Bioinformatic Analysis of lncRNA Mediated CeRNA Network in Intestinal Ischemia/Reperfusion Injury

Zhu, Lin; Yang, Xiao; Yao, Zhiwen; Wang, Ziyi; Lai, Yupei; Xu, Shiting; Liu, Ke-Xuan; Zhao, Bing-Cheng

doi:10.1016/j.jss.2022.11.063

Cited by 2 publications

(10 citation statements)

References 43 publications

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“…We predicted targets of DEmiRNAs between groups A and B using the miRWalk 20 database ( ). To visualize the relationship between active ingredients-mRNA-miRNA, we utilized Cytoscape 3.8.2 based on the intersection of mRNA of predicted targets of YWD and DEmiRNAs and DEmRNAs.…”

Section: Methodsmentioning

confidence: 99%

Exploring the Mechanism of Yiwei Decoction in the Intervention of a Premature Ovarian Insufficiency Rat Based on Network Pharmacology and the miRNA-mRNA Regulatory Network

Fan,

Lei,

et al. 2024

ACS Omega

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Objective: our aim is to explore the mechanism of action of Yiwei decoction (YWD) in addressing premature ovarian insufficiency (POI) through a combination of transcriptomics and network pharmacology. By doing so, we hope to identify important pathways of action, key targets, and active components that contribute to the efficacy of YWD. Materials and Methods: group A comprised of the model + traditional Chinese medicine group, while group B was the model control group and group C was the normal control group. After gavage, serum AMH and E2 levels were measured by using ELISA. HE staining was used to study the impact of YWD on ovarian follicle recovery in POI rats. Additionally, RNA-seq sequencing technology was employed to analyze the transcription levels of mRNAs and miRNAs in the ovarian tissues of each group, and the resulting data were examined using R. YWD used UPLC-Q-TOF-HRMS to analyze its active ingredients. Upon obtaining the sequencing results, the miRWalk database was utilized to forecast the targets of DEmiRNAs. Network pharmacology was then applied to predict the targets of active ingredients present in YWD, ultimately constructing a regulatory network consisting of active ingredients-mRNA-miRNA. The coexpression relationship between mRNAs and miRNAs was calculated using the Pearson correlation coefficient, and high correlation coefficients between miRNA-mRNA were confirmed through miRanda sequence combination. Results: the application of YWD resulted in improved serum levels of AMH and E2, as well as an increased number of ovarian follicles in rats with POI. However, there was a minimal impact on the infiltration of ovarian lymphocytes. Through GSEA pathway enrichment analysis, we found that YWD may have a regulatory effect on PI3K-Akt, ovarian steroidogenesis, and protein digestion and absorption, which could aid in the treatment of POI. Additionally, our research discovered a total of 6 DEmiRNAs between groups A and B, including 2 new DEmiRNAs. YWD contains 111 active compounds, and our analysis of the active component-mRNA regulatory network revealed 27 active components and 73 mRNAs. Furthermore, the coexpression network included 5 miRNAs and 18 mRNAs. Our verification of MiRanda binding demonstrated that 12 of the sequence binding sites were stable. Conclusions: our research has uncovered the regulatory network mechanism of active ingredients, mRNA, and miRNA in YWD POI treatment. However, further research is needed to determine the effect of the active ingredients on key miRNAs and mRNAs.

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Section: Methodsmentioning

confidence: 99%

Exploring the Mechanism of Yiwei Decoction in the Intervention of a Premature Ovarian Insufficiency Rat Based on Network Pharmacology and the miRNA-mRNA Regulatory Network

Fan,

Lei,

et al. 2024

ACS Omega

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“…In our literature search, 15 studies made use of transcriptomics technology to study intestinal IR injury versus sham surgery in animals [10][11][12][13][14][15][16][17][18][19][20][21][22][23][24] (Table 1, part I). The aims of these studies ranged from exploring overall changes in gene expression in intestinal IR for a better understanding of the pathological process and/or to identify potential therapeutic targets [10,16,17,21], to specific testing of a therapeutic intervention [11,13,15,18,19], or both [12,14,23,24]. For these studies, mice were most commonly used to establish an intestinal IR model [11,13,[15][16][17][18][19]21], and two studies made use of rats [10,14].…”

Section: Transcriptomicsmentioning

confidence: 99%

“…The aims of these studies ranged from exploring overall changes in gene expression in intestinal IR for a better understanding of the pathological process and/or to identify potential therapeutic targets [10,16,17,21], to specific testing of a therapeutic intervention [11,13,15,18,19], or both [12,14,23,24]. For these studies, mice were most commonly used to establish an intestinal IR model [11,13,[15][16][17][18][19]21], and two studies made use of rats [10,14].…”

Section: Transcriptomicsmentioning

confidence: 99%

“…After a suitable IR model was established and sample collection was performed, transcriptome data were generated, mostly by microarray [10][11][12][13][14][15][16][17][18]21], and more recently, RNA sequencing (RNA-seq) [19,23]. Most research focused on gene expression in the small intestine, with the exception of the study of Zhang et al, in which intestinal tissue exosomes were sequenced [23], and the study of Chang et al that, in addition to intestinal tissue, also examined kidney and muscle [10].…”

Section: Transcriptomicsmentioning

confidence: 99%

“…Transcriptomics data were either generated in house or an existing data set was obtained from platforms such as the Gene Expression Omnibus (GEO) or the European Nucleotide Archive (ENA). Most of the selected studies looked at mRNA [10,16,18,19], however, since gene regulation relies on complex interactions between coding and noncoding RNAs, other studies looked at combinations of mRNA with noncoding RNA types [15,17,21], while some focused on miRNA [11][12][13][14]24] or circular RNA [23] only. To analyze the transcriptomic data, most studies performed Gene Ontology (GO) functional analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and establishment of a protein-protein interaction (PPI) network, or a combination thereof [15-17, 19, 21].…”

Section: Transcriptomicsmentioning

confidence: 99%

See 2 more Smart Citations

Unveiling the molecular complexity of intestinal ischemia–reperfusion injury through omics technologies

Alicehajic,

Duivenvoorden,

Lenaerts

2024

Proteomics

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Intestinal ischemia–reperfusion injury (IR) is implicated in various clinical conditions and causes damage to the intestinal epithelium resulting in intestinal barrier loss. This presents a substantial clinical challenge, emphasizing the importance of gaining a comprehensive understanding of molecular events to aid in the identification of novel therapeutic targets. This review systematically explores the extent to which omics technologies—transcriptomics, proteomics, metabolomics, and metagenomics—have already contributed to deciphering the molecular mechanisms contributing to intestinal IR injury, in in vivo and in vitro animal and human models, and in clinical samples. Recent breakthroughs involve applying omics methodologies on exosomes, organoids, and single cells, shedding light on promising avenues and valuable targets to reduce intestinal IR injury. Future directions aimed at expediting clinical translation are discussed as well and include multi‐omics data integration to facilitate the identification of key regulatory nodes driving intestinal IR injury and advancing human organoid models based on the novel insights by single‐cell omics technologies, offering hope for clinical application of therapeutic strategies in the years to come.

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Bioinformatic Analysis of lncRNA Mediated CeRNA Network in Intestinal Ischemia/Reperfusion Injury

Cited by 2 publications

References 43 publications

Exploring the Mechanism of Yiwei Decoction in the Intervention of a Premature Ovarian Insufficiency Rat Based on Network Pharmacology and the miRNA-mRNA Regulatory Network

Exploring the Mechanism of Yiwei Decoction in the Intervention of a Premature Ovarian Insufficiency Rat Based on Network Pharmacology and the miRNA-mRNA Regulatory Network

Unveiling the molecular complexity of intestinal ischemia–reperfusion injury through omics technologies

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