILD samples from the Gene Expression Omnibus (GEO) database. Logistic regression analysis was performed to screen and verify the key gene related to SSc-ILD. CIBERSORT algorithms were utilized to analyze immune cell infiltration. Moreover, the correlation between the key genes and genes relevant to cancer was also evaluated. Furthermore, non-coding RNAs (ncRNAs) linking to PTGS2 were also explored.Results: In this study, we first performed WGCNA analysis for three GEO databases to find the potential hub genes in SSc-ILD. Subsequently, we determined PTGS2 was the key gene in SSC-ILD. Furthermore, in CIBERSORT analyses, PTGS2 were tightly correlated with immune cells such as regulatory T cells (Tregs) and was negatively correlated with CD20 expression. Moreover, PTGS2 was associated with tumor growth. Then, MALAT1, NEAT1, NORAD, XIST identified might be the most potential upstream lncRNAs, and LIMS1 and RANBP2 might be the two most potential upstream circRNAs.Conclusion: Collectively, our findings elucidated that ncRNAs-mediated downregulation of PTGS2, as a key gene in SSc-ILD, was positively related to the occurrence of SSc-ILD and abnormal immunocyte infiltration. It could be a promising factor for SSc-ILD progression to malignancy.

Gene Differential Expression and Interaction Networks Illustrate the Biomarkers and Molecular Mechanisms of Atherosclerotic Cerebral Infarction

Atherosclerotic cerebral infarction (ACI) seriously threatens the health of the senile patients, and the strategies are urgent for the diagnosis and treatment of ACI. This study investigated the mRNA profiling of the patients with ischemic stroke and atherosclerosis via excavating the datasets in the GEO database and attempted to reveal the biomarkers and molecular mechanism of ACI. In this study, GES16561 and GES100927 were obtained from Gene Expression Omnibus (GEO) database, and the related differentially expressed genes (DEGs) were analyzed with R language. Furthermore, the DEGs were analyzed with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Besides, the protein-protein interaction (PPI) network of DEGs was analyzed by STRING database and Cytoscape. The results showed that 133 downregulated DEGs and 234 upregulated DEGs were found in GES16561, 25 downregulated DEGs and 104 upregulated DEGs were found in GSE100927, and 6 common genes were found in GES16561 and GES100927. GO enrichment analysis showed that the functional models of the common genes were involved in neutrophil activation, neutrophil degranulation, neutrophil activation, and immune response. KEGG enrichment analysis showed that the DEGs in both GSE100927 and GSE16561 were connected with the pathways including Cell adhesion molecules (CAMs), Cytokine-cytokine receptor interaction, Phagosome, Antigen processing and presentation, and Staphylococcus aureus infection. The PPI network analysis showed that 9 common DEGs were found in GSE100927 and GSE16561, and a cluster with 6 nodes and 12 edges was also identified by PPI network analysis. In conclusion, this study suggested that FCGR3A and MAPK pathways were connected with ACI.

Identification of Molecular Biomarkers and Key Pathways for Esophageal Carcinoma (EsC): A Bioinformatics Approach

Esophageal carcinoma (EsC) is a member of the cancer group that occurs in the esophagus; globally, it is known as one of the fatal malignancies. In this study, we used gene expression analysis to identify molecular biomarkers to propose therapeutic targets for the development of novel drugs. We consider EsC associated four different microarray datasets from the gene expression omnibus database. Statistical analysis is performed using R language and identified a total of 1083 differentially expressed genes (DEGs) in which 380 are overexpressed and 703 are underexpressed. The functional study is performed with the identified DEGs to screen significant Gene Ontology (GO) terms and associated pathways using the Database for Annotation, Visualization, and Integrated Discovery repository (DAVID). The analysis revealed that the overexpressed DEGs are principally connected with the protein export, axon guidance pathway, and the downexpressed DEGs are principally connected with the L13a-mediated translational silencing of ceruloplasmin expression, formation of a pool of free 40S subunits pathway. The STRING database used to collect protein-protein interaction (PPI) network information and visualize it with the Cytoscape software. We found 10 hub genes from the PPI network considering three methods in which the interleukin 6 (IL6) gene is the top in all methods. From the PPI, we found that identified clusters are associated with the complex I biogenesis, ubiquitination and proteasome degradation, signaling by interleukins, and Notch-HLH transcription pathway. The identified biomarkers and pathways may play an important role in the future for developing drugs for the EsC.

Exploration of the Role of Serine Proteinase Inhibitor A3 in Alcohol Dependence Using Gene Expression Omnibus Database

Background: Alcohol dependence is an overall health-related challenge; however, the specific mechanisms underlying alcohol dependence remain unclear. Serine proteinase inhibitor A3 (SERPINA3) plays crucial roles in multiple human diseases; however, its role in alcohol dependence clinical practice has not been confirmed.Methods: We screened Gene Expression Omnibus (GEO) expression profiles, and identified differentially expressed genes (DEGs). Protein-protein interaction (PPI) networks were generated using STRING and Cytoscape, and the key clustering module was identified using the MCODE plugin. SERPINA3-based target microRNA prediction was performed using online databases. Functional enrichment analysis was performed. Fifty-eight patients with alcohol dependence and 20 healthy controls were recruited. Clinical variables were collected and follow-up was conducted for 8 months for relapse.Results:SERPINA3 was identified as a DEG. ELANE and miR-137 were identified after PPI analysis. The enriched functions and pathways included acute inflammatory response, response to stress, immune response, and terpenoid backbone biosynthesis. SERPINA3 concentrations were significantly elevated in the alcohol dependence group than in healthy controls (P &lt; 0.001). According to the median value of SERPINA3 expression level in alcohol dependence group, patients were divided into high SERPINA3 (≥2677.33 pg/ml, n = 29) and low SERPINA3 groups (&lt;2677.33 pg/ml, n = 29). Binary logistic analysis indicated that IL-6 was statistically significant (P = 0.015) Kaplan-Meier survival analysis did not indicate any difference in event-free survival between patients with low and high SERPINA3 levels (P = 0.489) after 8 months of follow-up. Receiver characteristic curve analysis revealed that SERPINA3 had an area under the curve of 0.921 (P &lt; 0.0001), with a sensitivity and specificity of 93.1 and 80.0%, respectively. Cox regression analysis revealed that aspartate transaminase level was a negative predictor of relapse (β = 0.003; hazard ratio = 1.003; P = 0.03).Conclusions:SERPINA3 level was remarkably elevated in patients with alcohol dependence than healthy controls, indicating that SERPINA3 is correlated with alcohol dependence. However, SERPINA3 may not be a potential predictive marker of relapse with patients in alcohol dependence.

Immune infiltration and a ferroptosis-related gene signature for predicting the prognosis of patients with cholangiocarcinoma

Background Cholangiocarcinoma (CHOL) is a digestive tract tumor with high malignancy and poor prognosis and is extremely challenging to treat. At present, induced cell death holds great promise in tumor therapy. Ferroptosis is a recently proposed pattern of programmed cell death, and numerous studies have shown that it is intimately involved in tumors. However, the roles of differentially expressed ferroptosis-related genes (DEFRGs) in CHOL have not been investigated. Methods Our study was based on the The Cancer Genome Atlas (TCGA) database, DEFRGs were obtained to construct a prognostic riskScore model of CHOL by univariate and multivariate Cox regression analyses. Subsequently, the model was evaluated by nomogram construction, survival analysis, receiver operating characteristic (ROC) analysis and exploration of the immune microenvironment, and the mRNA and protein expression levels of each gene in the model were validated by Gene Expression Omnibus (GEO) database and quantitative real-time PCR (qRT-PCR). Results We screened four DEFRGs from the TCGA database to construct a prognostic model. The construction of a nomogram confirmed the predictive value of the model for overall survival (OS), and it was confirmed to have high diagnostic value by ROC analysis. The GSEA results suggested that these genes were mainly enriched in ferroptosis- and metabolism-related pathways. Finally, our experimental results validated the expression levels of the four DEFRGs, which were almost consistent with our bioinformatics results. Conclusion Our study found that the prognostic model showed extremely high diagnostic and prognostic value and could predict the possibility of immunotherapy, thus providing a new direction for individualized treatment of patients with CHOL.