scholarly journals Identification of key genes and pathways in the hPSC-derived lungs infected by the SARS-CoV-2

2020 ◽  
Author(s):  
Hanming Gu ◽  
Gongsheng Yuan
Keyword(s):  
Gene Expression ◽  
Severe Acute Respiratory Syndrome ◽  
Signaling Pathways ◽  
Gene Expression Profile ◽  
Homo Sapiens ◽  
Brain Disorders ◽  
Functional Categories ◽  
Mitochondrial Dysfunctions ◽  
The World ◽  
Key Genes

Abstract Coronavirus disease 2019 (COVID-19) is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has led to numerous infections and deaths in the world. Our research is to explore the differentially expressed genes (DEGs) and signaling pathways in hPSC-derived lungs by using a bioinformatics method to clarify their potential pathogenesis. The gene expression profile of GSE155241 dataset was originally created by using an Illumina NovaSeq 6000 (Homo sapiens) platform. Functional categories and significant pathways were identified by the KEGG and GO analysis. The results suggested that brain disorders and mitochondrial dysfunctions are the main signaling pathways affected by the SARS-CoV-2 infection. Furthermore, key genes e.g. CDC20, NCBP1 and inhibitors e.g. MEK1-2-inhibitor, tivozanib may paly critical roles in COVID-19. Therefore, our study provides insights into the treatment of COVID-19 and related disorders.

scholarly journals Identification of potential key genes for SARS-CoV-2 infected human bronchial organoids based on bioinformatics analysis

2020 ◽  
Author(s):  
Hanming Gu ◽  
Gongsheng Yuan
Keyword(s):  
Signaling Pathways ◽  
Bioinformatics Analysis ◽  
Homo Sapiens ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Receptor Interaction ◽  
Functional Categories ◽  
P53 Signaling ◽  
Key Genes ◽  
P53 Signaling Pathway

AbstractThere is an urgent need to understand the pathogenesis of the severe acute respiratory syndrome coronavirus clade 2 (SARS-CoV-2) that leads to COVID-19 and respiratory failure. Our study is to discover differentially expressed genes (DEGs) and biological signaling pathways by using a bioinformatics approach to elucidate their potential pathogenesis. The gene expression profiles of the GSE150819 datasets were originally produced using an Illumina NextSeq 500 (Homo sapiens). KEGG (Kyoto Encyclopedia of Genes and Genomes) and GO (Gene Ontology) were utilized to identify functional categories and significant pathways. KEGG and GO results suggested that the Cytokine-cytokine receptor interaction, P53 signaling pathway, and Apoptosis are the main signaling pathways in SARS-CoV-2 infected human bronchial organoids (hBOs). Furthermore, NFKBIA, C3, and CCL20 may be key genes in SARS-CoV-2 infected hBOs. Therefore, our study provides further insights into the therapy of COVID-19.

scholarly journals AB0005 IDENTIFICATION OF KEY GENES AND PATHWAYS FOR PSORIASIS BASED ON GEO DATABASES BY BIOINFORMATICS ANALYSIS

2021 ◽  
Vol 80 (Suppl 1) ◽  
pp. 1037.2-1038
Author(s):  
X. Sun ◽  
S. X. Zhang ◽  
S. Song ◽  
T. Kong ◽  
C. Zheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathways ◽  
Differentially Expressed Genes ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Shanxi Province ◽  
Receptor Interaction ◽  
Term Therapy ◽  
Pathway Enrichment Analysis ◽  
Key Genes

Background:Psoriasis is an immune-mediated, genetic disease manifesting in the skin or joints or both, and also has a strong genetic predisposition and autoimmune pathogenic traits1. The hallmark of psoriasis is sustained inflammation that leads to uncontrolled keratinocyte proliferation and dysfunctional differentiation. And it’s also a chronic relapsing disease, which often necessitates a long-term therapy2.Objectives:To investigate the molecular mechanisms of psoriasis and find the potential gene targets for diagnosis and treating psoriasis.Methods:Total 334 gene expression data of patients with psoriasis research (GSE13355 GSE14905 and GSE30999) were obtained from the Gene Expression Omnibus database. After data preprocessing and screening of differentially expressed genes (DEGs) by R software. Online toll Metascape3 was used to analyze Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs. Interactions of proteins encoded by DEGs were discovered by Protein-protein interaction network (PPI) using STRING online software. Cytoscape software was utilized to visualize PPI and the degree of each DEGs was obtained by analyzing the topological structure of the PPI network.Results:A total of 611 DEGs were found to be differentially expressed in psoriasis. GO analysis revealed that up-regulated DEGs were mostly associated with defense and response to external stimulus while down-regulated DEGs were mostly associated with metabolism and synthesis of lipids. KEGG enrichment analysis suggested they were mainly enriched in IL-17 signaling, Toll-like receptor signaling and PPAR signaling pathways, Cytokine-cytokine receptor interaction and lipid metabolism. In addition, top 9 key genes (CXCL10, OASL, IFIT1, IFIT3, RSAD2, MX1, OAS1, IFI44 and OAS2) were identified through Cytoscape.Conclusion:DEGs of psoriasis may play an essential role in disease development and may be potential pathogeneses of psoriasis.References:[1]Boehncke WH, Schon MP. Psoriasis. Lancet 2015;386(9997):983-94. doi: 10.1016/S0140-6736(14)61909-7 [published Online First: 2015/05/31].[2]Zhang YJ, Sun YZ, Gao XH, et al. Integrated bioinformatic analysis of differentially expressed genes and signaling pathways in plaque psoriasis. Mol Med Rep 2019;20(1):225-35. doi: 10.3892/mmr.2019.10241 [published Online First: 2019/05/23].[3]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].Acknowledgements:This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).Disclosure of Interests:None declared

scholarly journals Application of Serial Analysis of Gene Expression to the Study of the Gene Expression Profile ofLeishmania infantum chagasiPromastigote

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Adelino Soares Lima Neto ◽  
Osvaldo Pompílio de Melo Neto ◽  
Carlos Henrique Nery Costa
Keyword(s):  
Gene Expression ◽  
Life Cycle ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Leishmania Infantum ◽  
Open Reading Frames ◽  
Genomic Sequences ◽  
Coding Sequences ◽  
Key Genes ◽  
Reading Frames

This study describes the application of the LongSAGE methodology to study the gene expression profile in promastigotes ofLeishmania infantum chagasi. A tag library was created using the LongSAGE method and consisted of 14,208 tags of 17 bases. Of these, 8,427 (59.3%) were distinct. BLAST research of the 1,645 most abundant tags showed that 12.8% of them identified the coding sequences of genes, while 82% (1,349/1,645) identified one or more genomic sequences that did not correspond with open reading frames. Only 5.2% (84/1,645) of the tags were not aligned to any position in theL. infantum genome. The UTR size ofLeishmaniaand the lack of CATG sites in some transcripts were decisive for the generation of tags in these regions. Additional analysis will allow a better understanding of the expression profile and discovering the key genes in this life cycle.

scholarly journals May the force be with you: Transfer of healthy mitochondria from stem cells to stroke cells

2018 ◽  
Vol 39 (2) ◽  
pp. 367-370 ◽  
Author(s):  
Cesar V Borlongan ◽  
Hung Nguyen ◽  
Trenton Lippert ◽  
Eleonora Russo ◽  
Julian Tuazon ◽  
...  
Keyword(s):  
United States ◽  
Stem Cells ◽  
Therapeutic Option ◽  
Critical Role ◽  
The United States ◽  
Brain Disorders ◽  
Mitochondrial Dysfunctions ◽  
Limited Therapeutic Option ◽  
The World

Stroke is a major cause of death and disability in the United States and around the world with limited therapeutic option. Here, we discuss the critical role of mitochondria in stem cell-mediated rescue of stroke brain by highlighting the concept that deleting the mitochondria from stem cells abolishes the cells’ regenerative potency. The application of innovative approaches entailing generation of mitochondria-voided stem cells as well as pharmacological inhibition of mitochondrial function may elucidate the mechanism underlying transfer of healthy mitochondria to ischemic cells, thereby providing key insights in the pathology and treatment of stroke and other brain disorders plagued with mitochondrial dysfunctions.

scholarly journals Nanostring-Based Identification of the Gene Expression Profile in Trigger Finger Samples

Healthcare ◽  
2021 ◽  
Vol 9 (11) ◽  
pp. 1592
Author(s):  
Ravindra Kolhe ◽  
Umar Ghilzai ◽  
Ashis K. Mondal ◽  
Chetan Pundkar ◽  
Pankaj Ahluwalia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathways ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Bioinformatic Analysis ◽  
Trigger Finger ◽  
Molecular Signaling ◽  
Genetic Characteristics ◽  
Initiation And Propagation ◽  
Collagen Genes

Trigger finger is a common yet vastly understudied fibroproliferative hand pathology, severely affecting patients’ quality of life. Consistent trauma due to inadequate positioning within the afflicted finger’s tendon/pulley system leads to cellular dysregulation and eventual fibrosis. While the genetic characteristics of the fibrotic tissue in the trigger finger have been studied, the pathways that govern the initiation and propagation of fibrosis are still unknown. The complete gene expression profile of the trigger finger has never been explored. Our study has used the Nanostring nCounter gene expression assay to investigate the molecular signaling involved in trigger finger pathogenesis. We collected samples from patients undergoing trigger finger (n = 4) release surgery and compared the gene expression to carpal tunnel tissue (n = 4). Nanostring nCounter analysis identified 165 genes that were differentially regulated; 145 of these genes were upregulated, whereas 20 genes were downregulated. We found that several collagen genes were significantly upregulated, and a regulatory matrix metalloproteinase (MMP), MMP-3, was downregulated. Bioinformatic analysis revealed that several known signaling pathways were dysregulated, such as the TGF-β1 and Wnt signaling pathways. We also found several novel signaling pathways (e.g., PI3K, MAPK, JAK-STAT, and Notch) differentially regulated in trigger finger. The outcome of our study helps in understanding the molecular signaling pathway involved in the pathogenesis of the trigger finger.

scholarly journals Identification of potential key genes associated with glioblastoma based on the gene expression profile

2017 ◽  
Vol 14 (2) ◽  
pp. 2045-2052 ◽  
Author(s):  
Lijuan Bo ◽  
Bo Wei ◽  
Chaohui Li ◽  
Zhanfeng Wang ◽  
Zheng Gao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profile ◽  
Expression Profile ◽  
Key Genes
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