Co-expression gene network analysis reveals novel regulatory pathways involved in porto-sinusoidal vascular disease

Hernández‐Gea, Virginia; Campreciós, Genís; Betancourt, Fabian; Pérez-Campuzano, Valeria; Seijó, Susana; Díaz, Alba; Gallego‐Durán, Rocío; Olivas, Pol; Orts, Lara; Magaz, Marta; Baiges, Anna; Turón, Fanny; Sidorova, Julia; Romero‐Gómez, Manuel; Lozano, Juanjo; García‐Pagán, Juan Carlos

doi:10.1016/j.jhep.2021.05.014

Cited by 20 publications

(25 citation statements)

References 30 publications

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“…Dysfunction in lipid metabolism may also play a role in PSVD etiology. Our transcriptomic analysis, showing that the top enriched DEGs are involved in lipid metabolism, is consistent with the reported results of a transcriptomic study of a human PSVD cohort 39. In addition, retinol metabolism is another enriched Kyoto Encyclopedia of Genes and Genomes pathway in our transcriptomic data.…”

Section: Discussionsupporting

confidence: 90%

Genetic predisposition to porto‐sinusoidal vascular disorder: A functional genomic‐based, multigenerational family study

et al. 2022

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Background and Aims: Porto-sinusoidal vascular disorder (PSVD) is a group of liver vascular diseases featuring lesions encompassing the portal venules and sinusoids unaccompanied by cirrhosis, irrespective of the presence/absence of portal hypertension. It can occur secondary to coagulation disorders or insult by toxic agents. However, the cause of PSVD remains unknown in most cases. Hereditary cases of PSVD are

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Section: Discussionsupporting

confidence: 90%

Genetic predisposition to porto‐sinusoidal vascular disorder: A functional genomic‐based, multigenerational family study

et al. 2022

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“…Using a biological network approach (co-expression gene network analysis) to compare 20 PSVD cases, 20 age and sex-matched patients with cirrhosis and 13 healthy individuals, transcriptomics has recently demonstrated that PSVD is characterised by a deregulation of pathways involved in vascular homeostasis. 84 Specifically, the study identified genes of the Serpin family (SERPINC1), the apolipoproteins (APOA, APOB, APOC), ATP synthases (ATP5G1, ATP5B), fibrinogen genes (FGB, FGA) and alpha-2macroglobulin as differentially expressed in PSVD. These genes are involved in vascular haemostasis, coagulation, lipid metabolism and oxidative phosphorylation, and in other areas of medicine they have been associated with vascular remodelling,…”

Section: Transcriptomicsmentioning

confidence: 99%

Porto-sinusoidal vascular disorder

Gottardi

Sempoux

Berzigotti

2022

Journal of Hepatology

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“…GS was used to measure the association degree between genes and external information. The individual gene expression associations with BITC exposure were quantified by defining GS as the correlation between the gene expression and the trait . For each module, a quantitative measure of MM was also defined as the ME gene correlation and the gene expression profile.…”

Section: Methodsmentioning

confidence: 99%

Transcriptome Analysis and Weighted Gene Co-expression Network Reveal Multitarget-Directed Antibacterial Mechanisms of Benzyl Isothiocyanate against Staphylococcus aureus

Ming

et al. 2021

J. Agric. Food Chem.

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Staphylococcus aureus can cause many diseases and has a strong tendency to develop resistance to multiple antibiotics. In this study, benzyl isothiocyanate (BITC) was shown to have an excellent inhibitory effect on S. aureus ATCC25923 and methicillin-resistant S. aureus strains, with a minimum inhibitory concentration of 10 μg/mL. Under a scanning electron microscope, shrinkage and lysis of the cellular envelope were observed when exposed to BITC, and a bactericidal mode of BITC against S. aureus was further confirmed through flow cytometry. Additionally, the RNA profiles of S. aureus cells exposed to BITC indicated a violent transcriptional response to BITC. Through Kyoto Encyclopedia of Genes and Genomes analysis, it was found that many pathways involving bacterial survival were significantly affected, such as RNA degradation, oxidative phosphorylation, arginine biosynthesis, and so forth. A gene co-expression network was constructed using weighted gene co-expression network analysis, and six biologically meaningful co-expression modules and 125 hub genes were identified from the network. Among them, EfeB, GroES, SmpB, and Lsp were possibly targeted by BITC, leading to the death of S. aureus. Our results indicated a great potential of BITC to be applied in food safety and pharmaceuticals, highlighting its multitarget-directed bactericidal effects on S. aureus.

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Co-expression gene network analysis reveals novel regulatory pathways involved in porto-sinusoidal vascular disease

Cited by 20 publications

References 30 publications

Genetic predisposition to porto‐sinusoidal vascular disorder: A functional genomic‐based, multigenerational family study

Genetic predisposition to porto‐sinusoidal vascular disorder: A functional genomic‐based, multigenerational family study

Porto-sinusoidal vascular disorder

Transcriptome Analysis and Weighted Gene Co-expression Network Reveal Multitarget-Directed Antibacterial Mechanisms of Benzyl Isothiocyanate against Staphylococcus aureus

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