Identification of Hub Genes of Keloid Fibroblasts by Coexpression Network Analysis and Degree Algorithm

Background. Keloid is a benign dermal tumor characterized by abnormal proliferation and invasion of fibroblasts. The establishment of biomarkers is essential for the diagnosis and treatment of keloids. Methods. We systematically identified coexpression modules using the weighted gene coexpression network analysis method (WGCNA). Differential expressed genes (DEGs) in GSE145725 and genes in significant modules were integrated to identify overlapping key genes. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were then performed, as well as protein-protein interaction (PPI) network construction for hub gene screening. Results. Using the R package of WGCNA, 22 coexpression modules consisting of different genes were identified from the top 5,000 genes with maximum mean absolute deviation in 19 human fibroblast samples. Blue-green and yellow modules were identified as the most important modules, where genes overlapping with DEGs were identified as key genes. We identified the most critical functions and pathways as extracellular structure organization, vascular smooth muscle contraction, and the cGMP-PKG signaling pathway. Hub genes from key genes as BMP4, MSX1, HAND2, TBX2, SIX1, IRX1, EDN1, DLX5, MEF2C, and DLX2 were identified. Conclusion. The blue-green and yellow modules may play an important role in the pathogenesis of keloid. 10 hub genes were identified as potential biomarkers and therapeutic targets for keloid.

Endophytic fungus Pseudodidymocyrtis lobariellae KL27 promotes taxol biosynthesis and accumulation in Taxus chinensis

Background Taxol from Taxus species is a precious drug used for the treatment of cancer and can effectively inhibit the proliferation of cancer cells. However, the growth of Taxus plants is very slow and the content of taxol is quite low. Therefore, it is of great significance to improve the yield of taxol by modern biotechnology without destroying the wild forest resources. Endophytic fungus which symbiosis with their host plants can promote the growth and secondary metabolism of medicinal plants. Results Here, an endophytic fungus KL27 was isolated from T. chinensis, and identified as Pseudodidymocyrtis lobariellae. The fermentation broth of KL27 (KL27-FB) could significantly promote the accumulation of taxol in needles of T. chinensis, reaching 0.361 ± 0.082 mg/g·DW (dry weight) at 7 days after KL27-FB treatment, which is 3.26-fold increase as compared to the control. The RNA-seq and qRT-PCR showed that KL27-FB could significantly increase the expression of key genes involved in the upstream pathway of terpene synthesis (such as DXS and DXR) and those in the taxol biosynthesis pathway (such as GGPPS, TS, T5OH, TAT, T10OH, T14OH, T2OH, TBT, DBAT and PAM), especially at the early stage of the stimulation. Moreover, the activation of jasmonic acid (JA) biosynthesis and JA signal transduction, and its crosstalk with other hormones, such as gibberellin acid (GA), ethylene (ET) and salicylic acid (SA), explained the elevation of most of the differential expressed genes related to taxol biosynthesis pathway. Moreover, TF (transcriptional factor)-encoding genes, including MYBs, ethylene-responsive transcription factors (ERFs) and basic/helix-loop-helix (bHLH), were detected as differential expressed genes after KL27-FB treatment, further suggested that the regulation of hormone signaling on genes of taxol biosynthesis was mediated by TFs. Conclusions Our results indicated that fermentation broth of endophytic fungus KL27-FB could effectively enhance the accumulation of taxol in T. chinensis needles by regulating the phytohormone metabolism and signal transduction and further up-regulating the expression of multiple key genes involved in taxol biosynthesis. This study provides new insight into the regulatory mechanism of how endophytic fungus promotes the production and accumulation of taxol in Taxus sp.

COVID-19 Transcriptomic Atlas: A Comprehensive Analysis of COVID-19 Related Transcriptomics Datasets

Background: To develop anti-viral drugs and vaccines, it is crucial to understand the molecular basis and pathology of COVID-19. An increase in research output is required to generate data and results at a faster rate, therefore bioinformatics plays a crucial role in COVID-19 research. There is an abundance of transcriptomic data from studies carried out on COVID-19, however, their use is limited by the confounding factors pertaining to each study. The reanalysis of all these datasets in a unified approach should help in understanding the molecular basis of COVID-19. This should allow for the identification of COVID-19 biomarkers expressed in patients and the presence of markers specific to disease severity and condition.Aim: In this study, we aim to use the multiple publicly available transcriptomic datasets retrieved from the Gene Expression Omnibus (GEO) database to identify consistently differential expressed genes in different tissues and clinical settings.Materials and Methods: A list of datasets was generated from NCBI’s GEO using the GEOmetadb package through R software. Search keywords included SARS-COV-2 and COVID-19. Datasets in human tissues containing more than ten samples were selected for this study. Differentially expressed genes (DEGs) in each dataset were identified. Then the common DEGs between different datasets, conditions, tissues and clinical settings were shortlisted.Results: Using a unified approach, we were able to identify common DEGs based on the disease conditions, samples source and clinical settings. For each indication, a different set of genes have been identified, revealing that a multitude of factors play a role in the level of gene expression.Conclusion: Unified reanalysis of publically available transcriptomic data showed promising potential in identifying core targets that can explain the molecular pathology and be used as biomarkers for COVID-19.

Exercise-Regulated Gene Differential Expression In The Hippocampal Region of C57BL/6J Mice Ameliorates Methamphetamine Dependence

Background: Methamphetamine (METH) is the highly addictive psychoactive drug which could harm to individual health and lead to great social problems. Various approaches have been adopted to address these problems, but relapse rates remain high. Recently, it has been found that comprehensive treatment combined with scientific and appropriate exercise intervention can improve mental state and physical fitness of drug addicts and promote their physical and mental rehabilitation. Long-term regular exercise improves the symptoms of METH withdrawal and reduce METH relapse. This study is to investigate the effects and regulated genes expression related to running exercise in METH addicted mice. Method: We used male C57BL/6J mice to construct METH addiction model and performed running exercise intervention, conditional place preference (CPP) was used to measure the effects of running intervention on METH addict mice. RNA sequencing(RNA-seq) and transcriptome analysis was performed on mice hippocampus, functions and differential expressed genes (DEGs) significantly regulated by exercise intervention in METH addict mice were analysed and noted.Results: The results showed that days of CPP preference was shortened to day 3 in METH addict mice given moderate exercise intervention, compared to preference to day 6 in METH addict mice without exercise. In addition, hippocampal transcriptome analysis revealed 12 DEGs significantly regulated by exercise intervention. By performing Gene ontology and KEGG analysis, function of immune responses was significant enriched in METH addiction mice with exercise. The expression of 12 differential expressed genes was verified by qRT-PCR, which showed that relative mRNA expression of DEGs was consistent with the RNA sequencing results.Conclusion: Running intervention can promote the recovery of METH addiction in mice, and the 12 candidate DEGs from mice hippocampus could use for further research on regulation mechanisms of exercise in METH addiction mice.

In silico analysis for potential proteins and microRNAs in Glioblastoma and Parkinsonism.

In todays world, neurodegenerative diseases such as Alzheimers disease, Parkinsons Disease, Huntingtons Disease as well as brain cancers such as astrocytomas, ependymomas, glioblastomas have become a great threat to us. In this study, we are trying to find a probable molecular connection associated with two very much different diseases, Glioblastoma, also known as Glioblastoma Multiforme (cancers of microglial cells of our brain) and Parkinsons disease. We at first downloaded the microarray datasets of these two diseases from Gene Expression Omnibus (GEO) and then analyzed them by the GEO2R tool. After analysis, we found 249 common upregulated differential expressed genes and 135 common downregulated differential expressed genes of these two diseases. Therefore the common differentially expressed genes, both upregulated and downregulated, were imported into STRING online tool to find out the protein-protein interactions. Now, this whole network was subjected to Cytoscape and the top ten hub genes were found by Cyto-Hubba plug-in. The top then hub genes are EGFR, CCNB1, CDK1, CCNA2, CHEK1, RAD51, MAD2L1, KIF20A, BUB1, and CCNB2. These all genes are upregulated in both diseases. To find out the biological processes, molecular functions, cellular components, and pathways associated with these hub genes Enrichr online software was used. We used miRNet software to determine the interactions of hub genes with microRNAs. This study will be useful in the future for drug targets discovery for these diseases.

ε-poly-L-lysine Affects the Vegetative Growth, Pathogenicity and Expression Regulation of Necrotrophic Pathogen Sclerotinia sclerotiorum and Botrytis cinerea

Microbial secondary metabolites produced by Streptomyces are applied to control plant diseases. The metabolite, ε-poly-L-lysine (ε-PL), is a non-toxic food preservative, but the potential application of this compound as a microbial fungicide in agriculture is rarely reported. In this study, the effect and mode of action of ε-PL on two necrotrophic pathogenic fungi, Sclerotinia sclerotiorum and Botrytis cinerea, were investigated. The results showed that ε-PL effectively inhibited the mycelial growth of S. sclerotiorum and B. cinerea with EC50 values of 283 μg/mL and 281 μg/mL, respectively. In addition, ε-PL at the dose of 150 and 300 μg/mL reduced S. sclerotiorum sclerotia formation. The results of the RNA-seq and RT-qPCR validation indicated that ε-PL significantly regulated the gene expression of critical differential expressed genes (DEGs) involved in fungal growth, metabolism, pathogenicity, and induced an increase in the expression of the fungal stress responses and the detoxification genes. These results provided new insights for understanding the modes of action of ε-PL on S. sclerotiorum and B. cinerea and improved the sustainable management of these plant diseases.

Comparative Analysis of the Mutational Profile in HBV-Related and Non-HBV-Related Hepatocellular Carcinoma

BackgroundHepatocellular carcinoma (HCC) is the sixth most commonly diagnosed cancer and the fourth leading cause of cancer death worldwide.The distinct molecular mechanism that regulates cancer progression associated with HBV-related HCC are still unclear.MethodsThe study population included all HCC patients from TCGA lihc_firehose.Mutational signatures of HBV-related HCC samples were calculated with MuSiCa Online website tools. Overall Survival (OS) and disease-free survival（DFS) were estimated according to the log rank in Cox proportional model.Analysis of differential expressed genes was finished with R (version 3.6.3) package DESeq2.Results AXIN1 and CACNA2D1 were significantly higher tested in patients with HBV-related HCC.Mutational signature 26,6 and 16 were detected in HBV-related HCC.TMB of non-HBV-related HCC was significantly higher than HBV-related . Mutations of TTN, MUC16, RYR2, DNAH7 and ARID2 had significant effects on OS in HBV-related but were not associated with prognosis of non-HBV-related HCC.ConclusionWnt/β-catenin and cell cycle signaling pathway may be potentially targets for treatment of HBV-related HCC.Mutation genes of TTN, MUC16, RYR2, DNAH7 and ARID2 may be used as biomarkers of the clinical prognosis and a useful strategy for management of HBV-related HCC.

Chromium Genotoxicity associated with Respiratory Disease

Chromium existing in the biosphere in prominent two forms Cr (III) and Cr (VI) is a well-studied heavy metal. Cr (III) is considered as non-harmful and necessary element in diet whereas Cr(VI) is extremely toxic exerting various negative health impacts on human and other organisms. Mining activity is must for extracting economic minerals and a large number of people are related to these sites as worker or habitants and a major source of chromium exposure. Present chapter discusses genotoxic nature of chromium considering respiratory disease resulted from chromium exposure. The genotoxicity is illustrated in terms of chromium induced differential expressed genes (DEGs), transcription factors and microRNA regulating the DEGs and their gene ontology.

Apolipoprotein B Is Associated With the Microenvironment of Cholangiocarcinoma

BackgroundCholangiocarcinoma (CCA) is a kind of devastating malignancy, which is correlated with the extremely high mortality. Due to the occult pathogenesis of CCA, most patients are diagnosed in the advanced stage. However, the efficacy of chemotherapy and immunotherapy is limited for these patients. The cause for this phenomenon is unclear, the recent researches indicate that it could be related to predisposing genetic factors and tumor microenvironment (TME) changes. The TME is created by the tumor and dominated by tumor-induced interactions. And the tumor prognosis could be influenced by the extent of infiltrating immune cells and stromal cells in TME.Materials and methodsThe abundance ratio of immune cells for each sample was obtained via the CIBERSORT algorithm, and we used ESTIMATE score system to calculate the immune and stromal scores in CCA. The CCA cases in TCGA database were categorized into high and low score groups according to their immune/stromal scores. And then, we identified the differential expressed genes (DEGs) in two groups. Functional enrichment analysis and protein‐protein interaction networks were carried out for DEGs. Interestingly, we found out that apolipoprotein B (APOB) is the most down-regulated among these genes. Then we performed the immunohistochemistry staining of APOB in a CCA tumor microarray which contained 100 CCA cases, APOB was down-regulated in CCA samples. Thus, we evaluated the APOB function in the TME of CCA through TIMER.Results and ConclusionThe results demonstrate that the infiltration degree of immune cells in CCA could be influenced by the expression of APOB, and the APOB expression could be mediated by DNA methylation. Our study not only indicates APOB is a potential target for CCA immunotherapy but also provides new ideas for researchers to explore the immunotherapy of various tumors.