Bioinformatics analysis of oxidative stress genes in the pathogenesis of ulcerative colitis based on a competing endogenous RNA regulatory network

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Bioinformatics and Genomics

Main article text

 

Introduction

Materials and Methods

Data resource

Identification of DE-lncRNAs, DE-miRNAs, and DE-mRNAs

Construction of ceRNA network

Identification of oxidative stress-associated genes

Prediction of drug interactions

Animals and treatment

Histological examination

Total RNA isolation and qRT-PCR

Myeloperoxidase (MPO) activity

Detection of the levels of GSH, GSSG, ROS, SOD, and HMGB-1

Flow cytometry analysis of ROS

Western blotting

Statistical analysis

Results

Data integration and analysis for lncRNA/mRNA and miRNA/mRNA association pairs

Establishment of a ceRNA regulatory network

Screening for genes related to oxidative stress

Relationships between oxidative stress genes and active UC pathogenesis

Relationships between oxidative stress genes and glucocorticoid resistance in active UC

Prediction of drug interactions

Validation in mice with DSS-induced UC

Discussion

Conclusion

Supplemental Information

The ARRIVE guidelines 2.0 author checklist.

DOI: 10.7717/peerj.17213/supp-2

Principal components analysis for lncRNA, miRNA and mRNA.

(A) Principal components analysis for lncRNA between control and UC samples in GSE75214 dataset. (B) Principal components analysis for miRNA between control and UC samples in GSE75214 dataset. (C) Principal components analysis for miRNA between control and UC samples in GSE48959 dataset. (D) Principal components analysis for mRNA between control and UC samples in GSE48959 dataset.

DOI: 10.7717/peerj.17213/supp-3

AUC and accuracy density distributions.

AUCand accuracydensitydistributions of GSE75214 (A) and GSE48959 (B) datasets.

DOI: 10.7717/peerj.17213/supp-4

The expression of inflammatory cytokines, pro-inflammatory effector factors and anti-inflammatory effector factors in different groups.

(A) The mRNA expression of inflammatory cytokines IL-17, TNF-α, IL-1β and IL-6 in different groups. (B) The mRNA expression of pro-inflammatory effector factors (COX-2 and TLR4) and anti-inflammatory effector factors (Foxp3 and SOCS3) in different groups. *P < 0.05, **P < 0.01, ***P < 0.001, ****P < 0.0001.

DOI: 10.7717/peerj.17213/supp-5

The clinical information of UC patients from GEO database.

DOI: 10.7717/peerj.17213/supp-6

Eigenvalues of two principal components in the GEO dataset.

DOI: 10.7717/peerj.17213/supp-7

List of differentially expressed lncRNA, miRNA and mRNA.

DOI: 10.7717/peerj.17213/supp-8

The DElncRNA-DEmRNA-DEmiRNA ceRNA network.

DOI: 10.7717/peerj.17213/supp-9

List of differentially expressed genes and pathway enrichment analysis in GSE75214 dataset.

(A) differentially expressed mRNA in cluster 1 and 2 from GSE75214. (B) GO and KEGG enrichment analysis for cluster 1. (C) GO and KEGG enrichment analysis for cluster 2.

DOI: 10.7717/peerj.17213/supp-10

List of differentially expressed genes and pathway enrichment analysis in GSE114603 dataset.

(A) differentially expressed mRNA in cluster 1 from GSE114603. (B) differentially expressed mRNA in cluster 2 from GSE114603. (C) differentially expressed mRNA in cluster 3 from GSE114603. (D) GO and KEGG enrichment analysis for cluster 1. (E) GO and KEGG enrichment analysis for cluster 2. (F) GO and KEGG enrichment analysis for cluster 3.

DOI: 10.7717/peerj.17213/supp-11

Additional Information and Declarations

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Qifang Li analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Yuan Liu performed the experiments, analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Bingbing Li analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Canlei Zheng performed the experiments, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Bin Yu conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Kai Niu analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Yi Qiao analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

Jining Medical University provided full approval for this research (approval number: JNMC-2023-DW-090).

Data Availability

The following information was supplied regarding data availability:

The data is available at NCBI GEO: GSE75214, GSE48959, GSE114603.

The raw data are available in the Supplemental Files and at figshare: Yu, Bin (2023). Supplementary Table S1-6.xlsx. figshare. Dataset. https://doi.org/10.6084/m9.figshare.24188217.v3.

Funding

This work was supported by National Natural Science Foundation of China (Project No: 81603509), Natural Science Foundation of Shandong Province (Project No: ZR2014HQ051), Key Research and Development Plan of Jining (Project No: 2021YXNS007). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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