Weighted Gene Co-Expression Network Analysis Reveals Dysregulation of Mitochondrial Oxidative Phosphorylation in Eating Disorders

Yang, Liulin; Li, Yun; Turki, Turki; Tan, Huizi; Wei, Zhi; Chang, Xiao

doi:10.3390/genes9070325

Cited by 4 publications

(3 citation statements)

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“…Also WGCNA method can group genes into the specified modules based on the high correlations between co-expression genes across the samples, resulting in a cluster of genes that share a similar function ( Langfelder and Horvath, 2008 ; Atila et al, 2009 ). Cumulative studies on the transcriptome data using the WGCNA method to investigate complex traits or disease in animals, such as obesity ( Kogelman et al, 2014 ), residual feed intake ( Kong et al, 2016 ), and fat deposition ( Oliveira et al, 2018 ), and in human, including brain evolution ( Oldham et al, 2006 ), schizophrenia ( Chang et al, 2017 ), autism ( Gupta et al, 2014 ), neuroblastoma ( Yang et al, 2018b ), and eating disorders ( Yang et al, 2018a ) has been reported. However, RNA-Seq has not been used to identify the candidate genes related to heat tolerance in buffaloes.…”

Section: Introductionmentioning

confidence: 99%

Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data

Liu

et al. 2019

Front. Genet.

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Heat stress has a detrimental effect on the physiological and production performance of buffaloes. Elucidating the underlying mechanisms of heat stress is challenging, therefore identifying candidate genes is urgent and necessary. We evaluated the response of buffaloes (n = 30) to heat stress using the physiological parameters, ELISA indexes, and hematological parameters. We then performed mRNA and microRNA (miRNA) expression profiles analysis between heat tolerant (HT, n = 4) and non-heat tolerant (NHT, n = 4) buffaloes, as well as the specific modules, significant genes, and miRNAs related to the heat tolerance identified using the weighted gene co-expression network analysis (WGCNA). The results indicated that the buffaloes in HT had a significantly lower rectal temperature (RT) and respiratory rate (RR) and displayed a higher plasma heat shock protein (HSP70 and HSP90) and cortisol (COR) levels than those of NHT buffaloes. Differentially expressed analysis revealed a total of 753 differentially expressed genes (DEGs) and 16 differentially expressed miRNAs (DEmiRNAs) were identified between HT and NHT. Using the WGCNA analysis, these DEGs assigned into 5 modules, 4 of which were significantly correlation with the heat stress indexes. Interestingly, 158 DEGs associated with heat tolerance in the turquoise module were identified, 35 of which were found within the protein-protein interaction network. Several hub genes (IL18RAP, IL6R, CCR1, PPBP, IL1B, and IL1R1) were identified that significantly enriched in the Cytokine-cytokine receptor interaction. The findings may help further elucidate the underlying mechanisms of heat tolerance in buffaloes.

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Section: Introductionmentioning

confidence: 99%

Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data

Liu

et al. 2019

Front. Genet.

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“…Weighted gene coexpression network analysis (WCGNA) was used to construct a coexpression network based on scale-free topology to detect coexpression modules of genes with similar patterns of expression (32). In our study, DEGs were input into the WGCNA package (v1.69) in R to construct weighted coexpression modules.…”

Section: Construction Of Gene Coexpression Networkmentioning

confidence: 99%

ASF1B: A Possible Prognostic Marker, Therapeutic Target, and Predictor of Immunotherapy in Male Thyroid Carcinoma

Qiu

Shi

et al. 2022

Front. Oncol.

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BackgroundThyroid carcinoma (TC) is the most common malignant endocrine tumor worldwide. Several studies have documented that male patients with TC have a higher rate of metastasis and disease recurrence than female patients. However, the mechanism underlying this observation is not completely clear. The goal of our research was to investigate the potential key candidate genes and pathways related to TC progression in male patients at the molecular level.MethodsA total of 320 samples were obtained from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. Hub genes were screened out using weighted gene coexpression network analysis (WGCNA) and a protein–protein interaction (PPI) network analysis. Survival analysis was used to identify hub genes associated with disease-free survival (DFS) rates. Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression (ESTIMATE) data were used to assess the relationship between hub genes and immune cell infiltration. The molecular mechanism and biological functions of hub genes were explored using RT-qPCR, Western blot, Cell Counting Kit-8 Assay, flow cytometry, Transwell assays, and scratch assays.ResultsForty-seven hub genes were identified, and the survival analysis demonstrated that anti-silencing function 1B (ASF1B) was the sole independent risk factor for poor DFS in male TC patients. Possible associations between the results from the ESTIMATE analysis showed that the ASF1B expression level was related to the ESTIMATE score, immune score, and T-cell regulatory (Treg) infiltration level. Through in vitro cell function experiments, we verified that knockdown of ASF1B inhibited KTC-1 cell proliferation, promoted cell apoptosis, and blocked cell cycle. The silencing of ASF1B reduced protein kinase B (AKT), phospho-AKT (p-AKT), and forkhead box p3 (FOXP3) in KTC-1 cells. Moreover, FOXP3 overexpression markedly restored the cell migration, invasion, and proliferation abilities repressed by ASF1B knockdown.ConclusionsOur results indicate that ASF1B can be considered a prognostic marker, therapeutic target, and predictor of immunotherapy response in male thyroid cancer patients. However, further in-depth studies are required to validate this finding.

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“…In the Diagnostic and Statistical Manual of Mental Disorders (Fifth Edition), EDs primarily include anorexia nervosa (AN), bulimia nervosa (BN), binge eating disorders (BEDs), avoidant/restrictive food intake disorder (ARFID), ruminant/reflux disorders, and pica. In recent years, many studies on EDs have been published, such as epidemiological studies (e.g., Mitchison & Mond, 2015; Udo & Grilo, 2018), clinical medical studies (e.g., Yang et al, 2018), and psychological studies (e.g., Marzilli et al, 2018), which indicate that researchers have long been concerned about EDs. By summarizing and contextualizing the reviews of recent epidemiologic data on EDs in Asia and the Pacific, Thomas et al (2016) found that regions with EDs are transnational in distribution and that the prevalence rate of eating disorders is very high.…”

Section: Introductionmentioning

confidence: 99%

Developing an Item Bank of Computerized Adaptive Testing for Eating Disorders in Chinese University Students

Liu

Zhang

et al. 2022

SAGE Open

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We aimed to develop an item bank of computerized adaptive testing for eating disorders (CAT-ED) in Chinese university students to increase measurement precision and improve test efficiency. A total of 1,025 Chinese undergraduate respondents answered a series of questions about eating disorders in a paper-pencil test. A total of 133 items from four well-validated Chinese-version scales of eating disorders were used to construct the item bank of CAT-ED with the following analysis. First, unidimensionality, model fit, local independence, item ﬁt, discrimination and differential item functioning (DIF) were tested. Then, two simulation studies were applied to test the CAT-ED’s effectivity and rationality by calculating concurrent criterion-related validity, sensitivity and speciﬁcity. The ﬁnal item bank comprised 77 items, which met the requirements of local independence, item ﬁt, high discrimination and no differential item functioning in CAT. The mean number of administered items in CAT with the stopping rule fixed at SE ≤ 0.3 was 11 items. The obtained results showed that CAT-ED had acceptable reliability, validity, sensitivity and speciﬁcity.

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Weighted Gene Co-Expression Network Analysis Reveals Dysregulation of Mitochondrial Oxidative Phosphorylation in Eating Disorders

Cited by 4 publications

References 40 publications

Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data

Identifying Hub Genes for Heat Tolerance in Water Buffalo (Bubalus bubalis) Using Transcriptome Data

ASF1B: A Possible Prognostic Marker, Therapeutic Target, and Predictor of Immunotherapy in Male Thyroid Carcinoma

Developing an Item Bank of Computerized Adaptive Testing for Eating Disorders in Chinese University Students

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