Gene Set Enrichment Analysis Reveals That Fucoidan Induces Type I IFN Pathways in BMDC

Choi, Su Mi; Jeon, Sol A; Heo, Bu Yeon; Kang, Jong-Ho; Jung, Yunju; Duong, Pham Thi Thuy; Song, Ik‐Chan; Kim, Jeong‐Hwan; Kim, Seon‐Young; Kwon, Jaeyul

doi:10.3390/nu14112242

Cited by 6 publications

(4 citation statements)

References 72 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To explore the effect of δ-zein gene on C. utilis metabolism, gene set enrichment analysis (GSEA) was performed on the sets of DEGs. GSEA was used to examine several pathways that exhibited significant enrichment among the identified DEGs ( Choi et al, 2022 ). In the analysis, the gene sets of interest were derived from GO terms and KEGG pathways.…”

Section: Resultsmentioning

confidence: 99%

An integrated transcriptomic and metabolic phenotype analysis to uncover the metabolic characteristics of a genetically engineered Candida utilis strain expressing δ-zein gene

He,

Gong,

Wan

et al. 2023

Front. Microbiol.

View full text Add to dashboard Cite

IntroductionCandida utilis (C. utilis) has been extensively utilized as human food or animal feed additives. With its ability to support heterologous gene expression, C. utilis proves to be a valuable platform for the synthesis of proteins and metabolites that possess both high nutritional and economic value. However, there remains a dearth of research focused on the characteristics of C. utilis through genomic, transcriptomic and metabolic approaches.MethodsWith the aim of unraveling the molecular mechanism and genetic basis governing the biological process of C. utilis, we embarked on a de novo sequencing endeavor to acquire comprehensive sequence data. In addition, an integrated transcriptomic and metabolic phenotype analysis was performed to compare the wild-type C. utilis (WT) with a genetically engineered strain of C. utilis that harbors the heterologous δ-zein gene (RCT).Resultsδ-zein is a protein rich in methionine found in the endosperm of maize. The integrated analysis of transcriptomic and metabolic phenotypes uncovered significant metabolic diversity between the WT and RCT C. utilis. A total of 252 differentially expressed genes were identified, primarily associated with ribosome function, peroxisome activity, arginine and proline metabolism, carbon metabolism, and fatty acid degradation. In the experimental setup using PM1, PM2, and PM4 plates, a total of 284 growth conditions were tested. A comparison between the WT and RCT C. utilis demonstrated significant increases in the utilization of certain carbon source substrates by RCT. Gelatin and glycogen were found to be significantly utilized to a greater extent by RCT compared to WT. Additionally, in terms of sulfur source substrates, RCT exhibited significantly increased utilization of O-Phospho-L-Tyrosine and L-Methionine Sulfone when compared to WT.DiscussionThe introduction of δ-zein gene into C. utilis may lead to significant changes in the metabolic substrates and metabolic pathways, but does not weaken the activity of the strain. Our study provides new insights into the transcriptomic and metabolic characteristics of the genetically engineered C. utilis strain harboring δ-zein gene, which has the potential to advance the utilization of C. utilis as an efficient protein feed in agricultural applications.

show abstract

Section: Resultsmentioning

confidence: 99%

An integrated transcriptomic and metabolic phenotype analysis to uncover the metabolic characteristics of a genetically engineered Candida utilis strain expressing δ-zein gene

He,

Gong,

Wan

et al. 2023

Front. Microbiol.

View full text Add to dashboard Cite

show abstract

“…Next, Cytoscape was used to visualize the co‐upregulated gene set enrichment results. Briefly, clusters are divided into five representative categories of terms, including “Signal transduction,” [ 29 ] “Stimulation and cell maturation,” [ 30 ] “Chemotaxis and migration,” [ 31 ] “Regulation of adaptive immune response,” [ 32 ] and “Regulation of immune balance” [ 33 ] (Figure 2G).…”

Section: Resultsmentioning

confidence: 99%

“…Culture of BMDCs: Bone marrow cells were aseptically isolated from the tibia and femur of SPF mice. As previously mentioned , [30] the cells were induced into DCs using a directed differentiation medium (RPMI medium containing 10% FBS, 1% penicillin/streptomycin, 20 ng mL −1 GM-CSF and 10 ng mL −1 IL-4). Replace half of the fresh medium on the third and fifth days respectively, and collect cells on the seventh day.…”

Section: Methodsmentioning

confidence: 99%

Synthetic Self‐Adjuvanted Lipopeptide Vaccines Conferred Protection against Helicobacter pylori Infection

Xue

Liu

Wang

et al. 2023

Adv Healthcare Materials

View full text Add to dashboard Cite

Helicobacter pylori (H. pylori) colonizes the stomach epithelium of half the world's population and is responsible for various digestive diseases and even stomach cancer. Vaccine‐mediated protection against H. pylori infection depends primarily on the specific mucosal and T‐cell responses. In this study, the synthetic lipopeptide vaccines, Hp4 (Pam2Cys modified UreB T‐cell epitope) and Hp10 (Pam2Cys modified CagA T/B cell combined epitope), not only induce the bone marrow derived dendritic cells (BMDCs) maturation by activating a variety of pattern‐recognition receptors (PRRs) such as Toll‐like receptor (TLR), Nod‐like receptor (NLR), and retinoic acid‐inducing gene (RIG) I‐like receptor (RLR), and but also stimulate BMDCs to secret cytokines that have the potential to modulate T‐cell activation and differentiation. Although intranasal immunization with Hp4 or Hp10 elicits robust epitope‐specific T‐cell responses in mice, only Hp10 confers protection against H. pylori infection, possibly due to the fact that Hp10 also induces substantial specific sIgA response at mucosal sites. Interestingly, Hp4 elevates the protective response against H. pylori infection of Hp10 when administrated in combination, characterized by better protective effect and enhanced specific T‐cell and mucosal antibody responses. The results suggest that synthetic lipopeptide vaccines based on the epitopes derived from the protective antigens are promising candidates for protection against H. pylori infection.

show abstract

“…Based on the gene expression level in training datasets, GSEA was adopted to screen the significantly correlated pathways with subtypes. 27 FDR less than 0.05 was considered to be significant.…”

Section: Methodsmentioning

confidence: 99%

An effective disease diagnostic model related to pyroptosis in ischemic cardiomyopathy

Jin,

Liu,

Zhang

et al. 2023

J Cellular Molecular Medi

View full text Add to dashboard Cite

Pyroptosis is involved in ischemic cardiomyopathy (ICM). The study aimed to investigate the pyroptosis‐related genes and clarify their diagnostic value in ICM. The bioinformatics method identified the differential pyroptosis genes between the normal control and ICM samples from online datasets. Then, protein–protein interaction (PPI) and function analysis were carried out to explore the function of these genes. Following, subtype analysis was performed using ConsensusClusterPlus, functions, immune score, stromal score, immune cell proportion and human leukocyte antigen (HLA) genes between subtypes were investigated. Moreover, optimal pyroptosis genes were selected using the least absolute shrinkage and selection operator (LASSO) analysis to construct a diagnostic model and evaluate its effectiveness using receiver operator characteristic (ROC) analysis. Twenty‐one differential expressed pyroptosis genes were identified, and these genes were related to immune and pyroptosis. Subtype analysis identified two obvious subtypes: sub‐1 and sub‐2. And LASSO identified 13 optimal genes used to construct the diagnostic model. The diagnostic model in ICM diagnosis with the area under ROC (AUC) was 0.965. Our results suggested that pyroptosis was tightly associated with ICM.

show abstract

Gene Set Enrichment Analysis Reveals That Fucoidan Induces Type I IFN Pathways in BMDC

Cited by 6 publications

References 72 publications

An integrated transcriptomic and metabolic phenotype analysis to uncover the metabolic characteristics of a genetically engineered Candida utilis strain expressing δ-zein gene

An integrated transcriptomic and metabolic phenotype analysis to uncover the metabolic characteristics of a genetically engineered Candida utilis strain expressing δ-zein gene

Synthetic Self‐Adjuvanted Lipopeptide Vaccines Conferred Protection against Helicobacter pylori Infection

An effective disease diagnostic model related to pyroptosis in ischemic cardiomyopathy

Contact Info

Product

Resources

About