PathIN: an integrated tool for the visualization of pathway interaction networks

Minadakis, George; Christodoulou, Kyproula; Tsouloupas, George; Spyrou, George M.

doi:10.1016/j.csbj.2022.12.028

Cited by 5 publications

(2 citation statements)

References 43 publications

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“…Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation of genes differently expressed in the presence of LPCs was conducted using the KEGG mapper ( : accessed on 6 November 2023) and ShinyGO ( : accessed on 6 November 2023) with a restricted false discovery rate (FDR) < 0.05. Pathway networks linked with influenza A pathways were analyzed using PathIN tools ( : accessed on 30 November 2023) [ 38 ].…”

Section: Methodsmentioning

confidence: 99%

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Lysophosphatidylcholines Promote Influenza Virus Reproduction through the MAPK/JNK Pathway in PMA-Differentiated THP-1 Macrophages

Cha,

Choi,

2024

IJMS

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Obesity and metabolic syndrome alter serum lipid profiles. They also increase vulnerability to viral infections and worsen the survival rate and symptoms after infection. How serum lipids affect influenza virus proliferation is unclear. Here, we investigated the effects of lysophosphatidylcholines on influenza A virus (IAV) proliferation. IAV particles in the culture medium were titrated using extraction-free quantitative PCR, and viral RNA and protein levels were assessed using real-time PCR and Western blot, respectively. RNA sequencing data were analyzed using PCA and heatmap analysis, and pathway analysis was performed using the KEGG mapper and PathIN tools. Statistical analysis was conducted using SPSS21.0. LPC treatment of THP-1 cells significantly increased IAV proliferation and IAV RNA and protein levels, and saturated LPC was more active in IAV RNA expression than unsaturated LPC was. The functional analysis of genes affected by LPCs showed that the expression of genes involved in IAV signaling, such as suppressor of cytokine signaling 3 (SOCS3), phosphoinositide-3-kinase regulatory subunit 3 (PI3K) and AKT serine/threonine kinase 3 (AKT3), Toll-like receptor 7 (TKR7), and interferon gamma receptor 1 (IFNGR1), was changed by LPC. Altered influenza A pathways were linked with MAPK and PI3K/AKT signaling. Treatment with inhibitors of MAPK or PI3K attenuated viral gene expression changes induced by LPCs. The present study shows that LPCs stimulated virus reproduction by modifying the cellular environment to one in which viruses proliferated better. This was mediated by the MAPK, JNK, and PI3K/AKT pathways. Further animal studies are needed to confirm the link between LPCs from serum or the respiratory system and IAV proliferation.

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Section: Methodsmentioning

confidence: 99%

“…sdstate.edu: accessed on 6 November 2023) with a restricted false discovery rate (FDR) < 0.05. Pathway networks linked with influenza A pathways were analyzed using PathIN tools (https://pathin.cing-big.hpcf.cyi.ac.cy: accessed on 30 November 2023) [38].…”

Section: Rna Profile Analysismentioning

confidence: 99%

Lysophosphatidylcholines Promote Influenza Virus Reproduction through the MAPK/JNK Pathway in PMA-Differentiated THP-1 Macrophages

Cha,

Choi,

2024

IJMS

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Integrative Analysis of Multi Omic Data

Yue,

Mohamed-Hussein

2024

Reference Module in Life Sciences

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miRNAs mediate the impact of smoking on dental pulp stem cells via the p53 pathway

Hardin,

Abid,

Vang

et al. 2024

Toxicological Sciences

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Cigarette smoke changes the genomic and epigenomic imprint of cells. In this study, we investigated the biological consequences of extended cigarette smoke exposure on dental pulp stem cells (DPSCs) and the potential roles of miRNAs. DPSCs were treated with various doses of cigarette smoke condensate (CSC) for up to six weeks. Cell proliferation, survival, migration, and differentiation were evaluated. Cytokine and miRNA expression were profiled. The results showed that extended exposure to CSC significantly impaired the regenerative capacity of the DPSCs. Bioinformatic analysis showed that the cell cycle pathway, cancer pathways (small cell lung cancer, pancreatic, colorectal, and prostate cancer), and pathways for TNF, TGF-β, p53, PI3K-Akt, mTOR and ErbB signal transduction, were associated with altered miRNA profiles. In particular, three miRNAs has-miR-26a-5p, has-miR-26b-5p and has-miR-29b-3p fine tune the p53 and cell cycle signaling pathways to regulate DPSC cellular activities. The work indicated that miRNAs are promising targets to modulate stem cell regeneration and understanding miRNA-targeted genes and their associated pathways in smoking individuals have significant implications for disease control and prevention.

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PathIN: an integrated tool for the visualization of pathway interaction networks

Cited by 5 publications

References 43 publications

Lysophosphatidylcholines Promote Influenza Virus Reproduction through the MAPK/JNK Pathway in PMA-Differentiated THP-1 Macrophages

Lysophosphatidylcholines Promote Influenza Virus Reproduction through the MAPK/JNK Pathway in PMA-Differentiated THP-1 Macrophages

Integrative Analysis of Multi Omic Data

miRNAs mediate the impact of smoking on dental pulp stem cells via the p53 pathway

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