STAT3 Is the Master Regulator for the Forming of 3D Spheroids of 3T3-L1 Preadipocytes

To elucidate the currently unknown mechanisms responsible for the diverse biological aspects between two-dimensional (2D) and three-dimensional (3D) cultured 3T3-L1 preadipocytes, RNA-sequencing analyses were performed. During a 7-day culture period, 2D- and 3D-cultured 3T3-L1 cells were subjected to lipid staining by BODIPY, qPCR for adipogenesis related genes, including peroxisome proliferator-activated receptor γ (Pparγ), CCAAT/enhancer-binding protein alpha (Cebpa), Ap2 (fatty acid-binding protein 4; Fabp4), leptin, and AdipoQ (adiponectin), and RNA-sequencing analysis. Differentially expressed genes (DEGs) were detected by next-generation RNA sequencing (RNA-seq) and validated by a quantitative reverse transcription–polymerase chain reaction (qRT–PCR). Bioinformatic analyses were performed on DEGs using a Gene Ontology (GO) enrichment analysis and an Ingenuity Pathway Analysis (IPA). Significant spontaneous adipogenesis was observed in 3D 3T3-L1 spheroids, but not in 2D-cultured cells. The mRNA expression of Pparγ, Cebpa, and Ap2 among the five genes tested were significantly higher in 3D spheroids than in 2D-cultured cells, thus providing support for this conclusion. RNA analysis demonstrated that a total of 826 upregulated and 725 downregulated genes were identified as DEGs. GO enrichment analysis and IPA found 50 possible upstream regulators, and among these, 6 regulators—transforming growth factor β1 (TGFβ1), signal transducer and activator of transcription 3 (STAT3), interleukin 6 (IL6), angiotensinogen (AGT), FOS, and MYC—were, in fact, significantly upregulated. Further analyses of these regulators by causal networks of the top 14 predicted diseases and functions networks (IPA network score indicated more than 30), suggesting that STAT3 was the most critical upstream regulator. The findings presented herein suggest that STAT3 has a critical role in regulating the unique biological properties of 3D spheroids that are produced from 3T3-L1 preadipocytes.

RegEnrich gene regulator enrichment analysis reveals a key role of the ETS transcription factor family in interferon signaling

Changes in a few key transcriptional regulators can lead to different biological states. Extracting the key gene regulators governing a biological state allows us to gain mechanistic insights. Most current tools perform pathway/GO enrichment analysis to identify key genes and regulators but tend to overlook the gene/protein regulatory interactions. Here we present RegEnrich, an open-source Bioconductor R package, which combines differential expression analysis, data-driven gene regulatory network inference, enrichment analysis, and gene regulator ranking to identify key regulators using gene/protein expression profiling data. By benchmarking using multiple gene expression datasets of gene silencing studies, we found that RegEnrich using the GSEA method to rank the regulators performed the best. Further, RegEnrich was applied to 21 publicly available datasets on in vitro interferon-stimulation of different cell types. Collectively, RegEnrich can accurately identify key gene regulators from the cells under different biological states, which can be valuable in mechanistically studying cell differentiation, cell response to drug stimulation, disease development, and ultimately drug development.

Selection of Cashmere Fineness Functional Genes by Translatomics

Cashmere fineness is an important index to evaluate cashmere quality. Liaoning Cashmere Goat (LCG) has a large cashmere production and long cashmere fiber, but its fineness is not ideal. Therefore, it is important to find genes involved in cashmere fineness that can be used in future endeavors aiming to improve this phenotype. With the continuous advancement of research, the regulation of cashmere fineness has made new developments through high-throughput sequencing and genome-wide association analysis. It has been found that translatomics can identify genes associated with phenotypic traits. Through translatomic analysis, the skin tissue of LCG sample groups differing in cashmere fineness was sequenced by Ribo-seq. With these data, we identified 529 differentially expressed genes between the sample groups among the 27197 expressed genes. From these, 343 genes were upregulated in the fine LCG group in relation to the coarse LCG group, and 186 were downregulated in the same relationship. Through GO enrichment analysis and KEGG enrichment analysis of differential genes, the biological functions and pathways of differential genes can be found. In the GO enrichment analysis, 491 genes were significantly enriched, and the functional region was mainly in the extracellular region. In the KEGG enrichment analysis, the enrichment of the human papillomavirus infection pathway was seen the most. We found that the COL6A5 gene may affect cashmere fineness.

A Network Pharmacology Perspective Investigation of the Pharmacological Mechanisms of the Herbal Drug FDY003 in Gastric Cancer

Gastric cancer (GC) is one of the most common and deadly malignant tumors worldwide. While the application of herbal drugs for GC treatment is increasing, the multicompound–multitarget pharmacological mechanisms involved are yet to be elucidated. By adopting a network pharmacology strategy, we investigated the properties of the anticancer herbal drug FDY003 against GC. We found that FDY003 reduced the viability of human GC cells and enhanced their chemosensitivity. We also identified 8 active phytochemical compounds in FDY003 that target 70 GC-associated genes and proteins. Gene ontology (GO) enrichment analysis suggested that the targets of FDY003 are involved in various cellular processes, such as cellular proliferation, survival, and death. We further identified various major FDY003 target GC-associated pathways, including PIK3-Akt, MAPK, Ras, HIF-1, ErbB, and p53 pathways. Taken together, the overall analysis presents insight at the systems level into the pharmacological activity of FDY003 against GC.

High Expression of PDE8B and DUOX2 Associated with Ability of Metastasis in Thyroid Carcinoma

Background. Hormone is an independent factor that induces differentiation of thyroid cancer (TC) cells. The thyroid-stimulating hormone (TSH) could promote the progression and invasion in TC cells. However, few genes related to hormone changes are studied in poorly differentiated metastatic TC. This study is aimed at constructing a gene set’s coexpression correlation network and verifying the changes of some hub genes involved in regulating hormone levels. Methods. Microarray datasets of TC samples were obtained from public Gene Expression Omnibus (GEO) databases. R software and bioinformatics packages were utilized to identify the differentially expressed genes (DEGs), important gene module eigengenes, and hub genes. Subsequently, the Gene Ontology (GO) enrichment analysis was constructed to explore important biological processes that are associated with the mechanism of poorly differentiated TC. Finally, some hub gene expressions were validated through real-time PCR and immunoblotting. Results. Gene chip with category number GSE76039 was analyzed, and 1190 DEGs were screened with criteria of P < 0.05 and ∣ log 2 foldchange ∣ > 2 . Our analysis showed that human dual oxidase 2 (DUOX2) and phosphodiesterase 8B (PDE8B) are the two important hub genes in a coexpression network. In addition, the validated experimental results showed that the expression levels of both DUOX2 and PDE8B were elevated in poorly differentiated metastatic TC tissues. Conclusion. This study identified and validated that DUOX2 and PDE8B were significantly associated with the metastasis ability of thyroid carcinoma.

Identification of Stage-related and Severity-Related Biomarkers and Exploration of Immune Landscape for Dengue by Comprehensive Analyses

At present, there are still no specific therapeutic drugs and appropriate vaccines for Dengue. Therefore, it is very important to explore distinct clinical diagnostic indicators. In this study, we combined differentially expressed genes (DEGs) analysis and weighted co-expression network analysis (WGCNA) to screen a stable and robust biomarker which can be used to distinguish three clinical stages of Dengue and severity of Dengue. CD38 can distinguish excellently Early Acute, Late Acute, Convalescent stages for Dengue patients, and ZNF595 can discriminate DHF from DF in whole acute stages. We also found that three clinical stages can be discriminated based on the fractions of Plasma cells, activated memory CD4+ T cells, and Monocytes. In different clinical stages different immune cells function positively. Negative inhibition of viral replication based on Gene Ontology (GO) enrichment, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Gene set enrichment analysis (GSEA), up-regulated autophagy genes and impairing immune system are potential reasons resulting in dengue hemorrhagic fever (DHF).

The Systematic Landscape of Nectin Family and Nectin-Like Molecules: Functions and Prognostic Value in Low Grade Glioma

Objective: Nectin and nectin-like molecules (Necls) are molecules that are involved in cell–cell adhesion and other vital cellular processes. This study aimed to determine the expression and prognostic value of nectin and Necls in low grade glioma (LGG).Materials and Methods: Differentially expressed nectin and Necls in LGG samples and the relationship of nectin family and Necls expression with prognosis, clinicopathological parameters, and survival were explored using The Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA), and Repository of Molecular Brain Neoplasia Data (REMBRANDT) databases. Univariate and multivariate Cox analysis models were performed to construct the prognosis-related gene signature. Kaplan-Meier curves and time-dependent receiver operating characteristic (ROC) curves and multivariate Cox regression analysis, were utilized to evaluate the prognostic capacity of the four-gene signature. Gene ontology (GO)enrichment analysis and Gene Set Enrichment Analyses (GSEA) were performed to further understand the underlying molecular mechanisms. The Tumor Immune Estimation Resource (TIMER) was used to explore the relationship between the four-gene signature and tumor immune infiltration.Results: Several nectin and Necls were differentially expressed in LGG. Kaplan–Meier survival analyses and Univariate Cox regression showed patients with high expression of NECTIN2 and PVR and low expression of CADM2 and NECTIN1 had worse prognosis among TCGA, CGGA, and REMBRANDT database. Then, a novel four-gene signature was built for LGG prognosis prediction. ROC curves, KM survival analyses, and multivariate COX regression indicated the new signature was an independent prognostic indicator for overall survival. Finally, GSEA and GO enrichment analyses revealed that immune-related pathways participate in the molecular mechanisms. The risk score had a strong negative correlation with tumor purity and data of TIMER showed different immune cell proportions (macrophage and myeloid dendritic cell) between high- and low-risk groups. Additionally, signature scores were positively related to multiple immune-related biomarkers (IL 2, IL8 and IFNγ).Conclusion: Our results offer an extensive analysis of nectin and Necls levels and a four-gene model for prognostic prediction in LGG, providing insights for further investigation of CADM2, NECTIN1/2, and PVR as potential clinical and immune targets in LGG.

Identification of Pathogenesis and Prognoses of Relapse in Myeloma by Bioinformatic Method

Background: Multiple myeloma (MM), the second most hematological malignancy, the molecular mechanism and pathogenesis of the relapse of MM is poorly understood. This study aimed to identify novel prognostic model for MM and explore potential mechanism of relapse. Methods: Gene expression data,clinical data(GSE24080) and HTseq-Counts files were downloaded from Gene Expression Omnibus (GEO) and TCGA database. Co-expression modules of genes were built by Weighted Correlation Network Analysis (WGCNA).KEGG and GO enrichment analysis were performed in each module. TATFs (tumor-associated transcription factors) were retrieved from the Cistrome. Twenty-two immune cell compositions was calculated by CIBERSORT algorithm.Univariate and multivariate Cox congression were performed and a predictive model by prognostic genes was constructed,the predictive power of the model was evaluated by Kaplan–Meier curve and time-dependent receiver operating characteristic (ROC) curves. Results: A total of 940 DEGs were identified,and in WGCNA analysis, yellow, brown and sky-blue modules were most associated with clinic traits.The yellow module related with the cell cycle and the brown and sky-blue modules correlated with cytokine and its receptors, where the M2 macrophage fraction is positively correlated with CCL18, CCL2, CCL8, CXCL12 and CCl23 were positively correlated with plasma cells by Cibersort analysis.Prognostic genes were identified and two genes (TPX2,PRAM1) were finally identified to construct a risk model for predicting EFS.

LncRNA-mRNA Expression Pattern in Invasive Pituitary Adenomas: A Microarray Analysis

Backgrounds: Long non-coding RNAs (lncRNAs) play important roles in tumorigenesis and progression of various cancer types; however, their roles in the development of invasive pituitary adenomas (PAs) remain to be investigated.Methods: lncRNA microarray was performed in three invasive and three noninvasive PAs. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis were performed, and coexpression networks between lncRNA and mRNA were constructed. Furthermore, three differentially expressed lncRNAs were selected for validation by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) in PA samples. The diagnostic values of these three lncRNAs were further evaluated by receiver operating characteristic (ROC) analysis.Results: A total of 8872 lncRNAs were identified in invasive and paired noninvasive PAs using lncRNA microarray. Among these, the differentially expressed lncRNAs included 81 that were upregulated and 165 that were downregulated. GO enrichment and KEGG pathway analysis showed that these differentially expressed lncRNAs were associated with post-translational modifications of proteins. Furthermore, we performed target gene prediction and coexpression analysis. The interrelationships between the lncRNAs and mRNAs with significant differential expression were identified. Additionally, three differentially expressed lncRNAs were selected for validation in 41 PA samples by qRT-PCR. The expression levels of FAM182B, LOC105371531, and LOC105375785 in the invasive PAs were significantly (P < 0.05) lower than in the noninvasive PAs, and these results were consistent with the microarray data. ROC analysis suggested that FAM182B and LOC105375785 expression levels could be used to distinguish invasive PAs from noninvasive PAs.Conclusion: Our findings demonstrated the lncRNAs expression patterns in invasive PAs. Thus, FAM182B and LOC105375785 may be involved in the invasiveness of PAs and serve as new candidate biomarkers for the diagnosis of invasive PAs.

Identification of transcriptomics biomarkers for the early prediction of the prognosis of septic shock from pneumopathies

Background Identifying the biological subclasses of septic shock might provide specific targeted therapies for the treatment and prognosis of septic shock. It might be possible to find biological markers for the early prediction of septic shock prognosis. Methods The data were obtained from the Gene Expression Omnibus databases (GEO) in NCBI. GO enrichment and KEGG pathway analyses were performed to investigate the functional annotation of up- and downregulated DEGs. ROC curves were drawn, and their areas under the curves (AUCs) were determined to evaluate the predictive value of the key genes. Results 117 DEGs were obtained, including 36 up- and 81 downregulated DEGs. The AUC for the MME gene was 0.879, as a key gene with the most obvious upregulation in septic shock. The AUC for the THBS1 gene was 0.889, as a key downregulated gene with the most obvious downregulation in septic shock. Conclusions The upregulation of MME via the renin-angiotensin system pathway and the downregulation of THBS1 through the PI3K–Akt signaling pathway might have implications for the early prediction of prognosis of septic shock in patients with pneumopathies.