Dataset Information

RNA-Seq Bayesian Network Exploration of Immune System in Bovine.

ABSTRACT: Background:The stress is one of main factors effects on production system. Several factors (both genetic and environmental elements) regulate immune response to stress. Objectives:In order to determine the major immune system regulatory genes underlying stress responses, a learning Bayesian network approach for those regulatory genes was applied to RNA-Seq data from a bovine leukocyte model system. Material and Methods:The transcriptome dataset GSE37447 was used from GEO and a Bayesian network on differentially expressed genes was learned to investigate the gene regulatory network. Results:Applying the method produced a strongly interconnected network with four genes (TERF2IP, PDCD10, DDX10 and CENPE) acting as nodes, suggesting these genes may be important in the transcriptome regulation program of stress response. Of these genes TERF2IP has been shown previously to regulate gene expression, act as a regulator of the nuclear factor-kappa B (NF-?B) signalling, and to activate expression of NF-?B target genes; PDCD10 encodes a conserved protein associated with cell apoptosis; DDX10 encodes a DEAD box protein and is believed to be associated with cellular growth and division; and CENPE involves unstable spindle microtubule capture at kinetochores. Together these genes are involved in DNA damage of apoptosis, RNA splicing, DNA repairing, and regulating cell division in the bovine genome. The topology of the learned Bayesian gene network indicated that the genes had a minimal interrelationship with each other. This type of structure, using the publically available computational tool, was also observed on human orthologous genes of the differentially expressed genes. Conclusions:Overall, the results might be used in transcriptomic-assisted selection and design of new drug targets to treat stress-related problems in bovines.

SUBMITTER: Behdani E

PROVIDER: S-EPMC7080973 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature

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RNA-Seq Bayesian Network Exploration of Immune System in Bovine.

Behdani Elham E Ghaderi-Zefrehei Mostafa M Rafeie Farjad F Bakhtiarizadeh Mohammad Reza MR Roshanfeker Hedayatollah H Fayazi Jamal J

Iranian journal of biotechnology 20190901 3

<h4>Background</h4>The stress is one of main factors effects on production system. Several factors (both genetic and environmental elements) regulate immune response to stress.<h4>Objectives</h4>In order to determine the major immune system regulatory genes underlying stress responses, a learning Bayesian network approach for those regulatory genes was applied to RNA-Seq data from a bovine leukocyte model system.<h4>Material and methods</h4>The transcriptome dataset GSE37447 was used from GEO an ...[more]

PMID: 32195281

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Project description:Individuals with diverticula or outpouchings of the colonic mucosa and submucosa through the colonic wall have diverticulosis, which is usually asymptomatic. In 10-25% of individuals, the diverticula become inflamed, resulting in diverticulitis. Very little is known about the pathophysiology or gene regulatory pathways involved in the development of diverticulitis. To identify these pathways, we deep sequenced RNAs isolated from full-thickness sections of sigmoid colon from diverticulitis patients and control individuals. Specifically for diverticulitis cases, we analyzed tissue adjacent to areas affected by chronic disease. Since the tissue was collected during elective sigmoid resection, the disease was in a quiescent state. A comparison of differentially expressed genes found that gene ontology (GO) pathways associated with the immune response were upregulated in diverticulitis patients compared with nondiverticulosis controls. Next, weighted gene coexpression network analysis was performed to identify the interaction among coexpressed genes. This analysis revealed RASAL3, SASH3, PTPRC, and INPP5D as hub genes within the brown module eigengene, which highly correlated (r = 0.67, P = 0.0004) with diverticulitis. Additionally, we identified elevated expression of downstream interacting genes. In summary, transcripts associated with the immune response were upregulated in adjacent tissue from the sigmoid colons of chronic, recurrent diverticulitis patients. Further elucidating the genetic or epigenetic mechanisms associated with these alterations can help identify those at risk for chronic disease and may assist in clinical decision management.NEW & NOTEWORTHY By using an unbiased approach to analyze transcripts expressed in unaffected colonic tissues adjacent to those affected by chronic diverticulitis, our study implicates that a defect in the immune response may be involved in the development of the disease. This finding expands on the current data that suggest the pathophysiology of diverticulitis is mediated by dietary, age, and obesity-related factors. Further characterizing the immunologic differences in diverticulitis may better inform clinical decision-making.

Dataset Information

RNA-Seq Bayesian Network Exploration of Immune System in Bovine.

Publications

RNA-Seq Bayesian Network Exploration of Immune System in Bovine.

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