scholarly journals System, Method and Software for Calculation of a Cannabis Drug Efficiency Index for the Reduction of Inflammation

2020 ◽  
Vol 22 (1) ◽  
pp. 388
Author(s):  
Nicolas Borisov ◽  
Yaroslav Ilnytskyy ◽  
Boseon Byeon ◽  
Olga Kovalchuk ◽  
Igor Kovalchuk
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Impact Analysis ◽  
Cannabis Sativa ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Efficiency Index ◽  
System Method ◽  
High Throughput Gene Expression ◽  
Drug Efficiency

There are many varieties of Cannabis sativa that differ from each other by composition of cannabinoids, terpenes and other molecules. The medicinal properties of these cultivars are often very different, with some being more efficient than others. This report describes the development of a method and software for the analysis of the efficiency of various cannabis extracts to detect the anti-inflammatory properties of the various cannabis extracts. The method uses high-throughput gene expression profiling data but can potentially use other omics data as well. According to the signaling pathway topology, the gene expression profiles are convoluted into the signaling pathway activities using a signaling pathway impact analysis (SPIA) method. The method was tested by inducing inflammation in human 3D epithelial tissues, including intestine, oral and skin, and then exposing these tissues to various extracts and then performing transcriptome analysis. The analysis showed a different efficiency of the various extracts in restoring the transcriptome changes to the pre-inflammation state, thus allowing to calculate a different cannabis drug efficiency index (CDEI).

scholarly journals High-Throughput Gene Expression Profiles to Define Drug Similarity and Predict Compound Activity

2018 ◽  
Vol 16 (3) ◽  
pp. 162-176 ◽  
Author(s):  
Hans De Wolf ◽  
Laure Cougnaud ◽  
Kirsten Van Hoorde ◽  
An De Bondt ◽  
Joerg K. Wegner ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Throughput ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
High Throughput Gene Expression ◽  
Drug Similarity

scholarly journals Proteasome Inhibitors Interrupt the Activation of Non-Canonical NF-κB Signaling Pathway and Induce Cell Apoptosis in Cytarabine-Resistant HL60 Cells

2021 ◽  
Vol 23 (1) ◽  
pp. 361
Author(s):  
Shuo-Yu Wang ◽  
Yin-Hwa Shih ◽  
Tzong-Ming Shieh ◽  
Yu-Hsin Tseng
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Proteasome Inhibitors ◽  
Gene Expression Profiles ◽  
Nuclear Factor Κb ◽  
High Dose ◽  
Hl60 Cells ◽  
Expression Arrays ◽  
Study Results

Over half of older patients with acute myeloid leukemia (AML) do not respond to cytotoxic chemotherapy, and most responders relapse because of drug resistance. Cytarabine is the main drug used for the treatment of AML. Intensive treatment with high-dose cytarabine can increase the overall survival rate and reduce the relapse rate, but it also increases the likelihood of drug-related side effects. To optimize cytarabine treatment, understanding the mechanism underlying cytarabine resistance in leukemia is necessary. In this study, the gene expression profiles of parental HL60 cells and cytarabine-resistant HL60 (R-HL60) cells were compared through gene expression arrays. Then, the differential gene expression between parental HL60 and R-HL60 cells was measured using KEGG software. The expression of numerous genes associated with the nuclear factor κB (NF-κB) signaling pathway changed during the development of cytarabine resistance. Proteasome inhibitors inhibited the activity of non-canonical NF-κB signaling pathway and induced the apoptosis of R-HL60 cells. The study results support the application and possible mechanism of proteasome inhibitors in patients with relapsed or refractory leukemia.

scholarly journals Identifying hub genes and immune infiltration of osteoarthritis using comprehensive bioinformatics analysis

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Zheng-yuan Wu ◽  
Gang Du ◽  
Yi-cai Lin
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Cell Activation ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Joint Space ◽  
Mast Cell Activation ◽  
Healthy Controls ◽  
Bioinformatics Analyses ◽  
Immune Infiltration

Abstract Background Osteoarthritis (OA) is the most common chronic degenerative joint disorder globally that is characterized by synovitis, cartilage degeneration, joint space stenosis, and sub-cartilage bone hyperplasia. However, the pathophysiologic mechanisms of OA have not been thoroughly investigated. Methods In this study, we conducted various bioinformatics analyses to identify hub biomarkers and immune infiltration in OA. The gene expression profiles of synovial tissues from 29 healthy controls and 36 OA samples were obtained from the gene expression omnibus database to identify differentially expressed genes (DEGs). The CIBERSORT algorithm was used to explore the association between immune infiltration and arthritis. Results Eighteen hub DEGs were identified as critical biomarkers for OA. Through gene ontology and pathway enrichment analyses, it was found that these DEGs were primarily involved in PI3K-Akt signaling pathway and Rap1 signaling pathway. Furthermore, immune infiltration analysis revealed differences in immune infiltration between patients with OA and healthy controls. The hub gene ZNF160 was closely related to immune cells, especially mast cell activation in OA. Conclusion Overall, this study presented a novel method to identify hub DEGs and their correlation with immune infiltration, which may provide novel insights into the diagnosis and treatment of patients with OA.

scholarly journals In silico gene expression profiling in Cannabis sativa

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 69 ◽  
Author(s):  
Luca Massimino
Keyword(s):  
Gene Expression ◽  
Expression Profiling ◽  
Developmental Stages ◽  
Cannabis Sativa ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Functional Genomic ◽  
Functional Genomic Data ◽  
Starting Point ◽  
Scientific Papers

The cannabis plant and its active ingredients (i.e., cannabinoids and terpenoids) have been socially stigmatized for half a century. Luckily, with more than 430,000 published scientific papers and about 600 ongoing and completed clinical trials, nowadays cannabis is employed for the treatment of many different medical conditions. Nevertheless, even if a large amount of high-throughput functional genomic data exists, most researchers feature a strong background in molecular biology but lack advanced bioinformatics skills. In this work, publicly available gene expression datasets have been analyzed giving rise to a total of 40,224 gene expression profiles taken from cannabis plant tissue at different developmental stages. The resource presented here will provide researchers with a starting point for future investigations with Cannabis sativa.

Microarray-Based Gene Expression Analysis Identifies Potential Diagnostic and Prognostic Biomarkers for Waldenström Macroglobulinemia

2018 ◽  
Vol 140 (2) ◽  
pp. 87-96
Author(s):  
Haitao Xu ◽  
Fusheng Yao
Keyword(s):  
Gene Expression ◽  
B Cell ◽  
Signaling Pathway ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Mitogen Activated Protein Kinase ◽  
Ppi Network ◽  
Waldenström Macroglobulinemia ◽  
Waldenstrom Macroglobulinemia

Waldenström macroglobulinemia (WM), also known as lymphoplasmacytic lymphoma, is rare but a clinicopathologically distinct B-cell malignancy. This study assessed differentially expressed genes (DEGs) to identify potential WM biomarkers and uncover the underlying the molecular mechanisms of WM progression using gene expression profiles from the Gene Expression Omnibus database. DEGs were identified using the LIMMA package and their potential functions were then analyzed by using the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses and the protein-protein interaction (PPI) network analysis by using the Search Tool for the Retrieval of Interacting Genes/Proteins database. Data showed that among 1,756 DEGs, 926 were upregulated and 830 were downregulated by comparing WM BM CD19+ with normal PB CD19+ B cell samples, whereas 241 DEGs (95 upregulated and 146 downregulated) were identified by comparing WM BM CD138+ with normal BM CD138+ plasma cell samples. The DEGs were enriched in different GO terms and pathways, including the apoptotic process, cell cycle arrest, immune response, cell adhesion, mitogen-activated protein kinase signaling pathway, toll-like receptor signaling pathway, and the gonadotropin-releasing hormone signaling pathway. Hub nodes in the PPI network included CDK1, JUN, CREBBP, EP300, CAD, CDK2, and MAPK14. Bioinformatics analysis of the GSE9656 dataset identified 7 hub genes that might play an important role in WM development and progression. Some of the candidate genes and pathways may serve as promising therapeutic targets for WM.

Identification of DMSA-Coated Fe3O4 Nanoparticles Induced-Apoptosis Response Genes in Human Monocytes by cDNA Microarrays

2013 ◽  
Vol 749 ◽  
pp. 377-383 ◽  
Author(s):  
Ying Xun Liu ◽  
Jian Yuan Huang ◽  
Dong Liang Wang ◽  
Jin Ke Wang
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Cell Apoptosis ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Dependent Manner ◽  
Receptor Signaling ◽  
Apoptosis Pathway ◽  
Receptor Signaling Pathway

This study investigated the cell apoptosis and gene expression profiles of human THP-1 monocytes in order to identify the molecular mechanism of cell apoptosis induced by meso-2,-3-dimercaptosuccinnic acid-coated Fe3O4magnetic nanoparticles. Cell apoptosis was visualized with flow cytometry after treated by 50 and 100 μg/ml Fe3O4nanoparticles, and the gene expression profiles were detected with Affymetrix Human Genome U133 Plus 2.0 GeneChips® microarrays. The transmission electron microscopy obserbation revealed that THP-1 cells were effectively labeled by the Fe3O4nanoparticles. The internalized Fe3O4nanoparticles increased cell apoptosis in a dose-dependent manner, but not decreased cell viability significantly. The cDNA microarray results showed that hundreds of genes were significantly regulated at the concentration of 50 and 100 μg/ml, and the level of these genes exhibited a dose response, includingCD14,CD86,CFLAR,IL-1,NFKBIA,NLRC4,NAIPandAIP3. The Fe3O4nanoparticles treatments resulted in significantly altered in Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and Cell apoptosis signaling pathway. Gene ontology analysis of these differentially expressed genes demonstrated that mainly up-regulated genes were related to cytokine production and cell apoptosis. These results showed that the Fe3O4nanoparticles induced THP-1 cells apoptosis and the level of lots of genes involved in extrinsic apoptosis pathway differentially expressed, which further revealed demonstrated the relation between Fe3O4MNPs treatment and cell apoptosis.

scholarly journals Potential genes and pathways associated with heterotopic ossification derived from analyses of gene expression profiles

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Zhanyu Yang ◽  
Delong Liu ◽  
Rui Guan ◽  
Xin Li ◽  
Yiwei Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Protein Kinase ◽  
Heterotopic Ossification ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Differentially Expressed ◽  
Heterotopic Bone ◽  
Hub Genes ◽  
Ppi Networks

Abstract Background Heterotopic ossification (HO) represents pathological lesions that refer to the development of heterotopic bone in extraskeletal tissues around joints. This study investigates the genetic characteristics of bone marrow mesenchymal stem cells (BMSCs) from HO tissues and explores the potential pathways involved in this ailment. Methods Gene expression profiles (GSE94683) were obtained from the Gene Expression Omnibus (GEO), including 9 normal specimens and 7 HO specimens, and differentially expressed genes (DEGs) were identified. Then, protein–protein interaction (PPI) networks and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed for further analysis. Results In total, 275 DEGs were differentially expressed, of which 153 were upregulated and 122 were downregulated. In the biological process (BP) category, the majority of DEGs, including EFNB3, UNC5C, TMEFF2, PTH2, KIT, FGF13, and WISP3, were intensively enriched in aspects of cell signal transmission, including axon guidance, negative regulation of cell migration, peptidyl-tyrosine phosphorylation, and cell-cell signaling. Moreover, KEGG analysis indicated that the majority of DEGs, including EFNB3, UNC5C, FGF13, MAPK10, DDIT3, KIT, COL4A4, and DKK2, were primarily involved in the mitogen-activated protein kinase (MAPK) signaling pathway, Ras signaling pathway, phosphatidylinositol-3-kinase/protein kinase B (PI3K/Akt) signaling pathway, and Wnt signaling pathway. Ten hub genes were identified, including CX3CL1, CXCL1, ADAMTS3, ADAMTS16, ADAMTSL2, ADAMTSL3, ADAMTSL5, PENK, GPR18, and CALB2. Conclusions This study presented novel insight into the pathogenesis of HO. Ten hub genes and most of the DEGs intensively involved in enrichment analyses may be new candidate targets for the prevention and treatment of HO in the future.

scholarly journals Comparative Transcriptome Analysis Provides Insights into the Polyunsaturated Fatty Acid Synthesis Regulation of Fat-1 Transgenic Sheep

2020 ◽  
Vol 21 (3) ◽  
pp. 1121
Author(s):  
Rongsong Luo ◽  
Zhong Zheng ◽  
Chunrong Yang ◽  
Xiaoran Zhang ◽  
Lei Cheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Transgenic Animals ◽  
Acid Synthesis ◽  
Abnormal Development ◽  
Pathogen Invasion ◽  
Transgenic Sheep ◽  
Synthesis Regulation

Transgenic technology has huge application potential in agriculture and medical fields, such as producing new livestock varieties with new valuable features and xenotransplantation. However, how an exogenous gene affects the host animal’s gene regulation networks and their health status is still poorly understood. In the current study, Fat-1 transgenic sheep were generated, and the tissues from 100-day abnormal (DAF_1) and normal (DAF_2) fetuses, postnatal lambs (DAF_4), transgenic-silencing (DAFG5), and -expressing (DAFG6) skin cells were collected and subjected to transcriptome sequencing, and their gene expression profiles were compared in multiple dimensions. The results were as follows. For DAF_1, its abnormal development was caused by pathogen invasion but not the introduction of the Fat-1 gene. Fat-1 expression down-regulated the genes related to the cell cycle; the NF-κB signaling pathway and the PI3K/Akt signaling pathway were down-regulated, and the PUFAs (polyunsaturated fatty acids) biosynthesis pathway was shifted toward the biosynthesis of high-level n-3 LC-PUFAs (long-chain PUFAs). Four key node genes, FADS2, PPARA, PRKACA, and ACACA, were found to be responsible for the gene expression profile shift from the Fat-1 transgenic 100-day fetus to postnatal lamb, and FADS2 may play a key role in the accumulation of n-3 LC-PUFAs in Fat-1 transgenic sheep muscle. Our study provides new insights into the FUFAs synthesis regulation in Fat-1 transgenic animals.

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