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.

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.

The DOMINO web-server for active module identification analysis

Active module identification (AMI) is an essential step in many omics analyses. Such algorithms receive a gene network and a gene activity profile as input and report subnetworks that show significant over-representation of accrued activity signal ("active modules"). Such modules can point out key molecular processes in the analyzed biological conditions. We recently introduced a novel AMI algorithm called DOMINO, and demonstrated that it detects active modules that capture biological signals with markedly improved rate of empirical validation. Here, we provide an online server that executes DOMINO, making it more accessible and user-friendly. To help the interpretation of solutions, the server provides GO enrichment analysis, module visualizations, and accessible output formats for customized downstream analysis. It also enables running DOMINO with various gene identifiers of different organisms. The server is available at http://domino.cs.tau.ac.il. Its codebase is available at https://github.com/Shamir-Lab.

Dimethyl itaconate alleviates the pyroptosis of macrophages through oxidative stress

Macrophages are involved in the pathophysiology of many diseases as critical cells of the innate immune system. Pyroptosis is a form of macrophage death that induces cytokinesis of phagocytic substances in the macrophages, thereby defending against infection. Dimethyl itaconate (DI) is an analog of itaconic acid with anti-inflammatory effects. However, the effect of dimethyl itaconate on macrophage pyroptosis has not been elucidated clearly. Thus, the present study aimed to analyze the effect of DI treatment on a macrophage pyroptosis model (Lipopolysaccharide, LPS + Adenosine Triphosphate, ATP). The results showed that 0.25 mM DI ameliorated macrophage pyroptosis and downregulated interleukin (IL)-1β expression. Then, real-time quantitative polymerase chain reaction (RT-qPCR) was used to confirm the result of RNA-sequencing of the upregulated oxidative stress-related genes (Gclc and Gss) and downregulated inflammation-related genes (IL-12β and IL-1β). In addition, Gene Ontology (GO) enrichment analysis showed that differential genes were associated with transcript levels and DNA replication. Kyoto encyclopedia of genes and genomes (KEGG) enrichment showed that signaling pathways, such as tumor necrosis factor (TNF), Jak, Toll-like receptor and IL-17, were altered after DI treatment. N-acetyl-L-cysteine (NAC) reversed the DI effect on the LPS + ATP-induced macrophage pyroptosis and upregulated the IL-1β expression. Oxidative stress-related protein Nrf2 is involved in the DI regulation of macrophage pyroptosis. Taken together, these findings suggested that DI alleviates the pyroptosis of macrophages through oxidative stress.

Transcriptome in Combination Proteome Unveils the Phenylpropane Pathway Involved in Garlic (Allium sativum) Greening

Garlic (Allium sativum) is an important vegetable crop that is widely used in cooking and medicine. The greening phenomenon of garlic severely decreases the quality of garlic and hinders garlic processing. To study the mechanism of garlic greening, comprehensive full-length transcript sets were constructed. We detected the differences in greening between Pizhou (PZ) garlic and Laiwu (LW) garlic that were both stored at −2.5°C and protected from light at the same time. The results showed that 60,087 unigenes were respectively annotated to the NR, KEGG, GO, Pfam, eggNOG and Swiss Prot databases, and a total of 30,082 unigenes were annotated. The analysis of differential genes and differential proteins showed that PZ garlic and LW garlic had 923 differentially expressed genes (DEGs), of which 529 genes were up regulated and 394 genes were downregulated. Through KEGG and GO enrichment analysis, it was found that the most significant way of enriching DEGs was the phenylpropane metabolic pathway. Proteomics analysis found that there were 188 differentially expressed proteins (DAPs), 162 up-regulated proteins, and 26 down-regulated proteins between PZ garlic and LW garlic. The content of 10 proteins related to phenylpropanoid biosynthesis in PZ garlic was significantly higher than that of LW garlic. This study explored the mechanisms of garlic greening at a molecular level and further discovered that the formation of garlic green pigment was affected significantly by the phenylpropanoid metabolic pathway. This work provided a theoretical basis for the maintenance of garlic quality during garlic processing and the future development of the garlic processing industries.

DNAJB11 predicts a poor prognosis and is associated with immune infiltration in thyroid carcinoma: a bioinformatics analysis

Objective To investigate the prognostic value of the co-chaperone protein DnaJ Heat Shock Protein Family (Hsp40) Member B11 (DNAJB11) in thyroid carcinoma (THCA). Methods This bioinformatics analysis study evaluated the prognostic value of DNAJB11 mRNA levels in THCA based on data from The Cancer Genome Atlas (TCGA). The levels of DNAJB11 mRNA in THCA and normal tissues were compared with Wilcoxon signed rank test. Kaplan–Meier survival curve analysis and Cox regression analysis were performed to evaluate the correlation between DNAJB11 mRNA levels and survival. Gene Ontology (GO) enrichment analysis was used to elucidate the functional enrichment difference. Results Data from the 502 patients with THCA from the TCGA database were analysed. DNAJB11 mRNA was downregulated in THCA tissues compared with normal tissues. Decreased levels of DNAJB11 mRNA were significantly correlated with T stage, N stage, pathological stage, histological type, extrathyroidal extension and BRAF gene status. The low levels of DNAJB11 mRNA were associated with a shorter progression-free interval. GO enrichment analysis showed that DNAJB11 was involved in immune-related biological processes. Conclusion Low levels of DNAJB11 mRNA were associated with poor prognosis in THCA.

A Comparative Transcriptome Analysis Reveals New Insights into Pre-Harvest Sprouting (PHS) in Wheat

Background: pre-harvest sprouting (PHS) is a significant cause of yield loss in cereal crops, and is an important topic of study for the improvement of wheat quality. Many studies have focused on PHS in wheat during the last 10 years, especially on the involvement of abscisic acid (ABA) in PHS, however, a lot remained unknown about this topic.Results: In this study, a PHS resistant line was isolated from an ethylmethane sulfonate (EMS) mutant population derived from the wheat cultivar ‘Long 13-3778’, namely ‘LQ18’. The mutant line LQ18 showed highly significant resistance to PHS compared with the wild-type. Transcriptome sequencing was conducted to determine the differences between the LQ18 mutant and the wild-type at the level of gene expression. The results showed no conclusive evidence that the ABA biosynthesis and signaling pathways contribute to the differences in PHS between the mutant and the wild-type, and some genes and their alleles associated with PHS tolerance showed differential expression between the mutant and wild-type lines. The most interesting result of this study was that the expression levels of the chitinase family genes showed significant differences between the mutant and the wild-type as determined by GO enrichment analysis, and a subsequent analysis of differential expression profiling of the chitinase genes led to the same conclusion.Conclusions: Transcriptomic analysis in this study have revealed the global transcriptome profiles of the PHS sensitive wheat cultivar ‘Long 13-3778’ and its PHS resistant mutants. Furthermore, this study has proposed a possible explanation of the connection between PHS and the chitinase family for the first time, which added to our understanding of PHS and seed dormancy in common wheat.

A Novel Defined Ferroptosis-Related Gene Signature for Predicting the Prognosis of Kidney Renal Clear Cell Carcinoma

Objective: Currently, the mechanism of ferroptosis in the progression of kidney renal clear cell carcinoma (KIRC) is still unclear. This paper aims to explore the potential mechanism of ferroptosis-related genes in KIRC.Methods: Using KIRC chip data in Gene Expression Synthesis (GEO) database, the differentially expressed genes (DEGs) between normal and tumor group were screened in GSE168845, GSE105261 and GSE11151 by limma package. Ferroptosis-related DEGs were gained by the intersection of DEGs and ferroptosis-related genes, which from the FerrDb database. Gene ontology (GO) enrichment analysis of ferroptosis-related DEGs was carried out by gene set enrichment analysis (GSEA). Univariate and multivariate Cox risk regression model was used to screen and establish gene prognosis risk prediction model. For ferroptosis-related DEGs, targeted small molecules are predicted for the treatment of KIRC.Results: In GSE168845, GSE105261 and GSE11151, 2532 DEGs were screened from normal group and tumor group. And 149 ferroptosis-related genes were obtained from the FerrDb database. Through the intersection of DEGs and ferroptosis-related genes, 17 ferroptosis-related DEGs were obtained. GO enrichment analysis indicated that primary biological processes of 17 ferroptosis-related DEGs enrichment had iron ion binding, microvillus membrane and regulation of transcription from RNA polymerase II promoter in response to stress. Based on univariate and multivariate Cox regression analysis, the multivariate prognostic risk prediction model composed of three ferroptosis DEGs including MT1G, LAMP2 and MIOX was constructed. The results of patient risk score indicated that the prognosis with high score was worse than those with low score. Meanwhile, we found that the exprssion of MT1G, LAMP2 and MIOX were related with methylation and immune infiltration in KIRC. Terroptosis-gene interaction and terroptosis-miRNA coregulatory network of MT1G, LAMP2 and MIOX were collected by Network Analyst. Then, the ferroptosis-related prognosis nomogram, including age, gender, grade, TNM and risk score, was found to predict the overall survival (OS) of KIRC patients. Finally, according to ferroptosis related DEGs, the potential therapeutic effects of emetine, cephaeline,scoulerline, sanguinarine, cicloheximide, tolfenamic acid, phenoxybenzamine and calmidazolium were predicted in KIRC.Conclusion: The risk prediction models of MT1G, LAMP2 and MIOX can effectively predict the prognosis of patients with KIRC. And MT1G, LAMP2 and MIOX are related to methylation and immune infiltration in KIRC, which is expected to play a guiding role in the clinical treatment of KIRC. Targeted these three genes, potential therapeutic drugs of emetine, cephaeline,scoulerline, sanguinarine, cicloheximide, tolfenamic acid, phenoxybenzamine and calmidazolium were also predicted in KIRC.