Identification of therapeutic targets and prognostic biomarkers in cholangiocarcinoma via WGCNA

Xu, Lei; Xiao, Ting; Xu, Ling; Yao, Wei

doi:10.3389/fonc.2022.977992

Cited by 3 publications

(1 citation statement)

References 52 publications

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“…WGCNA and Expression-Based Transcriptome and Metabolome Correlation Analysis. The weighted gene coexpression network analysis (WGCNA) was performed using WGCNA package in R. 28 "Spearman" algorithm was used to set a threshold value of correlation coefficient for the differentially expressed genes and differential metabolites in selected module integration, and the OPLS-DA model was used to measure the role of differentially expressed genes in metabolic variation.…”

Section: Generation Of Uvhst2 Gene Deletion and Complementedmentioning

confidence: 99%

Histone Deacetylase UvHST2 Is a Global Regulator of Secondary Metabolism in Ustilaginoidea virens

Liu,

Wang,

Duan

et al. 2023

J. Agric. Food Chem.

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Ustilaginoidea virens, the causal agent of rice false smut, produces a large amount of mycotoxins, including ustilaginoidins and sorbicillinoids. However, little is known about the regulatory mechanism of mycotoxin biosynthesis inU. virens.Here, we demonstrate that the NAD + -dependent histone deacetylase UvHST2 negatively regulates ustilaginoidin biosynthesis. UvHst2 knockout caused retarded hypha growth and reduced conidiation and pathogenicity inU. virens. Transcriptome analysis revealed that the transcription factor genes, transporter genes, and other tailoring genes in eight biosynthetic gene clusters (BGCs) including ustilaginoidin and sorbicillinoid BGCs were upregulated in ΔUvhst2. Interestingly, the UvHst2 deletion affects alternative splicing. Metabolomics revealed that UvHST2 negatively regulates the biosynthesis of various mycotoxins including ustilaginoidins, sorbicillin, ochratoxin B, zearalenone, and O-M-sterigmatocystin. Combined transcriptome and metabolome analyses uncover that UvHST2 positively regulates pathogenicity but negatively modulates the expression of BGCs involved in secondary metabolism. Collectively, UvHST2 functions as a global regulator of secondary metabolism inU. virens.

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Section: Generation Of Uvhst2 Gene Deletion and Complementedmentioning

confidence: 99%

Histone Deacetylase UvHST2 Is a Global Regulator of Secondary Metabolism in Ustilaginoidea virens

Liu,

Wang,

Duan

et al. 2023

J. Agric. Food Chem.

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Gene-network based analysis of human placental trophoblast subtypes identifies critical genes as potential targets of therapeutic drugs

Lackner,

Pollheimer,

Latos

et al. 2023

Journal of Integrative Bioinformatics

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During early pregnancy, extravillous trophoblasts (EVTs) play a crucial role in modifying the maternal uterine environment. Failures in EVT lineage formation and differentiation can lead to pregnancy complications such as preeclampsia, fetal growth restriction, and pregnancy loss. Despite recent advances, our knowledge on molecular and external factors that control and affect EVT development remains incomplete. Using trophoblast organoid in vitro models, we recently discovered that coordinated manipulation of the transforming growth factor beta (TGFβ) signaling is essential for EVT development. To further investigate gene networks involved in EVT function and development, we performed weighted gene co-expression network analysis (WGCNA) on our RNA-Seq data. We identified 10 modules with a median module membership of over 0.8 and sizes ranging from 1005 (M1) to 72 (M27) network genes associated with TGFβ activation status or in vitro culturing, the latter being indicative for yet undiscovered factors that shape the EVT phenotypes. Lastly, we hypothesized that certain therapeutic drugs might unintentionally interfere with placentation by affecting EVT-specific gene expression. We used the STRING database to map correlations and the Drug-Gene Interaction database to identify drug targets. Our comprehensive dataset of drug-gene interactions provides insights into potential risks associated with certain drugs in early gestation.

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Long Non-Coding RNA AGAP2-AS1: A Comprehensive Overview on Its Biological Functions and Clinical Significances in Human Cancers

Ma,

Zhang,

Wang

et al. 2024

Molecules

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Long non-coding RNAs (lncRNAs) are well known for their oncogenic or anti-oncogenic roles in cancer development. AGAP2-AS1, a new lncRNA, has been extensively demonstrated as an oncogenic lncRNA in various cancers. Abundant experimental results have proved the aberrantly high level of AGAP2-AS1 in a great number of malignancies, such as glioma, colorectal, lung, ovarian, prostate, breast, cholangiocarcinoma, bladder, colon and pancreatic cancers. Importantly, the biological functions of AGAP2-AS1 have been extensively demonstrated. It could promote the proliferation, migration and invasion of cancer cells. Simultaneously, the clinical significances of AGAP2-AS1 were also illustrated. AGAP2-AS1 was exceptionally overexpressed in various cancer tissues. Clinical studies disclosed that the abnormal overexpression of AGAP2-AS1 was tightly connected with overall survival (OS), lymph nodes metastasis (LNM), clinical stage, tumor infiltration, high histological grade (HG), serous subtype and PFI times. However, to date, the biological actions and clinical significances of AGAP2-AS1 have not been systematically reviewed in human cancers. In the present review, the authors overviewed the biological actions, potential mechanisms and clinical features of AGAP2-AS1 according to the previous studies. In summary, AGAP2-AS1, as a vital oncogenic gene, is a promising biomarker and potential target for carcinoma prognosis and therapy.

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Identification of therapeutic targets and prognostic biomarkers in cholangiocarcinoma via WGCNA

Cited by 3 publications

References 52 publications

Histone Deacetylase UvHST2 Is a Global Regulator of Secondary Metabolism in Ustilaginoidea virens

Histone Deacetylase UvHST2 Is a Global Regulator of Secondary Metabolism in Ustilaginoidea virens

Gene-network based analysis of human placental trophoblast subtypes identifies critical genes as potential targets of therapeutic drugs

Long Non-Coding RNA AGAP2-AS1: A Comprehensive Overview on Its Biological Functions and Clinical Significances in Human Cancers

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